Help - About Nucleotide And Protein Sequence Formats
Sequence formats are simply the way in which the amino acid or DNA sequence is recorded in a computer file. Different programs expect different formats, so if you are to submit a job successfully, it is important to understand what the various formats look like.
In order to successfully submit a job it is important to understand what
the various sequence formats used for describing biological sequences
are and what their basic structure is. The job submission forms are fairly
flexible but cannot cope with too much inconsistency.
You can submit sequence to the search and analysis programs in any of
the formats mentioned in the options your chosen tool.
If you are submitting sequences to ClustalW2 or pratt you may the normal format, as described below, just making sure that the sequences follow each other and are separated from each other with the format´s separator. In the case of EMBL format this would be `//´.
In order to aid the user with the process of converting sequences to appropriate formats please use the following link: READSEQ.
- ALN/ClustalW2 format
- AMPS Block file format
- ClustalW2
- Codata
- EMBL
- GCG/MSF
- GDE
- Genebank
- FASTA (Pearson)
- NBRF/PIR
- PDB format
- Pfam/Stockholm format
- Phylip
- Raw
- RSF
- UniProtKB/Swiss-Prot
e.g. "CLUSTAL W (2.1) multiple sequence alignment"
The type of clustal program is "W" and the version is 2.1.
The alignment is written in blocks of 60 residues.
Every block starts with the sequence names, obtained from the input sequence, and a count of the total number of residues is shown at the end of the line.
The information about which residues match is shown below each block of residues:
"*" means that the residues or nucleotides in that column are identical in all sequences in the alignment.
":" means that conserved substitutions have been observed.
"." means that semi-conserved substitutions are observed.
An example is shown below.
The first part of a block-file contains the identifier codes of the sequences that are to follow. Each code is prefixed by the > symbol, codes must not contain spaces. e.g.
>HAHU
>Trypsin
>A0046
>Seq1
etc.
The number of ">" symbols is read in the beginning of the file until a * symbol is found. The * signals the beginning of the multiple alignment which is stored VERTICALLY, thus columns are individual sequences, whilst rows are aligned positions. The * symbol must lie over the first sequence. A further star in the same column signals the end of the alignment. Software then uses the number of ">" symbols at the beginning of the file to work out how many columns to read from the * position. It is therefore important that the only ">" symbols in the file are those that define the identifiers, and the only symbols are those defining the start and end of the multiple alinnment. A simple, small block-file is shown below.
Codata Format:
The first line starts with the text ENTRY". The end of a sequence is delineated by "///". The "SEQUENCE" line specifies the beginning of the sequence lines (starting on the next line), and no sequence is assumed to appear in the entry if the "SEQUENCE" line is missing.
-
ENTRY IXI_234 SEQUENCE 5 10 15 20 25 30 1 T S P A S I R P P A G P S S R P A M V S S R R T R P S P P G 31 P R R P T G R P C C S A A P R R P Q A T G G W K T C S G T C 61 T T S T S T R H R G R S G W S A R T T T A A C L R A S R K S 91 M R A A C S R S A G S R P N R F A P T L M S S C I T S T T G 121 P P A W A G D R S H E /// ENTRY IXI_235 SEQUENCE 5 10 15 20 25 30 1 T S P A S I R P P A G P S S R - - - - - - - - - R P S P P G 31 P R R P T G R P C C S A A P R R P Q A T G G W K T C S G T C 61 T T S T S T R H R G R S G W - - - - - - - - - - R A S R K S 91 M R A A C S R S A G S R P N R F A P T L M S S C I T S T T G 121 P P A W A G D R S H E /// ENTRY IXI_236 SEQUENCE 5 10 15 20 25 30 1 T S P A S I R P P A G P S S R P A M V S S R - - R P S P P P 31 P R R P P G R P C C S A A P P R P Q A T G G W K T C S G T C 61 T T S T S T R H R G R S G W S A R T T T A A C L R A S R K S 91 M R A A C S R - - G S R P P R F A P P L M S S C I T S T T G 121 P P P P A G D R S H E /// ENTRY IXI_237 SEQUENCE 5 10 15 20 25 30 1 T S P A S L R P P A G P S S R P A M V S S R R - R P S P P G 31 P R R P T - - - - C S A A P R R P Q A T G G Y K T C S G T C 61 T T S T S T R H R G R S G Y S A R T T T A A C L R A S R K S 91 M R A A C S R - - G S R P N R F A P T L M S S C L T S T T G 121 P P A Y A G D R S H E ///
The EMBL entries(as below) in the database are structured so as to be usable by human readers as well as by computer programs. Each entry in the database is composed of lines. Different types of lines, each with its own format, which are used to record the various types of data which make up the entry. Some entries will not contain all of the line types, and some line types occur many times in a single entry. As noted, each entry begins with an identification line (ID) and ends with a terminator line (//). Consult the EMBL user manual for a more comprehensive guide.
- The ID (IDentification line) line is always the first line of an entry. The general form of the ID line is:
Term Primary accession number Sequence Version Number dataclass molecule Data Class Taxonomic division sequencelength (Base Pairs) e.g. X14897 SV 1 linear mRNA STD MUS 4145 BP
- The XX line contains no data or comments. It is used instead of blank lines to avoid confusion with the sequence data lines.
- The AC (Accession Number) line lists the accession numbers associated with this entry.
- The DT (DaTe) line shows the date/release number of creation, date/release number of the last modification of the entry and the version number.
- The DE (DEscription) lines contain general descriptive information about the sequence stored.
- The KW (KeyWord) lines provide information which can be used to generate cross-reference indexes of the sequence entries based on functional, structural, or other categories deemed important. The keywords chosen for each entry serve as a subject reference for the sequence, and will be expanded as work with the database continues. Often several KW lines are necessary for a single entry.
- The OS (Organism Species) line specifies the preferred scientific name of the organism which was
the source of the stored sequence.
- The OC (Organism Classification) lines contain the taxonomic classification of the source organism.
- The RN (Reference Number) line gives a unique number to each reference citation within an entry.
- The RC (Reference Comment) line type is an optional line type which appears if the reference has a comment.
- The RP (Reference Position) line type is an optional line type which appears if one or more contiguous base spans of the presented sequence can be attributed to the reference in question.
- The RX (Reference Cross-reference) line type is an optional line type which contains a cross-reference to an external citation or abstract database.
- The RA (Reference Author) lines list the authors of the paper (or other work) cited.
- The RT (Reference Title) lines give the title of the paper (or other work).
- The RL (Reference Location) line contains the conventional citation information for the reference.
- The PE (Protein Existance) line describes the evidence evidence for the existence of a protein.
- The DR (Database Cross-Reference) line cross-references other databases which contain information related to the entry in which the DR line appears.
- The CC lines are free text comments about the entry, and may be used to convey any sort of information thought to be useful.
- The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen. The lines contain no data and may be ignored by computer programs.
- The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data. Regions or sites in the sequence which are of interest are listed in the table. A complete and definitive description of the feature table is given here.
- The SQ (SeQuence header) line marks the beginning of the sequence data and gives a summary of its content.
- The sequence data lines has lines of code starting with two blanks. The sequence is written 60 bases per line, in groups of 10 bases separated by a blank character, beginning in position 6 of the line. The direction listed is always 5' to 3'
- The // (terminator) line also contains no data or comments. It designates the end of an entry.
-
ID X14897; SV 1; linear; mRNA; STD; MUS; 4145 BP. XX AC X14897; XX DT 23-NOV-1989 (Rel. 21, Created) DT 18-APR-2005 (Rel. 83, Last updated, Version 3) XX DE Mouse fosB mRNA XX KW fos cellular oncogene; fosB oncogene; oncogene. XX OS Mus musculus (house mouse) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; OC Muridae; Murinae; Mus. XX RN [1] RP 1-4145 RX PUBMED; 2498083. RA Zerial M., Toschi L., Ryseck R.P., Schuermann M., Mueller R., Bravo R.; RT "The product of a novel growth factor activated gene, fos B, interacts with RT JUN proteins enhancing their DNA binding activity"; RL EMBO J. 8(3):805-813(1989). XX DR TRANSFAC; T00291; T00291. XX CC clone=AC113-1; cell line=NIH3T3; XX FH Key Location/Qualifiers FH FT source 1..4145 FT /organism="Mus musculus" FT /mol_type="mRNA" FT /db_xref="taxon:10090" FT CDS 1202..2218 FT /note="fosB protein (AA 1-338)" FT /db_xref="GOA:P13346" FT /db_xref="InterPro:IPR000837" FT /db_xref="InterPro:IPR004827" FT /db_xref="InterPro:IPR008917" FT /db_xref="InterPro:IPR011700" FT /db_xref="UniProtKB/Swiss-Prot:P13346" FT /protein_id="CAA33026.1" FT /translation="MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECA FT GLGEMPGSFVPTVTAITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSY FT STPGLSAYSTGGASGSGGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRE FT RNKLAAAKCRNRRRELTDRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGC FT KIPYEEGPGPGPLAEVRDLPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLF FT THSEVQVLGDPFPVVSPSYTSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL" XX SQ Sequence 4145 BP; 960 A; 1186 C; 1007 G; 991 T; 1 other; ataaattctt attttgacac tcaccaaaat agtcacctgg aaaacccgct ttttgtgaca 60 aagtacagaa ggcttggtca catttaaatc actgagaact agagagaaat actatcgcaa 120 actgtaatag acattacatc cataaaagtt tccccagtcc ttattgtaat attgcacagt 180 gcaattgcta catggcaaac tagtgtagca tagaagtcaa agcaaaaaca aaccaaagaa 240 aggagccaca agagtaaaac tgttcaacag ttaatagttc aaactaagcc attgaatcta 300 tcattgggat cgttaaaatg aatcttccta caccttgcag tgtatgattt aacttttaca 360 gaacacaagc caagtttaaa atcagcagta gagatattaa aatgaaaagg tttgctaata 420 gagtaacatt aaataccctg aaggaaaaaa aacctaaata tcaaaataac tgattaaaat 480 tcacttgcaa attagcacac gaatatgcaa cttggaaatc atgcagtgtt ttatttaaga 540 aaacataaaa caaaactatt aaaatagttt tagagggggt aaaatccagg tcctctgcca 600 ggatgctaaa attagacttc aggggaattt tgaagtcttc aattttgaaa cctattaaaa 660 agcccatgat tacagttaat taagagcagt gcacgcaaca gtgacacgcc tttagagagc 720 attactgtgt atgaacatgt tggctgctac cagccacagt caatttaaca aggctgctca 780 gtcatgaact taatacagag agagcacgcc taggcagcaa gcacagcttg ctgggccact 840 ttcctccctg tcgtgacaca atcaatccgt gtacttggtg tatctgaagc gcacgctgca 900 ccgcggcact gcccggcggg tttctgggcg gggagcgatc cccgcgtcgc cccccgtgaa 960 accgacagag cctggacttt caggaggtac agcggcggtc tgaaggggat ctgggatctt 1020 gcagagggaa cttgcatcga aacttgggca gttctccgaa ccggagacta agcttccccg 1080 agcagcgcac tttggagacg tgtccggtct actccggact cgcatctcat tccactcggc 1140 catagccttg gcttcccggc gacctcagcg tggtcacagg ggcccccctg tgcccaggga 1200 aatgtttcaa gcttttcccg gagactacga ctccggctcc cggtgtagct catcaccctc 1260 cgccgagtct cagtacctgt cttcggtgga ctccttcggc agtccaccca ccgccgccgc 1320 ctcccaggag tgcgccggtc tcggggaaat gcccggctcc ttcgtgccaa cggtcaccgc 1380 aatcacaacc agccaggatc ttcagtggct cgtgcaaccc accctcatct cttccatggc 1440 ccagtcccag gggcagccac tggcctccca gcctccagct gttgaccctt atgacatgcc 1500 aggaaccagc tactcaaccc caggcctgag tgcctacagc actggcgggg caagcggaag 1560 tggtgggcct tcaaccagca caaccaccag tggacctgtg tctgcccgtc cagccagagc 1620 caggcctaga agaccccgag aagagacact taccccagaa gaagaagaaa agcgaagggt 1680 tcgcagagag cggaacaagc tggctgcagc taagtgcagg aaccgtcgga gggagctgac 1740 agatcgactt caggcggaaa ctgatcagct tgaagaggaa aaggcagagc tggagtcgga 1800 gatcgccgag ctgcaaaaag agaaggaacg cctggagttt gtcctggtgg cccacaaacc 1860 gggctgcaag atcccctacg aagaggggcc ggggccaggc ccgctggccg aggtgagaga 1920 tttgccaggg tcaacatccg ctaaggaaga cggcttcggc tggctgctgc cgccccctcc 1980 accacccccc ctgcccttcc agagcagccg agacgcaccc cccaacctga cggcttctct 2040 ctttacacac agtgaagttc aagtcctcgg cgaccccttc cccgttgtta gcccttcgta 2100 cacttcctcg tttgtcctca cctgcccgga ggtctccgcg ttcgccggcg cccaacgcac 2160 cagcggcagc gagcagccgt ccgacccgct gaactcgccc tcccttcttg ctctgtaaac 2220 tctttagaca aacaaaacaa acaaacccgc aaggaacaag gaggaggaag atgaggagga 2280 gaggggagga agcagtccgg gggtgtgtgt gtggaccctt tgactcttct gtctgaccac 2340 ctgccgcctc tgccatcgga catgacggaa ggacctcctt tgtgttttgt gctccgtctc 2400 tggttttctg tgccccggcg agaccggaga gctggtgact ttggggacag ggggtggggc 2460 ggggatggac acccctcctg catatctttg tcctgttact tcaacccaac ttctggggat 2520 agatggctgg ctgggtgggt agggtggggt gcaacgccca cctttggcgt cttgcgtgag 2580 gctggagggg aaagggtgct gagtgtgggg tgcagggtgg gttgaggtcg agctggcatg 2640 cacctccaga gagacccaac gaggaaatga cagcaccgtc ctgtccttct tttcccccac 2700 ccacccatcc accctcaagg gtgcagggtg accaagatag ctctgttttg ctccctcggg 2760 ccttagctga ttaacttaac atttccaaga ggttacaacc tcctcctgga cgaattgagc 2820 ccccgactga gggaagtcga tgcccccttt gggagtctgc taaccccact tcccgctgat 2880 tccaaaatgt gaacccctat ctgactgctc agtctttccc tcctgggaaa actggctcag 2940 gttggatttt tttcctcgtc tgctacagag ccccctccca actcaggccc gctcccaccc 3000 ctgtgcagta ttatgctatg tccctctcac cctcaccccc accccaggcg cccttggccg 3060 tcctcgttgg gccttactgg ttttgggcag cagggggcgc tgcgacgccc atcttgctgg 3120 agcgctttat actgtgaatg agtggtcgga ttgctgggtg cgccggatgg gattgacccc 3180 cagccctcca aaactttccc tgggcctccc cttcttccac ttgcttcctc cctccccttg 3240 acagggagtt agactcgaaa ggatgaccac gacgcatccc ggtggccttc ttgctcaggc 3300 cccagacttt ttctctttaa gtccttcgcc ttccccagcc taggacgcca acttctcccc 3360 accctgggag ccccgcatcc tctcacagag gtcgaggcaa ttttcagaga agttttcagg 3420 gctgaggctt tggctcccct atcctcgata tttgaatccc caaatatttt tggactagca 3480 tacttaagag ggggctgagt tcccactatc ccactccatc caattccttc agtcccaaag 3540 acgagttctg tcccttccct ccagctttca cctcgtgaga atcccacgag tcagatttct 3600 attttttaat attggggaga tgggccctac cgcccgtccc ccgtgctgca tggaacattc 3660 cataccctgt cctgggccct aggttccaaa cctaatccca aaccccaccc ccagctattt 3720 atccctttcc tggttcccaa aaagcactta tatctattat gtataaataa atatattata 3780 tatgagtgtg cgtgtgtgtg cgtgtgcgtg cgtgcgtgcg tgcgtgcgag cttccttgtt 3840 ttcaagtgtg ctgtggagtt caaaatcgct tctggggatt tgagtcagac tttctggctg 3900 tccctttttg tcaccttttt gttgttgtct cggctcctct ggctgttgga gacagtcccg 3960 gcctctccct ttatcctttc tcaagtctgt ctcgctcaga ccacttccaa catgtctcca 4020 ctctcaatga ctctgatctc cggtntgtct gttaattctg gatttgtcgg ggacatgcaa 4080 ttttacttct gtaagtaagt gtgactgggt ggtagatttt ttacaatcta tatcgttgag 4140 aattc 4145 //
FASTA Format:
- This format contains a single header line providing the sequence name, and optionally a description, followed by lines of sequence data.
- Sequences in FASTA formatted files are preceded by a line starting with a " >" symbol.
- The first word on this line is the name of the sequence. The rest of the line is a description of the sequence.
Term Entry Name Molecule Type Gene Name Sequence Length
e.g. FOSB_MOUSE Protein fosB 338 bp
- The remaining lines contain the sequence itself, usually formated to 60 characters per line.
- Depending on the application blank lines in a FASTA file are ignored or treated as terminating the sequence
- Depending on the application spaces or other non-sequence symbols (dashes, underscores, periods) in a sequence are either ignored or treated as gaps.
- FASTA files containing multiple sequences are just the same, with one sequence listed right after another. This format is accepted for many multiple sequence alignment programs.
>FOSB_MOUSE Protein fosB. 338 bp
MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA
ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS
GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT
DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD
LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY
TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL
GCG/MSF Format
- The file may begin with as many lines of comment or description as required.
- The comments are terminated with a line starting with two slashes.
- The first mandatory line that is recognised as part of the MSF file is the line containing the text "MSF:", this line also includes the sequence length, type and date plus an internal check sum value.
- The next line is a mandatory blank line inserted before the sequence names.
- There then follows one line per sequence describing the sequence name, length, checksum and a weight value. Only one name per line is allowed; the qualifier "Name: " is followed by the sequence name. Names are restricted to 10 characters or less. Extra characters, between the sequence names and "Len: " are acceptable if they contain no blank characters. Another blank line is added followed by a line starting with two slashes "//" , this indicates the end of the name list.
- There then follows another blank line.
- Sequences are interleaved on separate lines with gaps represented by periods. Each sequence line starts with the sequence name which is separated from the aligned sequence residues by white space.
-
MSF: 510 Type: P Check: 7736 .. Name: ACHE_BOVIN oo Len: 510 Check: 7842 Weight: 16.0 Name: ACHE_HUMAN oo Len: 510 Check: 8553 Weight: 17.8 Name: ACHE_MOUSE oo Len: 510 Check: 229 Weight: 12.5 Name: ACHE_RAT oo Len: 510 Check: 8410 Weight: 14.2 Name: ACHE_XENLA oo Len: 510 Check: 2702 Weight: 39.2 // ACHE_BOVIN MAGALLCALL LLQLLGRGEG KNEELRLYHY LFDTYDPGRR PVQEPEDTVT ACHE_HUMAN MARAPLGVLL LLGLLGRGVG KNEELRLYHH LFNNYDPGSR PVREPEDTVT ACHE_MOUSE MAGALLGALL LLTLFGRSQG KNEELSLYHH LFDNYDPECR PVRRPEDTVT ACHE_RAT MTMALLGTLL LLALFGRSQG KNEELSLYHH LFDNYDPECR PVRRPEDTVT ACHE_XENLA MESGVRILSL LILLHNSLAS ESEESRLIKH LFTSYDQKAR PSKGLDDVVP ACHE_BOVIN ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSKG DFGGVETLRV ACHE_HUMAN ISLKVTLTNL ISLNEKEETL TTSVWIGIDW QDYRLNYSKD DFGGIETLRV ACHE_MOUSE ITLKVTLTNL ISLNEKEETL TTSVWIGIDW HDYRLNYSKD DFAGVGILRV ACHE_RAT ITLKVTLTNL ISLNEKEETL TTSVWIGIEW QDYRLNFSKD DFAGVEILRV ACHE_XENLA VTLKLTLTNL IDLNEKEETL TTNVWVQIAW NDDRLVWNVT DYGGIGFVPV
GDE Format:
GDE format is a tagged field format used for storing all available information about a sequence. The format matches very closely the GDE internal structures for sequence data. The format consists of text records starting and ending with braces ('{}'). Between the open and close braces are several tagged field lines specifying different pieces of information about a given sequence. The tag values can be wrapped with double quote characters ('""') as needed. If quotes are not used, the first white space delimited string is taken as the value.Any fields that are not specified are assumed to be the default values. Offsets can be negative as well as positive. Genbank entries written out in this format will have all (") converted to ('), and all ({}) converted to ([]) to avoid confusion in the parser. Leading and trailing gaps are removed prior to writing each sequence. This format is deliberately verbose in order to be simple to duplicate.
-
{ name "Short name for sequence"
longname "Long (more descriptive) name for sequence"
sequence-ID "Unique ID number"
creation-date "mm/dd/yy hh:mm:ss"
direction [-1|1]
strandedness [1|2]
type [DNA|RNA||PROTEIN|TEXT|MASK]
offset (-999999,999999)
group-ID (0,999)
creator "Author's name"
descrip "Verbose description"
comments "Lines of comments that can be fairly arbitrary text about a
sequence. Return characters are allowed, but no internal double quotes
or brace characters. Remember to close with a double quote"
sequence "gctagctagctagctagctcttagctgtagtcgtagctgatgctagct
gatgctagctagctagctagctgatcgatgctagctgatcgtagctgacg
gactgatgctagctagctagctagctgtctagtgtcgtagtgcttattgc" }
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Although there is daily exchange of information with the EMBL Nucleotide Sequence Database, it has it's own sequence format shown below. Each GenBank entry includes a concise description of the sequence, the scientific name and taxonomy of the source organism, and a table of features that identifies coding regions and other sites of biological significance, such as transcription units, sites of mutations or modifications, and repeats. Protein translations for coding regions are included in the feature table. Bibliographic references are included along with a link to the Medline unique identifier for all published sequences. Each sequence entry is composed of lines. Different types of lines, each with their own format, are used to record the various data that make up the entry.
- LOCUS: Short name for this sequence (Maximum of 32 characters).
- DEFINITION: Definition of sequence (Maximum of 80 characters).
- ACCESSION: accession number of the entry.
- VERSION: Version of the entry.
- DBSOURCE: Shows the source, the date of creation and last modification of the database entry.
- KEYWORDS: Keywords for the entry.
- AUTHORS: Authors for the work.
- TITLE: Title of the publication.
- JOURNAL: Journal reference for the entry.
- MEDLINE: Medline ID.
- COMMENT: Lines of comments.
- SOURCE ORGANISM: The organism from which the sequence was derived.
- ORGANISM: Full name of organism (Maximum of 80 characters).
- AUTHORS: Authors of this sequence (Maximum of 80 characters).
- ACCESSION: ID Number for this sequence (Maximum of 80 characters).
- FEATURES: Features of the sequence.
- ORIGIN: Beginning of sequence data.
- // End of sequence data.
-
LOCUS MMFOSB 4145 bp mRNA linear ROD 12-SEP-1993 DEFINITION Mouse fosB mRNA. ACCESSION X14897 VERSION X14897.1 GI:50991 KEYWORDS fos cellular oncogene; fosB oncogene; oncogene. SOURCE Mus musculus. ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus. REFERENCE 1 (bases 1 to 4145) AUTHORS Zerial,M., Toschi,L., Ryseck,R.P., Schuermann,M., Muller,R. and Bravo,R. TITLE The product of a novel growth factor activated gene, fos B, interacts with JUN proteins enhancing their DNA binding activity JOURNAL EMBO J. 8 (3), 805-813 (1989) MEDLINE 89251612 PUBMED 2498083 COMMENT clone=AC113-1; cell line=NIH3T3. FEATURES Location/Qualifiers source 1..4145 /organism="Mus musculus" /db_xref="taxon:10090" CDS 1202..2218 /note="fosB protein (AA 1-338)" /codon_start=1 /protein_id="CAA33026.1" /db_xref="GI:50992" /db_xref="MGD:95575" /db_xref="SWISS-PROT:P13346" /translation="MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQEC AGLGEMPGSFVPTVTAITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGT SYSTPGLSAYSTGGASGSGGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRV RRERNKLAAAKCRNRRRELTDRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAH KPGCKIPYEEGPGPGPLAEVRDLPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNL TASLFTHSEVQVLGDPFPVVSPSYTSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPS LLAL" BASE COUNT 960 a 1186 c 1007 g 991 t 1 others ORIGIN 1 ataaattctt attttgacac tcaccaaaat agtcacctgg aaaacccgct ttttgtgaca 61 aagtacagaa ggcttggtca catttaaatc actgagaact agagagaaat actatcgcaa 121 actgtaatag acattacatc cataaaagtt tccccagtcc ttattgtaat attgcacagt 181 gcaattgcta catggcaaac tagtgtagca tagaagtcaa agcaaaaaca aaccaaagaa 241 aggagccaca agagtaaaac tgttcaacag ttaatagttc aaactaagcc attgaatcta 301 tcattgggat cgttaaaatg aatcttccta caccttgcag tgtatgattt aacttttaca 361 gaacacaagc caagtttaaa atcagcagta gagatattaa aatgaaaagg tttgctaata 421 gagtaacatt aaataccctg aaggaaaaaa aacctaaata tcaaaataac tgattaaaat 481 tcacttgcaa attagcacac gaatatgcaa cttggaaatc atgcagtgtt ttatttaaga 541 aaacataaaa caaaactatt aaaatagttt tagagggggt aaaatccagg tcctctgcca 601 ggatgctaaa attagacttc aggggaattt tgaagtcttc aattttgaaa cctattaaaa 661 agcccatgat tacagttaat taagagcagt gcacgcaaca gtgacacgcc tttagagagc 721 attactgtgt atgaacatgt tggctgctac cagccacagt caatttaaca aggctgctca 781 gtcatgaact taatacagag agagcacgcc taggcagcaa gcacagcttg ctgggccact 841 ttcctccctg tcgtgacaca atcaatccgt gtacttggtg tatctgaagc gcacgctgca 901 ccgcggcact gcccggcggg tttctgggcg gggagcgatc cccgcgtcgc cccccgtgaa 961 accgacagag cctggacttt caggaggtac agcggcggtc tgaaggggat ctgggatctt 1021 gcagagggaa cttgcatcga aacttgggca gttctccgaa ccggagacta agcttccccg 1081 agcagcgcac tttggagacg tgtccggtct actccggact cgcatctcat tccactcggc 1141 catagccttg gcttcccggc gacctcagcg tggtcacagg ggcccccctg tgcccaggga 1201 aatgtttcaa gcttttcccg gagactacga ctccggctcc cggtgtagct catcaccctc 1261 cgccgagtct cagtacctgt cttcggtgga ctccttcggc agtccaccca ccgccgccgc 1321 ctcccaggag tgcgccggtc tcggggaaat gcccggctcc ttcgtgccaa cggtcaccgc 1381 aatcacaacc agccaggatc ttcagtggct cgtgcaaccc accctcatct cttccatggc 1441 c
NBRF/PIR Format:
- A sequence in PIR format consists of:
- One line starting with
- a ">" (greater-than) sign, followed by
- a two-letter code describing the sequence type (P1, F1, DL, DC, RL, RC, or XX), followed by
- a semicolon, followed by
- the sequence identification code (the database ID-code).
- One line containing a textual description of the sequence.
- One or more lines containing the sequence itself. The end of the sequence is marked by a "*" (asterisk) character.
- One line starting with
- A file in PIR format may comprise more than one sequence.
| Sequence type | Code |
|---|---|
| Protein (complete) | P1 |
| Protein (fragment) | F1 |
| DNA (linear) | DL |
| DNA (circular) | DC |
| RNA (linear) | RL |
| RNA (circular) | RC |
| tRNA | N3 |
| other functional RNA | N1 |
-
>P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK*
Basic Notions of the Format Description
Character Set
Only non-control ASCII characters, as well as the space and end-of-line indicator, appear in a PDB coordinate entry file. Namely:
abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ
1234567890
` - = [ ] \ ; ' , . / ~ ! @ # $ % ^ & * ( ) _ + { } | : "
< > ?
the space, and end-of-line. The end-of-line indicator is system-specific. Unix uses a line feed character; other systems may use a carriage return followed by a line feed.
Special Characters
Greek letters are spelled out, i.e., alpha, beta, gamma, etc.
Bullets are represented as (DOT).
Right arrow is represented as -->.
Left arrow is represented as <--.
Superscripts are initiated and terminated by double equal signs, e.g., S==2+==.
Subscripts are initiated and terminated by single equal signs, e.g., F=c=.
If "=" is surrounded by at least one space on each side, then it is assumed to be an equal sign, e.g., 2 + 4 = 6.
Commas, colons, and semi-colons are used as list delimiters in records which have one of the following data types:
List
SList
Specification List
Specification
If a comma, colon, or semi-colon is used in any context other than as a delimiting character, then the character must be escaped, i.e., immediately preceded by a backslash, "\". Examples of this use are found in line 4 of each of the following:
-
COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE SYNTHETASE; COMPND 3 CHAIN: NULL; COMPND 4 SYNONYM: GAMMA-L-GLUTAMYL-L-CYSTEINE\:GLYCINE LIGASE COMPND 5 (ADP-FORMING); COMPND 6 EC: 6.3.2.3; COMPND 7 ENGINEERED: YES COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHETASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MAT, ATP\:L-METHIONINE S-ADENOSYLTRANSFERASE; COMPND 5 EC: 2.5.1.6; COMPND 6 ENGINEERED: YES; COMPND 7 BIOLOGICAL_UNIT: TETRAMER; COMPND 8 OTHER_DETAILS: TETRAGONAL MODIFICATIONs
The "Pfam/Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types.
Header:
The first line in the file must contain a format and version identifier, currently:
# STOCKHOLM 1.0
The sequence alignment:
<
seqname> <aligned sequence>
<
seqname> <aligned sequence>
<
seqname> <aligned sequence>
.
.
//
<seqname> stands for "sequence name", typically in the form "name/start-end" or just "name".
The "//" line indicates the end of the alignment.
Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".
Wrap-around alignments are allowed in principle, mainly for historical reasons, but are not used in e.g. Pfam. Wrapped alignments are discouraged since they are much harder to parse.
The alignment mark-up:
Mark-up lines may include any characters except whitespace. Use underscore ("_") instead of space.
#=GF <feature> <Generic per-File annotation, free text>
#=GC <feature> <Generic per-Column annotation, exactly 1 char per column>
#=GS <seqname> <feature> <Generic per-Sequence annotation, free text>
#=GR <seqname> <feature> <Generic per-Sequence AND per-Column markup, exactly 1 char per column>
Example:
-
# STOCKHOLM 1.0
#=GF ID CBS
#=GF AC PF00571
#=GF DE CBS domain
#=GF AU Bateman A
#=GF CC CBS domains are small intracellular modules mostly found
#=GF CC in 2 or four copies within a protein.
#=GF SQ 67
#=GS O31698/18-71 AC O31698
#=GS O83071/192-246 AC O83071
#=GS O83071/259-312 AC O83071
#=GS O31698/88-139 AC O31698
#=GS O31698/88-139 OS Bacillus subtilis
O83071/192-246 MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS
#=GR O83071/192-246 SA 999887756453524252..55152525....36463774777
O83071/259-312 MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY
#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE
O31698/18-71 MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS
#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH
O31698/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH
#=GC SS_cons CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH
O31699/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
#=GR O31699/88-139 AS ________________*__________________________
#=GR_O31699/88-139_IN ____________1______________2__________0____
//
- The first line of the input file contains the number of species, the number of sequences and their length (in characters)separated by blanks.
- The next line contains the sequence name, followed by the sequence in blocks of 10 characters.
-
1 338 I
FOSB_MOUSE MFQAFPGDYD SGSRCSSSPS AESQYLSSVD SFGSPPTAAA SQECAGLGEM
PGSFVPTVTA ITTSQDLQWL VQPTLISSMA QSQGQPLASQ PPAVDPYDMP
GTSYSTPGLS AYSTGGASGS GGPSTSTTTS GPVSARPARA RPRRPREETL
TPEEEEKRRV RRERNKLAAA KCRNRRRELT DRLQAETDQL EEEKAELESE
IAELQKEKER LEFVLVAHKP GCKIPYEEGP GPGPLAEVRD LPGSTSAKED
GFGWLLPPPP PPPLPFQSSR DAPPNLTASL FTHSEVQVLG DPFPVVSPSY
TSSFVLTCPE VSAFAGAQRT SGSEQPSDPL NSPSLLAL
Like text/plain format except that it removes any white space or digits, accepts only alphabetic characters and rejects anything else. This means that it is safer to use this format that plain format. If you have digits and spaces or TAB characters, these are removed and ignored. If you have other non-alphabetic characters (for example, punctuation characters), then the sequence will be rejected as erroneous.
-
ataaattcttattttgacactcaccaaaatagtcacctggaaaacccgctttttgtgaca aagtacagaaggcttggtcacatttaaatcactgagaactagagagaaatactatcgcaa actgtaatagacattacatccataaaagtttccccagtccttattgtaatattgcacagt gcaattgctacatggcaaactagtgtagcatagaagtcaaagcaaaaacaaaccaaagaa aggagccacaagagtaaaactgttcaacagttaatagttcaaactaagccattgaatcta tcattgggatcgttaaaatgaatcttcctacaccttgcagtgtatgatttaacttttaca
RSF means rich sequence format and it is created by the Editor in SeqLab. The format is recognised by the word !!RICH_SEQUENCE at the beginning of
the file. It contains one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information such as:
- Creator/author of the sequence
- Sequence weight
- Creation date
- One-line description of the sequence
- Offset, or the number of leading gaps in a sequence that is part of an alignment or fragment assembly project
Known sequence features
-
!!RICH_SEQUENCE 1.0 .. { name chkhba type DNA longname chkhba checksum 980 creation-date 4/15/98 16:42:47 strand 1 sequence ACACAGAGGTGCAACCATGGTGCTGTCCGCTGCTGACAAGAACAACGTCAAGGGCATCTT CACCAAAATCGCCGGCCATGCTGAGGAGTATGGCGCCGAGACCTTGGAAAGGATGTTCAC CACCTACCCCCCAACCAAGACCTACTTCCCCCACTTCGATCTGTCACACGGCTCCGCTCA ... } { name davagl type DNA longname davagl checksum 7399 creation-date 4/15/98 16:42:47 strand 1 sequence GTGCTCTCGGATGCTGACAAGACTCACGTGAAAGCCATCTGGGGTAAGGTGGGAGGCCAC GCCGGTGCCTACGCAGCTGAAGCTCTTGCCAGAACCTTCCTCTCCTTCCCCACTACCAAA ... }
Macsim Format:
<!-- This is the Document Type Definition (DTD) for Macsim. -->
<!-- A DTD for describing Multiple Alignments of Complete Sequences -->
<!-- and Information Mining -->
<!-- This DTD was created by Julie Thompson (julie@igbmc.u-strasbg.fr) -->
<!-- Institut de Genetique et de Biologie Moleculaire et Cellulaire, -->
<!-- Strasbourg, France. -->
<!-- Email the above address for corrections and suggestions. -->
<!-- This DTD's DISTRIBUTION and USE is UNLIMITED under the condition -->
<!-- that its entire content remains intact. -->
<!-- THIS DTD AND DOCUMENTATION IS PROVIDED 'AS IS,' AND COPYRIGHT -->
<!-- HOLDERS MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED,-->
<!-- INCLUDING BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY OR -->
<!-- FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF THE DTD -->
<!-- OR DOCUMENTATION WILL NOT INFRINGE ANY THIRD PARTY PATENTS, -->
<!-- COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS. -->
<!-- COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, -->
<!-- SPECIAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF ANY USE OF THE -->
<!-- DTD OR DOCUMENTATION. -->
<!-- The name and trademarks of the copyright holder may NOT be used in-->
<!-- advertising or publicity pertaining to the DTD without -->
<!-- specific, written prior permission. Title to copyright in this -->
<!-- DTD and any associated documentation will at all times remain -->
<!-- with copyright holders. -->
<!-- Version 1.1 : -->
<!-- Version 1.2 : 2005/01/04 Julie added taxid -->
<!-- Version 1.3 : 2005/01/17 Raymond changed aln-txt to freetext and -->
<!-- : add owner+type in freetext and consensus -->
<!-- Version 1.4 : 2005/03/16 Raymond added ? to fscore? -->
<!-- Version 1.5 : 2005/03/29 Julie added sense -1 0 1 -->
<!-- Version 1.6 : 2006/07/11 Julie added surface accessibility and -->
<!-- residue contact list -->
<!ELEMENT macsim (alignment)>
<!ELEMENT alignment (aln-name,
aln-score?,
aln-note?,
(sequence | freetext | consensus | column-score | surface-accessibility)+)>
<!ELEMENT aln-name (#PCDATA)>
<!ELEMENT aln-score (#PCDATA)>
<!ELEMENT aln-note (#PCDATA)>
<!-- owner signification : 0 for all, 1-n for group, seq-name for sequence -->
<!ELEMENT freetext (freetext-name,
freetext-owner,
freetext-type,
freetext-data)>
<!ELEMENT consensus (cons-name,
cons-owner,
cons-type,
cons-data)>
<!ELEMENT column-score (colsco-name,
colsco-owner,
colsco-type,
colsco-data)>
<!ELEMENT surface-accessibility (suracc-name,
suracc-owner,
suracc-type,
suracc-data)>
<!ELEMENT freetext-name (#PCDATA)>
<!ELEMENT freetext-owner (#PCDATA)>
<!ELEMENT freetext-type (#PCDATA)>
<!ELEMENT freetext-data (#PCDATA)>
<!ELEMENT cons-name (#PCDATA)>
<!ELEMENT cons-owner (#PCDATA)>
<!ELEMENT cons-type (#PCDATA)>
<!ELEMENT cons-data (#PCDATA)>
<!ELEMENT colsco-name (#PCDATA)>
<!ELEMENT colsco-owner (#PCDATA)>
<!ELEMENT colsco-type (#PCDATA)>
<!ELEMENT colsco-data (#PCDATA)>
<!ELEMENT suracc-name (#PCDATA)>
<!ELEMENT suracc-owner (#PCDATA)>
<!ELEMENT suracc-type (#PCDATA)>
<!ELEMENT suracc-data (#PCDATA)>
<!-- A sequence must minimally have a name with a type
attribute and some sequence data, the info is optional -->
<!ELEMENT sequence (seq-name,
seq-info?,
seq-data)>
<!ATTLIST sequence seq-type (Protein | DNA | PDB) #REQUIRED>
<!ELEMENT seq-name (#PCDATA)>
<!ELEMENT seq-data (#PCDATA)>
<!-- The info section can contain any of the following, in any order -->
<!ELEMENT seq-info (accession | nid | definition | organism | taxid | lifedomain | ec
| hydrophobicity | fragment | keywordlist | complex | pub | ftable | residue-contact-list |
dbxreflist | length | weight | group | cksum | score | sense | status)+>
<!ELEMENT accession (#PCDATA)>
<!ELEMENT nid (#PCDATA)>
<!ELEMENT definition (#PCDATA)>
<!ELEMENT organism (#PCDATA)>
<!ELEMENT taxid (#PCDATA)>
<!ELEMENT lifedomain (#PCDATA)>
<!ELEMENT ec (#PCDATA)>
<!ELEMENT hydrophobicity (#PCDATA)>
<!ELEMENT fragment EMPTY>
<!ATTLIST fragment status (Yes | No) "No">
<!ELEMENT keywordlist (keyword+)>
<!ELEMENT keyword (#PCDATA)>
<!ELEMENT complex (#PCDATA)>
<!ELEMENT pub (pubxref | authors | journal | other | title)*>
<!ELEMENT authors (#PCDATA)>
<!ELEMENT journal (#PCDATA)>
<!ELEMENT other (#PCDATA)>
<!ELEMENT pubxref (#PCDATA)>
<!ELEMENT title (#PCDATA)>
<!ELEMENT ftable (fitem+)>
<!ELEMENT fitem (ftype,
fstart,
fstop,
fcolor,
fscore?,
fnote?)>
<!ATTLIST fitem status (Confirmed | Predicted) "Confirmed">
<!ELEMENT ftype (#PCDATA)>
<!ELEMENT fstart (#PCDATA)>
<!ELEMENT fstop (#PCDATA)>
<!ELEMENT fcolor (#PCDATA)>
<!ELEMENT fscore (#PCDATA)>
<!ELEMENT fnote (#PCDATA)>
<!ELEMENT residue-contact-list (contact-residue1 , residue-contact+)>
<!ELEMENT residue-contact (contact-residue2,
contact-distance?,
contact-note?)>
<!ELEMENT contact-residue2 (#PCDATA)>
<!ELEMENT contact-distance (#PCDATA)>
<!ELEMENT contact-note (#PCDATA)>
<!ELEMENT dbxreflist (#PCDATA)>
<!ELEMENT dbxref (dbname,
dbid,
dbnote?,
dbnumber?)>
<!ELEMENT dbname (#PCDATA)>
<!ELEMENT dbid (#PCDATA)>
<!ELEMENT dbnote (#PCDATA)>
<!ELEMENT dbnumber (#PCDATA)>
<!ELEMENT length (#PCDATA)>
<!ELEMENT weight (#PCDATA)>
<!ELEMENT group (#PCDATA)>
<!ELEMENT cksum (#PCDATA)>
<!ELEMENT score (#PCDATA)>
<!ELEMENT sense (#PCDATA)>
<!ELEMENT status (#PCDATA)>
UniProtKB/Swiss-Prot Format:
UniProtKB/Swiss-Prot is an annotated protein sequence database. The UniProtKB/Swiss-Prot protein knowledgebase consists of sequence entries. Sequence entries are composed of different line types, each with their own format. For standardisation purposes the format of UniProtKB/Swiss-Prot follows as closely as possible that of the EMBL Nucleotide Sequence Database. The UniProtKB/Swiss-Prot user manual is available here. The entries in the UniProtKB/Swiss-Prot database are structured so as to be usable by human readers as well as by computer programs. The explanations, descriptions, classifications and other comments are in ordinary English. Wherever possible, symbols familiar to biochemists, protein chemists and molecular biologists are used. Each sequence entry is composed of lines. Different types of lines, each with their own format, are used to record the various data that make up the entry.
- The ID (IDentification) line is always the first line of an entry. The general form of the ID line is:
Term ID ENTRY_NAME STATUS SEQUENCE_LENGTH. e.g. ID FOSB_MOUSE Reviewed 338 AA
- Entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence. The entry name consists of up to ten uppercase alphanumeric characters.
- Status: To distinguish the fully annotated entries in the Swiss-Prot section of the UniProt Knowledgebase from the computer-annotated entries in the TrEMBL section, the 'status' of each entry is indicated in the first (ID) line of each entry. The two defined classes are:
- Reviewed
Entries that have been manually reviewed and annotated by UniProtKB curators (Swiss-Prot section of the UniProt Knowledgebase). - Unreviewed
Computer-annotated entries that have not been reviewed by UniProtKB curators (TrEMBL section of the UniProt Knowledgebase).
- Reviewed
- Length of the molecule: The sequence length in amino acids.
- Entry name: The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence. The entry name consists of up to ten uppercase alphanumeric characters.
- The AC (ACcession number) line lists the accession number(s) associated with an entry.
- The DT (DaTe) lines shows the date of creation and last modification of the database entry.
- The DE (DEscription) lines contain general descriptive information about the sequence stored.
- The GN (Gene Name) line contains the name(s) of the gene(s) that code for the stored protein sequence.
- The OS (Organism Species) line specifies the organism(s) which was (were) the source of the stored sequence.
- The OG (OrGanelle) line indicates if the gene coding for a protein originates from the mitochondria, the chloroplast, a cyanelle, or a plasmid.
- The PR (PRoject) line shows the International Nucleotide Sequence Database Collaboration (INSDC) Project Identifier that has been assigned to the entry.
- The OC (Organism Classification) lines contain the taxonomic classification of the source organism.
- The OX (Organism taxonomy Cross-Reference) line is used to indicate the identifier to a specific organism in a taxonomic database.
- The RN (Reference Number) line gives a sequential number to each reference citation in an entry.
- The RP (Reference Position) line describes the extent of the work carried out by the authors of the reference cited.
- The RC (Reference Comment) lines are optional lines which are used to store comments relevant to the reference cited.
- The RX (Reference Cross-Reference) line is an optional line which is used to indicate the identifier assigned to a specific reference in a bibliographic database.
- The RA (Reference Author) lines list the authors of the paper (or other work) cited.
- The RT (Reference Title) lines give the title of the paper (or other work) cited.
- The RL (Reference Location) lines contain the conventional citation information for the reference.
- The CC lines are free text comments on the entry, and are used to convey any useful information.
- The DR (Database cross-Reference) lines are used as pointers to information related to UniProtKB/Swiss-Prot entries and found in other data collections.
- The KW (KeyWord) lines provide information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
- The FT (Feature Table) lines provide a precise but simple means for the annotation of the sequence data. The table describes regions or sites of interest in the sequence. In general the feature table lists posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references.
- The SQ (SeQuence header) line marks the beginning of the sequence data and gives a quick summary of its content.
- The sequence data line has a line code consisting of two blanks rather than the two-letter codes used until now. The sequence counts 60 amino acids per line, in groups of 10 amino acids, beginning in position 6 of the line.
- The // (terminator) line contains no data or comments and designates the end of an entry.
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ID FOSB_MOUSE Reviewed; 338 AA. AC P13346; DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot. DT 01-JAN-1990, sequence version 1. DT 20-FEB-2007, entry version 54. DE Protein fosB. GN Name=Fosb; OS Mus musculus (Mouse). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; OC Muroidea; Muridae; Murinae; Mus. OX NCBI_TaxID=10090; RN [1] RP NUCLEOTIDE SEQUENCE [MRNA]. RX MEDLINE=89251612; PubMed=2498083; RA Zerial M., Toschi L., Ryseck R.-P., Schuermann M., Mueller R., RA Bravo R.; RT "The product of a novel growth factor activated gene, fos B, interacts RT with JUN proteins enhancing their DNA binding activity."; RL EMBO J. 8:805-813(1989). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=92158623; PubMed=1741260; DOI=10.1093/nar/20.2.343; RA Lazo P.S., Dorfman K., Noguchi T., Mattei M.-G., Bravo R.; RT "Structure and mapping of the fosB gene. FosB downregulates the RT activity of the fosB promoter."; RL Nucleic Acids Res. 20:343-350(1992). CC -!- FUNCTION: FosB interacts with Jun proteins enhancing their DNA CC binding activity. CC -!- SUBUNIT: Heterodimer (By similarity). CC -!- SUBCELLULAR LOCATION: Nucleus. CC -!- INDUCTION: By growth factors. CC -!- SIMILARITY: Belongs to the bZIP family. Fos subfamily. CC -!- SIMILARITY: Contains 1 bZIP domain. CC ----------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution-NoDerivs License CC ----------------------------------------------------------------------- DR EMBL; X14897; CAA33026.1; -; mRNA. DR EMBL; AF093624; AAD13196.1; -; Genomic_DNA. DR PIR; S35477; TVMSFB. DR UniGene; Mm.248335; -. DR HSSP; P01100; 1FOS. DR SMR; P13346; 157-215. DR DIP; DIP:1067N; -. DR TRANSFAC; T00291; -. DR Ensembl; ENSMUSG00000003545; Mus musculus. DR KEGG; mmu:14282; -. DR MGI; MGI:95575; Fosb. DR ArrayExpress; P13346; -. DR GermOnline; ENSMUSG00000003545; Mus musculus. DR InterPro; IPR011700; bZIP_2. DR InterPro; IPR008917; Euk_TF_DNA_bd. DR InterPro; IPR000837; Leuzip_Fos. DR InterPro; IPR004827; TF_bZIP. DR Pfam; PF07716; bZIP_2; 1. DR PRINTS; PR00042; LEUZIPPRFOS. DR SMART; SM00338; BRLZ; 1. DR PROSITE; PS50217; BZIP; 1. DR PROSITE; PS00036; BZIP_BASIC; 1. KW DNA-binding; Nuclear protein. FT CHAIN 1 338 Protein fosB. FT /FTId=PRO_0000076477. FT DOMAIN 183 211 Leucine-zipper. FT DNA_BIND 161 179 Basic motif. SQ SEQUENCE 338 AA; 35977 MW; E9D031A4BEAE48EC CRC64; MFQAFPGDYD SGSRCSSSPS AESQYLSSVD SFGSPPTAAA SQECAGLGEM PGSFVPTVTA ITTSQDLQWL VQPTLISSMA QSQGQPLASQ PPAVDPYDMP GTSYSTPGLS AYSTGGASGS GGPSTSTTTS GPVSARPARA RPRRPREETL TPEEEEKRRV RRERNKLAAA KCRNRRRELT DRLQAETDQL EEEKAELESE IAELQKEKER LEFVLVAHKP GCKIPYEEGP GPGPLAEVRD LPGSTSAKED GFGWLLPPPP PPPLPFQSSR DAPPNLTASL FTHSEVQVLG DPFPVVSPSY TSSFVLTCPE VSAFAGAQRT SGSEQPSDPL NSPSLLAL //
Known biosequence format Extensions
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ID Name Read Write Int'leaf Document Content-type Suffix 1 IG|Stanford yes yes -- -- biosequence/ig .ig 2 GenBank|GB yes yes -- yes biosequence/genbank .gb 3 NBRF yes yes -- -- biosequence/nbrf .nbrf 4 EMBL yes yes -- yes biosequence/embl .embl 5 GCG yes yes -- -- biosequence/gcg .gcg 6 DNAStrider yes yes -- -- biosequence/strider .strider 7 Fitch -- -- -- -- biosequence/fitch .fitch 8 Pearson|FASTA yes yes -- -- biosequence/fasta .fasta 9 Zuker -- -- -- -- biosequence/zuker .zuker 10 Olsen -- -- yes -- biosequence/olsen .olsen 11 Phylip3.2 yes yes yes -- biosequence/phylip2 .phylip2 12 Phylip|Phylip4 yes yes yes -- biosequence/phylip .phylip 13 Plain|Raw yes yes -- -- biosequence/plain .seq 14 PIR|CODATA yes yes -- -- biosequence/codata .pir 15 MSF yes yes yes -- biosequence/msf .msf 16 PAUP|NEXUS yes yes yes -- biosequence/nexus .nexus 17 Pretty -- yes yes -- biosequence/pretty .pretty 18 XML yes yes -- yes biosequence/xml .xml 19 BLAST yes -- yes -- biosequence/blast .blast 20 SCF yes -- -- -- biosequence/scf .scf 21 ASN.1 -- -- -- -- biosequence/asn1 .asn
CLUSTAL W 2.1 multiple sequence alignment FOSB_MOUSE ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS 60 FOSB_HUMAN ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPVVDPYDMPGTSYSTPGMSGYSSGGASGS 60 ********************************.***************:*.**:******