 |
|
EBI DbfetchID AF304123; SV 1; linear; mRNA; STD; INV; 774 BP. XX AC AF304123; XX DT 18-JAN-2001 (Rel. 66, Created) DT 15-APR-2005 (Rel. 83, Last updated, Version 2) XX DE Caenorhabditis elegans adenylate kinase 1 (XL906) mRNA, complete cds. XX KW Worm Transcriptome Project. XX OS Caenorhabditis elegans OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; OC Rhabditidae; Peloderinae; Caenorhabditis. XX RN [1] RP 1-774 RA Kohara Y., Shin'i T., Suzuki Y., Sugano S., Potdevin M., Thierry-Mieg Y., RA Thierry-Mieg D., Thierry-Mieg J.; RT ; RL Unpublished. XX RN [2] RP 1-774 RA Kohara Y., Shin'i T., Thierry-Mieg D., Thierry-Mieg J.; RT ; RL Submitted (11-SEP-2000) to the EMBL/GenBank/DDBJ databases. RL National Institute of Genetics, Mishima, Japan XX CC Complete mRNA for adenylate kinase 1 (ATP AMP transphosphorylase) CC gene XL906 (YK4845) in C. elegans, enriched in young embryos. CC This gene is located on chromosome X on the reverse strand, its CC 3' end is in megabase 12, near kilobase 906. It is encoded by CC cosmid F38B2 from base 13588 to base 12449. Its extrapolated CC genetic position is (X; 3.10). No phenotype has yet been reported CC to our knowledge; this gene's function is yet unknown. CC Clones CC This mRNA is represented by 5 clones, all compatible with a single CC mRNA type, 4 clones containing the entire CDS have been fully CC sequenced (yk242b5, yk254c8, yk473g2, yk623E1). Clones match the CC mRNA starting on base: CC yk473g2 -> base 0 ; yk254c8 -> base 1 ; CC yk242b5 -> base 1 ; yk623E1 -> base 1 ; CC yk484c6 -> base 8 ; CC Transcripts from this gene are present mostly in young embryos. 5 CC of 5 staged clones come from young embryos. CC The 5'UTR contains 3 bp: CC AAA CC The transpliced leader SL1 (...GAG) is likely present in the mRNA CC in front of the submitted sequence. The first ATG starts at CC nucleotide 4. CC Splicing CC Comparison to the genome sequence confirms genome sequence accuracy CC and shows that the 4/4 introns follow the consensus [gt-ag] rule. CC Coordinates of the introns in the template genomic DNA, where 1 CC denotes the first genomic base matching the RNA, are CC [ type ] start end length CC [ gt_ag ] 247 316 70 bp CC [ gt_ag ] 437 551 115 bp CC [ gt_ag ] 635 704 70 bp CC [ gt_ag ] 814 924 111 bp CC The 3'UTR contains alternatively 121 or 138 bp immediately followed CC by the polyA. The longuest 3'UTR is : CC TTGTTTTTTTTTGTCAACTATCCATCAATTTTCGGAAAACTAGACCATCA CC TTGCTTTACTTACATCTAAAAAAAATTATTCTATGCTCCAAAAATAAAAT CC GTTTAAATTTCTGTACTTAATAAATTTTTCTAGTTTTA CC The standard AATAAA polyadenylation signal is seen 18 to 23 bp CC before the polyA of the short variant and is seen 15 to 20 bp CC before the polyA in the long variant CC Conceptual translation CC The protein encoded between the first in frame amino acid and the CC stop codon contains 210 residues (MW: 22.6 kDa; pI: 6.85). The CC sequence exactly matches the predicted gene F38B2.4 (210 AA). CC Homology CC BLASTp search run at NCBI on database nr on Aug 21, 2000 shows 128 CC hits with expectancy < 0.001. CC There are 6 hits in C. elegans: this gene belongs to a multigene CC family. CC Lineage report CC Based on S. Federhen and S. Shavirin's tax BLAST at NCBI, homologs CC to this gene are found in cellular organisms (a-proteobacteria, CC actinomycetes, animals, apicomplexa, aquificales, b-proteobacteria, CC birds, bony fishes, chlamydias, ciliates, cyanobacteria, CC e-proteobacteria, enterobacteria, eubacteria, eudicots, eukaryotes, CC euryarchaeotes, ferns, flatworms, flies, fungi, g-proteobacteria, CC kinetoplastids, low GC Gram+, mammals, monocots, mycoplasmas, CC nematodes, spirochetes, thermotogales). CC PFAM analysis, carried on Sean Eddy's server at CC http://pfam.wustl.edu on Aug 21, 2000 shows significant hits to : CC Motif Adenylate kinase, from 25 to 182, score 278.8, E=2.7e-81 CC 1 non relevant hit (negative score) CC Neighbors CC The XL906 gene is in a 40 kb region coding for 5 well transcribed CC genes. The closest neighbors are XL893 (on the opposite strand) CC and XL914 (on the same strand). CC Please mail any question to mieg@ncbi.nlm.nih.gov. CC Map location: XL906. XX FH Key Location/Qualifiers FH FT source 1..774 FT /organism="Caenorhabditis elegans" FT /mol_type="mRNA" FT /db_xref="taxon:6239" FT CDS 4..636 FT /codon_start=1 FT /gene="XL906" FT /product="adenylate kinase 1" FT /db_xref="GOA:Q20140" FT /db_xref="HSSP:3ADK" FT /db_xref="InterPro:IPR006267" FT /db_xref="UniProtKB/Swiss-Prot:Q20140" FT /experiment="experimental evidence, no additional details FT recorded" FT /protein_id="AAG50236.1" FT /translation="MAPTVERKNINLAPLKAAGVPIFFIVGGPGSGKGTQCDKIVAKYG FT LTHLSSGDLLRDEVKSGSPRGAQLTAIMESGALVPLEVVLDLVKEAMLKAIEKGSKGFL FT IDGYPREVAQGQQFESEIQEAKLVLFFDVAEETLVKRLLHRAQTSGRADDNADTIKKRL FT HTFVTSTAPVVDYYESKGKLVRINAEGSVDDIFAVVVANLDKATSKL" XX SQ Sequence 774 BP; 230 A; 165 C; 159 G; 220 T; 0 other; aaaatggcac caaccgttga gcgtaaaaat atcaatttgg ctccattaaa agctgccggt 60 gttccaatct tcttcattgt tggaggacca ggatctggaa agggaaccca atgtgacaaa 120 attgttgcca agtatggatt gactcacttg tcatccggag atcttctccg tgacgaagta 180 aaatctggat ctccacgtgg agcccagctc accgctatca tggagtccgg agccctcgtt 240 ccattggaag ttgttctgga cttggtcaaa gaagcaatgc tcaaggctat tgaaaaggga 300 agcaagggat tcctcattga cggataccca agagaagttg ctcaaggaca gcagttcgag 360 tctgagatcc aagaagccaa gttggtattg ttctttgatg tcgccgaaga aacgttggtc 420 aagagactct tgcatcgcgc tcaaaccagt ggaagagccg atgacaacgc tgacactatc 480 aaaaagcgtc tccatacctt tgttacctcc actgccccag ttgttgatta ctacgagtcc 540 aaaggaaaac ttgttagaat caatgccgaa ggttccgttg atgatatttt tgctgtcgta 600 gtggcaaacc tcgataaagc aacatctaag ctctaattgt ttttttttgt caactatcca 660 tcaattttcg gaaaactaga ccatcattgc tttacttaca tctaaaaaaa attattctat 720 gctccaaaaa taaaatgttt aaatttctgt acttaataaa tttttctagt ttta 774 // |
|