Accessing the marker portal via REST URLs

The marker portal is a special section of the data warehouse, with a new domain id "marker". The marker domain used by this portal allows the search of a single marker (using a marker symbol listed below) and any taxonomic search to narrow the results to the taxa of interest. No other fields are currently searchable for this domain.

Markers

There are currently 22 coding and 5 noncoding markers available for searching:

Marker symbol Marker description
ACACA Acetyl-CoA carboxylase
ATP5B ATP synthase beta-subunit
BETA-ACTIN Actin, beta
COX1 Cytochrome C oxidase subunit I
CYTB Cytochrome B
EEF1A Elongation factor 1-alpha
EEF2K Eukaryotic elongation factor-2 kinase
MATK Maturase K
MDH Malate dehydrogenase
NAD1 NADH dehydrogenase subunit 1 (ndhA)
NAD2 NADH dehydrogenase subunit 2 (ndhB)
NAD3 NADH dehydrogenase subunit 3 (ndhC)
NAD4 NADH dehydrogenase subunit 4 (ndhD)
NAD5 NADH dehydrogenase subunit 5 (ndhF)
PETD petD cytochrome b6/f complex subunit 4
POLR2B Polymerase (RNA) II (DNA directed) polypeptide B
RAG1 Recombination activating gene 1
RAG2 Recombination activating gene 2
RBCL Ribulose bisophosphate carboxylase
RHOD Rhodopsin
TUBA Alpha tubulin
TUBB Tubulin, beta class I
12S 12S rRNA
16S 16S rRNA
18S 18S rRNA
23S 23S rRNA
28S 28S rRNA

Result IDs

Downloading/displaying reports, sequences and taxonomic coverage information, all require the result to be set. The valid result IDs for these searches are:

  • Coding markers: coding_release and coding_update
  • Non-coding markers: noncoding_release and noncoding_udpate

Examples

Download all CDS and parent accessions for mammalian COX1 sequences from the latest release:
http://www.ebi.ac.uk/ena/data/warehouse/search?query="marker="COX1"%20AND%20tax_tree(40674)"&domain=marker&result=coding_release&fields=parent_accession&display=report

Display FASTA sequences for all mammalian COX1 sequences from the latest release:
http://www.ebi.ac.uk/ena/data/warehouse/search?query="marker="COX1"%20AND%20tax_tree(40674)"&domain=marker&result=coding_release&display=fasta

Display the mammalian taxonomic coverage (with sequence counts) for COX1 from the latest release:
http://www.ebi.ac.uk/ena/data/warehouse/search?query="marker="COX1"%20AND%20tax_tree(40674)"&domain=marker&result=coding_release&display=marker

Note to download the taxonomic coverage above, append &download=marker to the end of the URL

Latest ENA news

11 Oct 2017: Read data download issues resolved

Read data download issues previously affecting ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk services now resolved.

06 Oct 2017: ENA read data download issues

Issues with read data download from ftp.sra.ebi.ac.uk and fasp.sra.ebi.ac.uk

04 Oct 2017: ENA Release 133

Release 133 of ENA's assembled/annotated sequences now available