Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2679

Cannot retrieve ENA crossreferences for Uniprot sequence corresponding to EnsemblGenomes example ID

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.0, 2.10.1, 2.10.2, 2.10.2b1
    • Fix Version/s: 2.10.3, 2.10.3b1
    • Component/s: data retrieval services
    • Labels:
      None

      Description

      EnsemblGenomes has an example ID:DDB_G0283883
      This has a crossreference to uniprot: Q54Q10

      1. Showing crossreference to Uniprot only yields a transcript & product containing many '*'s (EAL65556). On 2.10.2, it takes several minutes to show this single CDS/Product sequence.

      2. Retrieving the Uniprot record Q54Q10, and then asking for ENA crossreferences results in an ENA record being retrieved, but no CDS/Protein window is shown. The corresponding record should be: EAL65284 (parent is AAFI01000105).

      Retrieving EAL65284 yields a protein with no corresponding Uniprot ID (?!) and the parent ENA record is also not retrievable.

        Attachments

          Issue Links

          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2892 Cannot recover CDS for an 'EMBLCDSPROTEIN' crossreference

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-2894 Cannot view crossreference for EnsemblGenomes: DDB_G0283883

          • Major - Major loss of function.
          • In Progress

          Bug - A problem which impairs or prevents the functions of the product. JAL-2666 No linked scrolling of CDS from peptide view of CDS/Protein products from gene query to Ensembl

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2893 Cannot roundtrip between EnsemblGenomes and Uniprot cross-refs for some IDs

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

            Activity

              People

              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: