Promote trembls to full PR ids
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#123 Promote trembls to full PR ids
The following Tremble records have been used by GOA as isoforms in their moue gaf (column 17) which are in PRO but are dynamic and not full pro records. I have provided a PMID that demonstrates experimental evidence that the protein exists. Once converted, we can change these from UniProtKB: in our db and gaf/gpad files, to PR: ids so they will be in the mouse gpi file.
Protein AC Gene Name Annotation PMID
A0A0R4J0I9 Lrp1 PMID:24305823
E9PYV8 Adamts9 PMID:20093484
F7AAP4 Atp2b4 PMID:18591664
G5E8P4 Cobl PMID:22114352
Q1A6U9 Inpp4b PMID:16631325
Q1A6V0 Inpp4b PMID:16631325
Q1A6V1 Inpp4b PMID:16631325
Q3V4A2 Mospd3 PMID:11591653
Q3V4B7 Krtap4-6 PMID:11591653
Q545N1 Dpm2 PMID:11591653
Q545R7 Dpm2 PMID:11591653
Q60I23 Sox2 PMID:21532573
Q6AXH7 Ezh2 PMID:23624931
Q7M753 Pank2 PMID:23152917
Q80XD5 Fryl PMID:11591653
Q8BTB4 Zfp748 PMID:15469996
Q8K0M3 Sorbs3 PMID:15836771
Q8K3G7 Rtn4 PMID:15034570
Q91ZE6 Sptbn4 PMID:11807096
Q9CRS6 Krt5 PMID:11591653
Q9CYE0 Ankrd24 PMID:11591653
Q9D122 Krtap4-2 PMID:11591653
Q9D195 Lce1g PMID:11591653
Q9D1I4 Lce1f PMID:11591653
Q9D1K4 Lce1a2 PMID:11591653
Q9D7Q2 Crct1 PMID:11591653
Hi Harold
Two quick questions:
1) Some of these (for example Q9D7Q2) do not have a Swiss-Prot parent term. In such cases are these to be treated as isoforms even though they can (potentially) become the "main" entry for the encoding gene in mouse?
2) How were the specific TrEMBL entries chosen? Did they map specifically to the paper? I ask because in some cases there are multiple sequence variants from the indicated gene, and only one of them would be an exact match to the reference proteome. For example, the last on the list (Q9D7Q2, encoded by Crct1) maps to MGI:1921425. If I search UniProtKB for that MGI, I get two hits, the one given above and Q6PAI5. They are identical except for a single amino acid difference, so one of them is the canonical and the other is a sequence variant. When I look at the consensus CDS linked from the MGI page, I see that the one you chose is the variant. None of this is an issue, but it all impacts how the terms are made in PRO.
Answer to 1: yes; I can furnish the gene it's suppose to belong to if need.
2. The entries chosen for the GOA mouse ones are their curator decisions. We assume they know what they are doing. Even single amino acid differences may be important. I have actually put in varients into RACEPRO at times .
The key here is that the ids get associated with the correct gene in MGI so that they can be used.
Hi Harold,
The terms have been created. All terms were added as isoforms except where indicated. Terms with specific notes are in bold below. Let me know if you want the stanzas pasted here.
A0A0R4J0I9 Lrp1 PMID:24305823 PR:A0A0R4J0I9
E9PYV8 Adamts9 PMID:20093484 PR:E9PYV8
F7AAP4 Atp2b4 PMID:18591664 PR:F7AAP4
G5E8P4 Cobl PMID:22114352 PR:G5E8P4
Q1A6U9 Inpp4b PMID:16631325 PR:Q1A6U9
Q1A6V0 Inpp4b PMID:16631325 PR:Q1A6V0
Q1A6V1 Inpp4b PMID:16631325 PR:Q1A6V1
Q3V4A2 Mospd3 PMID:11591653 PR:Q3V4A2
Q3V4B7 Krtap4-6 PMID:11591653 PR:Q3V4B7
Q545N1 Dpm2 PMID:11591653 PR:P56873-1 (PRO term already exists; PR:Q545N1 added as alt_id; wrong gene indicated here, should be Sssca1)
Q545R7 Dpm2 PMID:11591653 PR:Q9Z324-1 (PRO term already exists; PR:Q545R7 added as an alt_id)
Q60I23 Sox2 PMID:21532573 PR:Q60I23 (sequence variant)
Q6AXH7 Ezh2 PMID:23624931 PR:Q6AXH7
Q7M753 Pank2 PMID:23152917 PR:Q7M753
Q80XD5 Fryl PMID:11591653 PR:Q8BTB4
Q8BTB4 Zfp748 PMID:15469996 PR:Q8BTB4
Q8K0M3 Sorbs3 PMID:15836771 PR:Q8K0M3
Q8K3G7 Rtn4 PMID:15034570 PR:Q8K3G7
Q91ZE6 Sptbn4 PMID:11807096 PR:Q91ZE6
Q9CRS6 Krt5 PMID:11591653 PR:Q9CRS6
Q9CYE0 Ankrd24 PMID:11591653 PR:Q9CYE0
Q9D122 Krtap4-2 PMID:11591653 PR:Q9D122
Q9D195 Lce1g PMID:11591653 PR:Q9D195
Q9D1I4 Lce1f PMID:11591653 PR:Q9D1I4
Q9D1K4 Lce1a2 PMID:11591653 PR:Q9D1K4
Q9D7Q2 Crct1 PMID:11591653 PR:Q9D7Q2