Suggestions for RefGen jamboree annotation targets (Archived): Difference between revisions
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[[Category:Reference Genome]] | |||
Please note here any genes that you think might be suitable for a Reference Genome jamboree. | Please note here any genes that you think might be suitable for a Reference Genome jamboree. | ||
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~17 papers | ~17 papers | ||
|(UniProtKB:P49337)~10 | |(UniProtKB:P49337)~10 | ||
| | |no ortholog in set | ||
| (UniProtKB:P56705)~70 | | (UniProtKB:P56705)~70 | ||
| (MGI:98957) ~65 | | (MGI:98957) ~65 | ||
| (RGD:621348) ~40 | | (RGD:621348) ~40 | ||
| (no ortholog) 0 | | (no ortholog) 0 | ||
| | |(no ortholog) 0 | ||
|ZDB-GENE-980526-352 wnt4a Q1RLW9 ~16; ZDB-GENE-000411-1 wnt4b Q9IAU3 ~2 | |ZDB-GENE-980526-352 wnt4a Q1RLW9 ~16; ZDB-GENE-000411-1 wnt4b Q9IAU3 ~2 | ||
|- | |- | ||
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|http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL916 | |http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL916 | ||
|none | |none | ||
| none | |none | ||
|(UniProtKB:P24014, FB:FBgn0003425) ~100 | |(UniProtKB:P24014, FB:FBgn0003425) ~100 | ||
| WB:WBGene00004854 (F40E10.4 · slt-1) · UniProtKB:Q20204 | | WB:WBGene00004854 (F40E10.4 · slt-1) · UniProtKB:Q20204 | ||
Line 47: | Line 48: | ||
|(UniProtKB:Q90WZ2, | |(UniProtKB:Q90WZ2, | ||
UniProtKB:Q90XG2, | UniProtKB:Q90XG2, | ||
UniProtKB:Q90Z44) | UniProtKB:Q90Z44)~10 papers | ||
|no ortholog in set | |||
| | |||
|(UniProtKB:O94813) ~60 | |(UniProtKB:O94813) ~60 | ||
|(MGI:1315205) ~35 | |(MGI:1315205) ~35 | ||
|(RGD:69310) ~40 | |(RGD:69310) ~40 | ||
|(no ortholog) 0 | |(no ortholog) 0 | ||
| | |(no ortholog) 0 | ||
| | | UniProtKB:Q3S2J2 · ZFIN:ZDB-GENE-030722-3 (slit1a) ~11, UniProtKB:Q3Y6S4 · ZFIN:ZDB-GENE-030722-4 (slit1b) ~8, UniProtKB:Q9DE36 · ZFIN:ZDB-GENE-010306-3 (slit2) ~12, UniProtKB:Q9DE37 · ZFIN:ZDB-GENE-010306-4 (slit3) ~11 | ||
|- | |- | ||
Line 66: | Line 65: | ||
| WB:WBGene00007048 (C16A3.7 · tag-182) · UniProtKB:Q18034 | | WB:WBGene00007048 (C16A3.7 · tag-182) · UniProtKB:Q18034 | ||
0 papers | 0 papers | ||
|(GenBank:XP_418890) | |(GenBank:XP_418890)No papers | ||
No papers | |||
| | | | ||
|(UniProtKB:Q12986) ~8 | |(UniProtKB:Q12986) ~8 | ||
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|(RGD:1310277) - 0 | |(RGD:1310277) - 0 | ||
|(SGD:S000004968) 7 | |(SGD:S000004968) 7 | ||
| | |(GeneDB_Spombe:SPCC18.03) No papers | ||
| | |No ortholog in set | ||
|- | |- | ||
| ATF6B (Cyclic AMP-dependent transcription factor ATF-6 beta) | | ATF6B (Cyclic AMP-dependent transcription factor ATF-6 beta) | ||
Line 85: | Line 82: | ||
~9 papers | ~9 papers | ||
|No ortholog | |No ortholog | ||
| | |no ortholog in set | ||
|(UniProtKB:Q99941) ~40 | |(UniProtKB:Q99941) ~40 | ||
|(MGI:105121) ~ 3 | |(MGI:105121) ~ 3 | ||
|(RGD:1303317) - 0 | |(RGD:1303317) - 0 | ||
|(no ortholog) 0 | |(no ortholog) 0 | ||
| | |(no ortholog) 0 | ||
| | |Q5RH85 si:ch211-199m3.9 ZDB-GENE-041014-328 ~0 | ||
|- | |- | ||
| SIR2 (NAD-dependent histone deacetylase SIR2 of the Sirtuin family involved in regulation of lifespan, EC=3.5.1.-) | | SIR2 (NAD-dependent histone deacetylase SIR2 of the Sirtuin family involved in regulation of lifespan, EC=3.5.1.-) | ||
|http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/Para1362 | |http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/Para1362 | ||
|(TAIR:AT5G55760) (UniProtKB:Q9FE17) ~2 | |(TAIR:AT5G55760) (UniProtKB:Q9FE17) ~2 | ||
| | | DDB_G0289967 (sir2D): none; there is another gene in the same family that has 1 paper | ||
|(UniProtKB:Q9VK34, FB:FBgn0024291) ~11 | |(UniProtKB:Q9VK34, FB:FBgn0024291) ~11 | ||
| WB:WBGene00004800 (R11A8.4 · sir-2.1) · UniProtKB:Q21921 (R11A8.4 · SIRT1_CAEEL · sir-2.1) | | WB:WBGene00004800 (R11A8.4 · sir-2.1) · UniProtKB:Q21921 (R11A8.4 · SIRT1_CAEEL · sir-2.1) | ||
~40 papers | ~40 papers | ||
|(UniProtKB:Q68BG0)1 paper | |(UniProtKB:Q68BG0)1 paper | ||
|(UniProtKB:P75960) | |(UniProtKB:P75960) ~ 5 | ||
|(UniProtKB:Q96EB6) ~115 | |(UniProtKB:Q96EB6) ~115 | ||
|(MGI:2135607) ~ 49 | |(MGI:2135607) ~ 49 | ||
|(RGD:1308542) ~36 | |(RGD:1308542) ~36 | ||
|(SGD:S000005429; SGD:S000005936; SGD:S000005551; SGD:S000002599; SGD:S000002200) ~640 [even if we chose to do JUST SIR2 and not the related 4 proteins, that would still be 592 papers] | |(SGD:S000005429; SGD:S000005936; SGD:S000005551; SGD:S000002599; SGD:S000002200) ~640 [even if we chose to do JUST SIR2 and not the related 4 proteins, that would still be 592 papers] | ||
|( | |(GeneDB_Spombe:Hst2,Hst4,Sir2) ~24 | ||
|UniProtKB:Q7ZVK3 · ZFIN:ZDB-GENE-030131-1028 (sirt2) ~0, UniProtKB:A1L2B7 · ZFIN:ZDB-GENE-070112-1762 (sirt3) ~0, UniProtKB:Q1LWD1 ZDB-GENE-061207-46 (si:dkey-103i16.6) ~0, ZFIN:ZDB-GENE-041010-65 (zgc:103539) UniProtKB:Q5XJ86 ~0, UniProtKB:Q6DHI5 · ZFIN:ZDB-GENE-040718-349 (sirt5) ~0, UniProtKB:Q6IQK0 · ZFIN:ZDB-GENE-031007-2 (sirt6) ~0, | |||
| | |||
|- | |- | ||
| ELAC2 (tRNA 3'-processing endonuclease; defects are involved in prostate cancer) | | ELAC2 (tRNA 3'-processing endonuclease; defects are involved in prostate cancer) | ||
|http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1557 | |http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1557 | ||
| | |(TAIR:AT1G52160,AT3G16260) 1 paper | ||
| | | DDB_G0276633, DDB_G0290623 and DDB_G0277337 None | ||
| | |(UniProtKB:Q8MKW7, FB:FBgn0028426) ~20 | ||
| WB:WBGene00001983 (hoe-1 · E04A4.4) · UniProtKB:O44476 | | WB:WBGene00001983 (hoe-1 · E04A4.4) · UniProtKB:O44476 | ||
1 paper | 1 paper | ||
| | | Genbank:XP_415584 No papers | ||
| | |no ortholog in set | ||
| (UniProtKB:Q9BQ52) ~6 | | (UniProtKB:Q9BQ52) ~6 | ||
| | | (MGI:1890496) ~3 | ||
| | | (RGD:628882) ~4 | ||
|(SGD:S000001787) ~13 | |(SGD:S000001787) ~13 | ||
| | |(GeneDB_Spombe:SPAC1D4.10) 1 paper | ||
| | |ZFIN:ZDB-GENE-041111-227 (im:7145112) · UniProtKB:Q6DG69 ~0 | ||
|- | |- | ||
|SURF1 (involved in assembly of cytochrome c oxidase; defects are a cause of Leigh syndrome) | |SURF1 (involved in assembly of cytochrome c oxidase; defects are a cause of Leigh syndrome) | ||
|http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1594 | |http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1594 | ||
| | |(TAIR:AT1G48510,AT3G17910) 1 paper for second gene, only a HTP one for the first | ||
| | | DDB_G0272889 none | ||
| | |(UniProtKB:Q9U4F3, FB:FBgn0029117) ~1 | ||
| WB:WBGene00004787 · UniProtKB:Q9N5N8 | | WB:WBGene00004787 · UniProtKB:Q9N5N8 | ||
0 papers | 0 papers | ||
| | |(UniProtKB:Q800L1) No papers | ||
| | |no ortholog in set | ||
| (UniProtKB:Q15526) ~30 | | (UniProtKB:Q15526) ~30 | ||
| | | (MGI:98443) ~10 | ||
| | | (RGD:620527) ~3 | ||
|(SGD:S000003344) ~41 | |(SGD:S000003344) ~41 | ||
| | |(GeneDB_Spombe:SPC1215.01) No papers | ||
| | |UniProtKB:A5WUL6 · ZFIN:ZDB-GENE-041108-2 (surf1) ~1 | ||
|- | |- | ||
|NIPBL (involved in sister chromatid cohesion; defects are the cause of Cornelia de Lange syndrome type 1 (CDLS1)) | |NIPBL (involved in sister chromatid cohesion; defects are the cause of Cornelia de Lange syndrome type 1 (CDLS1)) | ||
|http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1223 | |http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1223 | ||
| | |(TAIR:AT5G15540) 2 papers | ||
| | | DDB_G0283099 none | ||
| | |(UniProtKB:Q7PLI2, FB:FBgn0026401) ~4 | ||
| WB:WBGene00004166 (Y43H11AL.3 · pqn-85) · UniProtKB:Q95XZ5 | | WB:WBGene00004166 (Y43H11AL.3 · pqn-85) · UniProtKB:Q95XZ5 | ||
2 papers | 2 papers | ||
| | | no ortholog | ||
| | |no ortholog in set | ||
|(UniProtKB:Q6KC79)~19 | |(UniProtKB:Q6KC79)~19 | ||
| | |(MGI:1913976) ~1 | ||
| | | (RGD:1306393) ~6 | ||
|(SGD:S000002588) ~ 45 | |(SGD:S000002588) ~ 45 | ||
| | |(G eneDB_Spombe:Mis4) ~13 | ||
| | |ENSEMBL:ENSDARP00000081088 ZDB-GENE-030131-6070 (nipblb) ~1, UniProtKB:A2BGN3 ZDB-GENE-060526-121 (nipbla) 0 | ||
|- | |- | ||
| | | |
Latest revision as of 09:42, 12 April 2019
Please note here any genes that you think might be suitable for a Reference Genome jamboree.
All groups that participate in the jamboree should note the amount of literature that is available for each proposed target. Therefore the aim would be to select two targets for a jamboree that have the widest spread of literature across all participating groups.
In addition, please indicate your preferred date for the RefGen call, by visiting: http://www.doodle.com/a4h2u7hdcmqieiir
Target Gene Name | PPOD URL | Arabidopsis ID & papers | Dicty ID & papers | Drosophila ID & papers | C.elegans ID & papers | Chicken ID & papers | E.coli ID & papers | Human ID & papers | Mouse ID & papers | Rat ID & papers | S.cerevisiae ID & papers | S.pombe ID & papers | Zebrafish ID & papers | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WNT4 (Ligand for frizzled family of transmembrane receptors. Probable developmental protein. Possible signaling molecule which affects the development of discrete regions of tissues) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL5001 | none | none | none | WB:WBGene00000857 (cwn-1 · K10B4.6) · UniProtKB:P34888
~17 papers |
(UniProtKB:P49337)~10 | no ortholog in set | (UniProtKB:P56705)~70 | (MGI:98957) ~65 | (RGD:621348) ~40 | (no ortholog) 0 | (no ortholog) 0 | ZDB-GENE-980526-352 wnt4a Q1RLW9 ~16; ZDB-GENE-000411-1 wnt4b Q9IAU3 ~2 | |
SLIT2 (molecular guidance cue in cellular migration) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL916 | none | none | (UniProtKB:P24014, FB:FBgn0003425) ~100 | WB:WBGene00004854 (F40E10.4 · slt-1) · UniProtKB:Q20204
~27 papers |
(UniProtKB:Q90WZ2,
UniProtKB:Q90XG2, UniProtKB:Q90Z44)~10 papers |
no ortholog in set | (UniProtKB:O94813) ~60 | (MGI:1315205) ~35 | (RGD:69310) ~40 | (no ortholog) 0 | (no ortholog) 0 | UniProtKB:Q3S2J2 · ZFIN:ZDB-GENE-030722-3 (slit1a) ~11, UniProtKB:Q3Y6S4 · ZFIN:ZDB-GENE-030722-4 (slit1b) ~8, UniProtKB:Q9DE36 · ZFIN:ZDB-GENE-010306-3 (slit2) ~12, UniProtKB:Q9DE37 · ZFIN:ZDB-GENE-010306-4 (slit3) ~11 | |
NFX1 (Nuclear transcription factor). In mammals may be involved in regulating duration of an inflammatory response) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL3955 | (TAIR:AT1G10170)(UniProtKB:Q9SY59) ~8 | DDB_G0293590 : 1 HTP | (UniProtKB:P40798, FB:FBgn0001978) ~3 | WB:WBGene00007048 (C16A3.7 · tag-182) · UniProtKB:Q18034
0 papers |
(GenBank:XP_418890)No papers | (UniProtKB:Q12986) ~8 | (MGI:1921414) ~ 2 | (RGD:1310277) - 0 | (SGD:S000004968) 7 | (GeneDB_Spombe:SPCC18.03) No papers | No ortholog in set | ||
ATF6B (Cyclic AMP-dependent transcription factor ATF-6 beta) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL4962 | none | none | (UniProtKB:Q8SX87, FB:FBgn0033010) 0 | WB:WBGene00000222 (F45E6.2 · atf-6) · UniProtKB:Q20435 (F45E6.2 · atf-6)
~9 papers |
No ortholog | no ortholog in set | (UniProtKB:Q99941) ~40 | (MGI:105121) ~ 3 | (RGD:1303317) - 0 | (no ortholog) 0 | (no ortholog) 0 | Q5RH85 si:ch211-199m3.9 ZDB-GENE-041014-328 ~0 | |
SIR2 (NAD-dependent histone deacetylase SIR2 of the Sirtuin family involved in regulation of lifespan, EC=3.5.1.-) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/Para1362 | (TAIR:AT5G55760) (UniProtKB:Q9FE17) ~2 | DDB_G0289967 (sir2D): none; there is another gene in the same family that has 1 paper | (UniProtKB:Q9VK34, FB:FBgn0024291) ~11 | WB:WBGene00004800 (R11A8.4 · sir-2.1) · UniProtKB:Q21921 (R11A8.4 · SIRT1_CAEEL · sir-2.1)
~40 papers |
(UniProtKB:Q68BG0)1 paper | (UniProtKB:P75960) ~ 5 | (UniProtKB:Q96EB6) ~115 | (MGI:2135607) ~ 49 | (RGD:1308542) ~36 | (SGD:S000005429; SGD:S000005936; SGD:S000005551; SGD:S000002599; SGD:S000002200) ~640 [even if we chose to do JUST SIR2 and not the related 4 proteins, that would still be 592 papers] | (GeneDB_Spombe:Hst2,Hst4,Sir2) ~24 | UniProtKB:Q7ZVK3 · ZFIN:ZDB-GENE-030131-1028 (sirt2) ~0, UniProtKB:A1L2B7 · ZFIN:ZDB-GENE-070112-1762 (sirt3) ~0, UniProtKB:Q1LWD1 ZDB-GENE-061207-46 (si:dkey-103i16.6) ~0, ZFIN:ZDB-GENE-041010-65 (zgc:103539) UniProtKB:Q5XJ86 ~0, UniProtKB:Q6DHI5 · ZFIN:ZDB-GENE-040718-349 (sirt5) ~0, UniProtKB:Q6IQK0 · ZFIN:ZDB-GENE-031007-2 (sirt6) ~0, | |
ELAC2 (tRNA 3'-processing endonuclease; defects are involved in prostate cancer) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1557 | (TAIR:AT1G52160,AT3G16260) 1 paper | DDB_G0276633, DDB_G0290623 and DDB_G0277337 None | (UniProtKB:Q8MKW7, FB:FBgn0028426) ~20 | WB:WBGene00001983 (hoe-1 · E04A4.4) · UniProtKB:O44476
1 paper |
Genbank:XP_415584 No papers | no ortholog in set | (UniProtKB:Q9BQ52) ~6 | (MGI:1890496) ~3 | (RGD:628882) ~4 | (SGD:S000001787) ~13 | (GeneDB_Spombe:SPAC1D4.10) 1 paper | ZFIN:ZDB-GENE-041111-227 (im:7145112) · UniProtKB:Q6DG69 ~0 | |
SURF1 (involved in assembly of cytochrome c oxidase; defects are a cause of Leigh syndrome) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1594 | (TAIR:AT1G48510,AT3G17910) 1 paper for second gene, only a HTP one for the first | DDB_G0272889 none | (UniProtKB:Q9U4F3, FB:FBgn0029117) ~1 | WB:WBGene00004787 · UniProtKB:Q9N5N8
0 papers |
(UniProtKB:Q800L1) No papers | no ortholog in set | (UniProtKB:Q15526) ~30 | (MGI:98443) ~10 | (RGD:620527) ~3 | (SGD:S000003344) ~41 | (GeneDB_Spombe:SPC1215.01) No papers | UniProtKB:A5WUL6 · ZFIN:ZDB-GENE-041108-2 (surf1) ~1 | |
NIPBL (involved in sister chromatid cohesion; defects are the cause of Cornelia de Lange syndrome type 1 (CDLS1)) | http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO3/OrthoMCL1223 | (TAIR:AT5G15540) 2 papers | DDB_G0283099 none | (UniProtKB:Q7PLI2, FB:FBgn0026401) ~4 | WB:WBGene00004166 (Y43H11AL.3 · pqn-85) · UniProtKB:Q95XZ5
2 papers |
no ortholog | no ortholog in set | (UniProtKB:Q6KC79)~19 | (MGI:1913976) ~1 | (RGD:1306393) ~6 | (SGD:S000002588) ~ 45 | (G eneDB_Spombe:Mis4) ~13 | ENSEMBL:ENSDARP00000081088 ZDB-GENE-030131-6070 (nipblb) ~1, UniProtKB:A2BGN3 ZDB-GENE-060526-121 (nipbla) 0 | |