Suggestions for RefGen jamboree annotation targets (Archived)

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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