reference genome annotation

pombase-admin commented 15 years ago

Spreadsheet http://spreadsheets.google.com/ccckey=pZhlLFuj8ewDe799QTmxzCA&hl=en12:42

eg http://proto.informatics.jax.org/prototypes/GOgraphEX/PPOD12\_Graph/ORTHOMCL1245.html

AUG-FEB PMID: 18820293 rps2 PMID: 2834104 PMID:14623272 ? done?

Need to add pre August list

Original comment by: ValWood

pombase-admin commented 15 years ago

suggested targets

pombelist

Original comment by: ValWood

pombase-admin commented 15 years ago

March curation targets are available here:

http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en

Original comment by: ValWood

pombase-admin commented 15 years ago

March curation targets are available here:

http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en

Original comment by: ValWood

pombase-admin commented 15 years ago

The April curation targets are now available on the google speadsheet: http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en

The list was compiled by Kara, is based on a protein suggested by Harold (GTF2I), the rest of the Reactome complex in which that protein is found + the TFIID complex to bring us to 27 targets.

Original comment by: ValWood

pombase-admin commented 15 years ago

priority: 5 --> 3

Original comment by: ValWood

pombase-admin commented 15 years ago

The annotation targets for May are ready: http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en

Original comment by: ValWood

pombase-admin commented 15 years ago

June targets are available:

http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en

I would like to bring your attention to OrthoMCL910: EIF5A : previously universally annotated as translation initiation factor but demonstrated in Nature a couple of weeks ago to have a role in elongation

Original comment by: ValWood

pombase-admin commented 15 years ago

Below are the targets for August; these are based on the PANTHER families, so while there are only three lines in the spreadsheet (http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en), there are more three proteins to do per MOD. ;) These are available via the wiki links in the spreadsheet and I also pasted them below. Thanks to E. coli folks for sending along the suggestions.

-Kara

* PTHR12383 HUMAN ENSEMBL:ENSG00000148950 UniProtKB=Q96LU5

PTHR12383 MOUSE MGI:MGI:3645325 NCBI=NP_001104750
PTHR12383 MOUSE MGI:MGI:1913791 UniProtKB=Q9CQU8
PTHR12383 RAT RGD:1565697 NCBI=XP_345414
PTHR12383 RAT RGD:1586505 NCBI=XP_001073644
PTHR12383 RAT RGD:1587441 NCBI=XP_001076990
PTHR12383 CHICK ENTREZ:771365 NCBI=XP_001233149
PTHR12383 DANRE ENSEMBL:ENSDARG00000045935 ENSEMBL=ENSDARP00000067519
PTHR12383 CAEEL WB:WBGene00007021 UniProtKB=Q9XVD2
PTHR12383 DROME FB:FBgn0030669 UniProtKB=Q8SZ24
PTHR12383 YEAST SGD:S000004758 UniProtKB=P28627
PTHR12383 SCHPO GeneDB_Spombe:SPBC2D10.07c UniProtKB=O74800
PTHR12383 DICDI dictyBase:DDB_G0283049 UniProtKB=Q54RP1
PTHR12383 HUMAN ENSEMBL:ENSG00000184903 UniProtKB=Q96T52
PTHR12383 MOUSE MGI:MGI:2135611 UniProtKB=Q8BPT6
PTHR12383 RAT RGD:1561404 NCBI=XP_576024
PTHR12383 CHICK ENTREZ:417780 NCBI=XP_416025
PTHR12383 DANRE ZFIN:ZDB-GENE-040808-9 UniProtKB=Q6AZD4
PTHR12383 CAEEL WB:WBGene00021925 UniProtKB=Q9N371
PTHR12383 DROME FB:FBgn0034535 UniProtKB=Q4QQ12
PTHR12383 YEAST SGD:S000004638 UniProtKB=P46972
PTHR12383 SCHPO GeneDB_Spombe:SPBC336.13c UniProtKB=Q9UST2
PTHR12383 ECOLI ECOLI:EG10530-MONOMER UniProtKB=P00803

* PTHR11679 HUMAN ENSEMBL:ENSG00000116266 UniProtKB=O00186

PTHR11679 MOUSE MGI:MGI:3586869 NCBI=NP_001025488
PTHR11679 MOUSE MGI:MGI:107362 UniProtKB=Q60770
PTHR11679 RAT RGD:619968 UniProtKB=Q99PV2
PTHR11679 CHICK ENTREZ:424341 UniProtKB=Q5ZIM9
PTHR11679 DANRE ZFIN:ZDB-GENE-040426-2833 UniProtKB=Q6PD84
PTHR11679 HUMAN ENSEMBL:ENSG00000184178 UniProtKB=Q8WU76
PTHR11679 MOUSE MGI:MGI:2443446 UniProtKB=Q8BTY8
PTHR11679 RAT RGD:1562708 UniProtKB=Q5U2R9
PTHR11679 CHICK ENTREZ:770088 NCBI=XP_001233406
PTHR11679 HUMAN ENSEMBL:ENSG00000076944 UniProtKB=Q15833
PTHR11679 MOUSE MGI:MGI:107370 UniProtKB=Q64324
PTHR11679 RAT RGD:619967 UniProtKB=Q62753
PTHR11679 DANRE ZFIN:ZDB-GENE-040426-2482 UniProtKB=Q6NUX6
PTHR11679 HUMAN ENSEMBL:ENSG00000136854 UniProtKB=P61764
PTHR11679 MOUSE MGI:MGI:107363 UniProtKB=O08599
PTHR11679 RAT RGD:3785 UniProtKB=P61765
PTHR11679 CHICK ENTREZ:404293 UniProtKB=Q6R748
PTHR11679 DANRE ENSEMBL:ENSDARG00000056036 UniProtKB=A2BGE0
PTHR11679 DANRE ZFIN:ZDB-GENE-050626-106 UniProtKB=Q4QRD0
PTHR11679 CAEEL WB:WBGene00020298 UniProtKB=O44412
PTHR11679 CAEEL WB:WBGene00006757 UniProtKB=P34815
PTHR11679 DROME FB:FBgn0004574 UniProtKB=Q07327
PTHR11679 YEAST SGD:S000002571 UniProtKB=P30619
PTHR11679 SCHPO GeneDB_Spombe:SPCC584.05 UniProtKB=O94590
PTHR11679 DICDI dictyBase:DDB_G0277343 UniProtKB=Q54ZW8
PTHR11679 DICDI dictyBase:DDB_G0283937 UniProtKB=Q54QC8
PTHR11679 HUMAN ENSEMBL:ENSG00000184056 UniProtKB=Q9H267
PTHR11679 MOUSE MGI:MGI:2446237 UniProtKB=P59016
PTHR11679 RAT RGD:620644 UniProtKB=Q63616
PTHR11679 CHICK ENTREZ:425858 UniProtKB=Q5ZL71
PTHR11679 DANRE ZFIN:ZDB-GENE-050327-73 UniProtKB=Q58EN8
PTHR11679 HUMAN ENSEMBL:ENSG00000139719 UniProtKB=Q96AX1
PTHR11679 MOUSE MGI:MGI:1924823 UniProtKB=Q9D2N9
PTHR11679 RAT RGD:620643 UniProtKB=Q63615
PTHR11679 CHICK ENTREZ:416861 NCBI=XP_415153
PTHR11679 DANRE ENSEMBL:ENSDARG00000067559 ENSEMBL=ENSDARP00000088013
PTHR11679 DANRE ENSEMBL:ENSDARG00000010902 ENSEMBL=ENSDARP00000013152
PTHR11679 CAEEL WB:WBGene00016960 UniProtKB=Q18891
PTHR11679 CAEEL WB:WBGene00015130 UniProtKB=P34260
PTHR11679 DROME FB:FBgn0039335 UniProtKB=Q9VBR1
PTHR11679 DROME FB:FBgn0000257 UniProtKB=Q9Y1I2
PTHR11679 YEAST SGD:S000004388 UniProtKB=P20795
PTHR11679 SCHPO GeneDB_Spombe:SPBC1703.15c UniProtKB=Q9P7V6
PTHR11679 DICDI dictyBase:DDB_G0276239 UniProtKB=Q552I9
PTHR11679 DICDI dictyBase:DDB_G0282017 UniProtKB=Q54T42
PTHR11679 DICDI dictyBase:DDB_G0291097 UniProtKB=Q54F53
PTHR11679 HUMAN ENSEMBL:ENSG00000136631 UniProtKB=Q9NRW7
PTHR11679 MOUSE MGI:MGI:891965 UniProtKB=P97390
PTHR11679 RAT RGD:621267 UniProtKB=O08700
PTHR11679 CHICK ENTREZ:770545 NCBI=XP_001233883
PTHR11679 CHICK ENTREZ:430741 UniProtKB=Q5ZJG4
PTHR11679 DANRE ENSEMBL:ENSDARG00000061180 ENSEMBL=ENSDARP00000081395
PTHR11679 CAEEL WB:WBGene00016643 UniProtKB=Q18609
PTHR11679 DROME FB:FBgn0037711 UniProtKB=Q9VHB5
PTHR11679 YEAST SGD:S000003063 UniProtKB=P38932
PTHR11679 SCHPO GeneDB_Spombe:SPAC2G11.03c UniProtKB=Q09805
PTHR11679 DICDI dictyBase:DDB_G0276205 UniProtKB=Q552H9
PTHR11679 DICDI dictyBase:DDB_G0290213 UniProtKB=Q54GE3
PTHR11679 HUMAN ENSEMBL:ENSG00000092108 UniProtKB=Q8WVM8
PTHR11679 MOUSE MGI:MGI:1924233 UniProtKB=Q8BRF7
PTHR11679 RAT RGD:619828 UniProtKB=Q62991
PTHR11679 CHICK ENTREZ:423307 NCBI=XP_421224
PTHR11679 DANRE ZFIN:ZDB-GENE-030116-3 UniProtKB=Q8AUT3
PTHR11679 CAEEL WB:WBGene00009654 UniProtKB=Q20364
PTHR11679 DROME FB:FBgn0015816 UniProtKB=Q24179
PTHR11679 YEAST SGD:S000002597 UniProtKB=P22213
PTHR11679 SCHPO GeneDB_Spombe:SPCC74.01 UniProtKB=O74534
PTHR11679 DICDI dictyBase:DDB_G0288719 UniProtKB=Q54IJ1

* PTHR11200 DROME FB:FBgn0038890 UniProtKB=Q9VD98

PTHR11200 HUMAN ENSEMBL:ENSG00000198825 UniProtKB=Q9Y2H2
PTHR11200 MOUSE MGI:MGI:2141867 UniProtKB=Q8CDA1
PTHR11200 RAT RGD:1305777 NCBI=XP_001080439
PTHR11200 CHICK ENTREZ:423932 NCBI=XP_421792
PTHR11200 DANRE ENSEMBL:ENSDARG00000061437 ENSEMBL=ENSDARP00000082038
PTHR11200 HUMAN ENSEMBL:ENSG00000211456 UniProtKB=Q9NTJ5
PTHR11200 MOUSE MGI:MGI:1933169 UniProtKB=Q9EP69
PTHR11200 RAT RGD:69223 UniProtKB=Q9ES21
PTHR11200 CHICK ENTREZ:420700 NCBI=XP_418799
PTHR11200 DANRE ZFIN:ZDB-GENE-060503-122 UniProtKB=A4VCH0
PTHR11200 DANRE ZFIN:ZDB-GENE-070112-542 UniProtKB=A1L244
PTHR11200 CAEEL WB:WBGene00012353 UniProtKB=Q9U330
PTHR11200 CAEEL WB:WBGene00009264 UniProtKB=Q93641
PTHR11200 DROME FB:FBgn0035195 UniProtKB=Q9W0I6
PTHR11200 YEAST SGD:S000001695 UniProtKB=P32368
PTHR11200 SCHPO GeneDB_Spombe:SPAC3C7.01c UniProtKB=O14127
PTHR11200 SCHPO GeneDB_Spombe:SPBC19F5.03 UniProtKB=O60162
PTHR11200 DICDI dictyBase:DDB_G0274537 UniProtKB=Q86HL0
PTHR11200 DICDI dictyBase:DDB_G0290653 UniProtKB=Q54FY6
PTHR11200 DICDI dictyBase:DDB_G0292392 UniProtKB=Q54D97
PTHR11200 DICDI dictyBase:DDB_G0271630 UniProtKB=Q55AW9
PTHR11200 HUMAN ENSEMBL:ENSG00000198574 UniProtKB=O14796
PTHR11200 MOUSE MGI:MGI:3622649 NCBI=NP_001028671
PTHR11200 RAT RGD:1589042 NCBI=XP_001065477
PTHR11200 RAT RGD:1590159 NCBI=XP_001076713
PTHR11200 RAT RGD:1563884 NCBI=XP_577284
PTHR11200 MOUSE MGI:MGI:1349420 UniProtKB=O35324
PTHR11200 RAT RGD:1563935 NCBI=XP_577285
PTHR11200 CHICK ENTREZ:418411 NCBI=XP_416626
PTHR11200 HUMAN ENSEMBL:ENSG00000183918 UniProtKB=O60880
PTHR11200 MOUSE MGI:MGI:1328352 UniProtKB=O88890
PTHR11200 RAT RGD:1562408 NCBI=XP_001059172
PTHR11200 HUMAN ENSEMBL:ENSG00000112367 UniProtKB=Q92562
PTHR11200 MOUSE MGI:MGI:2143585 UniProtKB=Q91WF7
PTHR11200 RAT RGD:1559789 NCBI=XP_574790
PTHR11200 RAT RGD:1311375 UniProtKB=Q0Z843
PTHR11200 CHICK ENTREZ:421762 NCBI=NP_001108095
PTHR11200 DANRE ENSEMBL:ENSDARG00000037566 ENSEMBL=ENSDARP00000054705
PTHR11200 CAEEL WB:WBGene00007912 UniProtKB=P90770
PTHR11200 DROME FB:FBgn0031611 UniProtKB=Q9VR06
PTHR11200 YEAST SGD:S000005269 UniProtKB=P42837
PTHR11200 SCHPO GeneDB_Spombe:SPAC1093.03 UniProtKB=Q7Z9H9
PTHR11200 DICDI dictyBase:DDB_G0281427 UniProtKB=Q54TZ3
PTHR11200 HUMAN ENSEMBL:ENSG00000132376 UniProtKB=Q9BT40
PTHR11200 MOUSE MGI:MGI:1194899 UniProtKB=Q8C5L6
PTHR11200 RAT RGD:1359130 UniProtKB=Q5XIU8
PTHR11200 CHICK ENTREZ:771549 NCBI=XP_001234813
PTHR11200 HUMAN ENSEMBL:ENSG00000185133 UniProtKB=Q15735
PTHR11200 MOUSE MGI:MGI:2158663 UniProtKB=P59644
PTHR11200 RAT RGD:620541 UniProtKB=Q9JMC1
PTHR11200 CHICK ENTREZ:416996 NCBI=XP_415287
PTHR11200 DROME FB:FBgn0034179 UniProtKB=Q7K161
PTHR11200 DROME FB:FBgn0030761 UniProtKB=Q9VXE7
PTHR11200 HUMAN ENSEMBL:ENSG00000168918 UniProtKB=Q92835
PTHR11200 MOUSE MGI:MGI:107357 UniProtKB=Q9ES52
PTHR11200 RAT RGD:2914 UniProtKB=P97573
PTHR11200 CHICK ENTREZ:424745 NCBI=XP_422567
PTHR11200 DANRE ENSEMBL:ENSDARG00000052515 UniProtKB=Q503S7
PTHR11200 DANRE ENSEMBL:ENSDARG00000070900 UniProtKB=Q1L8C4
PTHR11200 HUMAN ENSEMBL:ENSG00000165458 UniProtKB=O15357
PTHR11200 MOUSE MGI:MGI:1333787 UniProtKB=Q6P549
PTHR11200 RAT RGD:68396 UniProtKB=Q9WVR3
PTHR11200 CHICK ENTREZ:428692 NCBI=XP_426250
PTHR11200 DANRE ENSEMBL:ENSDARG00000034319 UniProtKB=Q2I6J0
PTHR11200 DANRE ENSEMBL:ENSDARG00000001442 UniProtKB=Q1LY73
PTHR11200 DANRE ENSEMBL:ENSDARG00000030146 ENSEMBL=ENSDARP00000041896
PTHR11200 HUMAN ENSEMBL:ENSG00000204084 UniProtKB=P32019
PTHR11200 MOUSE MGI:MGI:103257 NCBI=NP_032411
PTHR11200 RAT RGD:1311511 UniProtKB=Q4G006
PTHR11200 CHICK ENTREZ:419609 NCBI=XP_417756
PTHR11200 DANRE ENSEMBL:ENSDARG00000042111 ENSEMBL=ENSDARP00000061705
PTHR11200 HUMAN ENSEMBL:ENSG00000122126 UniProtKB=Q01968
PTHR11200 MOUSE MGI:MGI:109589 NCBI=NP_796189
PTHR11200 RAT RGD:1594526 NCBI=XP_229106
PTHR11200 CHICK ENTREZ:422136 NCBI=XP_420138
PTHR11200 DANRE ZFIN:ZDB-GENE-061110-61 UniProtKB=A0JMC7
PTHR11200 CAEEL WB:WBGene00012016 UniProtKB=Q17762
PTHR11200 CAEEL WB:WBGene00007620 UniProtKB=O17590
PTHR11200 DROME FB:FBgn0023508 UniProtKB=O46094
PTHR11200 SCHPO GeneDB_Spombe:SPAC9G1.10c UniProtKB=O14306
PTHR11200 YEAST SGD:S000005050 UniProtKB=P50942
PTHR11200 YEAST SGD:S000005635 UniProtKB=Q12271
PTHR11200 YEAST SGD:S000005426 UniProtKB=Q08227
PTHR11200 YEAST SGD:S000001264 UniProtKB=P40559
PTHR11200 SCHPO GeneDB_Spombe:SPBC577.13 UniProtKB=Q9USQ6
PTHR11200 SCHPO GeneDB_Spombe:SPBC2G2.02 UniProtKB=O43001
PTHR11200 DICDI dictyBase:DDB_G0279927 UniProtKB=Q54W40
PTHR11200 DICDI dictyBase:DDB_G0284187 UniProtKB=Q54PV1
PTHR11200 HUMAN ENSEMBL:ENSG00000148384 UniProtKB=Q9NRR6
PTHR11200 MOUSE MGI:MGI:1927753 UniProtKB=Q9JII1
PTHR11200 RAT RGD:620478 UniProtKB=Q9WVR1
PTHR11200 CHICK ENTREZ:417135 NCBI=XP_415418
PTHR11200 DROME FB:FBgn0036273 UniProtKB=Q9VTW2
PTHR11200 HUMAN ENSEMBL:ENSG00000078269 UniProtKB=O15056
PTHR11200 MOUSE MGI:MGI:1201671 UniProtKB=Q9D2G5
PTHR11200 RAT RGD:69436 UniProtKB=O55207
PTHR11200 HUMAN ENSEMBL:ENSG00000159082 UniProtKB=O43426
PTHR11200 MOUSE MGI:MGI:1354961 UniProtKB=Q8CHC4
PTHR11200 RAT RGD:69434 UniProtKB=Q62910
PTHR11200 CHICK ENTREZ:418498 NCBI=XP_416706
PTHR11200 DANRE ENSEMBL:ENSDARG00000068267 UniProtKB=A2BGK3
PTHR11200 DANRE ZFIN:ZDB-GENE-030131-9180 UniProtKB=Q5XUX5
PTHR11200 CAEEL WB:WBGene00016802 UniProtKB=P34370
PTHR11200 CAEEL WB:WBGene00006763 UniProtKB=Q9GT42
PTHR11200 DROME FB:FBgn0034691 UniProtKB=Q5U0V7

Original comment by: ValWood

pombase-admin commented 15 years ago

September targets

PTHR10906 >SCHPO GeneDB_Spombe:SPBC19G7.17
PTHR10906 >SCHPO GeneDB_Spombe:SPBC354.02c
PTHR12309 >SCHPO GeneDB_Spombe:SPAC4G8.02c
PTHR13509 >SCHPO GeneDB_Spombe:SPBC2G2.03c
PTHR20856 >SCHPO GeneDB_Spombe:SPAC4G9.08c
PTHR20856 >SCHPO GeneDB_Spombe:SPBP23A10.07
PTHR20856 >SCHPO GeneDB_Spombe:SPAC23G3.01
PTHR24096 >SCHPO GeneDB_Spombe:SPBP4H10.11c
PTHR24096 >SCHPO GeneDB_Spombe:SPBC18H10.02

Original comment by: ValWood

pombase-admin commented 11 years ago

Ticket moved from /p/pombase/go-annotation/6/

Original comment by: mah11

pombase-admin commented 10 years ago

status: open --> closed-out-of-date

Original comment by: ValWood

pombase / curation

reference genome annotation #297