Pig genome annotation: A Gene Wish List

A Wish List of Genes for Annotation (version 3.26)

(Matches to BACs by their Genome Locations Based on Pig Genome Build v.9 (Data Downloads as of Mar. 7, 2010 )

Info:

Purpose: Help users to find where to go from gene names to their genome locations/BACs in order to locate a starting spot in the pig genome to bring into Otterlace for annotations.
Methods: The gene locations are determined in 2 ways: Ensembl predictions and Blasts. Clones are sought based on their overlapping genome locations with that of your gene.
Terms: Finished BACs: A total of 811 "finished" clones that met the "golden standard" of finished sequencing quality. Unfinished clones: Out of 15,837 clones on the "unfinished clones" list, only 1,769 have been processed to have genome locations. FPC clones: 254K+ of those clones in the sequencing pipeline
Related links:

HINTS:

Owner/Status info: : Someone has this gene on their wish-list to annotate. : This gene is to be annotated. : This gene has been annotated (click to check for details - maybe only a gene variant is annotated. The ultimate annotator list is from Otterlace entries; This list only provides a working reference).
Additional info: : have orthologous gene information. : have refseq information. : details (click for more)
Ensembl Gene ID, Genome Locations, and BAC names are all hyper-linked to Ensembl database

( Go to genes whose symbol start with: 1, 5, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z )
Search results:	Show Finished BAC Show unFinished BAC

User Gene List			Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)
Symbol	Owner/ Status	Ensembl Gene ID	Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)

TXK		location ⇒	8:32508934-32508867		CU915496,CH242-393C5,8:32504856-32516642 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
TXK		location ⇒	8:32512567-32512354		CU915496,CH242-393C5,8:32504856-32516642 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
TXLNA		ENSSSCG00000003617	6:60914156-60926352
TXLNB		ENSSSCG00000004143	1:26574140-26613539
TXN		ENSSSCG00000005453	1:263983103-264032572
TXN		ENSSSCG00000005453	1:263983103-264032572
TXN		location ⇒	1:110119178-110119101		CU929866,CH242-13A12,1:110100332-110200592 (Clone quality: bE13A12 on chr=1; Num_of_Contigs=4; )
TXN		location ⇒	1:110119178-110119101		CU929866,CH242-13A12,1:110100332-110200592 (Clone quality: bE13A12 on chr=1; Num_of_Contigs=4; )
TXN		location ⇒	1:263983366-263983261		CU457438,CH242-191P2,1:263966357-263987981 (Clone quality: bE191P2 on chr=1; Num_of_Contigs=12; )
TXN		location ⇒	1:263983995-263983925		CU457438,CH242-191P2,1:263966357-263987981 (Clone quality: bE191P2 on chr=1; Num_of_Contigs=12; )
TXN		location ⇒	1:263991823-263991717		CU457438,CH242-191P2,1:263988082-263993151 (Clone quality: bE191P2 on chr=1; Num_of_Contigs=12; )
TXN2		ENSSSCG00000000144	5:7704458-7717661		CU928818,CH242-252E6,5:7696847-7741655 (Clone quality: bE252E6 on chr=5; Num_of_Contigs=9; )
TXNDC11		ENSSSCG00000007896	3:28086893-28126599
TXNDC12		ENSSSCG00000003867	6:113960876-113975266
TXNDC17		ENSSSCG00000017891	12:47981543-47984235		CU571053,CH242-64E15,12:47942312-48004602 (Clone quality: bE64E15 on chr=12; Num_of_Contigs=3; )
TXNDC3		ENSSSCG00000015448	9:101211852-101246073
TXNDC6		ENSSSCG00000011659	13:64961858-64970348		CU915328,CH242-252D2,13:64912315-64972199 (Clone quality: bE252D2 on chr=13; Num_of_Contigs=10; )
TXNDC8		ENSSSCG00000005454	1:263995182-264015173
TXNIP		ENSSSCG00000006681	4:103433742-103437296		CU151864,CH242-277H11,4:103383388-103453720 (Clone quality: bE277H11 on chr=4; Num_of_Contigs=7; )
TXNIP		ENSSSCG00000006681	4:103433742-103437296		CU151864,CH242-277H11,4:103383388-103453720 (Clone quality: bE277H11 on chr=4; Num_of_Contigs=7; )
TXNIP		location ⇒	4:103434046-103434298		CU151864,CH242-277H11,4:103383388-103453720 (Clone quality: bE277H11 on chr=4; Num_of_Contigs=7; )
TXNIP		location ⇒	4:103435592-103435850		CU151864,CH242-277H11,4:103383388-103453720 (Clone quality: bE277H11 on chr=4; Num_of_Contigs=7; )
TXNIP		location ⇒	4:103436219-103436374		CU151864,CH242-277H11,4:103383388-103453720 (Clone quality: bE277H11 on chr=4; Num_of_Contigs=7; )
TXNIP		location ⇒	4:103436930-103437034		CU151864,CH242-277H11,4:103383388-103453720 (Clone quality: bE277H11 on chr=4; Num_of_Contigs=7; )
TXNL1		ENSSSCG00000004537	1:109164800-109204634
TXNL4A		ENSSSCG00000005777	1:290997073-291013175		CU041273,CH242-39O17,1:290960996-291029484 (Clone quality: bE39O17 on chr=1; Num_of_Contigs=4; )
TXNL4B		ENSSSCG00000002751	6:10797840-10800771		CU914723,CH242-491H10,6:10781997-10802656 (Clone quality: bE491H10 on chr=6; Num_of_Contigs=16; )
TXNRD1		ENSSSCG00000000843	5:75140645-75208149
TXNRD2		ENSSSCG00000010131	14:52609540-52638915		CT737290,CH242-153A5,14:52550615-52684021 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
TYK2		ENSSSCG00000013648	2:53126801-53152421
Tyk2		ENSSSCG00000013648	2:53126801-53152421
Tyk2		location ⇒	2:53145844-53145999		CU657936,CH242-239H17,2:53128518-53215272 (Clone quality: bE239H17 on chr=2; Num_of_Contigs=8; )
Tyk2		location ⇒	2:53146917-53147069		CU657936,CH242-239H17,2:53128518-53215272 (Clone quality: bE239H17 on chr=2; Num_of_Contigs=8; )
Tyk2		location ⇒	2:53147897-53148092		CU657936,CH242-239H17,2:53128518-53215272 (Clone quality: bE239H17 on chr=2; Num_of_Contigs=8; )
Tyk2		location ⇒	2:53148928-53149104		CU657936,CH242-239H17,2:53128518-53215272 (Clone quality: bE239H17 on chr=2; Num_of_Contigs=8; )
TYMS		location ⇒	6:122633774-122633258		CU928926,CH242-254O3,6:122583641-122659305 (Clone quality: bE254O3 on chr=6; Num_of_Contigs=7; )
TYR		ENSSSCG00000001969	7:74188390-74210719
TYR		ENSSSCG00000002431	7:119621566-119707343
TYR		ENSSSCG00000007098	17:27602731-27721837
TYR		location ⇒	9:22725269-22725627		FP236346,CH242-474N9,9:22719915-22732477 (Clone quality: bE474N9 on chr=9; Num_of_Contigs=5; )
TYR		location ⇒	9:22906705-22906521		FP236346,CH242-474N9,9:22905155-22920106 (Clone quality: bE474N9 on chr=9; Num_of_Contigs=5; )
TYR		location ⇒	9:22906705-22906521		FP236346,CH242-474N9,9:22905155-22920106 (Clone quality: bE474N9 on chr=9; Num_of_Contigs=5; )
TYRO3		ENSSSCG00000004744	1:136222813-136239205		CU633572,CH242-274F1,1:136202998-136286247 (Clone quality: bE274F1 on chr=1; Num_of_Contigs=12; )
TYRO3		location ⇒	1:136223249-136221764		CU633572,CH242-274F1,1:136202998-136286247 (Clone quality: bE274F1 on chr=1; Num_of_Contigs=12; )
TYRO3		location ⇒	1:136225954-136225815		CU633572,CH242-274F1,1:136202998-136286247 (Clone quality: bE274F1 on chr=1; Num_of_Contigs=12; )
TYRO3		location ⇒	1:136226298-136226139		CU633572,CH242-274F1,1:136202998-136286247 (Clone quality: bE274F1 on chr=1; Num_of_Contigs=12; )
TYRO3		location ⇒	1:136227131-136227009		CU633572,CH242-274F1,1:136202998-136286247 (Clone quality: bE274F1 on chr=1; Num_of_Contigs=12; )
TYROBP		ENSSSCG00000002919	6:30466058-30469384		CU466979,CH242-510C11,6:30452219-30481257 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
TYROBP		location ⇒	6:30466284-30466060		CU466979,CH242-510C11,6:30452219-30481257 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
TYROBP		location ⇒	6:30466284-30466166		CU466979,CH242-510C11,6:30452219-30481257 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-8

Report problems to zhu

iastate.edu

$version: 3.26; Updates: Mar. 6, 2010; Apr. 20, 2010; Aug 21, 2010

Related publications:

Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, ... Denis Milan, Hendrik-Jan Megens, ... Zhi-Liang Hu, Sean J. Humphray, ... James M. Reecy, ..., Gary A. Rohrer, ... Shuhong Zhao, Jane Rogers, Carol Churcher & Lawrence B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).