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)

TCF3		location ⇒	2:46604357-46604233		CU972485,CH242-416N2,2:46568566-46699601 (Clone quality: bE416N2 on chr=2; Num_of_Contigs=2; )
TCF4		ENSSSCG00000004535	1:107583639-107940776
TCF4		ENSSSCG00000010638	14:129166368-129394453
TCF4		location ⇒	1:107583844-107583677		CU929941,CH242-488L10,1:107582453-107585257 (Clone quality: bE488L10 on chr=1; Num_of_Contigs=3; )
TCF4		location ⇒	1:107585804-107585573		CU929941,CH242-488L10,1:107585358-107637032 (Clone quality: bE488L10 on chr=1; Num_of_Contigs=3; )
TCF4		location ⇒	1:107589229-107589065		CU929941,CH242-488L10,1:107585358-107637032 (Clone quality: bE488L10 on chr=1; Num_of_Contigs=3; )
TCF4		location ⇒	1:107681260-107680943		CU929941,CH242-488L10,1:107671730-107682516 (Clone quality: bE488L10 on chr=1; Num_of_Contigs=3; )
TCF7		ENSSSCG00000014297	2:124253752-124260539
TCF7		location ⇒	2:124256553-124256654		CU694278,CH242-390O19,2:124253014-124258074 (Clone quality: bE390O19 on chr=2; Num_of_Contigs=22; )
TCF7		location ⇒	2:124257100-124257262		CU694278,CH242-390O19,2:124253014-124258074 (Clone quality: bE390O19 on chr=2; Num_of_Contigs=22; )
TCF7		location ⇒	2:124257353-124257414		CU694278,CH242-390O19,2:124253014-124258074 (Clone quality: bE390O19 on chr=2; Num_of_Contigs=22; )
TCF7L1		ENSSSCG00000008241	3:54227917-54247923
TCF7L1		location ⇒	3:54229569-54229495		CU951451,CH242-157C24,3:54215273-54246342 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
TCF7L1		location ⇒	3:54230965-54230855		CU951451,CH242-157C24,3:54215273-54246342 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
TCF7L1		location ⇒	3:54231220-54231061		CU951451,CH242-157C24,3:54215273-54246342 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
TCF7L2		ENSSSCG00000010638	14:129166368-129394453
TCF7L2		ENSSSCG00000011274	13:20905977-20950024		CU861524,CH242-156J19,13:20905383-20993819 (Clone quality: bE156J19 on chr=13; Num_of_Contigs=6; )
TCF7L2		location ⇒	14:129166368-129166612		CT826377,CH242-112P17,14:129048119-129167383 (Clone quality: bE112P17 on chr=14; Num_of_Contigs=2; )
TCF7L2		location ⇒	14:129166885-129166953		CT826377,CH242-112P17,14:129048119-129167383 (Clone quality: bE112P17 on chr=14; Num_of_Contigs=2; )
TCF7L2		location ⇒	14:129167154-129167214		CT826377,CH242-112P17,14:129048119-129167383 (Clone quality: bE112P17 on chr=14; Num_of_Contigs=2; )
TCF8		ENSSSCG00000011025	10:40357121-40554534
TCF8		location ⇒	10:40554444-40554533		CU914393,CH242-102C5,10:40538526-40554569 (Clone quality: bE102C5 on chr=10; Num_of_Contigs=10; )
TCF8		location ⇒	10:40570800-40570275		CU914393,CH242-102C5,10:40554670-40570814 (Clone quality: bE102C5 on chr=10; Num_of_Contigs=10; )
TCHHL1		ENSSSCG00000006609	4:101039712-101042878		CU469439,CH242-256E21,4:100997235-101089062 (Clone quality: bE256E21 on chr=4; Num_of_Contigs=4; )
TCHP		ENSSSCG00000009926	14:41219471-41239706		CU640887,CH242-377K8,14:41152094-41308016 (Clone quality: bE377K8 on chr=14; Num_of_Contigs=2; )
TCIRG1		ENSSSCG00000012890	2:3193403-3205475
TCIRG1		location ⇒	2:3193546-3193408		CU856479,CH242-200O4,2:3088400-3194485 (Clone quality: bE200O4 on chr=2; Num_of_Contigs=4; )
TCIRG1		location ⇒	2:3193805-3193627		CU856479,CH242-200O4,2:3088400-3194485 (Clone quality: bE200O4 on chr=2; Num_of_Contigs=4; )
TCIRG1		location ⇒	2:3195252-3195038		CU856479,CH242-200O4,2:3194586-3214494 (Clone quality: bE200O4 on chr=2; Num_of_Contigs=4; )
TCIRG1		location ⇒	2:3196294-3196156		CU856479,CH242-200O4,2:3194586-3214494 (Clone quality: bE200O4 on chr=2; Num_of_Contigs=4; )
TCL1A		ENSSSCG00000002498	7:125764448-125768777	CT867964,CH242-267C2,7:125614014-125812235 (Clone quality: bE267C2 on chr=7; Num_of_Contigs=1; )
TCL1B		ENSSSCG00000002497	7:125742462-125747424	CT867964,CH242-267C2,7:125614014-125812235 (Clone quality: bE267C2 on chr=7; Num_of_Contigs=1; )
TCN1		location ⇒	2:9615584-9615659		FP074885,CH242-183I22,2:9614544-9696063 (Clone quality: bE183I22 on chr=2; Num_of_Contigs=1; )
TCN2		ENSSSCG00000010011	14:48302979-48320699
TCOF1		ENSSSCG00000014450	2:136877104-136888949
TCP1		ENSSSCG00000004048	1:8717456-8728025	CU855864,CH242-178J19,1:8688737-8737378 (Clone quality: bE178J19 on chr=1; Num_of_Contigs=11; )
TCP11		ENSSSCG00000001535	7:35485030-35509484
TCP11L2		ENSSSCG00000000170	5:12272726-12309816		CU462865,CH242-104E3,5:12271346-12333720 (Clone quality: bE104E3 on chr=5; Num_of_Contigs=9; )
TCPZ_PIG		ENSSSCG00000007746	3:15355394-15395652
TCR-a		ENSSSCG00000002103	7:83876720-83877016
TCR-a		ENSSSCG00000002102	7:83858052-83858351		CU468442,CH242-70A24,7:83737240-83877014 (Clone quality: bE70A24 on chr=7; Num_of_Contigs=2; )
TCR-a		ENSSSCG00000002094	7:83749950-83750501		CU468442,CH242-70A24,7:83737240-83877014 (Clone quality: bE70A24 on chr=7; Num_of_Contigs=2; )
TCR-a		ENSSSCG00000002104	7:83881471-83881978		CU468442,CH242-70A24,7:83877115-83932341 (Clone quality: bE70A24 on chr=7; Num_of_Contigs=2; )
TCR-a		ENSSSCG00000002077	7:83389981-83390457		CU467527,CH242-199B11,7:83367687-83404680 (Clone quality: bE199B11 on chr=7; Num_of_Contigs=11; )
TCR-a		ENSSSCG00000002093	7:83740376-83741088		CU468442,CH242-70A24,7:83737240-83877014 (Clone quality: bE70A24 on chr=7; Num_of_Contigs=2; )
TCR-a		ENSSSCG00000002091	7:83685523-83761354
TCR-a		ENSSSCG00000002076	7:83359778-83360490		CU467527,CH242-199B11,7:83358562-83364786 (Clone quality: bE199B11 on chr=7; Num_of_Contigs=11; )
TCR-a		ENSSSCG00000002058	7:83022227-83022672		CU468882,CH242-63B2,7:83001624-83076399 (Clone quality: bE63B2 on chr=7; Num_of_Contigs=5; )
TCR-a		ENSSSCG00000002066	7:83149922-83150367		CU571294,CH242-414N2,7:83105900-83181462 (Clone quality: bE414N2 on chr=7; Num_of_Contigs=4; )
TCR-a		location ⇒	7:82668728-82668825		CU407030,CH242-171E18,7:82618242-82670161 (Clone quality: bE171E18 on chr=7; Num_of_Contigs=3; )

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

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$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).