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)

T		ENSSSCG00000004025	1:3360697-3368706
T		ENSSSCG00000016436	18:5054144-5058667		FP102583,CH242-165F21,18:5049308-5059326 (Clone quality: bE165F21 on chr=18; Num_of_Contigs=16; )
T		location ⇒	1:3363663-3363727		CU570672,CH242-87O7,1:3329096-3366195 (Clone quality: bE87O7 on chr=1; Num_of_Contigs=6; )
T		location ⇒	1:3365320-3365493		CU570672,CH242-87O7,1:3329096-3366195 (Clone quality: bE87O7 on chr=1; Num_of_Contigs=6; )
T1		ENSSSCG00000000173	5:13278670-13312392		CU914692,CH242-143P14,5:13271941-13360701 (Clone quality: bE143P14 on chr=5; Num_of_Contigs=6; )
T1		ENSSSCG00000013316	2:26543912-26544559	CU695128,CH242-211D14,2:26542927-26556260 (Clone quality: bE211D14 on chr=2; Num_of_Contigs=7; )
T1		ENSSSCG00000013115	2:9524678-9534242		CU914270,CH242-323D11,2:9520060-9538986 (Clone quality: bE323D11 on chr=2; Num_of_Contigs=11; )
T1		ENSSSCG00000012648	X:103026366-103027499	CU550660,CH242-196N11,X:102984061-103140424 (Clone quality: bE196N11 on chr=X; Num_of_Contigs=1; )
T1		ENSSSCG00000009468	11:47976064-47977044		CT956058,CH242-156P24,11:47940321-47985298 (Clone quality: bE156P24 on chr=11; Num_of_Contigs=6; )
T1		ENSSSCG00000003451	6:50299906-50308519		FP236409,CH242-139N22,6:50299882-50316412 (Clone quality: bE139N22 on chr=6; Num_of_Contigs=12; )
T1		ENSSSCG00000003743	6:83007355-83137932
T1		ENSSSCG00000004510	1:102229469-102256875
T1		ENSSSCG00000005934	4:1712609-2190793
T1		ENSSSCG00000008374	3:73228974-73230080
T22D3_PIG		ENSSSCG00000012563	X:86347451-86351177
T22D3_PIG		ENSSSCG00000012559	X:86096769-86100600		FP074898,CH242-294L14,X:86058638-86138881 (Clone quality: bE294L14 on chr=X; Num_of_Contigs=4; )
TA-NFKBH		ENSSSCG00000002917	6:30455154-30461706		CU466979,CH242-510C11,6:30452219-30481257 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
TAAR1		ENSSSCG00000004182	1:32539798-32540802		CU041311,CH242-393L4,1:32529640-32588123 (Clone quality: bE393L4 on chr=1; Num_of_Contigs=2; )
TAAR2		ENSSSCG00000004183	1:32564895-32565908		CU041311,CH242-393L4,1:32529640-32588123 (Clone quality: bE393L4 on chr=1; Num_of_Contigs=2; )
TAAR5		ENSSSCG00000004185	1:32595925-32596938	CU074298,CH242-141E21,1:32588124-32781733 (Clone quality: bE141E21 on chr=1; Num_of_Contigs=3; )
TAAR6		ENSSSCG00000004188	1:32632368-32633393	CU074298,CH242-141E21,1:32588124-32781733 (Clone quality: bE141E21 on chr=1; Num_of_Contigs=3; )
TAAR8		ENSSSCG00000004186	1:32607328-32608356	CU074298,CH242-141E21,1:32588124-32781733 (Clone quality: bE141E21 on chr=1; Num_of_Contigs=3; )
TAC1		location ⇒	9:72502237-72501910		CU929465,CH242-53M16,9:72494621-72539554 (Clone quality: bE53M16 on chr=9; Num_of_Contigs=10; )
TAC1		location ⇒	9:72510084-72509951		CU929465,CH242-53M16,9:72494621-72539554 (Clone quality: bE53M16 on chr=9; Num_of_Contigs=10; )
TAC1		location ⇒	9:72621472-72621605		CU855713,CH242-128I7,9:72617262-72645479 (Clone quality: bE128I7 on chr=9; Num_of_Contigs=8; )
TAC1		location ⇒	9:72629318-72629645		CU855713,CH242-128I7,9:72617262-72645479 (Clone quality: bE128I7 on chr=9; Num_of_Contigs=8; )
TAC3		ENSSSCG00000000418	5:21342429-21350344		FP236389,CH242-191L18,5:21313775-21350609 (Clone quality: bE191L18 on chr=5; Num_of_Contigs=7; )
TAC4		ENSSSCG00000017554	12:23438877-23448361		CU442715,CH242-56F15,12:23390749-23462544 (Clone quality: bE56F15 on chr=12; Num_of_Contigs=9; )
TAC4		location ⇒	12:23439261-23439054		CU442715,CH242-56F15,12:23390749-23462544 (Clone quality: bE56F15 on chr=12; Num_of_Contigs=9; )
TAC4		location ⇒	12:23440972-23440909		CU442715,CH242-56F15,12:23390749-23462544 (Clone quality: bE56F15 on chr=12; Num_of_Contigs=9; )
TAC4		location ⇒	12:23444601-23444505		CU442715,CH242-56F15,12:23390749-23462544 (Clone quality: bE56F15 on chr=12; Num_of_Contigs=9; )
TAC4		location ⇒	12:23448335-23448132		CU442715,CH242-56F15,12:23390749-23462544 (Clone quality: bE56F15 on chr=12; Num_of_Contigs=9; )
TACC3		ENSSSCG00000008677	8:196236-205962
TACO1		ENSSSCG00000017293	12:12893622-12898053		CU929939,CH242-45G1,12:12889620-12949393 (Clone quality: bE45G1 on chr=12; Num_of_Contigs=5; )
TACR2		ENSSSCG00000010254	14:75610214-75621758		CU407057,CH242-241O22,14:75572743-75651187 (Clone quality: bE241O22 on chr=14; Num_of_Contigs=5; )
TACR3		ENSSSCG00000009160	8:100864091-100920219
TACSTD1		location ⇒	3:86466088-86465654		CU928288,CH242-3M15,3:86465591-86482117 (Clone quality: bE3M15 on chr=3; Num_of_Contigs=9; )
TACSTD1		location ⇒	3:86470867-86470667		CU928288,CH242-3M15,3:86465591-86482117 (Clone quality: bE3M15 on chr=3; Num_of_Contigs=9; )
TACSTD1		location ⇒	3:86476945-86476705		CU928288,CH242-3M15,3:86465591-86482117 (Clone quality: bE3M15 on chr=3; Num_of_Contigs=9; )
TACSTD1		location ⇒	3:86477336-86477227		CU928288,CH242-3M15,3:86465591-86482117 (Clone quality: bE3M15 on chr=3; Num_of_Contigs=9; )
TACSTD2		ENSSSCG00000003832	6:109161614-109162585		CU929656,CH242-501P8,6:109138346-109187890 (Clone quality: bE501P8 on chr=6; Num_of_Contigs=7; )
TACTILE		ENSSSCG00000011935	13:111588741-111625422
TADA1L		ENSSSCG00000006318	4:87540259-87552627		CU207249,CH242-383G23,4:87517520-87566826 (Clone quality: bE383G23 on chr=4; Num_of_Contigs=5; )
TADA2L		ENSSSCG00000017697	12:37128863-37160717
TADA3L		ENSSSCG00000011551	13:55258010-55266399		CU633418,CH242-443E24,13:55210129-55267796 (Clone quality: bE443E24 on chr=13; Num_of_Contigs=9; )
TAF11		ENSSSCG00000001533	7:35262638-35274226	CT797453,CH242-109D12,7:35137121-35327761 (Clone quality: bE109D12 on chr=7; Num_of_Contigs=2; )
TAF13		ENSSSCG00000006839	4:115482436-115492756		CU207233,CH242-432M23,4:115446550-115504367 (Clone quality: bE432M23 on chr=4; Num_of_Contigs=7; )
TAF15		ENSSSCG00000017707	12:37489471-37527374		CU914398,CH242-121H9,12:37483147-37597733 (Clone quality: bE121H9 on chr=12; Num_of_Contigs=11; )
TAF1A		ENSSSCG00000010833	10:11400101-11421860		CU929023,CH242-218C2,10:11328820-11437324 (Clone quality: bE218C2 on chr=10; Num_of_Contigs=4; )

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).