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)

ARPP-19		location ⇒	1:123948196-123948320		CU326376,CH242-262C7,1:123940935-123960591 (Clone quality: bE262C7 on chr=1; Num_of_Contigs=2; )
ARPP-19		location ⇒	1:123951310-123951481		CU326376,CH242-262C7,1:123940935-123960591 (Clone quality: bE262C7 on chr=1; Num_of_Contigs=2; )
ARPP-21		ENSSSCG00000011238	13:17665852-17815679
ARPP19		ENSSSCG00000004618	1:123932964-123952385
ARR3		ENSSSCG00000012379	X:54919356-54933199	CU463005,CH242-411O22,X:54745943-54944013 (Clone quality: bE411O22 on chr=X; Num_of_Contigs=1; )
ARR3		location ⇒	X:54922555-54922418	CU463005,CH242-411O22,X:54745943-54944013 (Clone quality: bE411O22 on chr=X; Num_of_Contigs=1; )
ARR3		location ⇒	X:54924623-54924558	CU463005,CH242-411O22,X:54745943-54944013 (Clone quality: bE411O22 on chr=X; Num_of_Contigs=1; )
ARR3		location ⇒	X:54924828-54924777	CU463005,CH242-411O22,X:54745943-54944013 (Clone quality: bE411O22 on chr=X; Num_of_Contigs=1; )
ARR3		location ⇒	X:54925157-54924958	CU463005,CH242-411O22,X:54745943-54944013 (Clone quality: bE411O22 on chr=X; Num_of_Contigs=1; )
ARRB1		ENSSSCG00000014852	9:9246543-9273876		CU655994,CH242-280C8,9:9240845-9289734 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
ARRB1		location ⇒	9:9246547-9246789		CU655994,CH242-280C8,9:9240845-9289734 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
ARRB1		location ⇒	9:9255696-9255894		CU655994,CH242-280C8,9:9240845-9289734 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
ARRB1		location ⇒	9:9264956-9265095		CU655994,CH242-280C8,9:9240845-9289734 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
ARRB1		location ⇒	9:9273087-9273418		CU655994,CH242-280C8,9:9240845-9289734 (Clone quality: bE280C8 on chr=9; Num_of_Contigs=8; )
ARRB2		ENSSSCG00000017918	12:49338282-49343582		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
ARRDC2		ENSSSCG00000013893	2:62235749-62238862		CU463003,CH242-317A24,2:62151810-62279750 (Clone quality: bE317A24 on chr=2; Num_of_Contigs=2; )
ARRDC3		ENSSSCG00000014156	2:87739789-87751839
ARRDC4		ENSSSCG00000002252	7:89915744-89925963		CT826396,CH242-251N22,7:89912666-90063931 (Clone quality: bE251N22 on chr=7; Num_of_Contigs=1; )
ARSB		ENSSSCG00000014106	2:76779233-76796561
ARSG		ENSSSCG00000017261	12:10034056-10118441
ARSK		ENSSSCG00000014139	2:82752097-82798024
ART1		ENSSSCG00000008548	3:104211286-104216776
ART1		location ⇒	9:5797419-5797098		FP103078,CH242-97F1,9:5795320-5801690 (Clone quality: bE97F1 on chr=9; Num_of_Contigs=12; )
ART1		location ⇒	9:5797758-5797655		FP103078,CH242-97F1,9:5795320-5801690 (Clone quality: bE97F1 on chr=9; Num_of_Contigs=12; )
ART1		location ⇒	9:5843068-5842747		CU928773,CH242-1I9,9:5824602-5854720 (Clone quality: bE1I9 on chr=9; Num_of_Contigs=1; )
ART1		location ⇒	9:5843407-5843304		CU928773,CH242-1I9,9:5824602-5854720 (Clone quality: bE1I9 on chr=9; Num_of_Contigs=1; )
ART3		ENSSSCG00000008976	8:61057752-61215246
ART4		ENSSSCG00000000607	5:55016603-55019846
ART5		ENSSSCG00000014798	9:5851938-5856786
ARTS-1		ENSSSCG00000014171	2:92440844-92468725
ARTS-1		location ⇒	2:92440000-92439484		CU469214,CH242-375N8,2:92430052-92444605 (Clone quality: bE375N8 on chr=2; Num_of_Contigs=13; )
ARTS-1		location ⇒	2:92440998-92440038		CU469214,CH242-375N8,2:92430052-92444605 (Clone quality: bE375N8 on chr=2; Num_of_Contigs=13; )
ARTS-1		location ⇒	2:92445157-92445014		CU469214,CH242-375N8,2:92444706-92493218 (Clone quality: bE375N8 on chr=2; Num_of_Contigs=13; )
ARTS-1		location ⇒	2:92445736-92445643		CU469214,CH242-375N8,2:92444706-92493218 (Clone quality: bE375N8 on chr=2; Num_of_Contigs=13; )
ARV1		ENSSSCG00000010179	14:61725714-61737747	CT737333,CH242-133K23,14:61634928-61823678 (Clone quality: bE133K23 on chr=14; Num_of_Contigs=2; )
ARVCF		ENSSSCG00000010133	14:52658177-52676881		CT737290,CH242-153A5,14:52550615-52684021 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
ARVCF		location ⇒	14:52667825-52667715		CT737290,CH242-153A5,14:52550615-52684021 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
ARVCF		location ⇒	14:52668152-52667989		CT737290,CH242-153A5,14:52550615-52684021 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
ARVCF		location ⇒	14:52673186-52673128		CT737290,CH242-153A5,14:52550615-52684021 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
ARX		ENSSSCG00000002876	6:29488702-29526486		CU929964,CH242-62K4,6:29482801-29678966 (Clone quality: bE62K4 on chr=6; Num_of_Contigs=2; )
AS3MT		ENSSSCG00000010592	14:118908266-118944708		CU424483,CH242-233G12,14:118903160-118983718 (Clone quality: bE233G12 on chr=14; Num_of_Contigs=4; )
ASAH2B		ENSSSCG00000010432	14:103609491-103682161		CU407016,CH242-121F9,14:103598725-103733348 (Clone quality: bE121F9 on chr=14; Num_of_Contigs=3; )
ASAP1		ENSSSCG00000005958	4:9410775-9576355
ASAP2		ENSSSCG00000008642	3:117328658-117460909		CU929910,CH242-294P3,3:117307789-117461375 (Clone quality: bE294P3 on chr=3; Num_of_Contigs=2; )
ASAP3		ENSSSCG00000003537	6:56296162-56303826
ASB1		ENSSSCG00000016340	15:130491268-130506514
ASB1		location ⇒	15:130493352-130493104		CU571360,CH242-35A9,15:130492037-130508002 (Clone quality: bE35A9 on chr=15; Num_of_Contigs=19; )
ASB1		location ⇒	15:130501106-130500847		CU571360,CH242-35A9,15:130492037-130508002 (Clone quality: bE35A9 on chr=15; Num_of_Contigs=19; )
ASB1		location ⇒	15:130503271-130503199		CU571360,CH242-35A9,15:130492037-130508002 (Clone quality: bE35A9 on chr=15; Num_of_Contigs=19; )
ASB11		ENSSSCG00000012133	X:11102986-11138511

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, 1751-32

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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).