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)

CAMK2G		location ⇒	14:79840294-79840049		CU640439,CH242-168L21,14:79822021-79894539 (Clone quality: bE168L21 on chr=14; Num_of_Contigs=4; )
CAMK2G		location ⇒	14:79840294-79840049		CU640439,CH242-168L21,14:79822021-79894539 (Clone quality: bE168L21 on chr=14; Num_of_Contigs=4; )
CAMK2N1		ENSSSCG00000003502	6:54051454-54051618		FP102733,CH242-56I17,6:54050937-54053068 (Clone quality: bE56I17 on chr=6; Num_of_Contigs=8; )
CAMK4		ENSSSCG00000014201	2:104603820-104824938
CAMKK1		ENSSSCG00000017873	12:47261846-47267888
CAMKK2		ENSSSCG00000009815	14:31348504-31405079
CAMLG		ENSSSCG00000014306	2:124715771-124718249		CU862042,CH242-222J18,2:124705772-124719510 (Clone quality: bE222J18 on chr=2; Num_of_Contigs=7; )
CAMLG		location ⇒	2:124715845-124716050		CU862042,CH242-222J18,2:124705772-124719510 (Clone quality: bE222J18 on chr=2; Num_of_Contigs=7; )
CAMLG		location ⇒	2:124717720-124718181		CU862042,CH242-222J18,2:124705772-124719510 (Clone quality: bE222J18 on chr=2; Num_of_Contigs=7; )
CAMP		ENSSSCG00000011349	13:26043606-26045922		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CAMP		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CAMP		location ⇒	13:26045596-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CAMSAP1		ENSSSCG00000005753	1:289692632-289700061
CAMTA2		ENSSSCG00000017902	12:49129543-49143792		FP015831,CH242-271O18,12:49076321-49169107 (Clone quality: bE271O18 on chr=12; Num_of_Contigs=4; )
CAND2		ENSSSCG00000011582	13:56984369-57012391		CU928558,CH242-268K10,13:56979951-57068856 (Clone quality: bE268K10 on chr=13; Num_of_Contigs=3; )
CANT1		location ⇒	3:38377017-38376728		FP102259,CH242-507E20,3:38318964-38457094 (Clone quality: bE507E20 on chr=3; Num_of_Contigs=3; )
CANX		ENSSSCG00000014020	2:68224484-68259810
CANX		location ⇒	2:68225190-68223288		FP015930,CH242-222N20,2:68151095-68227732 (Clone quality: bE222N20 on chr=2; Num_of_Contigs=11; )
CANX		location ⇒	2:68231776-68231559		FP015930,CH242-222N20,2:68227833-68248246 (Clone quality: bE222N20 on chr=2; Num_of_Contigs=11; )
CANX		location ⇒	2:68236244-68236054		FP015930,CH242-222N20,2:68227833-68248246 (Clone quality: bE222N20 on chr=2; Num_of_Contigs=11; )
CANX		location ⇒	2:68237241-68237048		FP015930,CH242-222N20,2:68227833-68248246 (Clone quality: bE222N20 on chr=2; Num_of_Contigs=11; )
CAP1		ENSSSCG00000003672	6:66065148-66073853
CAP1		ENSSSCG00000003672	6:66065148-66073853
CAP1		ENSSSCG00000006693	4:103708512-103740596		CU467072,CH242-100P4,4:103582921-103758989 (Clone quality: bE100P4 on chr=4; Num_of_Contigs=2; )
CAP1		ENSSSCG00000006693	4:103708512-103740596		CU467072,CH242-100P4,4:103582921-103758989 (Clone quality: bE100P4 on chr=4; Num_of_Contigs=2; )
CAP1		location ⇒	6:66065056-66064760	CR974432,PigE-204L22,6:65914672-66073853 (No clone quality info on bT204L22)
CAP1		location ⇒	6:66065939-66065138	CR974432,PigE-204L22,6:65914672-66073853 (No clone quality info on bT204L22)
CAP1		location ⇒	6:66067973-66067787	CR974432,PigE-204L22,6:65914672-66073853 (No clone quality info on bT204L22)
CAP1		location ⇒	6:66070236-66070180	CR974432,PigE-204L22,6:65914672-66073853 (No clone quality info on bT204L22)
CAP2		ENSSSCG00000001068	7:13773929-13891161
CAPB2		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CAPG		ENSSSCG00000008239	3:54148993-54163461		CU951451,CH242-157C24,3:54090565-54166505 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
CAPN1		ENSSSCG00000012999	2:5397982-5423807	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CAPN1		location ⇒	2:5398749-5398013	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CAPN1		location ⇒	2:5400222-5399444	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CAPN1		location ⇒	2:5403236-5403026	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CAPN1		location ⇒	2:5422981-5422705	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CAPN11		ENSSSCG00000001698	7:45697249-45712418	CR956360,CH242-245E12,7:45529239-45714745 (No clone quality info on bE245E12)
CAPN12		ENSSSCG00000002967	6:32817428-32829624
CAPN2		location ⇒	2:5420656-5420537	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
CAPN3		ENSSSCG00000004728	1:135190712-135267979
CAPN3		location ⇒	1:135199837-135199626		CU694786,CH242-266K24,1:135189684-135203771 (Clone quality: bE266K24 on chr=1; Num_of_Contigs=5; )
CAPN3		location ⇒	1:135201278-135201104		CU694786,CH242-266K24,1:135189684-135203771 (Clone quality: bE266K24 on chr=1; Num_of_Contigs=5; )
CAPN3		location ⇒	1:135233459-135233290		CU463161,CH242-286I1,1:135227749-135313166 (Clone quality: bE286I1 on chr=1; Num_of_Contigs=2; )
CAPN3		location ⇒	1:135267797-135267447		CU463161,CH242-286I1,1:135227749-135313166 (Clone quality: bE286I1 on chr=1; Num_of_Contigs=2; )
CAPN5		ENSSSCG00000014875	9:11085353-11121685
CAPN6		ENSSSCG00000012584	X:89158081-89186799
CAPN9		ENSSSCG00000010182	14:61911963-61952789
CAPNS1		location ⇒	16:69409140-69408457		CU915698,CH242-91L11,16:69407506-69415986 (Clone quality: bE91L11 on chr=16; Num_of_Contigs=4; )
CAPRIN1		ENSSSCG00000013305	2:25242333-25284579	CU929607,CH242-257K17,2:25128827-25332127 (Clone quality: bE257K17 on chr=2; Num_of_Contigs=6; )

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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).