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)

CD217		ENSSSCG00000000765	5:65217498-65222396		CU467896,CH242-34G22,5:65212731-65224619 (Clone quality: bE34G22 on chr=5; Num_of_Contigs=20; )
CD218a		ENSSSCG00000008158	3:47478525-47483065		FP102458,CH242-99M17,3:47400904-47486342 (Clone quality: bE99M17 on chr=3; Num_of_Contigs=2; )
CD218b		ENSSSCG00000008157	3:47435344-47462772		FP102458,CH242-99M17,3:47400904-47486342 (Clone quality: bE99M17 on chr=3; Num_of_Contigs=2; )
CD22		ENSSSCG00000002894	6:30118885-30123429		CU694505,CH242-50N19,6:30118807-30135716 (Clone quality: bE50N19 on chr=6; Num_of_Contigs=14; )
CD22		location ⇒	6:120972115-120972012		CU467721,CH242-292B22,6:120966122-121040855 (Clone quality: bE292B22 on chr=6; Num_of_Contigs=5; )
CD22		location ⇒	6:22043246-22043175		FP102989,CH242-160M21,6:22021486-22059819 (Clone quality: bE160M21 on chr=6; Num_of_Contigs=4; )
CD22		location ⇒	6:34075003-34074912		FP236582,CH242-238L13,6:34073901-34079026 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CD22		location ⇒	6:74063649-74063590		CU463096,CH242-501D20,6:73918542-74097119 (Clone quality: bE501D20 on chr=6; Num_of_Contigs=2; )
CD220		ENSSSCG00000013560	2:50473534-50476068		CU986279,CH242-45E14,2:50473212-50490770 (Clone quality: bE45E14 on chr=2; Num_of_Contigs=23; )
CD221		ENSSSCG00000004812	1:145050345-145349833
CD223		ENSSSCG00000000688	5:59967002-59972761		CU457492,CH242-370K21,5:59963772-59976892 (Clone quality: bE370K21 on chr=5; Num_of_Contigs=10; )
CD224		ENSSSCG00000010056	14:50598536-50614341		CU468600,CH242-236F16,14:50578935-50621062 (Clone quality: bE236F16 on chr=14; Num_of_Contigs=6; )
CD226		location ⇒	1:159968167-159968513		FP102352,CH242-84I3,1:159960422-159976944 (Clone quality: bE84I3 on chr=1; Num_of_Contigs=11; )
CD226		location ⇒	1:160032808-160032864		CU856319,CH242-135L3,1:160026133-160039230 (Clone quality: bE135L3 on chr=1; Num_of_Contigs=8; )
CD226		location ⇒	1:160038691-160038796		CU856319,CH242-135L3,1:160026133-160039230 (Clone quality: bE135L3 on chr=1; Num_of_Contigs=8; )
CD226		location ⇒	1:160047914-160047567		CU856319,CH242-135L3,1:160039331-160052816 (Clone quality: bE135L3 on chr=1; Num_of_Contigs=8; )
CD228		ENSSSCG00000011837	13:100347976-100371822
CD229		ENSSSCG00000006375	4:93151439-93178107		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD23		ENSSSCG00000013577	2:51062170-51072262		CU929919,CH242-334A8,2:51060964-51078871 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
CD230		ENSSSCG00000007039	17:13140304-13151006		CU694293,CH242-140G16,17:13136598-13170134 (Clone quality: bE140G16 on chr=17; Num_of_Contigs=2; )
CD231		ENSSSCG00000012238	X:34083565-34108599		FP102385,CH242-81B3,X:34005128-34178208 (Clone quality: bE81B3 on chr=X; Num_of_Contigs=2; )
CD232		ENSSSCG00000000907	5:83803502-83940444
CD233		ENSSSCG00000017358	12:16859433-16871908		CU468984,CH242-216D12,12:16857125-16875764 (Clone quality: bE216D12 on chr=12; Num_of_Contigs=22; )
CD234		ENSSSCG00000006416	4:94777387-94778855		CU462834,CH242-199I10,4:94761474-94795889 (Clone quality: bE199I10 on chr=4; Num_of_Contigs=5; )
CD235a		ENSSSCG00000009046	8:72508182-72536774		CU856644,CH242-197H16,8:72428832-72562979 (Clone quality: bE197H16 on chr=8; Num_of_Contigs=2; )
CD236		ENSSSCG00000015724	15:24313500-24313697		CU928614,CH242-504F3,15:24289485-24314494 (Clone quality: bE504F3 on chr=15; Num_of_Contigs=13; )
CD238		ENSSSCG00000016472	18:6126541-6146298		CU928245,CH242-100K20,18:6102984-6180022 (Clone quality: bE100K20 on chr=18; Num_of_Contigs=3; )
CD23A		ENSSSCG00000013577	2:51062170-51072262		CU929919,CH242-334A8,2:51060964-51078871 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
CD23A		location ⇒	2:51063011-51062890		CU929919,CH242-334A8,2:51060964-51078871 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
CD24		location ⇒	1:111016924-111016874		CU499013,CH242-5D7,1:111015529-111033169 (Clone quality: bE5D7 on chr=1; Num_of_Contigs=13; )
CD24		location ⇒	1:111132661-111132711		CU467101,CH242-394A18,1:111114207-111134635 (Clone quality: bE394A18 on chr=1; Num_of_Contigs=15; )
CD24		location ⇒	1:76650303-76649690		FP102527,CH242-496G17,1:76638049-76650303 (Clone quality: bE496G17 on chr=1; Num_of_Contigs=4; )
CD24		location ⇒	1:76651475-76650407		FP102527,CH242-496G17,1:76650404-76657546 (Clone quality: bE496G17 on chr=1; Num_of_Contigs=4; )
CD241		ENSSSCG00000001735	7:50903221-50928391		CU655813,CH242-388J22,7:50876348-50973828 (Clone quality: bE388J22 on chr=7; Num_of_Contigs=3; )
CD242		ENSSSCG00000013654	2:53200243-53201315		CU657936,CH242-239H17,2:53128518-53215272 (Clone quality: bE239H17 on chr=2; Num_of_Contigs=8; )
CD244		ENSSSCG00000006374	4:93137091-93149861		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD244		location ⇒	4:93137181-93137424		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD244		location ⇒	4:93137512-93137788		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD244		location ⇒	4:93140888-93140968		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD246		ENSSSCG00000008533	3:103131578-103185564
CD247		ENSSSCG00000006309	4:86799324-86892177	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
CD248		location ⇒	2:4448059-4449485		CU462998,CH242-142J19,2:4447933-4472453 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
CD248		location ⇒	2:4449646-4450390		CU462998,CH242-142J19,2:4447933-4472453 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
CD248		location ⇒	2:4450442-4450655		CU462998,CH242-142J19,2:4447933-4472453 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
CD249		ENSSSCG00000009132	8:96061729-96121292
CD25		ENSSSCG00000012397	X:56853523-56857235		CU468205,CH242-6A14,X:56849541-56908124 (Clone quality: bE6A14 on chr=X; Num_of_Contigs=4; )
CD258		ENSSSCG00000013549	2:50037626-50041232		CU694937,CH242-71B7,2:49979846-50046985 (Clone quality: bE71B7 on chr=2; Num_of_Contigs=4; )
CD26		ENSSSCG00000015894	15:63908071-63990308
CD265		ENSSSCG00000004898	1:165992452-166024819		CU234199,CH242-216F10,1:165980062-166061275 (Clone quality: bE216F10 on chr=1; Num_of_Contigs=4; )
CD269		ENSSSCG00000007888	3:27825419-27829389		FP102753,CH242-85B21,3:27808581-27831338 (No clone quality info on )

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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).