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)

CDKN1A		ENSSSCG00000010743	14:142126292-142138279		CT841550,CH242-252A14,14:142117451-142165612 (Clone quality: bE252A14 on chr=14; Num_of_Contigs=5; )
CDKN1A		ENSSSCG00000014878	9:11710480-11791400
CDKN1A		location ⇒	7:36987623-36987708	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
CDKN1A		location ⇒	7:36992376-36992833	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
CDKN1A		location ⇒	7:36992563-36992752	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
CDKN1A		location ⇒	7:36995154-36996704	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )
CDKN2A		ENSSSCG00000015779	15:42097166-42100256		CU694719,CH242-351H16,15:42082383-42103959 (Clone quality: bE351H16 on chr=15; Num_of_Contigs=9; )
CDKN2A		ENSSSCG00000014300	2:124454245-124462131		CU570753,CH242-461C23,2:124437899-124463515 (Clone quality: bE461C23 on chr=2; Num_of_Contigs=12; )
CDKN2A		ENSSSCG00000005134	1:209529377-209532177		CU915634,CH242-510N24,1:209528899-209535205 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2A		location ⇒	1:209501880-209502128		CU915634,CH242-510N24,1:209483379-209504275 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2A		location ⇒	1:209515657-209515403		CU915634,CH242-510N24,1:209509548-209517332 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2A		location ⇒	1:209529405-209529354		CU915634,CH242-510N24,1:209528899-209535205 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2A		location ⇒	1:209532177-209531868		CU915634,CH242-510N24,1:209528899-209535205 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2AIP		ENSSSCG00000015779	15:42097166-42100256		CU694719,CH242-351H16,15:42082383-42103959 (Clone quality: bE351H16 on chr=15; Num_of_Contigs=9; )
CDKN2AIPNL		ENSSSCG00000014300	2:124454245-124462131		CU570753,CH242-461C23,2:124437899-124463515 (Clone quality: bE461C23 on chr=2; Num_of_Contigs=12; )
CDKN2B		ENSSSCG00000005132	1:209499306-209529714
CDKN2B		location ⇒	1:209499306-209499470		CU915634,CH242-510N24,1:209483379-209504275 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2B		location ⇒	1:209501880-209502170		CU915634,CH242-510N24,1:209483379-209504275 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2B		location ⇒	1:209532177-209531929		CU915634,CH242-510N24,1:209528899-209535205 (Clone quality: bE510N24 on chr=1; Num_of_Contigs=8; )
CDKN2C		ENSSSCG00000003876	6:114985843-114990244		FP015924,CH242-136C1,6:114963846-114998258 (Clone quality: bE136C1 on chr=6; Num_of_Contigs=9; )
CDKN2C		location ⇒	6:114986598-114985449		FP015924,CH242-136C1,6:114963846-114998258 (Clone quality: bE136C1 on chr=6; Num_of_Contigs=9; )
CDKN2C		location ⇒	6:114990125-114989982		FP015924,CH242-136C1,6:114963846-114998258 (Clone quality: bE136C1 on chr=6; Num_of_Contigs=9; )
CDKN2C		location ⇒	6:114990977-114990577		FP015924,CH242-136C1,6:114963846-114998258 (Clone quality: bE136C1 on chr=6; Num_of_Contigs=9; )
CDKN2D		ENSSSCG00000013643	2:52949774-52951945		CU993813,CH242-86K24,2:52943491-52988729 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
CDKN2D		location ⇒	2:52949963-52950365		CU993813,CH242-86K24,2:52943491-52988729 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
CDKN2D		location ⇒	2:52951386-52952344		CU993813,CH242-86K24,2:52943491-52988729 (Clone quality: bE86K24 on chr=2; Num_of_Contigs=13; )
CDKN3		ENSSSCG00000005047	1:192401013-192415532
CDKN3		location ⇒	1:192403410-192403484		CU074294,CH242-134E21,1:192395025-192414617 (Clone quality: bE134E21 on chr=1; Num_of_Contigs=4; )
CDKN3		location ⇒	1:192405085-192405143		CU074294,CH242-134E21,1:192395025-192414617 (Clone quality: bE134E21 on chr=1; Num_of_Contigs=4; )
CDKN3		location ⇒	1:192408337-192408562		CU074294,CH242-134E21,1:192395025-192414617 (Clone quality: bE134E21 on chr=1; Num_of_Contigs=4; )
CDKN3		location ⇒	1:192415444-192415679		CU074294,CH242-134E21,1:192414718-192423212 (Clone quality: bE134E21 on chr=1; Num_of_Contigs=4; )
CDNF		ENSSSCG00000011053	10:44724121-44743194		CU929591,CH242-21K12,10:44713086-44749054 (Clone quality: bE21K12 on chr=10; Num_of_Contigs=3; )
CDO1		ENSSSCG00000014219	2:108663727-108676684		FP017291,CH242-139C12,2:108594376-108687090 (Clone quality: bE139C12 on chr=2; Num_of_Contigs=3; )
CDR2L		ENSSSCG00000017218	12:4427855-4437903		CU640421,CH242-384L19,12:4424022-4438549 (Clone quality: bE384L19 on chr=12; Num_of_Contigs=8; )
CDS1		ENSSSCG00000009231	8:115191877-115286354
CDSN		ENSSSCG00000001389	7:27478704-27482013	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
CDT1		ENSSSCG00000002651	6:497730-502217
CDV1		ENSSSCG00000009818	14:31564609-31653974
CDV3		ENSSSCG00000011637	13:61360915-61373350		CU466342,CH242-17F10,13:61360897-61373622 (Clone quality: bE17F10 on chr=13; Num_of_Contigs=4; )
CDw210a		ENSSSCG00000015085	9:44231877-44244316		FP102136,CH242-1A1,9:44193617-44246637 (Clone quality: bE1A1 on chr=9; Num_of_Contigs=15; )
CDw293		ENSSSCG00000009191	8:106689479-106700258		CU972439,CH242-452J6,8:106683308-106709026 (Clone quality: bE452J6 on chr=8; Num_of_Contigs=3; )
CDw92		ENSSSCG00000005425	1:258582618-258743259
CDW92		ENSSSCG00000005425	1:258582618-258743259
CDw93		ENSSSCG00000007116	17:31744235-31746961		CU606974,CH242-23K16,17:31739767-31793889 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
CDX1		ENSSSCG00000014445	2:136682841-136696916		CU914366,CH242-274B11,2:136663427-136711757 (Clone quality: bE274B11 on chr=2; Num_of_Contigs=10; )
CDX2		ENSSSCG00000009317	11:4881086-4886834		CU861636,CH242-487J22,11:4880927-4888573 (Clone quality: bE487J22 on chr=11; Num_of_Contigs=10; )
CEACAM1		ENSSSCG00000006084	4:39386638-39417590		CU571149,CH242-82O8,4:39360823-39418721 (Clone quality: bE82O8 on chr=4; Num_of_Contigs=6; )
CEACAM1		location ⇒	6:34003800-34004564		FP236582,CH242-238L13,6:33993771-34008076 (Clone quality: bE238L13 on chr=6; Num_of_Contigs=11; )
CEACAM1		location ⇒	6:34760830-34760691		FP015926,CH242-183C8,6:34727569-34762148 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )
CEACAM1		location ⇒	6:34761789-34761094		FP015926,CH242-183C8,6:34727569-34762148 (Clone quality: bE183C8 on chr=6; Num_of_Contigs=15; )

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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).