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)

CNBD1		location ⇒	4:51560433-51560340		CU633179,CH242-142B23,4:51537897-51579432 (Clone quality: bE142B23 on chr=4; Num_of_Contigs=19; )
CNBD1		location ⇒	4:51733073-51732980		CU582847,CH242-277M17,4:51673937-51840247 (Clone quality: bE277M17 on chr=4; Num_of_Contigs=1; )
CNDP2		ENSSSCG00000004870	1:157042761-157061754		CU862032,CH242-156K20,1:157038848-157066907 (Clone quality: bE156K20 on chr=1; Num_of_Contigs=4; )
CNDP2		location ⇒	1:157043930-157043778		CU862032,CH242-156K20,1:157038848-157066907 (Clone quality: bE156K20 on chr=1; Num_of_Contigs=4; )
CNDP2		location ⇒	1:157045929-157045762		CU862032,CH242-156K20,1:157038848-157066907 (Clone quality: bE156K20 on chr=1; Num_of_Contigs=4; )
CNDP2		location ⇒	1:157052177-157052012		CU862032,CH242-156K20,1:157038848-157066907 (Clone quality: bE156K20 on chr=1; Num_of_Contigs=4; )
CNDP2		location ⇒	1:157058919-157058855		CU862032,CH242-156K20,1:157038848-157066907 (Clone quality: bE156K20 on chr=1; Num_of_Contigs=4; )
CNG-1		location ⇒	8:32382737-32384133		CU915496,CH242-393C5,8:32381806-32387883 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
CNG-1		location ⇒	8:32467861-32467922		CU915496,CH242-393C5,8:32460490-32475189 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
CNG-1		location ⇒	8:32473991-32474076		CU915496,CH242-393C5,8:32460490-32475189 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
CNG-1		location ⇒	8:32474856-32474967		CU915496,CH242-393C5,8:32460490-32475189 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
CNGA1		ENSSSCG00000008814	8:32382648-32384153		CU915496,CH242-393C5,8:32381806-32387883 (Clone quality: bE393C5 on chr=8; Num_of_Contigs=11; )
CNGA2		ENSSSCG00000012753	X:121321939-121326832		CU927968,CH242-32J16,X:121284132-121386575 (Clone quality: bE32J16 on chr=X; Num_of_Contigs=7; )
CNGA4		ENSSSCG00000014630	9:2703568-2708959		CU915603,CH242-135E13,9:2696901-2725698 (Clone quality: bE135E13 on chr=9; Num_of_Contigs=12; )
CNGB1		ENSSSCG00000002811	6:19792002-19846064
CNGB3		ENSSSCG00000006134	4:51946984-52023562
CNIH		ENSSSCG00000012954	2:4479842-4485547		CU462998,CH242-142J19,2:4472554-4485664 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
CNIH		ENSSSCG00000010848	10:13324618-13426458
CNIH		location ⇒	1:192249376-192249491		CU074294,CH242-134E21,1:192248038-192273875 (Clone quality: bE134E21 on chr=1; Num_of_Contigs=4; )
CNIH		location ⇒	1:192421933-192422462		CU074294,CH242-134E21,1:192414718-192423212 (Clone quality: bE134E21 on chr=1; Num_of_Contigs=4; )
CNIH2		ENSSSCG00000012954	2:4479842-4485547		CU462998,CH242-142J19,2:4472554-4485664 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
CNIH3		ENSSSCG00000010848	10:13324618-13426458
CNKSR2		ENSSSCG00000012164	X:16475825-16714819
CNKSR3		ENSSSCG00000004071	1:13095284-13138196
CNKSR3		location ⇒	1:13114952-13114896		CU914574,CH242-133L8,1:13082326-13127130 (Clone quality: bE133L8 on chr=1; Num_of_Contigs=13; )
CNKSR3		location ⇒	1:13130174-13129970		CU914574,CH242-133L8,1:13127231-13143393 (Clone quality: bE133L8 on chr=1; Num_of_Contigs=13; )
CNKSR3		location ⇒	1:13218952-13218897		CU914574,CH242-133L8,1:13203288-13230549 (Clone quality: bE133L8 on chr=1; Num_of_Contigs=13; )
CNKSR3		location ⇒	1:13219521-13219444		CU914574,CH242-133L8,1:13203288-13230549 (Clone quality: bE133L8 on chr=1; Num_of_Contigs=13; )
CNN1		ENSSSCG00000013614	2:52229462-52231583		CU856608,CH242-517F5,2:52214444-52231801 (Clone quality: bE517F5 on chr=2; Num_of_Contigs=7; )
CNN2		location ⇒	4:127079066-127079034		CU639441,CH242-134D14,4:127074067-127113549 (Clone quality: bE134D14 on chr=4; Num_of_Contigs=7; )
CNN2		location ⇒	4:127079182-127079107		CU639441,CH242-134D14,4:127074067-127113549 (Clone quality: bE134D14 on chr=4; Num_of_Contigs=7; )
CNN2		location ⇒	4:127079183-127079107		CU639441,CH242-134D14,4:127074067-127113549 (Clone quality: bE134D14 on chr=4; Num_of_Contigs=7; )
CNN2		location ⇒	4:127100210-127100166		CU639441,CH242-134D14,4:127074067-127113549 (Clone quality: bE134D14 on chr=4; Num_of_Contigs=7; )
CNN3		ENSSSCG00000006887	4:127077068-127100464		CU639441,CH242-134D14,4:127074067-127113549 (Clone quality: bE134D14 on chr=4; Num_of_Contigs=7; )
CNNM1		ENSSSCG00000010536	14:115241549-115301415
CNNM2		ENSSSCG00000010593	14:118966775-119133301
CNNM3		ENSSSCG00000008201	3:52183938-52201595		FP102744,CH242-70H5,3:52166217-52203121 (Clone quality: bE70H5 on chr=3; Num_of_Contigs=11; )
CNNM4		ENSSSCG00000008202	3:52207087-52215282
CNOT1		ENSSSCG00000002799	6:19251945-19325733
CNOT2		ENSSSCG00000000502	5:33183472-33417601
CNOT3		ENSSSCG00000003264	6:40564012-40579928
CNOT4		ENSSSCG00000016528	18:12109730-12142135
CNOT6		ENSSSCG00000014009	2:67360786-67509564
CNOT6L		ENSSSCG00000008989	8:62657111-62727232
CNOT7		ENSSSCG00000006986	17:4820813-4832125		CU606905,CH242-40L10,17:4819387-4842262 (Clone quality: bE40L10 on chr=17; Num_of_Contigs=4; )
CNOT8		ENSSSCG00000017067	16:65689274-65708517		CU633659,CH242-20B14,16:65657649-65722171 (Clone quality: bE20B14 on chr=16; Num_of_Contigs=6; )
CNP		ENSSSCG00000017420	12:18491526-18498055		CU856598,CH242-362F6,12:18453794-18511165 (Clone quality: bE362F6 on chr=12; Num_of_Contigs=5; )
CNPY1		ENSSSCG00000016418	18:1964304-1970939
CNPY2		ENSSSCG00000000394	5:20713522-20716976		CU498845,CH242-111P13,5:20699391-20717983 (Clone quality: bE111P13 on chr=5; Num_of_Contigs=18; )
CNPY3		ENSSSCG00000001651	7:43861770-43872144	CR956379,CH242-196P11,7:43779717-43958428 (No clone quality info on bE196P11)

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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).