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)

TRIM6-TRIM34		ENSSSCG00000014672	9:3275880-3281846		CU856599,CH242-369B20,9:3224576-3283748 (Clone quality: bE369B20 on chr=9; Num_of_Contigs=3; )
TRIM61		ENSSSCG00000008861	8:38110698-38111231		CU693419,CH242-30B6,8:38110476-38116415 (Clone quality: bE30B6 on chr=8; Num_of_Contigs=7; )
TRIM62		ENSSSCG00000003620	6:61047931-61081743
TRIM65		ENSSSCG00000017195	12:3825525-3829867		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
TRIM66		ENSSSCG00000014567	9:19098-28703		FP102759,CH242-92D2,9:11540-30140 (Clone quality: bE92D2 on chr=9; Num_of_Contigs=7; )
TRIM67		ENSSSCG00000010177	14:61594178-61630858
TRIM68		ENSSSCG00000014768	9:4662264-4669953
TRIM69		ENSSSCG00000004681	1:132562840-132579708
TRIM72		ENSSSCG00000007757	3:15794562-15798544		CU464163,CH242-418M3,3:15771570-15802232 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
TRIM77		ENSSSCG00000014932	9:23110991-23111362		FP015793,CH242-134A11,9:23098775-23112427 (Clone quality: bE134A11 on chr=9; Num_of_Contigs=8; )
TRIM8		ENSSSCG00000010587	14:118662408-118675520		CT971490,CH242-33G15,14:118660960-118687883 (Clone quality: bE33G15 on chr=14; Num_of_Contigs=9; )
TRIM9		ENSSSCG00000005025	1:189001278-189104857
TRIML1		ENSSSCG00000006998	17:7112332-7118581		CU606978,CH242-286D19,17:7097366-7120140 (Clone quality: bE286D19 on chr=17; Num_of_Contigs=12; )
TRIML2		ENSSSCG00000006997	17:7064452-7074028		CU606978,CH242-286D19,17:7063050-7097265 (Clone quality: bE286D19 on chr=17; Num_of_Contigs=12; )
TRIO		ENSSSCG00000000126	5:6756169-6851030
TRIO		ENSSSCG00000016781	16:2980222-3204046
TRIO		location ⇒	16:3037116-3036884		CU571120,CH242-240G18,16:3025928-3042034 (Clone quality: bE240G18 on chr=16; Num_of_Contigs=8; )
TRIO		location ⇒	16:3050880-3050755		CU571120,CH242-240G18,16:3050450-3100139 (Clone quality: bE240G18 on chr=16; Num_of_Contigs=8; )
TRIO		location ⇒	16:3063327-3063133		CU571120,CH242-240G18,16:3050450-3100139 (Clone quality: bE240G18 on chr=16; Num_of_Contigs=8; )
TRIO		location ⇒	16:3079113-3078941		CU571120,CH242-240G18,16:3050450-3100139 (Clone quality: bE240G18 on chr=16; Num_of_Contigs=8; )
TRIOBP		ENSSSCG00000000126	5:6756169-6851030
TRIP		ENSSSCG00000008362	3:71232949-71233887		CU467929,CH242-297N18,3:71213957-71263753 (Clone quality: bE297N18 on chr=3; Num_of_Contigs=5; )
TRIP		ENSSSCG00000004552	1:110848744-111122527
TRIP		ENSSSCG00000004470	1:91844234-91847249		CU074282,CH242-124C3,1:91840945-91977429 (Clone quality: bE124C3 on chr=1; Num_of_Contigs=2; )
TRIP		ENSSSCG00000003612	6:60841813-60848666
TRIP		ENSSSCG00000002445	7:121544786-121617082
TRIP10		ENSSSCG00000013554	2:50223982-50301699
TRIP11		ENSSSCG00000002445	7:121544786-121617082
TRIP4		ENSSSCG00000004552	1:110848744-111122527
TRIP4		ENSSSCG00000010285	14:78256680-78301386
TRIP4		ENSSSCG00000004359	1:70840268-70860876		CU104757,CH242-114J14,1:70838053-70862278 (Clone quality: bE114J14 on chr=1; Num_of_Contigs=18; )
TRIP4		location ⇒	1:110849047-110848763		CU571342,CH242-151D21,1:110734263-110859048 (Clone quality: bE151D21 on chr=1; Num_of_Contigs=2; )
TRIP4		location ⇒	1:110891016-110890799		CU571342,CH242-151D21,1:110859149-110892399 (Clone quality: bE151D21 on chr=1; Num_of_Contigs=2; )
TRIP4		location ⇒	1:110902082-110902366		CU499013,CH242-5D7,1:110899010-110907229 (Clone quality: bE5D7 on chr=1; Num_of_Contigs=13; )
TRIP4		location ⇒	1:110992621-110992405		CU499013,CH242-5D7,1:110991010-110998796 (Clone quality: bE5D7 on chr=1; Num_of_Contigs=13; )
TRIT1		ENSSSCG00000003667	6:65714447-65759702
TRMT1		ENSSSCG00000013744	2:56260041-56315971
TRMT11		ENSSSCG00000004220	1:38527045-38588195		CU302387,CH242-264H12,1:38487384-38605780 (Clone quality: bE264H12 on chr=1; Num_of_Contigs=3; )
TRMT112		ENSSSCG00000013029	2:6168931-6169795
TRMT12		ENSSSCG00000005972	4:14750927-14752246		CU468433,CH242-46N16,4:14735693-14762168 (Clone quality: bE46N16 on chr=4; Num_of_Contigs=6; )
TRMT2A		ENSSSCG00000010136	14:52744119-52748290		CT737345,CH242-178J1,14:52723116-52857619 (Clone quality: bE178J1 on chr=14; Num_of_Contigs=3; )
TRMT2B		ENSSSCG00000012489	X:76036829-76078909
TRMT6		ENSSSCG00000007046	17:13913853-13925453		CU311185,CH242-222G18,17:13889408-14007446 (Clone quality: bE222G18 on chr=17; Num_of_Contigs=4; )
TRMT61B		ENSSSCG00000008537	3:103317915-103324783		CU915390,CH242-227M18,3:103316351-103328541 (Clone quality: bE227M18 on chr=3; Num_of_Contigs=14; )
TRMU		ENSSSCG00000000007	5:175376-187326		FP016092,CH242-185O3,5:173761-188766 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
TRNT1		ENSSSCG00000011529	13:50269310-50295275
TROAP		ENSSSCG00000000200	5:14198438-14205398		CU856470,CH242-396N13,5:14196631-14218178 (Clone quality: bE396N13 on chr=5; Num_of_Contigs=7; )
TROAP		ENSSSCG00000000196	5:14048035-14054995		CU633660,CH242-20J14,5:13996651-14067250 (Clone quality: bE20J14 on chr=5; Num_of_Contigs=3; )
TROAP		location ⇒	5:14048379-14048535		CU633660,CH242-20J14,5:13996651-14067250 (Clone quality: bE20J14 on chr=5; Num_of_Contigs=3; )
TROAP		location ⇒	5:14048659-14048846		CU633660,CH242-20J14,5:13996651-14067250 (Clone quality: bE20J14 on chr=5; Num_of_Contigs=3; )

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, 1751-1800, 1801-1850, 1851-8

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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).