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)

TROAP		location ⇒	5:14204774-14204587		CU856470,CH242-396N13,5:14196631-14218178 (Clone quality: bE396N13 on chr=5; Num_of_Contigs=7; )
TROAP		location ⇒	5:14205054-14204898		CU856470,CH242-396N13,5:14196631-14218178 (Clone quality: bE396N13 on chr=5; Num_of_Contigs=7; )
TROP		ENSSSCG00000003832	6:109161614-109162585		CU929656,CH242-501P8,6:109138346-109187890 (Clone quality: bE501P8 on chr=6; Num_of_Contigs=7; )
TROP		location ⇒	X:47378215-47376039		CU928851,CH242-119O9,X:47360054-47409767 (Clone quality: bE119O9 on chr=X; Num_of_Contigs=9; )
TROP		location ⇒	X:47457627-47459803		CU856438,CH242-133L21,X:47452437-47526061 (Clone quality: bE133L21 on chr=X; Num_of_Contigs=8; )
TROVE2		ENSSSCG00000010804	10:1709289-1818022
TRPA1		ENSSSCG00000006186	4:65646472-65696166		CU571032,CH242-276M8,4:65603920-65758454 (Clone quality: bE276M8 on chr=4; Num_of_Contigs=2; )
TRPC1		ENSSSCG00000011681	13:68029290-68098554
TRPC3		ENSSSCG00000009092	8:87672988-87728335
TRPC3		location ⇒	8:87712745-87712968		CU570952,CH242-424C2,8:87704036-87718589 (Clone quality: bE424C2 on chr=8; Num_of_Contigs=7; )
TRPC3		location ⇒	8:87725365-87725442		CU570952,CH242-424C2,8:87721145-87729703 (Clone quality: bE424C2 on chr=8; Num_of_Contigs=7; )
TRPC3		location ⇒	8:87728048-87728179		CU570952,CH242-424C2,8:87721145-87729703 (Clone quality: bE424C2 on chr=8; Num_of_Contigs=7; )
TRPC4		ENSSSCG00000009362	11:12925120-13083775
TRPC4AP		ENSSSCG00000007289	17:40444809-40467374
TRPC4AP		location ⇒	17:40466274-40466483		CU633434,CH242-93B19,17:40458604-40469407 (Clone quality: bE93B19 on chr=17; Num_of_Contigs=7; )
TRPC4AP		location ⇒	17:40466688-40466885		CU633434,CH242-93B19,17:40458604-40469407 (Clone quality: bE93B19 on chr=17; Num_of_Contigs=7; )
TRPC4AP		location ⇒	17:40466955-40467608		CU633434,CH242-93B19,17:40458604-40469407 (Clone quality: bE93B19 on chr=17; Num_of_Contigs=7; )
TRPC4AP		location ⇒	17:40512402-40512611		CU633434,CH242-93B19,17:40502263-40519368 (Clone quality: bE93B19 on chr=17; Num_of_Contigs=7; )
TRPC5		ENSSSCG00000012587	X:89642310-89770790
TRPC7		ENSSSCG00000014318	2:125704774-125885430
TRPM1		ENSSSCG00000004843	1:151404761-151495800
TRPM3		ENSSSCG00000005257	1:234286063-234571680
TRPM6		ENSSSCG00000005269	1:238288062-238409204
TRPM7		ENSSSCG00000004636	1:126114248-126203370
TRPM7		location ⇒	1:126146987-126147041		CU469118,CH242-119H7,1:126126637-126222260 (Clone quality: bE119H7 on chr=1; Num_of_Contigs=2; )
TRPM7		location ⇒	1:126157482-126157764		CU469118,CH242-119H7,1:126126637-126222260 (Clone quality: bE119H7 on chr=1; Num_of_Contigs=2; )
TRPM7		location ⇒	1:126171398-126172116		CU469118,CH242-119H7,1:126126637-126222260 (Clone quality: bE119H7 on chr=1; Num_of_Contigs=2; )
TRPM7		location ⇒	1:126184835-126184900		CU469118,CH242-119H7,1:126126637-126222260 (Clone quality: bE119H7 on chr=1; Num_of_Contigs=2; )
TRPM8		ENSSSCG00000016314	15:126944280-127020166	CU407086,CH242-496M8,15:126923063-127047825 (Clone quality: bE496M8 on chr=15; Num_of_Contigs=6; )
TRPS1		ENSSSCG00000006018	4:22821955-22892300
TRPT1		ENSSSCG00000013040	2:6268712-6271743		CU861533,CH242-1H13,2:6266781-6274991 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
TRPV1		ENSSSCG00000017863	12:46971284-46995144		FP016040,CH242-164K7,12:46938248-47005076 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
TRPV2		ENSSSCG00000018032	12:56177051-56192414
TRPV3		ENSSSCG00000017862	12:46933382-46963485
TRPV4		ENSSSCG00000009929	14:41337022-41358318		CU640887,CH242-377K8,14:41308117-41358969 (Clone quality: bE377K8 on chr=14; Num_of_Contigs=2; )
TRPV5		ENSSSCG00000016470	18:6112105-6120110		CU928245,CH242-100K20,18:6102984-6180022 (Clone quality: bE100K20 on chr=18; Num_of_Contigs=3; )
TRPV6		ENSSSCG00000016469	18:6086943-6102595		CU928245,CH242-100K20,18:6058604-6102883 (Clone quality: bE100K20 on chr=18; Num_of_Contigs=3; )
TRUB1		ENSSSCG00000010653	14:131145416-131187908		CU329682,CH242-56I1,14:131100241-131232014 (Clone quality: bE56I1 on chr=14; Num_of_Contigs=2; )
TRUB2		ENSSSCG00000005645	1:283381158-283391035		CU234126,CH242-282L14,1:283270038-283452033 (Clone quality: bE282L14 on chr=1; Num_of_Contigs=4; )
TRYP_PIG		ENSSSCG00000016483	18:6491040-6496748
TSC1		ENSSSCG00000008040	3:36414708-36451005
TSC1		ENSSSCG00000009649	14:9151231-9155342		CT978650,CH242-252H13,14:9123196-9234608 (Clone quality: bE252H13 on chr=14; Num_of_Contigs=2; )
TSC1		location ⇒	1:22203225-22203313		CU234155,CH242-220C4,1:22178545-22204108 (Clone quality: bE220C4 on chr=1; Num_of_Contigs=7; )
TSC1		location ⇒	1:2579353-2579259		FP089482,CH242-213J15,1:2579035-2630305 (Clone quality: bE213J15 on chr=1; Num_of_Contigs=5; )
TSC1		location ⇒	1:34784982-34784930		CU311188,CH242-291B3,1:34751265-34900086 (Clone quality: bE291B3 on chr=1; Num_of_Contigs=1; )
TSC1		location ⇒	1:8405698-8405646		FP017297,CH242-205C17,1:8387441-8416507 (Clone quality: bE205C17 on chr=1; Num_of_Contigs=7; )
TSC2		ENSSSCG00000008040	3:36414708-36451005
TSC22D1		ENSSSCG00000009422	11:21398956-21510318
TSC22D2		ENSSSCG00000011708	13:73626553-73675763		CU582886,CH242-286B9,13:73571562-73683239 (Clone quality: bE286B9 on chr=13; Num_of_Contigs=3; )
TSEN15		ENSSSCG00000015564	9:117657734-117693523		CU655916,CH242-251G9,9:117646192-117696689 (Clone quality: bE251G9 on chr=9; Num_of_Contigs=5; )

Go to records:
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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).