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)

ITM2B		location ⇒	11:18926994-18926222		FP085602,CH242-266M16,11:18913685-18928244 (Clone quality: bE266M16 on chr=11; Num_of_Contigs=8; )
ITM2B		location ⇒	11:18929276-18929121		FP085602,CH242-266M16,11:18928345-18955098 (Clone quality: bE266M16 on chr=11; Num_of_Contigs=8; )
ITM2B		location ⇒	11:18931337-18931131		FP085602,CH242-266M16,11:18928345-18955098 (Clone quality: bE266M16 on chr=11; Num_of_Contigs=8; )
ITM2B		location ⇒	11:18933199-18933069		FP085602,CH242-266M16,11:18928345-18955098 (Clone quality: bE266M16 on chr=11; Num_of_Contigs=8; )
ITM2C		ENSSSCG00000016267	15:124040914-124054783		CU571100,CH242-126N17,15:123990604-124093801 (Clone quality: bE126N17 on chr=15; Num_of_Contigs=2; )
ITM2C		ENSSSCG00000016267	15:124040914-124054783		CU571100,CH242-126N17,15:123990604-124093801 (Clone quality: bE126N17 on chr=15; Num_of_Contigs=2; )
ITM2C		location ⇒	15:124040993-124041163		CU571100,CH242-126N17,15:123990604-124093801 (Clone quality: bE126N17 on chr=15; Num_of_Contigs=2; )
ITM2C		location ⇒	15:124051165-124051355		CU571100,CH242-126N17,15:123990604-124093801 (Clone quality: bE126N17 on chr=15; Num_of_Contigs=2; )
ITM2C		location ⇒	15:124052588-124052738		CU571100,CH242-126N17,15:123990604-124093801 (Clone quality: bE126N17 on chr=15; Num_of_Contigs=2; )
ITM2C		location ⇒	15:124053494-124053590		CU571100,CH242-126N17,15:123990604-124093801 (Clone quality: bE126N17 on chr=15; Num_of_Contigs=2; )
ITPA		ENSSSCG00000007158	17:34041420-34054746
ITPK1		ENSSSCG00000002457	7:122500435-122566510		CU468886,CH242-145B2,7:122436020-122571421 (Clone quality: bE145B2 on chr=7; Num_of_Contigs=2; )
ITPKA		ENSSSCG00000004746	1:136277482-136285872		CU633572,CH242-274F1,1:136202998-136286247 (Clone quality: bE274F1 on chr=1; Num_of_Contigs=12; )
ITPKC		ENSSSCG00000003000	6:33719166-33730459		CU928654,CH242-130A3,6:33678287-33731769 (Clone quality: bE130A3 on chr=6; Num_of_Contigs=6; )
ITPR1		ENSSSCG00000011533	13:51178156-51227873
ITPR1		location ⇒	13:51047691-51047800		CU914792,CH242-10D7,13:51042795-51055141 (Clone quality: bE10D7 on chr=13; Num_of_Contigs=6; )
ITPR1		location ⇒	13:51145644-51145761		CU914792,CH242-10D7,13:51119023-51160269 (Clone quality: bE10D7 on chr=13; Num_of_Contigs=6; )
ITPR1		location ⇒	13:51156406-51156570		CU914792,CH242-10D7,13:51119023-51160269 (Clone quality: bE10D7 on chr=13; Num_of_Contigs=6; )
ITPR1		location ⇒	13:51158765-51158865		CU914792,CH242-10D7,13:51119023-51160269 (Clone quality: bE10D7 on chr=13; Num_of_Contigs=6; )
ITPR3		ENSSSCG00000001518	7:34243825-34308622	CU481857,CH242-122A6,7:34237512-34415946 (Clone quality: bE122A6 on chr=7; Num_of_Contigs=5; )
ITPRIP		ENSSSCG00000010613	14:120362980-120364635		CU041373,CH242-42A8,14:120244674-120398124 (Clone quality: bE42A8 on chr=14; Num_of_Contigs=3; )
ITSN2		ENSSSCG00000008583	3:106677444-106717483
IVD		ENSSSCG00000004774	1:137362220-137377017		CU234165,CH242-252B18,1:137339871-137454558 (Clone quality: bE252B18 on chr=1; Num_of_Contigs=2; )
IVL		ENSSSCG00000006595	4:100516908-100518594		CU210949,CH242-471G17,4:100442582-100566951 (Clone quality: bE471G17 on chr=4; Num_of_Contigs=4; )
IVNS1ABP		ENSSSCG00000015570	9:118908927-118928310
IVNS1ABP		location ⇒	9:118909700-118908813		CU972398,CH242-133N16,9:118830470-118917038 (Clone quality: bE133N16 on chr=9; Num_of_Contigs=2; )
IVNS1ABP		location ⇒	9:118911217-118911050		CU972398,CH242-133N16,9:118830470-118917038 (Clone quality: bE133N16 on chr=9; Num_of_Contigs=2; )
IVNS1ABP		location ⇒	9:118912821-118912595		CU972398,CH242-133N16,9:118830470-118917038 (Clone quality: bE133N16 on chr=9; Num_of_Contigs=2; )
IVNS1ABP		location ⇒	9:118919149-118918974		CU570727,CH242-209D22,9:118917039-118996352 (Clone quality: bE209D22 on chr=9; Num_of_Contigs=3; )
IWS1		ENSSSCG00000015865	15:55959051-55972597
IYD		ENSSSCG00000004093	1:16565065-16581970
IZUMO1		ENSSSCG00000003142	6:37634960-37638212		CU929759,CH242-294C24,6:37595303-37722216 (Clone quality: bE294C24 on chr=6; Num_of_Contigs=3; )
IZUMO1		location ⇒	6:37634587-37635203		CU929759,CH242-294C24,6:37595303-37722216 (Clone quality: bE294C24 on chr=6; 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, 1101-33

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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).