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)

STAT2		location ⇒	5:44476299-44476363		CU633308,CH242-523H4,5:44467589-44476707 (Clone quality: bE523H4 on chr=5; Num_of_Contigs=8; )
STAT2		location ⇒	5:77536059-77535974		CU915488,CH242-364N12,5:77529492-77540703 (Clone quality: bE364N12 on chr=5; Num_of_Contigs=15; )
STAT3		ENSSSCG00000000482	5:31819517-31824009
STAT3		ENSSSCG00000017409	12:18246329-18310664		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT3		ENSSSCG00000016916	16:32637552-32684001
STAT3		ENSSSCG00000016915	16:32560494-32608590		CU469029,CH242-408B13,16:32547189-32619563 (Clone quality: bE408B13 on chr=16; Num_of_Contigs=3; )
STAT3		ENSSSCG00000013154	2:10604681-10606545		CU929527,CH242-208E7,2:10603479-10641058 (Clone quality: bE208E7 on chr=2; Num_of_Contigs=8; )
STAT3		ENSSSCG00000009997	14:48017985-48020973	CT827833,CH242-227A13,14:47931258-48074674 (Clone quality: bE227A13 on chr=14; Num_of_Contigs=2; )
STAT3		ENSSSCG00000009996	14:47999037-48002022	CT827833,CH242-227A13,14:47931258-48074674 (Clone quality: bE227A13 on chr=14; Num_of_Contigs=2; )
STAT3		ENSSSCG00000005215	1:226776007-227058933
STAT3		ENSSSCG00000004158	1:28600713-28617035		CU633940,CH242-211F12,1:28551423-28622774 (Clone quality: bE211F12 on chr=1; Num_of_Contigs=6; )
STAT3		location ⇒	12:17955399-17955184		CU914191,CH242-236G5,12:17951908-17956244 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
STAT3		location ⇒	12:17968198-17968039		CU914191,CH242-236G5,12:17956345-17980585 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
STAT3		location ⇒	12:18251724-18251509		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT3		location ⇒	12:18264646-18264487		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT4		ENSSSCG00000016059	15:90131471-90155731
STAT4		ENSSSCG00000011730	13:78412462-78420147		CU466518,CH242-80G23,13:78393559-78436172 (Clone quality: bE80G23 on chr=13; Num_of_Contigs=6; )
STAT4		location ⇒	15:16799554-16799473		CU861619,CH242-316B4,15:16796209-16801143 (Clone quality: bE316B4 on chr=15; Num_of_Contigs=13; )
STAT4		location ⇒	15:23371695-23371574		CU683890,CH242-491G23,15:23368723-23372445 (Clone quality: bE491G23 on chr=15; Num_of_Contigs=5; )
STAT4		location ⇒	15:24407096-24407039		CU928614,CH242-504F3,15:24396908-24418159 (Clone quality: bE504F3 on chr=15; Num_of_Contigs=13; )
STAT4		location ⇒	15:923335-923222		CU855629,CH242-138C11,15:923238-993627 (Clone quality: bE138C11 on chr=15; Num_of_Contigs=4; ) FP015824,CH242-13P22,15:881001-923237 (Clone quality: bE13P22 on chr=15; Num_of_Contigs=1; )
STAT5A		ENSSSCG00000017530	12:22160826-22171733
STAT5A		location ⇒	12:17941845-17942053		CU914191,CH242-236G5,12:17933540-17951807 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
STAT5A		location ⇒	12:17945700-17945926		CU914191,CH242-236G5,12:17933540-17951807 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
STAT5A		location ⇒	12:18168652-18168733		CU570902,CH242-109J6,12:18151068-18197440 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT5A		location ⇒	12:18242239-18242465		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT5B		ENSSSCG00000017406	12:18153996-18182276		CU570902,CH242-109J6,12:18151068-18197440 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT5B		location ⇒	12:17941846-17942053		CU914191,CH242-236G5,12:17933540-17951807 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
STAT5B		location ⇒	12:18172893-18173100		CU570902,CH242-109J6,12:18151068-18197440 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT5B		location ⇒	12:18238385-18238592		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
STAT5B		location ⇒	12:22170650-22170857		CU570713,CH242-166L13,12:22169411-22171897 (Clone quality: bE166L13 on chr=12; Num_of_Contigs=17; )
STAT6		location ⇒	18:14224727-14224634		CU467575,CH242-383L21,18:14082196-14224814 (Clone quality: bE383L21 on chr=18; Num_of_Contigs=4; )
STAT6		location ⇒	18:21509005-21508944		CU464173,CH242-66N3,18:21485158-21660167 (Clone quality: bE66N3 on chr=18; Num_of_Contigs=1; )
STAT6		location ⇒	18:7466908-7466815		CU861954,CH242-234F22,18:7394978-7580916 (Clone quality: bE234F22 on chr=18; Num_of_Contigs=1; )
STAT6		location ⇒	18:8405990-8405933		CU638864,CH242-6M9,18:8382463-8423216 (Clone quality: bE6M9 on chr=18; Num_of_Contigs=3; )
STAU2		ENSSSCG00000006179	4:64451450-64490934
STBD1		ENSSSCG00000008982	8:61420722-61421504		CU856443,CH242-338M6,8:61414315-61434215 (Clone quality: bE338M6 on chr=8; Num_of_Contigs=9; )
STC1		ENSSSCG00000009642	14:7918917-7930360		CT990469,CH242-243C21,14:7815268-7931902 (Clone quality: bE243C21 on chr=14; Num_of_Contigs=2; )
STC2		ENSSSCG00000016983	16:48332183-48344135		CU466292,CH242-395M8,16:48326540-48370340 (Clone quality: bE395M8 on chr=16; Num_of_Contigs=10; )
STEAP		location ⇒	9:122958439-122958359		CU928431,CH242-12J10,9:122912528-122996434 (Clone quality: bE12J10 on chr=9; Num_of_Contigs=5; )
STEAP		location ⇒	9:123583923-123583831		CU972375,CH242-105J20,9:123582026-123592131 (Clone quality: bE105J20 on chr=9; Num_of_Contigs=6; )
STEAP		location ⇒	9:47050044-47050129		CU633338,CH242-137B6,9:47034976-47082437 (Clone quality: bE137B6 on chr=9; Num_of_Contigs=4; )
STEAP		location ⇒	9:51087164-51087075		CU915794,CH242-478B11,9:51080781-51092251 (Clone quality: bE478B11 on chr=9; Num_of_Contigs=8; )
STEAP1		ENSSSCG00000015301	9:65785000-65796284		CU914275,CH242-373L10,9:65776213-65811631 (Clone quality: bE373L10 on chr=9; Num_of_Contigs=5; )
STEAP2		ENSSSCG00000015302	9:65847479-65857394
STEAP4		ENSSSCG00000015299	9:63942552-63964482		CU695059,CH242-345H3,9:63879805-64040257 (Clone quality: bE345H3 on chr=9; Num_of_Contigs=1; )
STIM1		ENSSSCG00000014792	9:5381538-5586171
STIM2		ENSSSCG00000008762	8:16702487-16731034		CU856215,CH242-182L6,8:16680955-16736351 (Clone quality: bE182L6 on chr=8; Num_of_Contigs=10; )
STIP1		ENSSSCG00000016644	18:31720823-31722275		CU655857,CH242-129N18,18:31715649-31724795 (Clone quality: bE129N18 on chr=18; Num_of_Contigs=19; )
STK10		ENSSSCG00000016996	16:49495671-49510095		CU914215,CH242-63G20,16:49494559-49516079 (Clone quality: bE63G20 on chr=16; Num_of_Contigs=4; )

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, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

Report problems to zhu

iastate.edu

$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).