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)

STK11		ENSSSCG00000013429	2:46447651-46456283		CU929580,CH242-161G11,2:46439429-46462140 (Clone quality: bE161G11 on chr=2; Num_of_Contigs=11; )
STK16		ENSSSCG00000016214	15:114271217-114284659		CU457453,CH242-470M7,15:114256624-114294054 (Clone quality: bE470M7 on chr=15; Num_of_Contigs=11; )
STK17A		ENSSSCG00000016758	18:49924155-49946223
STK17A		location ⇒	1:91106496-91106030		CU469095,CH242-266C13,1:91105840-91114190 (Clone quality: bE266C13 on chr=1; Num_of_Contigs=10; )
STK17B		ENSSSCG00000016067	15:93659840-93691267
STK19		ENSSSCG00000001426	7:27881478-27889410	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
STK24		ENSSSCG00000009511	11:68447042-68468895
STK25		ENSSSCG00000016372	15:131938383-131948522
STK3		ENSSSCG00000009511	11:68447042-68468895
STK31		ENSSSCG00000016719	18:47252048-47313597		CU928519,CH242-26I21,18:47147788-47314181 (Clone quality: bE26I21 on chr=18; Num_of_Contigs=1; )
STK32A		ENSSSCG00000014418	2:134410201-134421029		CU929881,CH242-197N20,2:134401004-134422217 (Clone quality: bE197N20 on chr=2; Num_of_Contigs=13; )
STK32C		ENSSSCG00000010761	14:147161054-147174410		CU640371,CH242-130L11,14:147152431-147174465 (Clone quality: bE130L11 on chr=14; Num_of_Contigs=20; )
STK35		ENSSSCG00000007179	17:34929686-34945063
STK38		ENSSSCG00000001563	7:36838086-36884053
STK38L		ENSSSCG00000009595	14:3608534-3655324		CU468808,CH242-138L4,14:3542194-3693716 (Clone quality: bE138L4 on chr=14; Num_of_Contigs=3; )
STK4		ENSSSCG00000007386	17:49278757-49431613
STK6_PIG		ENSSSCG00000007493	17:59489642-59506801	CR956640,CH242-155M9,17:59463698-59643740 (No clone quality info on bE155M9)
STMN1		location ⇒	4:59033664-59033608		CU151844,CH242-179G3,4:59006340-59061577 (Clone quality: bE179G3 on chr=4; Num_of_Contigs=3; )
STMN2		ENSSSCG00000006160	4:59025859-59078572
STMN4		ENSSSCG00000009662	14:11105003-11125261		CT990535,CH242-108M15,14:11101852-11251924 (Clone quality: bE108M15 on chr=14; Num_of_Contigs=1; )
STOM		ENSSSCG00000005516	1:274982993-275004479
STOML1		ENSSSCG00000001913	7:64878679-64886961		CU468908,CH242-516A11,7:64870441-64902976 (Clone quality: bE516A11 on chr=7; Num_of_Contigs=3; )
STOML2		ENSSSCG00000005302	1:247003832-247007302		CU856695,CH242-238C15,1:246903923-247036412 (Clone quality: bE238C15 on chr=1; Num_of_Contigs=2; )
STOML3		ENSSSCG00000009366	11:13859119-13872086		CU633806,CH242-181G7,11:13853188-13875740 (Clone quality: bE181G7 on chr=11; Num_of_Contigs=20; )
STON2		ENSSSCG00000002412	7:111473737-111482027		CU407292,CH242-513J1,7:111441197-111499266 (Clone quality: bE513J1 on chr=7; Num_of_Contigs=13; )
STOX1		ENSSSCG00000010245	14:74990609-75130244
STOX2		ENSSSCG00000015780	15:42171975-42375631
STP4_PIG		ENSSSCG00000012723	X:116939969-116940741		CU928242,CH242-119C15,X:116938106-116966293 (Clone quality: bE119C15 on chr=X; Num_of_Contigs=9; )
STRA6		ENSSSCG00000001909	7:64750793-64773183	CT797479,CH242-196N13,7:64639731-64852331 (Clone quality: bE196N13 on chr=7; Num_of_Contigs=2; )
STRA8		ENSSSCG00000016533	18:12434131-12453268		FP236477,CH242-106A2,18:12433462-12473644 (Clone quality: bE106A2 on chr=18; Num_of_Contigs=4; )
STRADA		ENSSSCG00000017290	12:12775235-12801493		CU466402,CH242-435H9,12:12768820-12803099 (Clone quality: bE435H9 on chr=12; Num_of_Contigs=7; )
STRADB		ENSSSCG00000016103	15:98644855-98655515
STRBP		ENSSSCG00000005582	1:278617855-278681727
STRN		ENSSSCG00000008499	3:96344030-96444056
STRN4		ENSSSCG00000003104	6:36334833-36360565
STS		ENSSSCG00000012099	X:2890480-2987988
STT3A		ENSSSCG00000015214	9:51283723-51310191		CU694782,CH242-247G18,9:51267226-51364229 (Clone quality: bE247G18 on chr=9; Num_of_Contigs=6; )
STT3B		ENSSSCG00000011229	13:15488388-15585171
Stt3b		ENSSSCG00000011229	13:15488388-15585171
Stt3b		location ⇒	13:15551425-15551493		CU633575,CH242-277F9,13:15517513-15618231 (Clone quality: bE277F9 on chr=13; Num_of_Contigs=3; )
Stt3b		location ⇒	13:15566139-15566192		CU633575,CH242-277F9,13:15517513-15618231 (Clone quality: bE277F9 on chr=13; Num_of_Contigs=3; )
Stt3b		location ⇒	13:15585294-15585369		CU633575,CH242-277F9,13:15517513-15618231 (Clone quality: bE277F9 on chr=13; Num_of_Contigs=3; )
Stt3b		location ⇒	13:15585979-15586030		CU633575,CH242-277F9,13:15517513-15618231 (Clone quality: bE277F9 on chr=13; Num_of_Contigs=3; )
STUB1		ENSSSCG00000008008	3:35751704-35754314
STX10		ENSSSCG00000013752	2:56360272-56363181		CU914348,CH242-473F11,2:56357700-56393953 (Clone quality: bE473F11 on chr=2; Num_of_Contigs=7; )
STX11		ENSSSCG00000004125	1:22168666-22169529		CU234155,CH242-220C4,1:22148264-22178444 (Clone quality: bE220C4 on chr=1; Num_of_Contigs=7; )
STX16		ENSSSCG00000007516	17:61457168-61485451	CR956405,CH242-240K6,17:61451226-61584906 (No clone quality info on bE240K6)
STX17		ENSSSCG00000005386	1:253319915-253408022
STX1A		ENSSSCG00000007714	3:9296397-9304749		CU655977,CH242-166N19,3:9275764-9314897 (Clone quality: bE166N19 on chr=3; Num_of_Contigs=8; )
STX1B		ENSSSCG00000007772	3:16022181-16030446		CU914342,CH242-27O18,3:15998449-16034524 (Clone quality: bE27O18 on chr=3; Num_of_Contigs=6; )

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).