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)

GLI		ENSSSCG00000016763	18:51447359-51456362		CU655978,CH242-170J15,18:51382351-51457200 (Clone quality: bE170J15 on chr=18; Num_of_Contigs=4; )
GLI		ENSSSCG00000003846	6:112482883-112610792
GLI		ENSSSCG00000005224	1:228152081-228256562
GLI		ENSSSCG00000005339	1:248082221-248105467
GLI2		ENSSSCG00000015733	15:28588628-28622619
GLI3		ENSSSCG00000016763	18:51447359-51456362		CU655978,CH242-170J15,18:51382351-51457200 (Clone quality: bE170J15 on chr=18; Num_of_Contigs=4; )
GLIPR1		ENSSSCG00000000519	5:38696540-38832572
GLIPR2		ENSSSCG00000005339	1:248082221-248105467
GLIS1		ENSSSCG00000003846	6:112482883-112610792
GLMN		ENSSSCG00000006904	4:128954136-129039420
GLMN		location ⇒	4:128968230-128968414		CU855851,CH242-211F5,4:128860316-128979239 (Clone quality: bE211F5 on chr=4; Num_of_Contigs=2; )
GLMN		location ⇒	4:128968961-128969016		CU855851,CH242-211F5,4:128860316-128979239 (Clone quality: bE211F5 on chr=4; Num_of_Contigs=2; )
GLMN		location ⇒	4:128970741-128970824		CU855851,CH242-211F5,4:128860316-128979239 (Clone quality: bE211F5 on chr=4; Num_of_Contigs=2; )
GLMN		location ⇒	4:128978269-128978334		CU855851,CH242-211F5,4:128860316-128979239 (Clone quality: bE211F5 on chr=4; Num_of_Contigs=2; )
GLO1		ENSSSCG00000001587	7:39112469-39139156		CT737323,CH242-25F9,7:39094968-39227607 (Clone quality: bE25F9 on chr=7; Num_of_Contigs=2; )
GLOD4		ENSSSCG00000017807	12:45000506-45017025
GLP1R		ENSSSCG00000001589	7:39462693-39491076
GLP2R		ENSSSCG00000017998	12:51727140-51782021		CU929537,CH242-329E9,12:51698515-51788687 (Clone quality: bE329E9 on chr=12; Num_of_Contigs=5; )
GLRA2		ENSSSCG00000012129	X:10398964-10534612
GLRA3		ENSSSCG00000009698	14:15039237-15119079
GLRA4		ENSSSCG00000012535	X:82279758-82300717		FP015842,CH242-149K17,X:82243037-82322562 (Clone quality: bE149K17 on chr=X; Num_of_Contigs=5; )
GLRB		ENSSSCG00000008872	8:39857260-39893655
GLRX1		ENSSSCG00000014167	2:91521702-91533080		CU462919,CH242-162P12,2:91518543-91556345 (Clone quality: bE162P12 on chr=2; Num_of_Contigs=4; )
GLRX1		location ⇒	13:116967792-116968342		CU915464,CH242-217J21,13:116947212-117082193 (Clone quality: bE217J21 on chr=13; Num_of_Contigs=2; )
GLRX1		location ⇒	13:19212151-19211597		CU633398,CH242-322L18,13:19166931-19224321 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
GLRX1		location ⇒	13:59925463-59925086		CU633391,CH242-298L24,13:59903334-59925463 (Clone quality: bE298L24 on chr=13; Num_of_Contigs=9; )
GLRX1		location ⇒	13:8954290-8954841		CU633256,CH242-256G23,13:8925482-8986246 (Clone quality: bE256G23 on chr=13; Num_of_Contigs=2; )
GLRX2		ENSSSCG00000010803	10:1687413-1695447		CU929655,CH242-497M20,10:1681278-1698567 (Clone quality: bE497M20 on chr=10; Num_of_Contigs=12; )
GLRX3		ENSSSCG00000010759	14:146334011-146369522
GLRX5		ENSSSCG00000002496	7:125616258-125626326	CT867964,CH242-267C2,7:125614014-125812235 (Clone quality: bE267C2 on chr=7; Num_of_Contigs=1; )
GLS		ENSSSCG00000016056	15:90021180-90077214
GLS2		ENSSSCG00000000401	5:20795624-20994823
GLT25D1		ENSSSCG00000013883	2:61869234-61891774		CU861959,CH242-254K17,2:61868948-61911665 (Clone quality: bE254K17 on chr=2; Num_of_Contigs=9; )
GLT25D2		ENSSSCG00000015562	9:117429717-117455394
GLT6D1		ENSSSCG00000005758	1:289821314-289825774		FP102268,CH242-95K10,1:289814837-289832607 (Clone quality: bE95K10 on chr=1; Num_of_Contigs=5; )
GLT8D1		ENSSSCG00000011448	13:29440268-29446477		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
GLT8D2		ENSSSCG00000000848	5:75596126-75615078
GLT8D4		ENSSSCG00000011519	13:45953661-46045601
GLTPD1		ENSSSCG00000003340	6:42922448-42923359		FP102596,CH242-173K23,6:42905835-42937819 (Clone quality: bE173K23 on chr=6; Num_of_Contigs=10; )
GLTPD2		ENSSSCG00000017914	12:49299359-49300998		CU929524,CH242-164N17,12:49282475-49313175 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
GLTP_PIG		ENSSSCG00000009928	14:41253890-41277076		CU640887,CH242-377K8,14:41152094-41308016 (Clone quality: bE377K8 on chr=14; Num_of_Contigs=2; )
GLUL		ENSSSCG00000015545	9:116109982-116119502		CU855743,CH242-470F20,9:116099941-116165911 (Clone quality: bE470F20 on chr=9; Num_of_Contigs=8; )
GLYAT		ENSSSCG00000013149	2:10448380-10467284
GLYATL2		ENSSSCG00000013148	2:10414084-10420349		CU467529,CH242-205D7,2:10366123-10446917 (Clone quality: bE205D7 on chr=2; Num_of_Contigs=2; )
GLYATL3		ENSSSCG00000001730	7:50698989-50707004		CU498923,CH242-269A6,7:50698490-50707948 (Clone quality: bE269A6 on chr=7; Num_of_Contigs=16; )
GLYCTK		ENSSSCG00000011432	13:28965980-28972214		CU915558,CH242-407L22,13:28951297-29012322 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
GLYR1		ENSSSCG00000007931	3:33588734-33625054		CU929765,CH242-314I20,3:33579794-33640862 (Clone quality: bE314I20 on chr=3; Num_of_Contigs=8; )
GM2A		location ⇒	7:35716527-35716673		CU571051,CH242-525J6,7:35686365-35735821 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )
GM2A		location ⇒	7:35717268-35717458		CU571051,CH242-525J6,7:35686365-35735821 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )
GM2A		location ⇒	7:35719088-35719327		CU571051,CH242-525J6,7:35686365-35735821 (Clone quality: bE525J6 on chr=7; Num_of_Contigs=14; )

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, 851-25

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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).