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)

TEK		ENSSSCG00000005122	1:205048089-205292942
TEKT1		ENSSSCG00000017884	12:47773366-47796657		CU655858,CH242-208J3,12:47772347-47942311 (Clone quality: bE208J3 on chr=12; Num_of_Contigs=1; )
TEKT2		ENSSSCG00000003633	6:62557601-62561852		CU929602,CH242-252C17,6:62540199-62574798 (Clone quality: bE252C17 on chr=6; Num_of_Contigs=6; )
TEKT3		ENSSSCG00000018028	12:55976790-56007152		FP102666,CH242-289K1,12:55944745-56010841 (Clone quality: bE289K1 on chr=12; Num_of_Contigs=2; )
TEKT5		ENSSSCG00000007904	3:28870021-28873428
TELO2		ENSSSCG00000008022	3:36061090-36069921		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
TENC1		ENSSSCG00000000254	5:16840647-16849864
TEP1		ENSSSCG00000002142	7:84953173-84968950		CU571042,CH242-348N17,7:84913444-85061275 (Clone quality: bE348N17 on chr=7; Num_of_Contigs=2; )
TEPP		ENSSSCG00000002809	6:19779450-19785191		CU466242,CH242-524K2,6:19767867-19845596 (Clone quality: bE524K2 on chr=6; Num_of_Contigs=12; )
TERF2		ENSSSCG00000002762	6:12494036-12519598		FP015939,CH242-384D23,6:12465602-12559923 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
TERF2		location ⇒	6:12494879-12494575		FP015939,CH242-384D23,6:12465602-12559923 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
TERF2		location ⇒	6:12498190-12498105		FP015939,CH242-384D23,6:12465602-12559923 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
TERF2		location ⇒	6:12503260-12502916		FP015939,CH242-384D23,6:12465602-12559923 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
TERF2IP		ENSSSCG00000002703	6:8697381-8707359		CU856392,CH242-53K23,6:8631869-8811363 (Clone quality: bE53K23 on chr=6; Num_of_Contigs=1; )
TERT		ENSSSCG00000017118	16:76746745-76762472		FP236205,CH242-148J9,16:76738084-76762531 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
TERT		location ⇒	16:76751939-76751747		FP236205,CH242-148J9,16:76738084-76762531 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
TERT		location ⇒	16:76755955-76755770		FP236205,CH242-148J9,16:76738084-76762531 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
TERT		location ⇒	16:76756847-76756660		FP236205,CH242-148J9,16:76738084-76762531 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
TERT		location ⇒	16:76758047-76757850		FP236205,CH242-148J9,16:76738084-76762531 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
TES		ENSSSCG00000016636	18:28679467-28719845
TESC		ENSSSCG00000009859	14:35646147-35702683		CT737179,CH242-7H2,14:35543952-35742587 (Clone quality: bE7H2 on chr=14; Num_of_Contigs=1; )
TESK1		ENSSSCG00000005310	1:247433798-247437472		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
TESK2		ENSSSCG00000003917	6:118797507-118924653
TESSP5		ENSSSCG00000011323	13:24685782-24694721		CU856704,CH242-520E7,13:24685733-24696129 (Clone quality: bE520E7 on chr=13; Num_of_Contigs=12; )
TET1		ENSSSCG00000010241	14:74616492-74828703
TET2		ENSSSCG00000009158	8:100101794-100102795		CU914254,CH242-242C13,8:100099332-100103890 (Clone quality: bE242C13 on chr=8; Num_of_Contigs=3; )
TET3		ENSSSCG00000008292	3:63435983-63515996
TEX10		ENSSSCG00000005389	1:253709925-253786514
TEX101		ENSSSCG00000003052	6:34876750-34879693		FP102750,CH242-80G20,6:34865935-34887494 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
TEX11		ENSSSCG00000012374	X:54576553-54685355
TEX12		ENSSSCG00000015038	9:38818660-38820310		CU657951,CH242-322L21,9:38781851-38831276 (Clone quality: bE322L21 on chr=9; Num_of_Contigs=9; )
TEX12		location ⇒	9:38818661-38818765		CU657951,CH242-322L21,9:38781851-38831276 (Clone quality: bE322L21 on chr=9; Num_of_Contigs=9; )
TEX12		location ⇒	9:38820167-38820395		CU657951,CH242-322L21,9:38781851-38831276 (Clone quality: bE322L21 on chr=9; Num_of_Contigs=9; )
TEX14		ENSSSCG00000017645	12:32834226-32934785
TEX15		ENSSSCG00000015841	15:51190638-51207333		CU855604,CH242-134L11,15:51172181-51225680 (Clone quality: bE134L11 on chr=15; Num_of_Contigs=7; )
TEX2		ENSSSCG00000017278	12:12375975-12435179
TEX264		ENSSSCG00000011424	13:28704345-28704635		CU928637,CH242-39L16,13:28695022-28704722 (Clone quality: bE39L16 on chr=13; Num_of_Contigs=10; )
TEX9		ENSSSCG00000004602	1:120067872-120240632
TF		ENSSSCG00000002860	6:28513318-28521227		FP102642,CH242-236J21,6:28490537-28523128 (Clone quality: bE236J21 on chr=6; Num_of_Contigs=9; )
TF		ENSSSCG00000014157	2:89790905-89800303
TF		ENSSSCG00000011640	13:61524641-61679984
TF		ENSSSCG00000002254	7:91195566-91206740
TF		ENSSSCG00000002507	7:129488051-129578748
TF		ENSSSCG00000008392	3:74933698-75032194
TFAM		ENSSSCG00000010418	14:96859049-96877073		CU041308,CH242-254J24,14:96855451-96895808 (Clone quality: bE254J24 on chr=14; Num_of_Contigs=14; )
TFAP2A		ENSSSCG00000001036	7:7630425-7648184
TFAP2C		ENSSSCG00000007499	17:59699490-59710020	CR974569,CH242-255C19,17:59643741-59745847 (Clone quality: bE255C19 on chr=17; Num_of_Contigs=2; )
TFAP2D		ENSSSCG00000001744	7:51793918-51856199	CT961054,CH242-15K4,7:51679957-51884764 (Clone quality: bE15K4 on chr=7; Num_of_Contigs=1; )
TFB1M		ENSSSCG00000004066	1:12418469-12500472
TFCP2L1		ENSSSCG00000015732	15:28314444-28372604

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).