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)

TBC1D17		ENSSSCG00000003193	6:38461255-38475871		CU694867,CH242-269H19,6:38449667-38488605 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
TBC1D19		ENSSSCG00000008761	8:16263161-16328814
TBC1D2		ENSSSCG00000005376	1:251555000-251596313
TBC1D20		ENSSSCG00000007205	17:36634170-36638203
TBC1D21		ENSSSCG00000001915	7:64962279-64975563		CU468908,CH242-516A11,7:64903077-65019161 (Clone quality: bE516A11 on chr=7; Num_of_Contigs=3; )
TBC1D22A		ENSSSCG00000000955	5:98889308-98920281
Tbc1d23		location ⇒	13:116723909-116723820		CU467063,CH242-505O10,13:116723439-116736742 (Clone quality: bE505O10 on chr=13; Num_of_Contigs=16; )
Tbc1d23		location ⇒	13:116733612-116733487		CU467063,CH242-505O10,13:116723439-116736742 (Clone quality: bE505O10 on chr=13; Num_of_Contigs=16; )
Tbc1d23		location ⇒	13:116738478-116738275		CU467063,CH242-505O10,13:116736843-116751301 (Clone quality: bE505O10 on chr=13; Num_of_Contigs=16; )
Tbc1d23		location ⇒	13:116742371-116742259		CU467063,CH242-505O10,13:116736843-116751301 (Clone quality: bE505O10 on chr=13; Num_of_Contigs=16; )
TBC1D2B		ENSSSCG00000001758	7:53680066-53896572
TBC1D30		ENSSSCG00000000467	5:28873101-28900079		CU914701,CH242-243G1,5:28804495-28903031 (Clone quality: bE243G1 on chr=5; Num_of_Contigs=4; )
TBC1D4		ENSSSCG00000009464	11:46481164-46632950
TBC1D5		ENSSSCG00000011199	13:3324000-3458002
TBC1D7		ENSSSCG00000001053	7:9854758-9876999
TBC1D8		ENSSSCG00000008169	3:48826867-49011811
TBC1D8B		ENSSSCG00000012552	X:85251680-85322100
TBC1D9		ENSSSCG00000009057	8:74577735-74584053
TBC1D9B		ENSSSCG00000014014	2:68024386-68073421	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
TBCA		ENSSSCG00000014100	2:75554071-75567973
TBCB		ENSSSCG00000002926	6:30576503-30586590		CU694686,CH242-213I9,6:30551266-30589235 (Clone quality: bE213I9 on chr=6; Num_of_Contigs=4; )
TBCCD1		ENSSSCG00000011797	13:93964284-93984260		CU466376,CH242-17J7,13:93934222-94016715 (Clone quality: bE17J7 on chr=13; Num_of_Contigs=6; )
TBCD		ENSSSCG00000017136	12:527340-554187		CU655877,CH242-167I20,12:500430-557427 (Clone quality: bE167I20 on chr=12; Num_of_Contigs=15; )
TBCE		ENSSSCG00000010154	14:57008167-57022424
TBCK		ENSSSCG00000009154	8:99228451-99239803
TBK1		ENSSSCG00000017515	12:21457362-21472440		CU655852,CH242-166I5,12:21455434-21477393 (Clone quality: bE166I5 on chr=12; Num_of_Contigs=13; )
TBKBP1		ENSSSCG00000017515	12:21457362-21472440		CU655852,CH242-166I5,12:21455434-21477393 (Clone quality: bE166I5 on chr=12; Num_of_Contigs=13; )
TBL1XR1		ENSSSCG00000011760	13:87635591-87885374
TBL2		ENSSSCG00000007709	3:9218471-9223521		CU655977,CH242-166N19,3:9184886-9228135 (Clone quality: bE166N19 on chr=3; Num_of_Contigs=8; )
TBPL1		ENSSSCG00000004173	1:31322270-31357557
TBPL2		ENSSSCG00000005059	1:193339625-193348140		CU104729,CH242-24I13,1:193332714-193365551 (Clone quality: bE24I13 on chr=1; Num_of_Contigs=8; )
TBR1		ENSSSCG00000015891	15:63434610-63442239		CU571357,CH242-300O22,15:63426524-63482865 (Clone quality: bE300O22 on chr=15; Num_of_Contigs=9; )
TBRG1		ENSSSCG00000015195	9:50325514-50336035		CU633633,CH242-140J10,9:50258982-50355264 (Clone quality: bE140J10 on chr=9; Num_of_Contigs=3; )
TBRG4		ENSSSCG00000016732	18:48830579-48841835
TBRG4		location ⇒	18:48832822-48833289		FP085442,CH242-169J21,18:48823970-48837953 (Clone quality: bE169J21 on chr=18; Num_of_Contigs=4; )
TBRG4		location ⇒	18:48836789-48837116		FP085442,CH242-169J21,18:48823970-48837953 (Clone quality: bE169J21 on chr=18; Num_of_Contigs=4; )
TBRG4		location ⇒	18:48837649-48837722		FP085442,CH242-169J21,18:48823970-48837953 (Clone quality: bE169J21 on chr=18; Num_of_Contigs=4; )
TBRG4		location ⇒	18:49128043-49127576		CU855998,CH242-199O17,18:49126074-49128629 (Clone quality: bE199O17 on chr=18; Num_of_Contigs=20; )
TBX1		ENSSSCG00000010126	14:52376729-52381969
TBX1		location ⇒	14:52377704-52377876		CU468497,CH242-430C1,14:52377267-52380662 (Clone quality: bE430C1 on chr=14; Num_of_Contigs=6; )
TBX1		location ⇒	14:52378619-52378725		CU468497,CH242-430C1,14:52377267-52380662 (Clone quality: bE430C1 on chr=14; Num_of_Contigs=6; )
TBX1		location ⇒	14:52380491-52380614		CU468497,CH242-430C1,14:52377267-52380662 (Clone quality: bE430C1 on chr=14; Num_of_Contigs=6; )
TBX1		location ⇒	14:52549571-52549465		CT737290,CH242-153A5,14:52547645-52550514 (Clone quality: bE153A5 on chr=14; Num_of_Contigs=5; )
TBX10		ENSSSCG00000012888	2:3133038-3293093
TBX15		ENSSSCG00000006725	4:106185873-106224591		CU302242,CH242-216F15,4:106185124-106285939 (Clone quality: bE216F15 on chr=4; Num_of_Contigs=3; )
TBX18		ENSSSCG00000004290	1:56181268-56209134		CU457713,CH242-172M17,1:56092202-56271538 (Clone quality: bE172M17 on chr=1; Num_of_Contigs=1; )
TBX19		ENSSSCG00000006299	4:85952777-85985919	CU151849,CH242-198O5,4:85931827-86135389 (Clone quality: bE198O5 on chr=4; Num_of_Contigs=5; )
TBX20		ENSSSCG00000016662	18:37800796-37841667
TBX21		ENSSSCG00000017517	12:21499519-21511736
TBX21		location ⇒	12:21511155-21511351		CU655852,CH242-166I5,12:21507781-21522386 (Clone quality: bE166I5 on chr=12; Num_of_Contigs=13; )

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, 1851-8

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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).