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)

TM4SF2		location ⇒	X:34093885-34094041		FP102385,CH242-81B3,X:34005128-34178208 (Clone quality: bE81B3 on chr=X; Num_of_Contigs=2; )
TM4SF2		location ⇒	X:34107849-34108810		FP102385,CH242-81B3,X:34005128-34178208 (Clone quality: bE81B3 on chr=X; Num_of_Contigs=2; )
TM4SF2		location ⇒	X:34254563-34254374		CU480860,CH242-49J12,X:34233168-34262767 (Clone quality: bE49J12 on chr=X; Num_of_Contigs=7; )
TM4SF20		ENSSSCG00000016247	15:121271850-121282115		CU550654,CH242-149P18,15:121250654-121308013 (Clone quality: bE149P18 on chr=15; Num_of_Contigs=6; )
TM4SF4		ENSSSCG00000011703	13:73108683-73108868		FP102113,CH242-334M8,13:73105519-73116656 (Clone quality: bE334M8 on chr=13; Num_of_Contigs=8; )
TM4SF5		ENSSSCG00000017916	12:49305583-49312784		CU929524,CH242-164N17,12:49282475-49313175 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
TM6SF1		ENSSSCG00000001800	7:57861320-57889792		CU407315,CH242-258B16,7:57856098-58033288 (Clone quality: bE258B16 on chr=7; Num_of_Contigs=2; )
TM7SF2		ENSSSCG00000013004	2:5477247-5481946	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
TM7SF3		ENSSSCG00000000553	5:45318043-45358454
TM7SF4		ENSSSCG00000006043	4:33221677-33228096		CU407249,CH242-439E22,4:33220861-33230984 (Clone quality: bE439E22 on chr=4; Num_of_Contigs=12; )
TM9SF1		ENSSSCG00000001999	7:81445770-81450586		CT961055,CH242-32K2,7:81442434-81553552 (Clone quality: bE32K2 on chr=7; Num_of_Contigs=2; )
TM9SF3		ENSSSCG00000010508	14:113066739-113131018
TM9SF4		ENSSSCG00000007246	17:37902899-38007577
TMBIM1		ENSSSCG00000016186	15:113484201-113562604
TMBIM4		ENSSSCG00000000473	5:30371879-30457804
TMC1		ENSSSCG00000005266	1:236628431-236704318		CU633948,CH242-289K24,1:236624664-236704765 (Clone quality: bE289K24 on chr=1; Num_of_Contigs=4; )
TMC2		ENSSSCG00000007172	17:34523474-34554512
TMC3		ENSSSCG00000001789	7:56265505-56320922
TMC4		ENSSSCG00000003266	6:40585304-40599638
TMC7		ENSSSCG00000007866	3:23754374-23802792
TMCC1		ENSSSCG00000011593	13:57529191-57711604
TMCC2		ENSSSCG00000015287	9:63086323-63108992
TMCC3		ENSSSCG00000000906	5:83632764-83643365		FP089488,CH242-226P9,5:83576552-83704049 (Clone quality: bE226P9 on chr=5; Num_of_Contigs=3; )
TMCO1		ENSSSCG00000006323	4:88398372-88448110
TMCO1		location ⇒	4:88414501-88414551		CU468989,CH242-231O3,4:88387394-88421643 (Clone quality: bE231O3 on chr=4; Num_of_Contigs=3; )
TMCO1		location ⇒	4:88416746-88416814		CU468989,CH242-231O3,4:88387394-88421643 (Clone quality: bE231O3 on chr=4; Num_of_Contigs=3; )
TMCO1		location ⇒	4:88428061-88428205		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
TMCO1		location ⇒	4:88447528-88447904		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
TMCO3		ENSSSCG00000009563	11:79036367-79042939		FP236199,CH242-118I8,11:79031110-79049627 (Clone quality: bE118I8 on chr=11; Num_of_Contigs=8; )
TMCO5A		ENSSSCG00000004794	1:140009967-140026153		CU302355,CH242-289C11,1:139924696-140125159 (Clone quality: bE289C11 on chr=1; Num_of_Contigs=1; )
TMCO5B		ENSSSCG00000002251	7:89255499-89267278		CT990632,CH242-89J20,7:89225483-89366939 (Clone quality: bE89J20 on chr=7; Num_of_Contigs=2; )
TMCO6		ENSSSCG00000014370	2:129360207-129367211		CU459055,CH242-430O11,2:129351567-129383244 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
TMED1		ENSSSCG00000013631	2:52700561-52703092		CU928849,CH242-1G23,2:52653544-52705251 (Clone quality: bE1G23 on chr=2; Num_of_Contigs=8; )
TMED10		ENSSSCG00000002382	7:106584035-106616508	CT737372,CH242-134B18,7:106458379-106624048 (Clone quality: bE134B18 on chr=7; Num_of_Contigs=4; )
TMED2		ENSSSCG00000009772	14:29502053-29511509		CU468658,CH242-245F7,14:29355652-29557150 (Clone quality: bE245F7 on chr=14; Num_of_Contigs=1; )
TMED3		ENSSSCG00000001774	7:54472115-54472339		CT827823,CH242-157K7,7:54469595-54479169 (Clone quality: bE157K7 on chr=7; Num_of_Contigs=4; )
TMED4		ENSSSCG00000016744	18:49251540-49253731		CU856650,CH242-209B3,18:49245387-49362964 (Clone quality: bE209B3 on chr=18; Num_of_Contigs=3; )
TMED5		ENSSSCG00000006896	4:128193102-128210314
TMED6		ENSSSCG00000002761	6:12483741-12491150		FP015939,CH242-384D23,6:12465602-12559923 (Clone quality: bE384D23 on chr=6; Num_of_Contigs=2; )
TMED7		ENSSSCG00000014218	2:108525762-108540583
TMED8		ENSSSCG00000002395	7:108312980-108408922
TMED9		ENSSSCG00000014037	2:69620682-69623173	FP067372,CH242-220F6,2:69614494-69671554 (Clone quality: bE220F6 on chr=2; Num_of_Contigs=8; )
TMEFF1		ENSSSCG00000005391	1:253874098-253968938
TMEFF2		ENSSSCG00000016064	15:91367270-91385182		CU693393,CH242-174B17,15:91344837-91454554 (Clone quality: bE174B17 on chr=15; Num_of_Contigs=2; )
TMEM100		ENSSSCG00000017607	12:29537519-29537923		CU896617,CH242-207F3,12:29443353-29557217 (Clone quality: bE207F3 on chr=12; Num_of_Contigs=5; )
TMEM101		ENSSSCG00000017371	12:17182691-17185439		CU914436,CH242-507H4,12:17174854-17187762 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )
TMEM104		ENSSSCG00000017230	12:4629885-4681812
TMEM106B		ENSSSCG00000015351	9:76772463-76793195		CU638720,CH242-196F17,9:76708535-76860205 (Clone quality: bE196F17 on chr=9; Num_of_Contigs=1; )
TMEM106B		location ⇒	7:98181620-98181718	CT827816,CH242-102G18,7:98049960-98250340 (Clone quality: bE102G18 on chr=7; Num_of_Contigs=1; )
TMEM106B		location ⇒	7:98181766-98181824	CT827816,CH242-102G18,7:98049960-98250340 (Clone quality: bE102G18 on chr=7; Num_of_Contigs=1; )

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).