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)

ARF4		ENSSSCG00000011466	13:32993713-33013712		CU467952,CH242-20F23,13:32987254-33018707 (Clone quality: bE20F23 on chr=13; Num_of_Contigs=11; )
ARF4		location ⇒	13:32994665-32993727		CU467952,CH242-20F23,13:32987254-33018707 (Clone quality: bE20F23 on chr=13; Num_of_Contigs=11; )
ARF4		location ⇒	13:32996594-32996468		CU467952,CH242-20F23,13:32987254-33018707 (Clone quality: bE20F23 on chr=13; Num_of_Contigs=11; )
ARF4		location ⇒	13:33003576-33003465		CU467952,CH242-20F23,13:32987254-33018707 (Clone quality: bE20F23 on chr=13; Num_of_Contigs=11; )
ARF4		location ⇒	13:33004119-33004036		CU467952,CH242-20F23,13:32987254-33018707 (Clone quality: bE20F23 on chr=13; Num_of_Contigs=11; )
ARF5		ENSSSCG00000016593	18:18820546-18823765		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
Arf6		ENSSSCG00000005012	1:188129273-188130037		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
ARF6		ENSSSCG00000005012	1:188129273-188130037		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
Arf6		ENSSSCG00000010582	14:118457562-118459640		CU498828,CH242-221N13,14:118456049-118461184 (Clone quality: bE221N13 on chr=14; Num_of_Contigs=8; )
ARF6		ENSSSCG00000010582	14:118457562-118459640		CU498828,CH242-221N13,14:118456049-118461184 (Clone quality: bE221N13 on chr=14; Num_of_Contigs=8; )
Arf6		location ⇒	1:188129370-188129897		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
ARFGAP2		ENSSSCG00000013245	2:13414544-13424685		CU469364,CH242-119B4,2:13316728-13478061 (Clone quality: bE119B4 on chr=2; Num_of_Contigs=2; )
ARFGAP3		ENSSSCG00000000037	5:2689009-2743987
ARFGEF1		ENSSSCG00000006201	4:70010733-70106988
ARFGEF2		ENSSSCG00000007460	17:53123866-53154021
ARFIP1		ENSSSCG00000009010	8:65246756-65274807		FP067352,CH242-97G17,8:65226996-65275891 (Clone quality: bE97G17 on chr=8; Num_of_Contigs=7; )
ARFIP2		ENSSSCG00000014624	9:2561209-2564779		CU972372,CH242-47M8,9:2561067-2567081 (Clone quality: bE47M8 on chr=9; Num_of_Contigs=7; )
ARG1		ENSSSCG00000004195	1:33295233-33296874		CU633754,CH242-254O2,1:33260152-33299053 (Clone quality: bE254O2 on chr=1; Num_of_Contigs=9; )
ARG1		ENSSSCG00000003600	6:60374014-60402308
ARG1		location ⇒	1:33296371-33296758		CU633754,CH242-254O2,1:33260152-33299053 (Clone quality: bE254O2 on chr=1; Num_of_Contigs=9; )
ARG1		location ⇒	1:33426914-33426753		CU570820,CH242-157N19,1:33425744-33562809 (Clone quality: bE157N19 on chr=1; Num_of_Contigs=1; )
ARG1		location ⇒	1:33429046-33428870		CU570820,CH242-157N19,1:33425744-33562809 (Clone quality: bE157N19 on chr=1; Num_of_Contigs=1; )
ARG1		location ⇒	1:33437104-33436835		CU570820,CH242-157N19,1:33425744-33562809 (Clone quality: bE157N19 on chr=1; Num_of_Contigs=1; )
ARG2		ENSSSCG00000002294	7:99749663-99791985
ARG2		location ⇒	7:99750760-99750827		CT868701,CH242-284D22,7:99745670-99775099 (Clone quality: bE284D22 on chr=7; Num_of_Contigs=4; )
ARG2		location ⇒	7:99782022-99782200		CT868701,CH242-284D22,7:99775200-99807567 (Clone quality: bE284D22 on chr=7; Num_of_Contigs=4; )
ARG2		location ⇒	7:99785689-99785853		CT868701,CH242-284D22,7:99775200-99807567 (Clone quality: bE284D22 on chr=7; Num_of_Contigs=4; )
ARG2		location ⇒	7:99788784-99788920		CT868701,CH242-284D22,7:99775200-99807567 (Clone quality: bE284D22 on chr=7; Num_of_Contigs=4; )
ARGFX		ENSSSCG00000011886	13:104462568-104464201
ARGLU1		ENSSSCG00000009536	11:74937071-74963254		CU019594,CH242-520K8,11:74866635-75013917 (Clone quality: bE520K8 on chr=11; Num_of_Contigs=2; )
ARHGAP1		ENSSSCG00000013256	2:14123252-14139957
ARHGAP10		ENSSSCG00000009029	8:69645143-69870230
ARHGAP11A		ENSSSCG00000004806	1:144116995-144137188
ARHGAP12		ENSSSCG00000011026	10:40850132-40943156
ARHGAP17		ENSSSCG00000007829	3:20078739-20136760
ARHGAP19		ENSSSCG00000010516	14:113643376-113648734
ARHGAP20		ENSSSCG00000015015	9:37456102-37493239
ARHGAP21		ENSSSCG00000011074	10:48473667-48561191		CU694887,CH242-322E23,10:48445672-48606813 (Clone quality: bE322E23 on chr=10; Num_of_Contigs=1; )
ARHGAP22		ENSSSCG00000010381	14:92887455-93092734
ARHGAP23		ENSSSCG00000018058	12:57345459-57424929
ARHGAP24		ENSSSCG00000009229	8:114105524-114148502
ARHGAP25		ENSSSCG00000008344	3:67570891-67662589		FP236183,CH242-146A7,3:67562689-67713568 (Clone quality: bE146A7 on chr=3; Num_of_Contigs=2; )
ARHGAP26		ENSSSCG00000014399	2:131030807-131358836
ARHGAP28		ENSSSCG00000003686	6:68741039-68899254
ARHGAP29		ENSSSCG00000006889	4:127399455-127439411
ARHGAP30		ENSSSCG00000006372	4:93012284-93020876
ARHGAP4		ENSSSCG00000012790	X:122752679-122766762		CU915581,CH242-139K22,X:122729751-122810838 (Clone quality: bE139K22 on chr=X; Num_of_Contigs=13; )
ARHGAP5		ENSSSCG00000001967	7:73422584-73433902		CU469344,CH242-418J4,7:73417862-73471928 (Clone quality: bE418J4 on chr=7; Num_of_Contigs=4; )
ARHGAP5		location ⇒	7:73327944-73327181		CU469344,CH242-418J4,7:73297487-73331028 (Clone quality: bE418J4 on chr=7; Num_of_Contigs=4; )
ARHGAP6		ENSSSCG00000012112	X:6754432-7036677

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, 1751-32

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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).