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)

A0MZ91_PIG		ENSSSCG00000014317	2:125685877-125689948		FP089688,CH242-222D16,2:125684803-125692587 (Clone quality: bE222D16 on chr=2; Num_of_Contigs=7; )
A0MZ91_PIG		ENSSSCG00000014312	2:125439092-125443178		CU928966,CH242-280I22,2:125408617-125488938 (Clone quality: bE280I22 on chr=2; Num_of_Contigs=4; )
A0ZQ17_PIG		ENSSSCG00000006433	4:95195977-95196918		CU469040,CH242-470B17,4:95191760-95223049 (Clone quality: bE470B17 on chr=4; Num_of_Contigs=8; )
A1CF		ENSSSCG00000010431	14:103519490-103590115
A1EAJ7_PIG		ENSSSCG00000015723	15:23915858-23939724
A1IU54_PIG		ENSSSCG00000008854	8:37626278-37660289
A1IU54_PIG		ENSSSCG00000008854	8:37626278-37660289
A1XQS1_PIG		ENSSSCG00000013581	2:51149776-51151307		CU929919,CH242-334A8,2:51145935-51174431 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
A1XQS6_PIG		ENSSSCG00000009063	8:75540542-75661117
A1XQT4_PIG		ENSSSCG00000014560	2:139873305-139874838		CU928488,CH242-163I11,2:139819049-139956868 (Clone quality: bE163I11 on chr=2; Num_of_Contigs=2; )
A1XQU0_PIG		ENSSSCG00000003683	6:67495737-67529487
A1XQU8_PIG		ENSSSCG00000005169	1:212291192-212294428		CU467038,CH242-92A4,1:212285112-212300111 (Clone quality: bE92A4 on chr=1; Num_of_Contigs=10; )
A1XQU8_PIG		ENSSSCG00000005169	1:212291192-212294428		CU467038,CH242-92A4,1:212285112-212300111 (Clone quality: bE92A4 on chr=1; Num_of_Contigs=10; )
A1YMU6_PIG		ENSSSCG00000015994	15:78418817-78444129
A1Z1R6_PIG		ENSSSCG00000016027	15:85825538-85957549
A1Z624_PIG		ENSSSCG00000002538	7:131853872-131889927
A1Z624_PIG		ENSSSCG00000002538	7:131853872-131889927
A2BP1		ENSSSCG00000007917	3:30842719-31223905
A2LD1		ENSSSCG00000009523	11:70163766-70164200		CU640422,CH242-387P22,11:70161004-70164885 (Clone quality: bE387P22 on chr=11; Num_of_Contigs=6; )
A2M		ENSSSCG00000000660	5:59126715-59171828
A2M		location ⇒	5:59134581-59134635		CU457747,CH242-208P14,5:58999708-59159045 (Clone quality: bE208P14 on chr=5; Num_of_Contigs=1; )
A2M		location ⇒	5:59135073-59135158		CU457747,CH242-208P14,5:58999708-59159045 (Clone quality: bE208P14 on chr=5; Num_of_Contigs=1; )
A2M		location ⇒	5:59136764-59136884		CU457747,CH242-208P14,5:58999708-59159045 (Clone quality: bE208P14 on chr=5; Num_of_Contigs=1; )
A2M		location ⇒	5:59137710-59137826		CU457747,CH242-208P14,5:58999708-59159045 (Clone quality: bE208P14 on chr=5; Num_of_Contigs=1; )
A2ML1		ENSSSCG00000000664	5:59354247-59385516
A3F780_PIG		ENSSSCG00000013398	2:43102231-43102368		CU467737,CH242-350F20,2:43090187-43110882 (Clone quality: bE350F20 on chr=2; Num_of_Contigs=16; )
A3F780_PIG		ENSSSCG00000013397	2:42887437-42905127
A3QT04_PIG		ENSSSCG00000015266	9:61473745-61530848
A3RL62_PIG		ENSSSCG00000003159	6:37882951-37883319		FP102974,CH242-517N5,6:37881072-37888050 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
A4L2Z4_PIG		ENSSSCG00000005284	1:241086471-241173644
A4L2Z4_PIG		ENSSSCG00000005284	1:241086471-241173644
A4URS8_PIG		ENSSSCG00000008458	3:90136508-90173107
A4URS9_PIG		ENSSSCG00000008455	3:90032835-90037387		CU914350,CH242-523I3,3:90032062-90039630 (Clone quality: bE523I3 on chr=3; Num_of_Contigs=9; )
A4URS9_PIG		ENSSSCG00000008453	3:89996780-90012511
A5A750_PIG		ENSSSCG00000000795	5:70514392-70621623
A5A750_PIG		ENSSSCG00000000795	5:70514392-70621623
A5A759_PIG		ENSSSCG00000000250	5:16536792-16558365
A5A762_PIG		ENSSSCG00000006272	4:82341176-82343659		CU582799,CH242-236C2,4:82319512-82374432 (Clone quality: bE236C2 on chr=4; Num_of_Contigs=4; )
A5A762_PIG		ENSSSCG00000006270	4:82228367-82230850		CU582881,CH242-218H22,4:82223745-82231976 (Clone quality: bE218H22 on chr=4; Num_of_Contigs=6; )
A5A768_PIG		ENSSSCG00000013456	2:47060746-47068119
A5A8X2_PIG		ENSSSCG00000001441	7:28113663-28126493	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
A5D9J7_PIG		ENSSSCG00000001466	7:29421485-29431994	BX323833,PigI-554F3,7:29352096-29473578 (No clone quality info on bS554F3)
A5D9J8_PIG		ENSSSCG00000001465	7:29405415-29413543	BX323833,PigI-554F3,7:29352096-29473578 (No clone quality info on bS554F3)
A5D9J9_PIG		ENSSSCG00000001450	7:29001619-29014999	BX323846,PigI-43B6,7:28994357-29074505 (No clone quality info on bS43B6)
A5D9J9_PIG		ENSSSCG00000001449	7:28977023-28990395	CT797454,CH242-173D7,7:28821097-28994356 (Clone quality: bE173D7 on chr=7; Num_of_Contigs=2; )
A5D9K1_PIG		ENSSSCG00000001448	7:28967232-28971126	CT797454,CH242-173D7,7:28821097-28994356 (Clone quality: bE173D7 on chr=7; Num_of_Contigs=2; )
A5D9K2_PIG		ENSSSCG00000001451	7:29020800-29030222	BX323846,PigI-43B6,7:28994357-29074505 (No clone quality info on bS43B6)
A5D9K2_PIG		ENSSSCG00000001447	7:28962576-28966713	CT797454,CH242-173D7,7:28821097-28994356 (Clone quality: bE173D7 on chr=7; Num_of_Contigs=2; )
A5D9K3_PIG		ENSSSCG00000001446	7:28948106-28956782	CT797454,CH242-173D7,7:28821097-28994356 (Clone quality: bE173D7 on chr=7; Num_of_Contigs=2; )

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).