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)

SLC2A13		ENSSSCG00000000783	5:67246988-67632770
SLC2A3		location ⇒	1:188087540-188087484		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SLC2A3		location ⇒	1:228874404-228874347		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
SLC2A4		ENSSSCG00000017933	12:49724474-49730697		CU681851,CH242-516E15,12:49723440-49731153 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
SLC2A7		ENSSSCG00000003390	6:46747411-46764316
SLC2A8		ENSSSCG00000005610	1:282275660-282284548		CU407118,CH242-357D18,1:282268300-282306854 (Clone quality: bE357D18 on chr=1; Num_of_Contigs=10; )
SLC30A10		ENSSSCG00000010819	10:9519849-9520268
SLC30A4		ENSSSCG00000004668	1:131868411-131911234
SLC30A6		ENSSSCG00000008520	3:101164019-101164513		CU469148,CH242-287E22,3:101145029-101165537 (Clone quality: bE287E22 on chr=3; Num_of_Contigs=23; )
SLC30A7		ENSSSCG00000006860	4:122192755-122269526
SLC30A9		ENSSSCG00000008801	8:27958847-28012412
SLC31A1		location ⇒	1:187872904-187872960		CU633502,CH242-240C20,1:187832890-187878221 (Clone quality: bE240C20 on chr=1; Num_of_Contigs=4; )
SLC31A1		location ⇒	1:188087521-188087465		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SLC31A1		location ⇒	1:188102003-188101947		CU606975,CH242-251A8,1:188088869-188146416 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SLC31A1		location ⇒	1:228874384-228874328		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
SLC31A2		ENSSSCG00000005476	1:266714638-266724118		CU856416,CH242-238G19,1:266686641-266767270 (Clone quality: bE238G19 on chr=1; Num_of_Contigs=3; )
SLC31A21318		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
SLC32A1		ENSSSCG00000007348	17:43975675-43979507		CU074389,CH242-105J10,17:43935195-43994731 (Clone quality: bE105J10 on chr=17; Num_of_Contigs=5; )
SLC34A2		ENSSSCG00000008758	8:15727824-15790748
SLC34A3		ENSSSCG00000005850	1:294353516-294354016		CU928955,CH242-34I15,1:294322778-294354935 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
SLC35A1		ENSSSCG00000004304	1:58538518-58635311
SLC35A3		ENSSSCG00000006871	4:122993671-123012299		CU179629,CH242-295D24,4:122951510-123028902 (Clone quality: bE295D24 on chr=4; Num_of_Contigs=8; )
SLC35A4		ENSSSCG00000014367	2:129331367-129332617		CU459055,CH242-430O11,2:129241445-129341031 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
SLC35A5		ENSSSCG00000011929	13:109832383-109888540
SLC35B1		ENSSSCG00000017550	12:23214953-23221521
SLC35B2		ENSSSCG00000001702	7:45773108-45775917	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
SLC35B3		ENSSSCG00000001033	7:5717721-5741682		CT826384,CH242-85G15,7:5669843-5817195 (Clone quality: bE85G15 on chr=7; Num_of_Contigs=3; )
SLC35B4		ENSSSCG00000016541	18:13156510-13175831		CU640368,CH242-127A17,18:13149061-13213882 (Clone quality: bE127A17 on chr=18; Num_of_Contigs=7; )
SLC35C1		ENSSSCG00000013272	2:14950879-14958651		FP101987,CH242-521A18,2:14928381-14965257 (Clone quality: bE521A18 on chr=2; Num_of_Contigs=9; )
SLC35D1		ENSSSCG00000003802	6:102460252-102468328
SLC35D2		ENSSSCG00000010935	10:25218787-25235460		CU914745,CH242-514E6,10:25215943-25290846 (Clone quality: bE514E6 on chr=10; Num_of_Contigs=8; )
SLC35D3		ENSSSCG00000004159	1:28738500-28740667
SLC35E1		ENSSSCG00000013861	2:61104481-61121417		CU929691,CH242-155H10,2:61082713-61143329 (Clone quality: bE155H10 on chr=2; Num_of_Contigs=7; )
SLC35E3		ENSSSCG00000000487	5:32253272-32268987		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
SLC35E4		ENSSSCG00000010012	14:48325509-48331197		CT827803,CH242-235K4,14:48304424-48349386 (Clone quality: bE235K4 on chr=14; Num_of_Contigs=6; )
SLC35F1		ENSSSCG00000004250	1:45536362-45739026
SLC35F2		ENSSSCG00000015001	9:35672696-35689703		CU928597,CH242-212P11,9:35657305-35694050 (Clone quality: bE212P11 on chr=9; Num_of_Contigs=11; )
SLC35F3		ENSSSCG00000010162	14:57987447-58102038
SLC35F4		ENSSSCG00000005068	1:195299632-195335735		CU861575,CH242-109O3,1:195212418-195335952 (Clone quality: bE109O3 on chr=1; Num_of_Contigs=2; )
SLC35F5		ENSSSCG00000015709	15:18357459-18373379		CU570942,CH242-29L23,15:18349132-18373863 (Clone quality: bE29L23 on chr=15; Num_of_Contigs=5; )
SLC36A1		ENSSSCG00000017085	16:68880881-69032425
SLC36A3		ENSSSCG00000005521	1:275341127-275378133		FP102199,CH242-285K13,1:275302391-275395813 (Clone quality: bE285K13 on chr=1; Num_of_Contigs=4; )
SLC36A4		ENSSSCG00000014940	9:26020342-26037429
SLC37A1		ENSSSCG00000012087	13:144969069-145022943		CU861585,CH242-155I2,13:144912279-145023593 (Clone quality: bE155I2 on chr=13; Num_of_Contigs=3; )
Slc37a2		location ⇒	9:50724084-50724148		CU570648,CH242-232B10,9:50627915-50762322 (Clone quality: bE232B10 on chr=9; Num_of_Contigs=1; )
Slc37a2		location ⇒	9:50724437-50724520		CU570648,CH242-232B10,9:50627915-50762322 (Clone quality: bE232B10 on chr=9; Num_of_Contigs=1; )
Slc37a2		location ⇒	9:50882996-50882913		FP236515,CH242-475N5,9:50875185-50906122 (Clone quality: bE475N5 on chr=9; Num_of_Contigs=6; )
Slc37a2		location ⇒	9:50883349-50883285		FP236515,CH242-475N5,9:50875185-50906122 (Clone quality: bE475N5 on chr=9; Num_of_Contigs=6; )
SLC37A4		ENSSSCG00000015105	9:44838158-44843313		CU695209,CH242-241K21,9:44763573-44853404 (Clone quality: bE241K21 on chr=9; Num_of_Contigs=5; )
SLC38A1		ENSSSCG00000000807	5:72756983-72802292

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, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

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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).