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)

ACCSL		ENSSSCG00000013283	2:16837215-16847439		CU457486,CH242-12J14,2:16813439-16854641 (Clone quality: bE12J14 on chr=2; Num_of_Contigs=7; )
ACE		ENSSSCG00000017296	12:12979813-12999627		CU929939,CH242-45G1,12:12949494-13027836 (Clone quality: bE45G1 on chr=12; Num_of_Contigs=5; )
ACE		location ⇒	12:12980273-12980033		CU929939,CH242-45G1,12:12949494-13027836 (Clone quality: bE45G1 on chr=12; Num_of_Contigs=5; )
ACE		location ⇒	12:12980619-12980432		CU929939,CH242-45G1,12:12949494-13027836 (Clone quality: bE45G1 on chr=12; Num_of_Contigs=5; )
ACE		location ⇒	12:12983884-12983658		CU929939,CH242-45G1,12:12949494-13027836 (Clone quality: bE45G1 on chr=12; Num_of_Contigs=5; )
ACE		location ⇒	12:12988238-12988044		CU929939,CH242-45G1,12:12949494-13027836 (Clone quality: bE45G1 on chr=12; Num_of_Contigs=5; )
ACE2		ENSSSCG00000012138	X:11368440-11416356
ACER2		ENSSSCG00000005168	1:212236032-212262012
ACER3		ENSSSCG00000014873	9:10953182-10979185		FP089538,CH242-169J5,9:10941070-10981181 (Clone quality: bE169J5 on chr=9; Num_of_Contigs=5; )
ACIN1		ENSSSCG00000002034	7:82318411-82356240
ACLY		ENSSSCG00000017421	12:18557550-18601933
ACMSD		ENSSSCG00000015699	15:15463454-15504357
ACN9		ENSSSCG00000006882	4:126550199-126718047
ACO2		ENSSSCG00000000064	5:3556655-3584401
ACOT12		ENSSSCG00000014130	2:79176151-79217133
ACOT13		ENSSSCG00000001093	7:20512373-20515879		CU468861,CH242-123E20,7:20499469-20564207 (Clone quality: bE123E20 on chr=7; Num_of_Contigs=4; )
ACOT4		ENSSSCG00000002349	7:105047482-105051233		CT943655,CH242-523I15,7:105020527-105084317 (Clone quality: bE523I15 on chr=7; Num_of_Contigs=3; )
ACOT6		ENSSSCG00000002348	7:105002659-105008378		CT943655,CH242-523I15,7:104924151-105020426 (Clone quality: bE523I15 on chr=7; Num_of_Contigs=3; )
ACOT8		ENSSSCG00000007426	17:50103794-50118957
ACOT9		ENSSSCG00000012172	X:18669837-18695906
ACOX1		ENSSSCG00000017198	12:3875075-3888168		CU928029,CH242-304M1,12:3750666-3894443 (Clone quality: bE304M1 on chr=12; Num_of_Contigs=9; )
ACOX2		ENSSSCG00000011477	13:33854738-33887465		CU927912,CH242-524I3,13:33839842-33907683 (Clone quality: bE524I3 on chr=13; Num_of_Contigs=9; )
ACOX3		ENSSSCG00000008724	8:3583822-3601955
ACOXL		ENSSSCG00000008109	3:40572050-40825484
ACP1		ENSSSCG00000008659	3:121527229-121540621		FP102370,CH242-323F11,3:121518511-121558380 (Clone quality: bE323F11 on chr=3; Num_of_Contigs=8; )
ACP1		location ⇒	3:121528199-121527231		FP102370,CH242-323F11,3:121518511-121558380 (Clone quality: bE323F11 on chr=3; Num_of_Contigs=8; )
ACP1		location ⇒	3:121528402-121528294		FP102370,CH242-323F11,3:121518511-121558380 (Clone quality: bE323F11 on chr=3; Num_of_Contigs=8; )
ACP1		location ⇒	3:121535981-121535868		FP102370,CH242-323F11,3:121518511-121558380 (Clone quality: bE323F11 on chr=3; Num_of_Contigs=8; )
ACP1		location ⇒	3:121540512-121540435		FP102370,CH242-323F11,3:121518511-121558380 (Clone quality: bE323F11 on chr=3; Num_of_Contigs=8; )
ACP2		ENSSSCG00000013242	2:13357967-13365882		CU469364,CH242-119B4,2:13316728-13478061 (Clone quality: bE119B4 on chr=2; Num_of_Contigs=2; )
ACP5		ENSSSCG00000013612	2:52188216-52188479		CU856608,CH242-517F5,2:52162696-52188481 (Clone quality: bE517F5 on chr=2; Num_of_Contigs=7; )
ACP6		ENSSSCG00000006697	4:104047409-104065118		CU210948,CH242-433C8,4:104032556-104114601 (Clone quality: bE433C8 on chr=4; Num_of_Contigs=3; )
ACPL2		ENSSSCG00000011670	13:66824893-66840366		CU633797,CH242-235H14,13:66818830-66846929 (Clone quality: bE235H14 on chr=13; Num_of_Contigs=5; )
ACPP		ENSSSCG00000011627	13:60289078-60325135
ACRBP		ENSSSCG00000000700	5:60132272-60142871		CU914489,CH242-100M5,5:60122581-60144950 (Clone quality: bE100M5 on chr=5; Num_of_Contigs=13; )
ACRC		ENSSSCG00000012401	X:57200452-57210073		FP015848,CH242-94E16,X:57182938-57245160 (Clone quality: bE94E16 on chr=X; Num_of_Contigs=6; )
ACSBG1		ENSSSCG00000001760	7:53773239-53782420		CU467054,CH242-222N19,7:53768635-53784640 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
ACSBG1		location ⇒	7:53768079-53768302		CU467054,CH242-222N19,7:53754536-53768534 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
ACSBG1		location ⇒	7:53774825-53775002		CU467054,CH242-222N19,7:53768635-53784640 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
ACSBG1		location ⇒	7:53776566-53776789		CU467054,CH242-222N19,7:53768635-53784640 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
ACSBG1		location ⇒	7:53780319-53780569		CU467054,CH242-222N19,7:53768635-53784640 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
ACSBG2		ENSSSCG00000013536	2:49633578-49677212		FP085490,CH242-168M3,2:49601380-49713388 (Clone quality: bE168M3 on chr=2; Num_of_Contigs=4; )
ACSF2		ENSSSCG00000017566	12:24210110-24211162		CU928099,CH242-256B20,12:24209205-24237171 (Clone quality: bE256B20 on chr=12; Num_of_Contigs=9; )
ACSL1		location ⇒	15:42967047-42967101		CU928824,CH242-353H16,15:42951275-42968693 (Clone quality: bE353H16 on chr=15; Num_of_Contigs=10; )
ACSL1		location ⇒	15:42970342-42970398		CU928824,CH242-353H16,15:42968794-42972024 (Clone quality: bE353H16 on chr=15; Num_of_Contigs=10; )
ACSL1		location ⇒	15:43226095-43226149		CU928291,CH242-45D7,15:43220738-43231454 (Clone quality: bE45D7 on chr=15; Num_of_Contigs=3; )
ACSL1		location ⇒	15:43229534-43229590		CU928291,CH242-45D7,15:43220738-43231454 (Clone quality: bE45D7 on chr=15; Num_of_Contigs=3; )
ACSL3		ENSSSCG00000016223	15:114830324-114879237		CU896599,CH242-260E21,15:114826498-114883355 (Clone quality: bE260E21 on chr=15; Num_of_Contigs=5; )
ACSL4		ENSSSCG00000012583	X:88859579-89033122
ACSL4		location ⇒	X:88860833-88859581		FP102602,CH242-17O13,X:88856316-88942322 (Clone quality: bE17O13 on chr=X; Num_of_Contigs=3; )

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).