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)

KIAA1407		ENSSSCG00000011913	13:108903143-108939281
KIAA1409		ENSSSCG00000002463	7:123234135-123348801
KIAA1429		ENSSSCG00000006100	4:42631931-42695753
KIAA1430		ENSSSCG00000015791	15:43533678-43556613
KIAA1432		ENSSSCG00000005208	1:226296221-226407246
KIAA1462		ENSSSCG00000011020	10:39142380-39144746		CU464147,CH242-17E15,10:39076095-39176474 (Clone quality: bE17E15 on chr=10; Num_of_Contigs=3; )
KIAA1467		ENSSSCG00000000619	5:56551117-56639660
KIAA1468		ENSSSCG00000004899	1:166068702-166177723
KIAA1486		ENSSSCG00000016239	15:119545017-119739575
KIAA1539		ENSSSCG00000005301	1:246999589-247002246		CU856695,CH242-238C15,1:246903923-247036412 (Clone quality: bE238C15 on chr=1; Num_of_Contigs=2; )
KIAA1543		ENSSSCG00000013583	2:51162128-51171195		CU929919,CH242-334A8,2:51145935-51174431 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
KIAA1549		ENSSSCG00000016513	18:8797246-8984725
KIAA1598		ENSSSCG00000010665	14:132938941-133037544	CT737198,CH242-101L9,14:132896369-133092131 (Clone quality: bE101L9 on chr=14; Num_of_Contigs=2; )
KIAA1602		ENSSSCG00000000209	5:14492188-14567574
KIAA1609		ENSSSCG00000002672	6:2751013-2765116
KIAA1614		ENSSSCG00000015538	9:114945973-114956939		CU856441,CH242-286M10,9:114941123-114998424 (Clone quality: bE286M10 on chr=9; Num_of_Contigs=7; )
KIAA1644		ENSSSCG00000000023	5:1606991-1621473
KIAA1671		ENSSSCG00000009953	14:43426653-43682540
KIAA1683		ENSSSCG00000013903	2:62473252-62473713		CU915655,CH242-228H4,2:62461677-62473824 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
KIAA1712		ENSSSCG00000009701	14:15419377-15435567
KIAA1712		location ⇒	14:15419315-15419071		CU407065,CH242-308M4,14:15402940-15423151 (Clone quality: bE308M4 on chr=14; Num_of_Contigs=5; )
KIAA1712		location ⇒	14:15419597-15419466		CU407065,CH242-308M4,14:15402940-15423151 (Clone quality: bE308M4 on chr=14; Num_of_Contigs=5; )
KIAA1712		location ⇒	14:15424598-15424390		CU407065,CH242-308M4,14:15423252-15444996 (Clone quality: bE308M4 on chr=14; Num_of_Contigs=5; )
KIAA1712		location ⇒	14:15428797-15428668		CU407065,CH242-308M4,14:15423252-15444996 (Clone quality: bE308M4 on chr=14; Num_of_Contigs=5; )
KIAA1731		ENSSSCG00000014946	9:26393152-26537127
KIAA1737		ENSSSCG00000002393	7:108175132-108189430		CU012040,CH242-394H10,7:108038511-108238028 (Clone quality: bE394H10 on chr=7; Num_of_Contigs=3; )
KIAA1755		ENSSSCG00000007344	17:43744311-43776487		CU915723,CH242-72A24,17:43730981-43777667 (Clone quality: bE72A24 on chr=17; Num_of_Contigs=4; )
KIAA1797		ENSSSCG00000005165	1:210693013-210713998
KIAA1826		ENSSSCG00000015000	9:35552988-35554375		FP089571,CH242-190H22,9:35544647-35610789 (Clone quality: bE190H22 on chr=9; Num_of_Contigs=1; )
KIAA1841		ENSSSCG00000008386	3:74393111-74453247
KIAA1875		ENSSSCG00000005916	4:595866-683192
KIAA1919		ENSSSCG00000004419	1:80767604-80775275		FP102400,CH242-288J22,1:80756792-80787442 (Clone quality: bE288J22 on chr=1; Num_of_Contigs=3; )
KIAA1958		ENSSSCG00000005469	1:266121219-266262286
KIAA1967		ENSSSCG00000009628	14:6853274-6866704		CU407060,CH242-266L24,14:6832388-6900516 (Clone quality: bE266L24 on chr=14; Num_of_Contigs=5; )
KIAA1984		ENSSSCG00000005830	1:294124723-294131498
KIAA2018		ENSSSCG00000011918	13:109214813-109237832		CU915398,CH242-257L23,13:109145832-109269113 (Clone quality: bE257L23 on chr=13; Num_of_Contigs=2; )
KIAA2022		ENSSSCG00000012423	X:59518219-59524314		FP102692,CH242-382D9,X:59517548-59526996 (Clone quality: bE382D9 on chr=X; Num_of_Contigs=6; )
KIAA2026		ENSSSCG00000005205	1:226015831-226130518
KIF11		ENSSSCG00000010471	14:109235274-109285389		CU467586,CH242-452J20,14:109181517-109354289 (Clone quality: bE452J20 on chr=14; Num_of_Contigs=2; )
KIF12		ENSSSCG00000005486	1:267752987-267760947		CU407201,CH242-322N22,1:267675230-267763474 (Clone quality: bE322N22 on chr=1; Num_of_Contigs=4; )
KIF13B		ENSSSCG00000009683	14:12979545-13109758
KIF14		ENSSSCG00000010912	10:24012085-24044009		CU694728,CH242-39O9,10:23973476-24051931 (Clone quality: bE39O9 on chr=10; Num_of_Contigs=4; )
KIF15		ENSSSCG00000011309	13:23900998-23965720
KIF16B		ENSSSCG00000007080	17:25364030-25629924
KIF17		ENSSSCG00000003508	6:54236829-54260157
KIF18A		ENSSSCG00000013332	2:30269029-30366616
KIF18B		ENSSSCG00000017342	12:16298608-16310308
KIF1A		ENSSSCG00000016401	15:134429941-134488923
KIF1B		ENSSSCG00000003401	6:47417271-47466746
KIF1C		ENSSSCG00000017900	12:49096001-49117929		FP015831,CH242-271O18,12:49076321-49169107 (Clone quality: bE271O18 on chr=12; Num_of_Contigs=4; )

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, 551-1

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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).