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)

KDM4B		ENSSSCG00000013518	2:48855089-48867852		CU942405,CH242-425A24,2:48844140-48880704 (Clone quality: bE425A24 on chr=2; Num_of_Contigs=11; )
KDM5A		ENSSSCG00000000750	5:63487418-63498758
KDM5B		ENSSSCG00000010928	10:24833795-25022842
KDM6A		ENSSSCG00000012262	X:39996571-40050956
KDM6B		ENSSSCG00000017962	12:50096589-50105333
KDR		ENSSSCG00000008844	8:36147302-36193200
KDR		location ⇒	8:36158661-36158786		CU914686,CH242-88C12,8:36155337-36178147 (Clone quality: bE88C12 on chr=8; Num_of_Contigs=7; )
KDR		location ⇒	8:36163435-36163590		CU914686,CH242-88C12,8:36155337-36178147 (Clone quality: bE88C12 on chr=8; Num_of_Contigs=7; )
KDR		location ⇒	8:36165127-36165243		CU914686,CH242-88C12,8:36155337-36178147 (Clone quality: bE88C12 on chr=8; Num_of_Contigs=7; )
KDR		location ⇒	8:36166863-36166971		CU914686,CH242-88C12,8:36155337-36178147 (Clone quality: bE88C12 on chr=8; Num_of_Contigs=7; )
KDSR		ENSSSCG00000004892	1:165144499-165181549		CU694588,CH242-25E9,1:165123981-165192820 (Clone quality: bE25E9 on chr=1; Num_of_Contigs=5; )
KEAP1		ENSSSCG00000013640	2:52913898-53030923
KEL		ENSSSCG00000016472	18:6126541-6146298		CU928245,CH242-100K20,18:6102984-6180022 (Clone quality: bE100K20 on chr=18; Num_of_Contigs=3; )
KEL		ENSSSCG00000015932	15:71311502-71329392
KERA		ENSSSCG00000000917	5:86841154-86846514		CU468030,CH242-511M16,5:86827823-86885994 (Clone quality: bE511M16 on chr=5; Num_of_Contigs=1; )
KGF		ENSSSCG00000004649	1:127607417-127608734		CU651647,CH242-194D8,1:127601936-127626058 (Clone quality: bE194D8 on chr=1; Num_of_Contigs=12; )
KGF		location ⇒	1:127607418-127607521		CU651647,CH242-194D8,1:127601936-127626058 (Clone quality: bE194D8 on chr=1; Num_of_Contigs=12; )
KGF		location ⇒	1:127608538-127608730		CU651647,CH242-194D8,1:127601936-127626058 (Clone quality: bE194D8 on chr=1; Num_of_Contigs=12; )
KGF		location ⇒	1:127700023-127700414		CU651647,CH242-194D8,1:127664859-127710848 (Clone quality: bE194D8 on chr=1; Num_of_Contigs=12; )
KGUA_PIG		ENSSSCG00000013990	2:66544256-66554037	FP085478,CH242-132B19,2:66476472-66645587 (Clone quality: bE132B19 on chr=2; Num_of_Contigs=3; )
KHDRBS1		location ⇒	15:2890871-2891220		CU929906,CH242-275A16,15:2877645-2903847 (Clone quality: bE275A16 on chr=15; Num_of_Contigs=5; )
KHDRBS2		ENSSSCG00000001490	7:31748440-32189584
KHDRBS3		ENSSSCG00000005941	4:5106428-5208907	CU151851,CH242-208N23,4:5053289-5236023 (Clone quality: bE208N23 on chr=4; Num_of_Contigs=4; )
KHK		ENSSSCG00000008556	3:104457493-104467487		CU896571,CH242-143O19,3:104398046-104492436 (Clone quality: bE143O19 on chr=3; Num_of_Contigs=6; )
KHNYN		ENSSSCG00000001984	7:81197763-81206013		CT997804,CH242-280B15,7:81187212-81281808 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
KHSRP		ENSSSCG00000013538	2:49790979-49802551
KI-1		ENSSSCG00000003437	6:49086313-49093755		FP102316,CH242-204J17,6:49079436-49098258 (Clone quality: bE204J17 on chr=6; Num_of_Contigs=9; )
KI-1		ENSSSCG00000010934	10:25144094-25177987
KIAA0020		ENSSSCG00000005227	1:229156677-229201086
KIAA0082		ENSSSCG00000001579	7:37639839-37702388
KIAA0090		ENSSSCG00000003489	6:53229972-53248622		FP236131,CH242-145H9,6:53229810-53250408 (Clone quality: bE145H9 on chr=6; Num_of_Contigs=4; )
KIAA0100		ENSSSCG00000017764	12:42585559-42598383
KIAA0141		ENSSSCG00000014396	2:130481133-130495396
KIAA0146		ENSSSCG00000006277	4:82895864-83188958
KIAA0174		ENSSSCG00000002743	6:10624717-10650368
KIAA0182		ENSSSCG00000002664	6:1883755-1905215		FP102138,CH242-240F2,6:1871997-1906677 (Clone quality: bE240F2 on chr=6; Num_of_Contigs=8; )
KIAA0196		ENSSSCG00000005969	4:14284184-14330423
KIAA0226		ENSSSCG00000011853	13:101112141-101149697	CU468995,CH242-240L11,13:100938456-101151836 (Clone quality: bE240L11 on chr=13; Num_of_Contigs=8; )
KIAA0232		ENSSSCG00000008713	8:2535187-2582273		FP017238,CH242-126E3,8:2523850-2595028 (Clone quality: bE126E3 on chr=8; Num_of_Contigs=5; )
KIAA0240		ENSSSCG00000001646	7:43743976-43777543	CR956428,PigE-259M5,7:43612102-43779716 (No clone quality info on bT259M5)
KIAA0247		ENSSSCG00000002311	7:101649403-101736004
KIAA0284		ENSSSCG00000002558	7:133194262-133214665		CU695123,CH242-103I13,7:133191685-133215699 (Clone quality: bE103I13 on chr=7; Num_of_Contigs=13; )
KIAA0317		ENSSSCG00000002370	7:106130033-106137490		CU498954,CH242-313I6,7:106090273-106137689 (Clone quality: bE313I6 on chr=7; Num_of_Contigs=5; )
KIAA0319		ENSSSCG00000001091	7:20393560-20448260
KIAA0319		location ⇒	7:20412950-20412857		CU368380,CH242-281C24,7:20402681-20479564 (Clone quality: bE281C24 on chr=7; Num_of_Contigs=6; )
KIAA0319		location ⇒	7:20414962-20414809		CU368380,CH242-281C24,7:20402681-20479564 (Clone quality: bE281C24 on chr=7; Num_of_Contigs=6; )
KIAA0319		location ⇒	7:20417726-20417576		CU368380,CH242-281C24,7:20402681-20479564 (Clone quality: bE281C24 on chr=7; Num_of_Contigs=6; )
KIAA0319		location ⇒	7:20419412-20419276		CU368380,CH242-281C24,7:20402681-20479564 (Clone quality: bE281C24 on chr=7; Num_of_Contigs=6; )
KIAA0355		ENSSSCG00000002872	6:29355894-29410218		CU929776,CH242-347I7,6:29332460-29417769 (Clone quality: bE347I7 on chr=6; Num_of_Contigs=4; )
KIAA0368		ENSSSCG00000005459	1:265119961-265223605

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).