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)

LASS6		ENSSSCG00000015922	15:70660544-70691842
LAT		ENSSSCG00000007811	3:16879098-16883505		FP236780,CH242-166K15,3:16872934-16887483 (Clone quality: bE166K15 on chr=3; Num_of_Contigs=12; )
LAT		ENSSSCG00000007809	3:16742604-16878319
LAT		location ⇒	3:16752047-16751939		CU928476,CH242-24P1,3:16739139-16769231 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
LAT		location ⇒	3:16755860-16755742		CU928476,CH242-24P1,3:16739139-16769231 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
LAT		location ⇒	3:16879562-16879454		FP236780,CH242-166K15,3:16872934-16887483 (Clone quality: bE166K15 on chr=3; Num_of_Contigs=12; )
LAT		location ⇒	3:16883361-16883243		FP236780,CH242-166K15,3:16872934-16887483 (Clone quality: bE166K15 on chr=3; Num_of_Contigs=12; )
LAT1		ENSSSCG00000002041	7:82432218-82469416		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
LAT1		ENSSSCG00000007811	3:16879098-16883505		FP236780,CH242-166K15,3:16872934-16887483 (Clone quality: bE166K15 on chr=3; Num_of_Contigs=12; )
LAT2		ENSSSCG00000002032	7:82233276-82298502
LAT2		location ⇒	3:16072-15971		FP102618,CH242-1B21,3:10473-20929 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
LAT2		location ⇒	3:25822-25757		FP102618,CH242-1B21,3:21030-75729 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
LAT2		location ⇒	3:27719-27622		FP102618,CH242-1B21,3:21030-75729 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
LAT2		location ⇒	3:41723-41618		FP102618,CH242-1B21,3:21030-75729 (Clone quality: bE1B21 on chr=3; Num_of_Contigs=5; )
LATS1		ENSSSCG00000004106	1:17257694-17290467
LAX1		ENSSSCG00000015275	9:62231885-62242353		CU655999,CH242-299D21,9:62221412-62245767 (Clone quality: bE299D21 on chr=9; Num_of_Contigs=9; )
LAX1		location ⇒	9:62231885-62232067		CU655999,CH242-299D21,9:62221412-62245767 (Clone quality: bE299D21 on chr=9; Num_of_Contigs=9; )
LAX1		location ⇒	9:62232635-62232829		CU655999,CH242-299D21,9:62221412-62245767 (Clone quality: bE299D21 on chr=9; Num_of_Contigs=9; )
LAX1		location ⇒	9:62237310-62237421		CU655999,CH242-299D21,9:62221412-62245767 (Clone quality: bE299D21 on chr=9; Num_of_Contigs=9; )
LAX1		location ⇒	9:62241609-62241746		CU655999,CH242-299D21,9:62221412-62245767 (Clone quality: bE299D21 on chr=9; Num_of_Contigs=9; )
LAYN		ENSSSCG00000015022	9:38354154-38374508
LBA1		ENSSSCG00000011239	13:18016601-18030757
LBH		ENSSSCG00000008528	3:102261545-102288828		CU856581,CH242-240L10,3:102186350-102314110 (Clone quality: bE240L10 on chr=3; Num_of_Contigs=4; )
LBP		ENSSSCG00000015732	15:28314444-28372604
LBP		ENSSSCG00000011235	13:16178022-16222958
LBP		ENSSSCG00000011266	13:19815582-19817564
LBX1		ENSSSCG00000010562	14:117132756-117134278		CU469143,CH242-260O10,14:117126914-117237018 (Clone quality: bE260O10 on chr=14; Num_of_Contigs=4; )
LBX2		ENSSSCG00000008278	3:63092669-63094297		CU468647,CH242-164C3,3:63071721-63110155 (Clone quality: bE164C3 on chr=3; Num_of_Contigs=12; )
LBXCOR1		ENSSSCG00000004956	1:172974539-172982727		CU062656,CH242-136G13,1:172966213-173164526 (Clone quality: bE136G13 on chr=1; Num_of_Contigs=2; )
LC8		ENSSSCG00000009904	14:40506277-40508870		CU468509,CH242-66D17,14:40499959-40518844 (Clone quality: bE66D17 on chr=14; Num_of_Contigs=12; )
LC8		location ⇒	14:40506897-40506758		CU468509,CH242-66D17,14:40499959-40518844 (Clone quality: bE66D17 on chr=14; Num_of_Contigs=12; )
LC8		location ⇒	14:40508513-40508381		CU468509,CH242-66D17,14:40499959-40518844 (Clone quality: bE66D17 on chr=14; Num_of_Contigs=12; )
LCA5		ENSSSCG00000004469	1:91778357-91778785		CU638835,CH242-191K23,1:91764791-91821548 (Clone quality: bE191K23 on chr=1; Num_of_Contigs=8; )
LCAT		ENSSSCG00000002765	6:12760583-12832697
LCE2A		ENSSSCG00000006597	4:100581718-100687572
LCE4A		ENSSSCG00000006600	4:100643912-100658399	CU076058,CH242-126J8,4:100634937-100826648 (Clone quality: bE126J8 on chr=4; Num_of_Contigs=7; )
LCK		ENSSSCG00000003608	6:60803106-60944551
LCK		ENSSSCG00000014016	2:68101464-68112459	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
LCK		location ⇒	6:60807025-60807102		FP102820,CH242-217B19,6:60804606-60808893 (Clone quality: bE217B19 on chr=6; Num_of_Contigs=18; )
LCK		location ⇒	6:60807194-60807293		FP102820,CH242-217B19,6:60804606-60808893 (Clone quality: bE217B19 on chr=6; Num_of_Contigs=18; )
LCLAT1		ENSSSCG00000008526	3:101887377-102006928
LCMT1		ENSSSCG00000007826	3:19717793-19765014
LCMT2		ENSSSCG00000004711	1:134217565-134219622	CU210852,CH242-452O20,1:134123075-134309699 (Clone quality: bE452O20 on chr=1; Num_of_Contigs=4; )
LCN1		location ⇒	X:1658691-1658585	FP102438,CH242-227G12,X:1614901-1722511 (Clone quality: bE227G12 on chr=X; Num_of_Contigs=2; )
LCN1		location ⇒	X:3146793-3146878	CU855720,CH242-512P21,X:3139536-3256746 (Clone quality: bE512P21 on chr=X; Num_of_Contigs=10; )
LCN1		location ⇒	X:3445016-3445137	CU694849,CH242-236E18,X:3326006-3459219 (Clone quality: bE236E18 on chr=X; Num_of_Contigs=4; )
LCN1		location ⇒	X:909980-910084	FP015839,CH242-119P2,X:827887-930674 (Clone quality: bE119P2 on chr=X; Num_of_Contigs=2; )
LCN10		ENSSSCG00000005836	1:294196759-294199699		FP236151,CH242-517G10,1:294180904-294209678 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
LCN12		ENSSSCG00000005831	1:294147746-294216648
LCN15		ENSSSCG00000005843	1:294263118-294264919

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, 851-45

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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).