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)

ASB13		ENSSSCG00000011145	10:61803824-61815416		FP016037,CH242-134E10,10:61783213-61818339 (Clone quality: bE134E10 on chr=10; Num_of_Contigs=5; )
ASB15		ENSSSCG00000016606	18:21981481-22000321	CU463288,CH242-205B13,18:21975793-22134892 (Clone quality: bE205B13 on chr=18; Num_of_Contigs=4; )
ASB18		ENSSSCG00000016318	15:128389446-128430250
ASB2		ENSSSCG00000002467	7:123499063-123520224		CU062574,CH242-419P8,7:123497626-123525644 (Clone quality: bE419P8 on chr=7; Num_of_Contigs=9; )
ASB2		location ⇒	7:123516332-123516490		CU062574,CH242-419P8,7:123497626-123525644 (Clone quality: bE419P8 on chr=7; Num_of_Contigs=9; )
ASB2		location ⇒	7:123519786-123520224		CU062574,CH242-419P8,7:123497626-123525644 (Clone quality: bE419P8 on chr=7; Num_of_Contigs=9; )
ASB3		ENSSSCG00000008415	3:81288784-81395614
ASB3		location ⇒	3:81375404-81375522		CU463868,CH242-125K13,3:81372578-81397826 (Clone quality: bE125K13 on chr=3; Num_of_Contigs=5; )
ASB3		location ⇒	3:81395202-81395614		CU463868,CH242-125K13,3:81372578-81397826 (Clone quality: bE125K13 on chr=3; Num_of_Contigs=5; )
ASB4		ENSSSCG00000015333	9:70340992-70423150
ASB5		ENSSSCG00000015768	15:35676901-35713159
ASB6		ENSSSCG00000005679	1:284558089-284560643
ASB7		ENSSSCG00000004821	1:146892674-146937863		CU372904,CH242-503E13,1:146764885-146968309 (Clone quality: bE503E13 on chr=1; Num_of_Contigs=1; )
ASC		ENSSSCG00000007758	3:15810753-15812359		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
ASC		ENSSSCG00000012099	X:2890480-2987988
ASC		ENSSSCG00000007284	17:40180021-40233330
ASC		ENSSSCG00000002864	6:28694053-28708979		CU638683,CH242-3F10,6:28679939-28721948 (Clone quality: bE3F10 on chr=6; Num_of_Contigs=8; )
ASC		ENSSSCG00000004552	1:110848744-111122527
ASC		ENSSSCG00000004359	1:70840268-70860876		CU104757,CH242-114J14,1:70838053-70862278 (Clone quality: bE114J14 on chr=1; Num_of_Contigs=18; )
ASC		location ⇒	3:15811361-15811064		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
ASC		location ⇒	3:15811650-15811590		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
ASC		location ⇒	3:15812315-15811995		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
ASCC1		ENSSSCG00000010285	14:78256680-78301386
ASCL3		ENSSSCG00000014572	9:268151-268690		FP102436,CH242-219P18,9:264557-276580 (Clone quality: bE219P18 on chr=9; Num_of_Contigs=6; )
ASCL4		ENSSSCG00000000159	5:10805895-10806413	CU407156,CH242-210C11,5:10769632-10836330 (Clone quality: bE210C11 on chr=5; Num_of_Contigs=10; )
ASF1A		ENSSSCG00000004247	1:44997783-45011236
ASF1B		ENSSSCG00000013772	2:57094846-57104342		FP086609,CH242-184K22,2:57093118-57123281 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
ASGR1		location ⇒	12:49687540-49687425		CU914703,CH242-254H21,12:49676666-49691218 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
ASGR1		location ⇒	12:49865475-49865590		CU681851,CH242-516E15,12:49861757-49868938 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
ASGR2		ENSSSCG00000017932	12:49677280-49695900
ASH1L		ENSSSCG00000006508	4:98260518-98532469
ASIP		ENSSSCG00000011103	10:53976861-54261515
ASIP		ENSSSCG00000007277	17:39717458-39801515		CU606946,CH242-245E11,17:39642724-39823287 (Clone quality: bE245E11 on chr=17; Num_of_Contigs=2; )
ASL		ENSSSCG00000007738	3:15149285-15158639		FP102327,CH242-280B6,3:15139374-15293790 (Clone quality: bE280B6 on chr=3; Num_of_Contigs=2; )
ASNA1		ENSSSCG00000013728	2:55979609-55989030		CU856041,CH242-32I13,2:55919380-55991729 (Clone quality: bE32I13 on chr=2; Num_of_Contigs=2; )
ASNS		ENSSSCG00000015340	9:72736488-72761463
ASPA		ENSSSCG00000017861	12:46906594-46924551
ASPH		ENSSSCG00000006229	4:74613582-74696991
ASPH		location ⇒	4:74657542-74657611		CU302247,CH242-42C23,4:74648868-74837242 (Clone quality: bE42C23 on chr=4; Num_of_Contigs=1; )
ASPH		location ⇒	4:74681909-74682047		CU302247,CH242-42C23,4:74648868-74837242 (Clone quality: bE42C23 on chr=4; Num_of_Contigs=1; )
ASPH		location ⇒	4:74686998-74687091		CU302247,CH242-42C23,4:74648868-74837242 (Clone quality: bE42C23 on chr=4; Num_of_Contigs=1; )
ASPH		location ⇒	4:74687469-74687816		CU302247,CH242-42C23,4:74648868-74837242 (Clone quality: bE42C23 on chr=4; Num_of_Contigs=1; )
ASPHD2		ENSSSCG00000009959	14:44776764-44783838		CT841533,CH242-245B12,14:44759242-44823985 (Clone quality: bE245B12 on chr=14; Num_of_Contigs=7; )
ASPM		ENSSSCG00000010896	10:21161647-21206427
ASPN		ENSSSCG00000008072	3:37453022-37479114
ASRGL1		ENSSSCG00000013065	2:7664992-7709096
ASRGL1		location ⇒	2:7677185-7677051		FP102181,CH242-239P5,2:7676786-7683030 (Clone quality: bE239P5 on chr=2; Num_of_Contigs=6; )
ASTE1		ENSSSCG00000011182	13:1223886-1238101		CU468391,CH242-198D4,13:1217404-1336536 (Clone quality: bE198D4 on chr=13; Num_of_Contigs=2; )
ASTL		ENSSSCG00000008126	3:41953840-42027679
ASTN1		ENSSSCG00000015513	9:111666916-112025075

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).