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)

AKT2		ENSSSCG00000002989	6:33533100-33560034		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
AKT2		location ⇒	6:33557762-33557675		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
AKT2		location ⇒	6:33558328-33558239		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
AKT2		location ⇒	6:33558539-33558435		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
AKT2		location ⇒	6:33559863-33559516		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
AKT3		ENSSSCG00000010872	10:16162075-16280499
AKT3		location ⇒	10:16118469-16117854		CU570926,CH242-205H3,10:16016755-16179951 (Clone quality: bE205H3 on chr=10; Num_of_Contigs=1; )
AKT3		location ⇒	10:16131783-16131679		CU570926,CH242-205H3,10:16016755-16179951 (Clone quality: bE205H3 on chr=10; Num_of_Contigs=1; )
ALAD		location ⇒	X:57564157-57564233		CU463320,CH242-207P9,X:57555533-57612952 (Clone quality: bE207P9 on chr=X; Num_of_Contigs=11; )
ALAS1		location ⇒	13:28813925-28814091		CU914695,CH242-195P19,13:28772257-28826761 (Clone quality: bE195P19 on chr=13; Num_of_Contigs=14; )
ALAS1		location ⇒	13:28815731-28816002		CU914695,CH242-195P19,13:28772257-28826761 (Clone quality: bE195P19 on chr=13; Num_of_Contigs=14; )
ALAS1		location ⇒	13:29061095-29060824		CU915558,CH242-407L22,13:29052287-29068589 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
ALAS1		location ⇒	13:29062901-29062735		CU915558,CH242-407L22,13:29052287-29068589 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
ALAS2		ENSSSCG00000012347	X:47573786-47597191
ALB		ENSSSCG00000008950	8:59081569-59100317		CU606945,CH242-230P13,8:59079400-59136397 (Clone quality: bE230P13 on chr=8; Num_of_Contigs=3; )
ALB		ENSSSCG00000008948	8:58915609-58935318
ALB		location ⇒	8:58915788-58915640		FP104530,CH242-172E18,8:58909574-58920879 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
ALB		location ⇒	8:58920212-58919989		FP104530,CH242-172E18,8:58909574-58920879 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
ALB		location ⇒	8:58926205-58925988		FP104530,CH242-172E18,8:58920980-58958079 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
ALB		location ⇒	8:58931600-58931392		FP104530,CH242-172E18,8:58920980-58958079 (Clone quality: bE172E18 on chr=8; Num_of_Contigs=16; )
ALCAM		ENSSSCG00000011946	13:113830563-113914544
ALCAM		location ⇒	13:113834693-113834897		FP236707,CH242-240L8,13:113809818-113842454 (Clone quality: bE240L8 on chr=13; Num_of_Contigs=15; )
ALCAM		location ⇒	13:113845054-113845118		FP236707,CH242-240L8,13:113842555-113861803 (Clone quality: bE240L8 on chr=13; Num_of_Contigs=15; )
ALCAM		location ⇒	13:113846300-113846367		FP236707,CH242-240L8,13:113842555-113861803 (Clone quality: bE240L8 on chr=13; Num_of_Contigs=15; )
ALDH16A1		ENSSSCG00000003168	6:37997472-38014266		FP102665,CH242-289C15,6:37963305-38017162 (Clone quality: bE289C15 on chr=6; Num_of_Contigs=6; )
ALDH18A1		ENSSSCG00000010495	14:112230668-112277349		CT737262,CH242-169I8,14:112174454-112352511 (Clone quality: bE169I8 on chr=14; Num_of_Contigs=1; )
ALDH1A2		location ⇒	1:118082792-118082976		CU915427,CH242-479A19,1:118082541-118086432 (Clone quality: bE479A19 on chr=1; Num_of_Contigs=13; )
ALDH1A2		location ⇒	1:118085192-118085352		CU915427,CH242-479A19,1:118082541-118086432 (Clone quality: bE479A19 on chr=1; Num_of_Contigs=13; )
ALDH1A2		location ⇒	1:250530514-250530554		CU914291,CH242-55I17,1:250530134-250549980 (Clone quality: bE55I17 on chr=1; Num_of_Contigs=1; )
ALDH1A2		location ⇒	1:250618742-250618782		CU210910,CH242-81E21,1:250549981-250664896 (Clone quality: bE81E21 on chr=1; Num_of_Contigs=4; )
ALDH1A3		ENSSSCG00000004822	1:147153622-147237244
ALDH1L2		ENSSSCG00000000839	5:74831523-74862608
ALDH2_PIG		ENSSSCG00000009889	14:39812424-39843035
ALDH3A1		ENSSSCG00000018044	12:56571896-56578748		FP003595,CH242-47E22,12:56532412-56616940 (Clone quality: bE47E22 on chr=12; Num_of_Contigs=5; )
ALDH3A1218		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
ALDH3A2		ENSSSCG00000018041	12:56525138-56541593
ALDH5A1		ENSSSCG00000001090	7:20358750-20382925
ALDH6A1		ENSSSCG00000002357	7:105377851-105396190		CT797481,CH242-31K14,7:105227853-105414617 (Clone quality: bE31K14 on chr=7; Num_of_Contigs=1; )
ALDH7A1		ENSSSCG00000014247	2:117403698-117445470
ALDH8A1		location ⇒	1:30616087-30616222		CU407206,CH242-337H22,1:30600382-30625532 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
ALDH8A1		location ⇒	1:30621796-30621948		CU407206,CH242-337H22,1:30600382-30625532 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
ALDH8A1		location ⇒	1:30625087-30625342		CU407206,CH242-337H22,1:30600382-30625532 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
ALDH8A1		location ⇒	1:30626144-30626295		CU407206,CH242-337H22,1:30625633-30632621 (Clone quality: bE337H22 on chr=1; Num_of_Contigs=9; )
ALDH9A1		ENSSSCG00000006324	4:88466756-88494201		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
ALDH9A1		location ⇒	4:88466756-88466973		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
ALDH9A1		location ⇒	4:88478051-88478248		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
ALDH9A1		location ⇒	4:88486151-88486342		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
ALDH9A1		location ⇒	4:88493424-88493739		CU468388,CH242-187I4,4:88421644-88589691 (Clone quality: bE187I4 on chr=4; Num_of_Contigs=2; )
ALDOB		ENSSSCG00000005395	1:254661098-254662263		CU469282,CH242-469F7,1:254657078-254662451 (Clone quality: bE469F7 on chr=1; Num_of_Contigs=22; )
ALDOC		ENSSSCG00000017759	12:42452109-42456794

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

Report problems to zhu

iastate.edu

$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).