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)

MALL		location ⇒	3:177267-177376		FP102523,CH242-174H19,3:176551-207230 (Clone quality: bE174H19 on chr=3; Num_of_Contigs=7; )
MALL		location ⇒	3:1882203-1882304		FP102725,CH242-525I24,3:1876563-1884196 (Clone quality: bE525I24 on chr=3; Note=un_improved;)
MALT1		location ⇒	1:168981916-168982067		CU856589,CH242-300P8,1:168974224-168989301 (Clone quality: bE300P8 on chr=1; Num_of_Contigs=5; )
MALT1		location ⇒	1:168984095-168984254		CU856589,CH242-300P8,1:168974224-168989301 (Clone quality: bE300P8 on chr=1; Num_of_Contigs=5; )
MALT1		location ⇒	1:169025735-169025576		CU464199,CH242-84G18,1:169014769-169084027 (Clone quality: bE84G18 on chr=1; Num_of_Contigs=5; )
MALT1		location ⇒	1:169027914-169027763		CU464199,CH242-84G18,1:169014769-169084027 (Clone quality: bE84G18 on chr=1; Num_of_Contigs=5; )
MAMDC1		ENSSSCG00000005002	1:185435791-185559863
MAMDC1		location ⇒	1:185618390-185618588		CU074334,CH242-163O24,1:185618367-185621398 (Clone quality: bE163O24 on chr=1; Num_of_Contigs=12; )
MAMDC2		ENSSSCG00000005253	1:233860965-233876054
MAMDC4		ENSSSCG00000005832	1:294154261-294158159		FP236151,CH242-517G10,1:294154139-294159223 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
MAML1		ENSSSCG00000014019	2:68164730-68220114		FP015930,CH242-222N20,2:68151095-68227732 (Clone quality: bE222N20 on chr=2; Num_of_Contigs=11; )
MAML2		ENSSSCG00000014971	9:28659881-28661420
MAMLD1		ENSSSCG00000012741	X:120339479-120389000		FP102038,CH242-116A16,X:120329164-120398795 (Clone quality: bE116A16 on chr=X; Num_of_Contigs=5; )
MAMSTR		ENSSSCG00000003143	6:37654017-37658453		CU929759,CH242-294C24,6:37595303-37722216 (Clone quality: bE294C24 on chr=6; Num_of_Contigs=3; )
MAN1A1		ENSSSCG00000004244	1:44525271-44698100
MAN1A2		ENSSSCG00000006730	4:107284061-107492370
MAN1C1		ENSSSCG00000003550	6:57208014-57343683
MAN2A1		ENSSSCG00000014195	2:103141933-103313268
MAN2A2		ENSSSCG00000001819	7:59041792-59058903	CT868688,CH242-510G16,7:59026976-59242142 (Clone quality: bE510G16 on chr=7; Num_of_Contigs=3; )
MAN2B1		ENSSSCG00000013720	2:55896394-55914377		CU856041,CH242-32I13,2:55839118-55919279 (Clone quality: bE32I13 on chr=2; Num_of_Contigs=2; )
MAN2C1		ENSSSCG00000001881	7:63504976-63517672		CT990537,CH242-196K6,7:63503819-63528405 (Clone quality: bE196K6 on chr=7; Num_of_Contigs=8; )
MANBA		ENSSSCG00000009166	8:101277552-101368784
MANEA		ENSSSCG00000004337	1:65995249-66033910		CU210884,CH242-180M5,1:65958520-66042428 (Clone quality: bE180M5 on chr=1; Num_of_Contigs=4; )
MAOA		ENSSSCG00000012257	X:38904253-39057000
MAP1A		ENSSSCG00000004705	1:133989978-134009015		CU861634,CH242-463N18,1:133988258-134019113 (Clone quality: bE463N18 on chr=1; Num_of_Contigs=7; )
MAP1B		ENSSSCG00000016974	16:45838185-45931543
MAP1LC3A		ENSSSCG00000007281	17:40015033-40016729		CU606894,CH242-217L16,17:40007253-40020363 (Clone quality: bE217L16 on chr=17; Num_of_Contigs=12; )
MAP1LC3B		ENSSSCG00000002655	6:804217-824752		FP236784,CH242-96O7,6:794845-824903 (Clone quality: bE96O7 on chr=6; Num_of_Contigs=5; )
MAP1LC3C		ENSSSCG00000010870	10:15460745-15466482		FP236465,CH242-40I12,10:15457879-15467208 (Clone quality: bE40I12 on chr=10; Num_of_Contigs=11; )
MAP1S		ENSSSCG00000013884	2:61969773-61995530		CU928970,CH242-349K2,2:61957948-62018496 (Clone quality: bE349K2 on chr=2; Num_of_Contigs=3; )
MAP2		ENSSSCG00000016151	15:105467444-105544481		CU570737,CH242-313M19,15:105372761-105547335 (Clone quality: bE313M19 on chr=15; Num_of_Contigs=1; )
MAP2K1		ENSSSCG00000004943	1:171538293-171625963
MAP2K1		location ⇒	1:171538293-171538725		CU062652,CH242-108M5,1:171491799-171560282 (Clone quality: bE108M5 on chr=1; Num_of_Contigs=3; )
MAP2K1		location ⇒	1:171580560-171580764		CU407297,CH242-524I5,1:171580414-171586323 (Clone quality: bE524I5 on chr=1; Num_of_Contigs=20; )
MAP2K1		location ⇒	1:171582582-171582731		CU407297,CH242-524I5,1:171580414-171586323 (Clone quality: bE524I5 on chr=1; Num_of_Contigs=20; )
MAP2K1		location ⇒	1:171590985-171591489		CU407297,CH242-524I5,1:171588824-171597421 (Clone quality: bE524I5 on chr=1; Num_of_Contigs=20; )
MAP2K2		location ⇒	2:48443790-48443569		CU929466,CH242-60A20,2:48440296-48455778 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
MAP2K2		location ⇒	2:48450428-48450213		CU929466,CH242-60A20,2:48440296-48455778 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
MAP2K2		location ⇒	2:48451193-48451055		CU929466,CH242-60A20,2:48440296-48455778 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
MAP2K2		location ⇒	2:48492922-48493084		CU929466,CH242-60A20,2:48455879-48498778 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
MAP2K3		location ⇒	12:9245867-9245668		CU640375,CH242-148N7,12:9167330-9263627 (Clone quality: bE148N7 on chr=12; Num_of_Contigs=3; )
MAP2K3		location ⇒	12:9260409-9260269		CU640375,CH242-148N7,12:9167330-9263627 (Clone quality: bE148N7 on chr=12; Num_of_Contigs=3; )
MAP2K3		location ⇒	12:9263333-9263204		CU640375,CH242-148N7,12:9167330-9263627 (Clone quality: bE148N7 on chr=12; Num_of_Contigs=3; )
MAP2K3		location ⇒	12:9358157-9357870		CU463221,CH242-390E10,12:9356516-9358781 (Clone quality: bE390E10 on chr=12; Num_of_Contigs=14; )
MAP2K4		location ⇒	12:53494509-53494630		CU929508,CH242-173D1,12:53449762-53612633 (Clone quality: bE173D1 on chr=12; Num_of_Contigs=2; )
MAP2K4		location ⇒	12:53505829-53506523		CU929508,CH242-173D1,12:53449762-53612633 (Clone quality: bE173D1 on chr=12; Num_of_Contigs=2; )
MAP2K5		ENSSSCG00000004955	1:172621117-172854523
MAP2K6		ENSSSCG00000017254	12:9245523-9358173
MAP2K7		ENSSSCG00000013588	2:51277686-51289806
MAP2K7		location ⇒	2:51283505-51283588		CU928575,CH242-46K5,2:51259004-51289315 (Clone quality: bE46K5 on chr=2; Num_of_Contigs=5; )

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, 1401-46

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).