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)

MEIS2		ENSSSCG00000004795	1:140989407-141052663		FP085555,CH242-87J22,1:140983230-141054028 (Clone quality: bE87J22 on chr=1; Num_of_Contigs=5; )
MEIS3		ENSSSCG00000003115	6:36922166-36999293
MELK		ENSSSCG00000005344	1:248618134-248731424
MEMO1		ENSSSCG00000008515	3:100804030-100918000
MEMO1		location ⇒	3:100804700-100804036		CU861984,CH242-378M9,3:100803018-100859230 (Clone quality: bE378M9 on chr=3; Num_of_Contigs=9; )
MEMO1		location ⇒	3:100824698-100824551		CU861984,CH242-378M9,3:100803018-100859230 (Clone quality: bE378M9 on chr=3; Num_of_Contigs=9; )
MEMO1		location ⇒	3:100846998-100846887		CU861984,CH242-378M9,3:100803018-100859230 (Clone quality: bE378M9 on chr=3; Num_of_Contigs=9; )
MEMO1		location ⇒	3:100850699-100850587		CU861984,CH242-378M9,3:100803018-100859230 (Clone quality: bE378M9 on chr=3; Num_of_Contigs=9; )
MEN1		ENSSSCG00000013019	2:5762005-5765616	FP101995,CH242-228D7,2:5761371-5766446 (Clone quality: bE228D7 on chr=2; Num_of_Contigs=13; )
MEN1		ENSSSCG00000013021	2:5792161-5805583
MEOX1		ENSSSCG00000017376	12:17343490-17344088		CU928405,CH242-149G4,12:17278473-17345758 (Clone quality: bE149G4 on chr=12; Num_of_Contigs=4; )
MEP1A		ENSSSCG00000001724	7:48989758-49026601	CT967297,CH242-157K17,7:48911843-49089775 (Clone quality: bE157K17 on chr=7; Num_of_Contigs=1; )
MEP1B		ENSSSCG00000003732	6:80402657-80436762		CU467523,CH242-187M19,6:80395300-80438879 (Clone quality: bE187M19 on chr=6; Num_of_Contigs=7; )
MEPE		ENSSSCG00000009218	8:112702381-112713904	CU856168,CH242-97B16,8:112550233-112746938 (Clone quality: bE97B16 on chr=8; Num_of_Contigs=1; )
MERTK		ENSSSCG00000008103	3:39750364-40021457
MERTK		location ⇒	3:39844423-39844336		CU929435,CH242-218N20,3:39817373-39885453 (Clone quality: bE218N20 on chr=3; Num_of_Contigs=5; )
MERTK		location ⇒	3:39863826-39863649		CU929435,CH242-218N20,3:39817373-39885453 (Clone quality: bE218N20 on chr=3; Num_of_Contigs=5; )
MERTK		location ⇒	3:39868428-39868324		CU929435,CH242-218N20,3:39817373-39885453 (Clone quality: bE218N20 on chr=3; Num_of_Contigs=5; )
MERTK		location ⇒	3:39883409-39882990		CU929435,CH242-218N20,3:39817373-39885453 (Clone quality: bE218N20 on chr=3; Num_of_Contigs=5; )
MESDC1		ENSSSCG00000001785	7:55969877-55971948
MESDC1		location ⇒	7:55969966-55970247		CT841542,CH242-241P18,7:55956858-55970849 (Clone quality: bE241P18 on chr=7; Num_of_Contigs=3; )
MESDC1		location ⇒	7:55970980-55971949		CT841542,CH242-241P18,7:55970950-56105857 (Clone quality: bE241P18 on chr=7; Num_of_Contigs=3; )
MESDC1		location ⇒	7:55971984-55972043		CT841542,CH242-241P18,7:55970950-56105857 (Clone quality: bE241P18 on chr=7; Num_of_Contigs=3; )
MESDC1		location ⇒	7:55972335-55972617		CT841542,CH242-241P18,7:55970950-56105857 (Clone quality: bE241P18 on chr=7; Num_of_Contigs=3; )
MESDC2		ENSSSCG00000001784	7:55945136-55954800		CT841542,CH242-241P18,7:55916689-55956757 (Clone quality: bE241P18 on chr=7; Num_of_Contigs=3; )
MESP1		ENSSSCG00000001847	7:60746869-60747922		CT737411,CH242-149F11,7:60738915-60829656 (Clone quality: bE149F11 on chr=7; Num_of_Contigs=3; )
MESP2		ENSSSCG00000001848	7:60767716-60769800		CT737411,CH242-149F11,7:60738915-60829656 (Clone quality: bE149F11 on chr=7; Num_of_Contigs=3; )
MEST		ENSSSCG00000016554	18:16496940-16510729		CU915599,CH242-89E18,18:16490128-16562210 (Clone quality: bE89E18 on chr=18; Num_of_Contigs=5; )
MET		ENSSSCG00000006243	4:78422054-78426548		CU462960,CH242-392H23,4:78385334-78466679 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
MET		ENSSSCG00000013232	2:13114682-13135473
MET		ENSSSCG00000016633	18:28212432-28297096
MET		ENSSSCG00000004591	1:117047112-117080996
MET		ENSSSCG00000009684	14:13641085-13868167
METAP1		ENSSSCG00000009186	8:103959846-104019022
METAP2		ENSSSCG00000000899	5:82956316-82964533		CU896600,CH242-366K23,5:82949454-82965890 (Clone quality: bE366K23 on chr=5; Num_of_Contigs=8; )
METRN		ENSSSCG00000008005	3:35721526-35723582		FP016225,CH242-86N4,3:35707195-35730781 (Clone quality: bE86N4 on chr=3; Num_of_Contigs=9; )
METRNL		ENSSSCG00000017137	12:557531-565425	FP236794,CH242-280M17,12:557428-577827 (Clone quality: bE280M17 on chr=12; Num_of_Contigs=6; )
METT10D		ENSSSCG00000017833	12:45972181-45992324
METTL11A		ENSSSCG00000005678	1:284547901-284556412
METTL11B		ENSSSCG00000006281	4:83916052-83934597	CU151872,CH242-290P9,4:83796851-83948417 (Clone quality: bE290P9 on chr=4; Num_of_Contigs=1; )
METTL13		ENSSSCG00000015483	9:107193240-107209087		CU928019,CH242-102L6,9:107032719-107220326 (Clone quality: bE102L6 on chr=9; Num_of_Contigs=1; )
METTL14		ENSSSCG00000009113	8:90573759-90609262
METTL4		ENSSSCG00000003696	6:71161662-71167918		CU929712,CH242-197D22,6:71150666-71170506 (Clone quality: bE197D22 on chr=6; Num_of_Contigs=11; )
METTL5		location ⇒	13:54808937-54808633		CU929960,CH242-56L24,13:54808537-54811324 (Clone quality: bE56L24 on chr=13; Num_of_Contigs=7; )
METTL5		location ⇒	13:54902610-54902914		CU929960,CH242-56L24,13:54901721-54935226 (Clone quality: bE56L24 on chr=13; Num_of_Contigs=7; )
METTL5		location ⇒	13:54903178-54903520		CU929960,CH242-56L24,13:54901721-54935226 (Clone quality: bE56L24 on chr=13; Num_of_Contigs=7; )
METTL6		ENSSSCG00000011190	13:2019189-2034452		CU915680,CH242-245B17,13:2010184-2056700 (Clone quality: bE245B17 on chr=13; Num_of_Contigs=5; )
METTL7B		ENSSSCG00000000357	5:20030940-20033314		CU855487,CH242-124H13,5:20020708-20045638 (Clone quality: bE124H13 on chr=5; Num_of_Contigs=8; )
METTL8		ENSSSCG00000015945	15:72651318-72714258
MEX3D		ENSSSCG00000006497	4:97896984-97901761		CU302298,CH242-261P14,4:97896859-97936068 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )

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

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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).