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)

MED1		ENSSSCG00000017505	12:20802497-20902249
MED10		ENSSSCG00000017106	16:72900438-72908115		CU915407,CH242-304C24,16:72868010-72973211 (Clone quality: bE304C24 on chr=16; Num_of_Contigs=2; )
MED11		ENSSSCG00000017919	12:49353100-49354768		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
MED12		ENSSSCG00000012396	X:56826433-56849719
MED12L		ENSSSCG00000011714	13:74060524-74102592		CU467754,CH242-404L12,13:74041525-74105862 (Clone quality: bE404L12 on chr=13; Num_of_Contigs=3; )
MED13		ENSSSCG00000017674	12:34610037-34657854
MED13		location ⇒	12:34518520-34519204		CU929908,CH242-288F7,12:34490067-34520589 (Clone quality: bE288F7 on chr=12; Num_of_Contigs=8; )
MED13		location ⇒	12:34540611-34541526		CU929908,CH242-288F7,12:34520690-34545169 (Clone quality: bE288F7 on chr=12; Num_of_Contigs=8; )
MED13		location ⇒	12:34608909-34606951		CU929908,CH242-288F7,12:34563929-34620377 (Clone quality: bE288F7 on chr=12; Num_of_Contigs=8; )
MED13		location ⇒	12:34610422-34608961		CU929908,CH242-288F7,12:34563929-34620377 (Clone quality: bE288F7 on chr=12; Num_of_Contigs=8; )
MED13L		ENSSSCG00000009864	14:36579069-36649083
MED14		ENSSSCG00000012250	X:36069913-36138839		FP067431,CH242-266E24,X:36049329-36150098 (Clone quality: bE266E24 on chr=X; Num_of_Contigs=2; )
MED15		ENSSSCG00000010107	14:51806120-51858409
MED16		ENSSSCG00000013416	2:46131429-46166759		FP015903,CH242-504E7,2:46128360-46188530 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
MED17		ENSSSCG00000014949	9:26566364-26588641		CU464153,CH242-27K5,9:26560904-26638658 (Clone quality: bE27K5 on chr=9; Num_of_Contigs=3; )
MED19		ENSSSCG00000013177	2:11246439-11254785
MED20		ENSSSCG00000001630	7:42646636-42650716
MED21		ENSSSCG00000000552	5:45307483-45313478		CU928020,CH242-142K16,5:45257797-45331341 (Clone quality: bE142K16 on chr=5; Num_of_Contigs=5; )
MED23		ENSSSCG00000004196	1:33301523-33339032		CU633754,CH242-254O2,1:33299154-33340304 (Clone quality: bE254O2 on chr=1; Num_of_Contigs=9; )
MED25		ENSSSCG00000003197	6:38517806-38532886		CU694867,CH242-269H19,6:38488706-38576788 (Clone quality: bE269H19 on chr=6; Num_of_Contigs=4; )
MED26		ENSSSCG00000013862	2:61124745-61174481
MED27		ENSSSCG00000005720	1:287164826-287368710
MED29		location ⇒	14:138665270-138665330		FP236263,CH242-159G20,14:138633964-138675291 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
MED29		location ⇒	14:138668511-138668754		FP236263,CH242-159G20,14:138633964-138675291 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
MED29		location ⇒	14:138669489-138669779		FP236263,CH242-159G20,14:138633964-138675291 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
MED29		location ⇒	14:35003929-35003986		CT737271,CH242-60M15,14:34957829-35020074 (Clone quality: bE60M15 on chr=14; Num_of_Contigs=3; )
MED30		ENSSSCG00000012391	X:56603491-56620375		FP101958,CH242-149A9,X:56529129-56685548 (Clone quality: bE149A9 on chr=4; Num_of_Contigs=1; )
MED4		ENSSSCG00000009404	11:18973025-18980781		FP085602,CH242-266M16,11:18971338-18989709 (Clone quality: bE266M16 on chr=11; Num_of_Contigs=8; )
MED6		ENSSSCG00000002328	7:102748762-102766682		CU469452,CH242-138O16,7:102745211-102787172 (Clone quality: bE138O16 on chr=7; Num_of_Contigs=9; )
MED7		ENSSSCG00000017058	16:63801506-63807759		CU972395,CH242-203E2,16:63794505-63875272 (Clone quality: bE203E2 on chr=16; Num_of_Contigs=4; )
MED8		ENSSSCG00000003943	6:120089926-120096191		CU694684,CH242-210N13,6:120086513-120110432 (Clone quality: bE210N13 on chr=6; Num_of_Contigs=11; )
MED9		ENSSSCG00000018053	12:56987304-56995161		CU927962,CH242-273I13,12:56891060-57001521 (Clone quality: bE273I13 on chr=12; Num_of_Contigs=8; )
MEF2A		ENSSSCG00000004815	1:146047187-146086379		CU618336,CH242-489F23,1:146029145-146105399 (Clone quality: bE489F23 on chr=1; Num_of_Contigs=13; )
MEF2C		ENSSSCG00000014149	2:85646913-85737797		CU462930,CH242-2C11,2:85577022-85765142 (Clone quality: bE2C11 on chr=2; Num_of_Contigs=1; )
MEF2C		location ⇒	2:85647764-85646913		CU462930,CH242-2C11,2:85577022-85765142 (Clone quality: bE2C11 on chr=2; Num_of_Contigs=1; )
MEF2C		location ⇒	2:85656817-85656643		CU462930,CH242-2C11,2:85577022-85765142 (Clone quality: bE2C11 on chr=2; Num_of_Contigs=1; )
MEF2C		location ⇒	2:85676626-85676438		CU462930,CH242-2C11,2:85577022-85765142 (Clone quality: bE2C11 on chr=2; Num_of_Contigs=1; )
MEF2C		location ⇒	2:85720301-85720095		CU462930,CH242-2C11,2:85577022-85765142 (Clone quality: bE2C11 on chr=2; Num_of_Contigs=1; )
MEF2D		ENSSSCG00000006482	4:97397214-97411009		CU633176,CH242-238D11,4:97382842-97427421 (Clone quality: bE238D11 on chr=4; Num_of_Contigs=11; )
MEFV		ENSSSCG00000007964	3:34967767-34974733		CU928670,CH242-433O3,3:34954996-34980834 (Clone quality: bE433O3 on chr=3; Num_of_Contigs=10; )
MEGF10		ENSSSCG00000014251	2:117876711-118003906
MEGF11		ENSSSCG00000004939	1:170966774-171161116
MEGF6		ENSSSCG00000003358	6:43580995-43754289
MEGF8		ENSSSCG00000003021	6:34194261-34220876
MEGF8		location ⇒	6:34180219-34180929		FP102452,CH242-68N5,6:34131281-34214206 (Clone quality: bE68N5 on chr=6; Num_of_Contigs=4; )
MEGF8		location ⇒	6:34286053-34285370		FP102858,CH242-504I8,6:34285368-34299030 (Clone quality: bE504I8 on chr=6; Num_of_Contigs=13; )
MEGF9		ENSSSCG00000005506	1:274191659-274330375
MEI1		ENSSSCG00000000065	5:3613869-3616629		CU633382,CH242-275I12,5:3612541-3617529 (Clone quality: bE275I12 on chr=5; Num_of_Contigs=9; )
MEIG1		ENSSSCG00000011050	10:44659789-44668517		CU929591,CH242-21K12,10:44569457-44680253 (Clone quality: bE21K12 on chr=10; Num_of_Contigs=3; )
MEIS1		ENSSSCG00000008355	3:69341513-69346048		CU929690,CH242-154E21,3:69239153-69346539 (Clone quality: bE154E21 on chr=3; Num_of_Contigs=3; )

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).