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)

MPO		location ⇒	12:310596-310660		FP236791,CH242-196C17,12:301343-317225 (Clone quality: bE196C17 on chr=12; Num_of_Contigs=8; )
MPP1		ENSSSCG00000012822	X:123668189-123689450	CU914693,CH242-146E2,X:123643095-123740591 (Clone quality: bE146E2 on chr=X; Num_of_Contigs=16; )
MPP2		ENSSSCG00000017367	12:17121733-17127201		CU914436,CH242-507H4,12:17113480-17130047 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )
MPP3		ENSSSCG00000017372	12:17209085-17234253
MPP5		ENSSSCG00000002287	7:99347300-99461509
MPP6		ENSSSCG00000016717	18:46554241-46614396
MPP7		ENSSSCG00000011070	10:47746029-47954356
MPPED2		ENSSSCG00000013327	2:28031590-28211524	CU463210,CH242-12K2,2:28008472-28224382 (Clone quality: bE12K2 on chr=2; Num_of_Contigs=7; )
MPST		ENSSSCG00000000134	5:7074316-7080037		CU633243,CH242-20D10,5:7039128-7109453 (Clone quality: bE20D10 on chr=5; Num_of_Contigs=6; )
MPV17L2		ENSSSCG00000013896	2:62353253-62356573		CU915655,CH242-228H4,2:62349388-62376255 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
MPZ		ENSSSCG00000006352	4:92655512-92659772		CU606874,CH242-28G15,4:92644819-92669165 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
MPZ		location ⇒	4:92656079-92655942		CU606874,CH242-28G15,4:92644819-92669165 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
MPZ		location ⇒	4:92656520-92656306		CU606874,CH242-28G15,4:92644819-92669165 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
MPZ		location ⇒	4:92656927-92656760		CU606874,CH242-28G15,4:92644819-92669165 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
MPZ		location ⇒	4:92659772-92659670		CU606874,CH242-28G15,4:92644819-92669165 (Clone quality: bE28G15 on chr=4; Num_of_Contigs=6; )
MPZL1		ENSSSCG00000006306	4:86542743-86614598		CU462923,CH242-281L8,4:86503385-86700412 (Clone quality: bE281L8 on chr=4; Num_of_Contigs=1; )
MPZL1		location ⇒	4:86557655-86557550		CU462923,CH242-281L8,4:86503385-86700412 (Clone quality: bE281L8 on chr=4; Num_of_Contigs=1; )
MPZL1		location ⇒	4:86559169-86558955		CU462923,CH242-281L8,4:86503385-86700412 (Clone quality: bE281L8 on chr=4; Num_of_Contigs=1; )
MPZL1		location ⇒	4:86565911-86565745		CU462923,CH242-281L8,4:86503385-86700412 (Clone quality: bE281L8 on chr=4; Num_of_Contigs=1; )
MPZL1		location ⇒	4:86614576-86614371		CU462923,CH242-281L8,4:86503385-86700412 (Clone quality: bE281L8 on chr=4; Num_of_Contigs=1; )
MPZL2		ENSSSCG00000015091	9:44452413-44463512		CU914235,CH242-177G19,9:44427804-44486043 (Clone quality: bE177G19 on chr=9; Num_of_Contigs=2; )
MPZL3		ENSSSCG00000015090	9:44424153-44449466
MR1		ENSSSCG00000015540	9:115035712-115040791		CU856441,CH242-286M10,9:114998525-115054427 (Clone quality: bE286M10 on chr=9; Num_of_Contigs=7; )
MR1		location ⇒	9:157632-157697		FP102759,CH242-92D2,9:157119-185482 (Clone quality: bE92D2 on chr=9; Num_of_Contigs=7; )
MR1		location ⇒	9:158639-158522		FP102759,CH242-92D2,9:157119-185482 (Clone quality: bE92D2 on chr=9; Num_of_Contigs=7; )
MR1		location ⇒	9:159644-159745		FP102759,CH242-92D2,9:157119-185482 (Clone quality: bE92D2 on chr=9; Num_of_Contigs=7; )
MR1		location ⇒	9:183545-183472		FP102759,CH242-92D2,9:157119-185482 (Clone quality: bE92D2 on chr=9; Num_of_Contigs=7; )
MRAP2		ENSSSCG00000004288	1:55569914-55610704
MRC1		location ⇒	10:42350452-42350619		CU466345,CH242-21O2,10:42349048-42370125 (Clone quality: bE21O2 on chr=10; Num_of_Contigs=6; )
MRC1		location ⇒	10:42353439-42353540		CU466345,CH242-21O2,10:42349048-42370125 (Clone quality: bE21O2 on chr=10; Num_of_Contigs=6; )
MRC1		location ⇒	10:42354545-42354691		CU466345,CH242-21O2,10:42349048-42370125 (Clone quality: bE21O2 on chr=10; Num_of_Contigs=6; )
MRC1		location ⇒	10:42355734-42355850		CU466345,CH242-21O2,10:42349048-42370125 (Clone quality: bE21O2 on chr=10; Num_of_Contigs=6; )
MRC2		ENSSSCG00000017300	12:13713466-13739068
MRC2		location ⇒	12:13726685-13726573		CU693409,CH242-262P12,12:13725516-13730566 (Clone quality: bE262P12 on chr=12; Num_of_Contigs=8; )
MRC2		location ⇒	12:13728045-13727825		CU693409,CH242-262P12,12:13725516-13730566 (Clone quality: bE262P12 on chr=12; Num_of_Contigs=8; )
MRC2		location ⇒	12:13728848-13728696		CU693409,CH242-262P12,12:13725516-13730566 (Clone quality: bE262P12 on chr=12; Num_of_Contigs=8; )
MRC2		location ⇒	12:13729367-13729292		CU693409,CH242-262P12,12:13725516-13730566 (Clone quality: bE262P12 on chr=12; Num_of_Contigs=8; )
MRE11A		ENSSSCG00000014955	9:26917745-26973677
MREG		ENSSSCG00000016175	15:111133427-111153443
MRFAP1		location ⇒	16:32461783-32461852		CU929824,CH242-50P12,16:32460431-32464737 (Clone quality: bE50P12 on chr=16; Num_of_Contigs=16; )
MRGPRD		ENSSSCG00000012877	2:2397331-2398278		CU463344,CH242-408M2,2:2386118-2419493 (Clone quality: bE408M2 on chr=2; Num_of_Contigs=8; )
MRGPRF		ENSSSCG00000012876	2:2366606-2373923		CU463344,CH242-408M2,2:2334405-2383164 (Clone quality: bE408M2 on chr=2; Num_of_Contigs=8; )
MRGPRX2		ENSSSCG00000013356	2:37514811-37515800		CU929490,CH242-88D19,2:37512413-37521556 (Clone quality: bE88D19 on chr=2; Num_of_Contigs=15; )
MRI1		ENSSSCG00000013756	2:56814487-56821176		CU855962,CH242-129F14,2:56772208-56824782 (Clone quality: bE129F14 on chr=2; Num_of_Contigs=2; )
MRM1		ENSSSCG00000017691	12:36259817-36265133		CU694881,CH242-311G5,12:36223352-36296162 (Clone quality: bE311G5 on chr=12; Num_of_Contigs=3; )
MRO		ENSSSCG00000004521	1:103561675-103584829
MRPL1		ENSSSCG00000008990	8:62869504-62917938
MRPL11		ENSSSCG00000012943	2:4296668-4299260		CU928034,CH242-426E24,2:4294202-4299914 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
MRPL13		ENSSSCG00000005996	4:18237830-18322798
MRPL14		ENSSSCG00000001696	7:45646267-45659708	CR956360,CH242-245E12,7:45529239-45714745 (No clone quality info on bE245E12)

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).