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)

PLUNC		location ⇒	17:38676341-38676485		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
PLUNC		location ⇒	17:38676659-38676818		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
PLUNC		location ⇒	17:38678234-38678343		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
PLUNC		location ⇒	17:38678932-38679081		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
PLXDC1		ENSSSCG00000017511	12:21113802-21174151
PLXDC2		ENSSSCG00000011091	10:51791279-52121327
PLXNA2		ENSSSCG00000015621	9:126926727-127037639		CU856391,CH242-362M22,9:126866901-127037893 (Clone quality: bE362M22 on chr=9; Num_of_Contigs=3; )
PLXNA4		ENSSSCG00000016547	18:14913273-14914460		CU469309,CH242-313B7,18:14912201-14916504 (Clone quality: bE313B7 on chr=18; Num_of_Contigs=16; )
PLXNB1		ENSSSCG00000011346	13:25916679-25938329
PLXNB1		location ⇒	13:25932651-25932824		FP102065,CH242-145E9,13:25919129-25944766 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PLXNB1		location ⇒	13:25932980-25933142		FP102065,CH242-145E9,13:25919129-25944766 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PLXNB1		location ⇒	13:25933222-25933374		FP102065,CH242-145E9,13:25919129-25944766 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PLXNB1		location ⇒	13:25937575-25938328		FP102065,CH242-145E9,13:25919129-25944766 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PLXNC1		ENSSSCG00000000907	5:83803502-83940444
PLXNC1		location ⇒	5:83803563-83804518		FP245493,CH242-228L4,5:83803193-83805996 (Clone quality: bE228L4 on chr=5; Num_of_Contigs=7; )
PLXNC1		location ⇒	5:83903802-83903866		FP245493,CH242-228L4,5:83897461-83906441 (Clone quality: bE228L4 on chr=5; Num_of_Contigs=7; )
PLXNC1		location ⇒	5:83913726-83913830		FP245493,CH242-228L4,5:83906542-83915403 (Clone quality: bE228L4 on chr=5; Num_of_Contigs=7; )
PLXNC1		location ⇒	5:83935395-83935598		FP245493,CH242-228L4,5:83933585-83940288 (Clone quality: bE228L4 on chr=5; Num_of_Contigs=7; )
PLXND1		ENSSSCG00000011592	13:57439347-57489073
PM20D2		ENSSSCG00000004314	1:59959287-59985402		CU075926,CH242-86H13,1:59921397-60144581 (Clone quality: bE86H13 on chr=1; Num_of_Contigs=1; )
PMAIP1		location ⇒	1:167846904-167847139		CU855866,CH242-18C13,1:167831711-167849989 (Clone quality: bE18C13 on chr=1; Num_of_Contigs=11; )
PMAIP1		location ⇒	1:167850090-167850629
PMAIP1		location ⇒	1:168066423-168065644		CU633494,CH242-198F23,1:168026905-168104475 (Clone quality: bE198F23 on chr=1; Num_of_Contigs=5; )
PMAIP1		location ⇒	1:168069259-168069024		CU633494,CH242-198F23,1:168026905-168104475 (Clone quality: bE198F23 on chr=1; Num_of_Contigs=5; )
PMAP-23		location ⇒	13:26044715-26044685		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-23		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-23		location ⇒	13:26045592-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-36		location ⇒	13:26044715-26044685		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-36		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-36		location ⇒	13:26045592-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-37		location ⇒	13:26044714-26044634		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-37		location ⇒	13:26045037-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMAP-37		location ⇒	13:26045579-26045382		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
PMCH		ENSSSCG00000000858	5:77325181-77325441		CU457436,CH242-54N2,5:77321248-77325842 (Clone quality: bE54N2 on chr=5; Num_of_Contigs=8; )
PMCH		location ⇒	5:77325168-77325429		CU457436,CH242-54N2,5:77321248-77325842 (Clone quality: bE54N2 on chr=5; Num_of_Contigs=8; )
PMEPA1		ENSSSCG00000007509	17:60601351-60655822	CR956367,PigE-122C21,17:60551850-60674969 (No clone quality info on bT122C21)
PMF1		ENSSSCG00000006493	4:97756474-97782681
PMFBP1		ENSSSCG00000002747	6:10728037-10755444
PML		ENSSSCG00000010235	14:74220079-74245927		CT997807,CH242-507P18,14:74104999-74249590 (Clone quality: bE507P18 on chr=14; Num_of_Contigs=4; )
PML		ENSSSCG00000010587	14:118662408-118675520		CT971490,CH242-33G15,14:118660960-118687883 (Clone quality: bE33G15 on chr=14; Num_of_Contigs=9; )
PML		ENSSSCG00000007667	3:6832679-6836677		CU928563,CH242-369L8,3:6786261-6837493 (Clone quality: bE369L8 on chr=3; Num_of_Contigs=1; )
PML		ENSSSCG00000006760	4:110919445-110948658		CU138563,CH242-230I15,4:110770286-110949832 (Clone quality: bE230I15 on chr=4; Num_of_Contigs=2; )
PML		ENSSSCG00000006033	4:29305063-29347624
PML		ENSSSCG00000001912	7:64835208-64876558
PML		ENSSSCG00000001509	7:34084220-34087457	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
PML		ENSSSCG00000000282	5:17804056-17815030
PML		ENSSSCG00000009299	11:3165368-3174969		CU633808,CH242-519P8,11:3156619-3186937 (Clone quality: bE519P8 on chr=11; Num_of_Contigs=11; )
PML		location ⇒	7:64855483-64855317		CU468908,CH242-516A11,7:64852332-64870340 (Clone quality: bE516A11 on chr=7; Num_of_Contigs=3; )
PML		location ⇒	7:64874669-64874210		CU468908,CH242-516A11,7:64870441-64902976 (Clone quality: bE516A11 on chr=7; Num_of_Contigs=3; )
PML		location ⇒	7:64876558-64876502		CU468908,CH242-516A11,7:64870441-64902976 (Clone quality: bE516A11 on chr=7; 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, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-21

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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).