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)

PCDHGA10		location ⇒	2:130064264-130064353		CU468962,CH242-385J20,2:130048708-130067538 (Clone quality: bE385J20 on chr=2; Num_of_Contigs=15; )
PCDHGA12		ENSSSCG00000014386	2:130044861-130047182		CU468962,CH242-385J20,2:130042453-130048607 (Clone quality: bE385J20 on chr=2; Num_of_Contigs=15; )
PCDHGB2		location ⇒	2:129909399-129908788		CU855722,CH242-107K9,2:129900796-129910052 (Clone quality: bE107K9 on chr=2; Num_of_Contigs=12; )
PCDHGB7		location ⇒	2:129900212-129900452		CU855722,CH242-107K9,2:129818680-129900695 (Clone quality: bE107K9 on chr=2; Num_of_Contigs=12; )
PCDHGB7		location ⇒	2:129909646-129909886		CU855722,CH242-107K9,2:129900796-129910052 (Clone quality: bE107K9 on chr=2; Num_of_Contigs=12; )
PCDHGB7		location ⇒	2:129958803-129959043		CU855722,CH242-107K9,2:129953568-129959136 (Clone quality: bE107K9 on chr=2; Num_of_Contigs=12; )
PCDHGB7		location ⇒	2:129968050-129968290		CU855722,CH242-107K9,2:129959237-129968352 (Clone quality: bE107K9 on chr=2; Num_of_Contigs=12; )
PCDHGC3		location ⇒	2:130036633-130037204		CU468962,CH242-385J20,2:129993001-130042352 (Clone quality: bE385J20 on chr=2; Num_of_Contigs=15; )
PCDHGC5		ENSSSCG00000014385	2:129887520-130064352
PCDHX		location ⇒	X:76373571-76375632		CU928627,CH242-204D4,X:76365010-76387026 (Clone quality: bE204D4 on chr=X; Num_of_Contigs=5; )
PCDHX		location ⇒	X:76427390-76426804		CU928627,CH242-204D4,X:76407652-76428556 (Clone quality: bE204D4 on chr=X; Num_of_Contigs=5; )
PCDHX		location ⇒	X:78242652-78243178		CU861973,CH242-28P8,X:78220777-78243431 (Clone quality: bE28P8 on chr=X; Num_of_Contigs=4; )
PCDHX		location ⇒	X:78269435-78269961	CU468400,CH242-230G24,X:78250753-78310970 (Clone quality: bE230G24 on chr=X; Num_of_Contigs=5; )
PCF11		ENSSSCG00000014901	9:17366234-17392430
PCGF1		ENSSSCG00000008277	3:63083177-63085659		CU468647,CH242-164C3,3:63071721-63110155 (Clone quality: bE164C3 on chr=3; Num_of_Contigs=12; )
PCGF3		ENSSSCG00000008672	8:40326-43297		FP102972,CH242-47L5,8:39031-43407 (Clone quality: bE47L5 on chr=8; Num_of_Contigs=13; )
PCGF5		ENSSSCG00000010462	14:107837673-107899751		CU656022,CH242-437I1,14:107776412-107956298 (Clone quality: bE437I1 on chr=14; Num_of_Contigs=1; )
PCGF6		ENSSSCG00000010596	14:119377001-119401958
PCID2		ENSSSCG00000009557	11:78871431-78886876		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
PCIF1		ENSSSCG00000007433	17:50200789-50212380		CU407252,CH242-441N18,17:50187934-50215613 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
PCK2		ENSSSCG00000002009	7:81528029-81538448		CT961055,CH242-32K2,7:81442434-81553552 (Clone quality: bE32K2 on chr=7; Num_of_Contigs=2; )
PCLKC		ENSSSCG00000014055	2:70338038-70367840	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
PCLKC		location ⇒	2:70347765-70347693	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
PCLKC		location ⇒	2:70350239-70349996	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
PCLKC		location ⇒	2:70352509-70352288	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
PCLO		ENSSSCG00000015401	9:90684965-91078418
PCM1		ENSSSCG00000006994	17:5733931-5751497		CU915455,CH242-181E13,17:5733285-5759705 (Clone quality: bE181E13 on chr=17; Num_of_Contigs=4; )
PCMT1		ENSSSCG00000004103	1:17161761-17232353
PCMT1		location ⇒	1:17162565-17161763		CU571230,CH242-42L8,1:17100560-17179490 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
PCMT1		location ⇒	1:17172527-17172309		CU571230,CH242-42L8,1:17100560-17179490 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
PCMT1		location ⇒	1:17182981-17182874		CU571230,CH242-42L8,1:17179591-17204757 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
PCMT1		location ⇒	1:17232347-17232250		CU571230,CH242-42L8,1:17229321-17232366 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
PCMTD1		ENSSSCG00000006267	4:81062167-81093696
PCNA		location ⇒	1:70000949-70000160		CU392850,CH242-150N9,1:69931777-70081701 (Clone quality: bE150N9 on chr=1; Num_of_Contigs=2; )
PCNA		location ⇒	1:70002413-70001432		CU392850,CH242-150N9,1:69931777-70081701 (Clone quality: bE150N9 on chr=1; Num_of_Contigs=2; )
PCNP		ENSSSCG00000011955	13:115643183-115660192		CU633680,CH242-251F9,13:115560062-115745735 (Clone quality: bE251F9 on chr=13; Num_of_Contigs=2; )
PCNX		ENSSSCG00000002330	7:102838376-102951722		CT841685,CH242-227F9,7:102835138-103015707 (Clone quality: bE227F9 on chr=7; Num_of_Contigs=1; )
PCNXL2		ENSSSCG00000010165	14:58980219-59269450
PCNXL3		ENSSSCG00000012983	2:5016425-5025292		CU914305,CH242-95H15,2:5007151-5027868 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
PCOLCE2		ENSSSCG00000011683	13:68109008-68193664
PCP2		ENSSSCG00000013580	2:51147843-51149709		CU929919,CH242-334A8,2:51145935-51174431 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
PCSK1		ENSSSCG00000014169	2:92001906-92024579
PCSK2		ENSSSCG00000007083	17:26293939-26554239
PCSK5		ENSSSCG00000005275	1:239615943-239706811
PCSK6		ENSSSCG00000005783	1:292192711-292222288
PCSK7		ENSSSCG00000015072	9:43264186-43289723		CU633260,CH242-267D22,9:43263576-43314400 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
PCTK1		ENSSSCG00000012269	X:41755754-41761927		FP015877,CH242-127N16,X:41748540-41773689 (Clone quality: bE127N16 on chr=X; Num_of_Contigs=6; )
PCTK2		ENSSSCG00000015290	9:63236256-63239434		FP102849,CH242-21K8,9:63234146-63239626 (Clone quality: bE21K8 on chr=9; Num_of_Contigs=13; )
PCTK2		location ⇒	10:66343616-66345137		CT956084,PigE-149L18,10:66256961-66421506 (Clone quality: bT149L18 on chr=10; Num_of_Contigs=4; )
PCTK2		location ⇒	10:66345668-66346483		CT956084,PigE-149L18,10:66256961-66421506 (Clone quality: bT149L18 on chr=10; 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, 1401-1450, 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).