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)

PGM2		ENSSSCG00000008773	8:24716205-24750431		FP016170,CH242-4M13,8:24709586-24766045 (Clone quality: bE4M13 on chr=8; Num_of_Contigs=8; )
PGM2L1		ENSSSCG00000014838	9:8322237-8391108		CU928090,CH242-136E14,9:8299567-8413046 (Clone quality: bE136E14 on chr=9; Num_of_Contigs=5; )
PGM3		ENSSSCG00000004456	1:87217538-87240764
PGM5		ENSSSCG00000005243	1:231945283-232031804
PGM5		location ⇒	1:232015430-232015243		CU928820,CH242-265K10,1:232003245-232047656 (Clone quality: bE265K10 on chr=1; Num_of_Contigs=5; )
PGM5		location ⇒	1:232160494-232160307		CU896594,CH242-392F14,1:232150410-232177717 (Clone quality: bE392F14 on chr=1; Num_of_Contigs=9; )
PGM5		location ⇒	1:232176863-232176725		CU896594,CH242-392F14,1:232150410-232177717 (Clone quality: bE392F14 on chr=1; Num_of_Contigs=9; )
PGM5		location ⇒	1:232214060-232213878		CU896594,CH242-392F14,1:232177818-232233439 (Clone quality: bE392F14 on chr=1; Num_of_Contigs=9; )
PGP		ENSSSCG00000008046	3:36571012-36572092		FP102909,CH242-324F20,3:36570133-36575737 (Clone quality: bE324F20 on chr=3; Num_of_Contigs=11; )
PGR		ENSSSCG00000014977	9:31935591-32027633
PGRMC1		ENSSSCG00000012625	X:96829528-96837569		FP245395,CH242-121G9,X:96820741-96846531 (Clone quality: bE121G9 on chr=X; Num_of_Contigs=4; )
PGRMC2		ENSSSCG00000009072	8:83255186-83272589
PGRMC2		location ⇒	8:83255208-83255298		CU928714,CH242-113P6,8:83224493-83256262 (Clone quality: bE113P6 on chr=8; Num_of_Contigs=4; )
PGRMC2		location ⇒	8:83255473-83255628		CU928714,CH242-113P6,8:83224493-83256262 (Clone quality: bE113P6 on chr=8; Num_of_Contigs=4; )
PGRMC2		location ⇒	8:83269336-83269492		CU640884,CH242-226K22,8:83256263-83282612 (Clone quality: bE226K22 on chr=8; Num_of_Contigs=10; )
PGRMC2		location ⇒	8:83271349-83271725		CU640884,CH242-226K22,8:83256263-83282612 (Clone quality: bE226K22 on chr=8; Num_of_Contigs=10; )
PHACTR1		ENSSSCG00000001052	7:9741648-9833750	CU407000,CH242-288B3,7:9672602-9855229 (Clone quality: bE288B3 on chr=7; Num_of_Contigs=1; )
PHACTR2		ENSSSCG00000004132	1:22569930-22640591
PHACTR3		ENSSSCG00000007528	17:62243186-62480144
PHAX		ENSSSCG00000014244	2:117308145-117318111		CU929657,CH242-507N1,2:117296080-117327134 (Clone quality: bE507N1 on chr=2; Num_of_Contigs=11; )
PHAX		location ⇒	2:117309834-117310395		CU929657,CH242-507N1,2:117296080-117327134 (Clone quality: bE507N1 on chr=2; Num_of_Contigs=11; )
PHAX		location ⇒	2:117313615-117313738		CU929657,CH242-507N1,2:117296080-117327134 (Clone quality: bE507N1 on chr=2; Num_of_Contigs=11; )
PHAX		location ⇒	2:117317604-117317883		CU929657,CH242-507N1,2:117296080-117327134 (Clone quality: bE507N1 on chr=2; Num_of_Contigs=11; )
PHAX		location ⇒	2:117318051-117318118		CU929657,CH242-507N1,2:117296080-117327134 (Clone quality: bE507N1 on chr=2; Num_of_Contigs=11; )
PHB		ENSSSCG00000017549	12:23036468-23049966
PHB		ENSSSCG00000009238	8:116245643-116265218
PHB		location ⇒	12:22743860-22742757		FP089505,CH242-505B8,12:22730721-22753703 (Clone quality: bE505B8 on chr=12; Num_of_Contigs=9; )
PHB		location ⇒	12:22752043-22751881		FP089505,CH242-505B8,12:22730721-22753703 (Clone quality: bE505B8 on chr=12; Num_of_Contigs=9; )
PHB		location ⇒	12:23040327-23040489		FP015993,CH242-478C13,12:23006539-23042574 (Clone quality: bE478C13 on chr=12; Num_of_Contigs=11; )
PHB		location ⇒	12:23049481-23050584		FP015993,CH242-478C13,12:23046451-23076096 (Clone quality: bE478C13 on chr=12; Num_of_Contigs=11; )
PHEX		ENSSSCG00000012167	X:16927787-17142215
PHF1		ENSSSCG00000001511	7:34122031-34127370	CU498854,CH242-216B14,7:34116847-34138577 (Clone quality: bE216B14 on chr=7; Num_of_Contigs=6; )
PHF11		ENSSSCG00000009396	11:18194315-18241044
PHF12		ENSSSCG00000017779	12:42860412-42903417
PHF14		ENSSSCG00000015349	9:75690930-75793821
PHF15		ENSSSCG00000014303	2:124541326-124575451
PHF16		ENSSSCG00000012267	X:41628945-41689390		FP015845,CH242-82O13,X:41557134-41706425 (Clone quality: bE82O13 on chr=X; Num_of_Contigs=2; )
PHF17		ENSSSCG00000009071	8:82760167-82817405
PHF19		ENSSSCG00000005510	1:274502145-274510098		CU466455,CH242-242H3,1:274500310-274512991 (Clone quality: bE242H3 on chr=1; Num_of_Contigs=15; )
PHF2		ENSSSCG00000008080	3:38133249-38161237
PHF20		ENSSSCG00000007311	17:41315754-41385404
PHF20L1		ENSSSCG00000005950	4:7375526-7414051		CU466322,CH242-207J24,4:7329244-7446694 (Clone quality: bE207J24 on chr=4; Num_of_Contigs=7; )
PHF21A		ENSSSCG00000013264	2:14569968-14840508
PHF21B		ENSSSCG00000000020	5:1072079-1102094		CU633627,CH242-122C3,5:1025372-1174052 (Clone quality: bE122C3 on chr=5; Num_of_Contigs=4; )
PHF23		ENSSSCG00000017937	12:49759396-49761426		CU681851,CH242-516E15,12:49759171-49766738 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
PHF3		ENSSSCG00000004267	1:47348386-47379288
PHF6		ENSSSCG00000012682	X:108347742-108398259
PHF6		location ⇒	X:108382897-108382948		CU468475,CH242-274C3,X:108371119-108420183 (Clone quality: bE274C3 on chr=X; Num_of_Contigs=6; )
PHF6		location ⇒	X:108398539-108399438		CU468475,CH242-274C3,X:108371119-108420183 (Clone quality: bE274C3 on chr=X; Num_of_Contigs=6; )
PHF6		location ⇒	X:108399532-108400999		CU468475,CH242-274C3,X:108371119-108420183 (Clone quality: bE274C3 on chr=X; Num_of_Contigs=6; )

Go to records:
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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).