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)

POPDC2		ENSSSCG00000011894	13:105363332-105382558		CU607003,CH242-303J2,13:105344285-105449516 (Clone quality: bE303J2 on chr=13; Num_of_Contigs=5; )
POPDC3		ENSSSCG00000004367	1:74921091-74940466
POSTN		ENSSSCG00000009361	11:12850024-12883428	CT476832,XX-BE284E13,11:12812461-12993238 (No clone quality info on bE284E13)
POSTN		location ⇒	11:12850549-12850157	CT476832,XX-BE284E13,11:12812461-12993238 (No clone quality info on bE284E13)
POSTN		location ⇒	11:12866003-12865869	CT476832,XX-BE284E13,11:12812461-12993238 (No clone quality info on bE284E13)
POSTN		location ⇒	11:12867595-12867459	CT476832,XX-BE284E13,11:12812461-12993238 (No clone quality info on bE284E13)
POSTN		location ⇒	11:12868933-12868783	CT476832,XX-BE284E13,11:12812461-12993238 (No clone quality info on bE284E13)
POT1		ENSSSCG00000016597	18:21034427-21172396
POU1F1		ENSSSCG00000011996	13:123180720-123196835		CU633644,CH242-171D11,13:123151316-123247028 (Clone quality: bE171D11 on chr=13; Num_of_Contigs=4; )
POU1F1		location ⇒	13:123180714-123180977		CU633644,CH242-171D11,13:123151316-123247028 (Clone quality: bE171D11 on chr=13; Num_of_Contigs=4; )
POU1F1		location ⇒	13:123192179-123192393		CU633644,CH242-171D11,13:123151316-123247028 (Clone quality: bE171D11 on chr=13; Num_of_Contigs=4; )
POU1F1		location ⇒	13:123195243-123195299		CU633644,CH242-171D11,13:123151316-123247028 (Clone quality: bE171D11 on chr=13; Num_of_Contigs=4; )
POU1F1		location ⇒	13:123196100-123196331		CU633644,CH242-171D11,13:123151316-123247028 (Clone quality: bE171D11 on chr=13; Num_of_Contigs=4; )
POU2AF1		ENSSSCG00000015016	9:37982388-37983385		CU856590,CH242-307A12,9:37981605-37996929 (Clone quality: bE307A12 on chr=9; Num_of_Contigs=14; )
POU2AF1		location ⇒	9:117125583-117125644		CU570827,CH242-238C10,9:117082384-117181431 (Clone quality: bE238C10 on chr=9; Num_of_Contigs=5; )
POU2AF1		location ⇒	9:37982654-37982388		CU856590,CH242-307A12,9:37981605-37996929 (Clone quality: bE307A12 on chr=9; Num_of_Contigs=14; )
POU2AF1		location ⇒	9:37983381-37983248		CU856590,CH242-307A12,9:37981605-37996929 (Clone quality: bE307A12 on chr=9; Num_of_Contigs=14; )
POU2AF1		location ⇒	9:38156842-38157303		CU856590,CH242-307A12,9:38155206-38161162 (Clone quality: bE307A12 on chr=9; Num_of_Contigs=14; )
POU2F1		ENSSSCG00000006310	4:86901332-87080880
POU2F1		location ⇒	4:86901904-86901348	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
POU2F1		location ⇒	4:86905291-86904943	CU151848,CH242-192N14,4:86700413-86905931 (Clone quality: bE192N14 on chr=4; Num_of_Contigs=2; )
POU2F1		location ⇒	4:86925938-86925755		CU393593,CH242-337J23,4:86905932-87049355 (Clone quality: bE337J23 on chr=4; Num_of_Contigs=1; )
POU2F1		location ⇒	4:86945554-86945364		CU393593,CH242-337J23,4:86905932-87049355 (Clone quality: bE337J23 on chr=4; Num_of_Contigs=1; )
POU2F2		location ⇒	6:34562902-34562822		FP102936,CH242-6G6,6:34562312-34565382 (Clone quality: bE6G6 on chr=6; Num_of_Contigs=31; )
POU2F2		location ⇒	6:34563026-34562944		FP102936,CH242-6G6,6:34562312-34565382 (Clone quality: bE6G6 on chr=6; Num_of_Contigs=31; )
POU2F2		location ⇒	6:63603218-63603161	CR956424,PigE-234J24,6:63579214-63695944 (No clone quality info on bT234J24)
POU2F2		location ⇒	6:63709641-63709698		FP102603,CH242-181G10,6:63708865-63716089 (Clone quality: bE181G10 on chr=6; Num_of_Contigs=12; )
POU3F1		ENSSSCG00000003646	6:63602998-63604350	CR956424,PigE-234J24,6:63579214-63695944 (No clone quality info on bT234J24)
POU3F1		location ⇒	6:63601454-63601567	CR956424,PigE-234J24,6:63579214-63695944 (No clone quality info on bT234J24)
POU3F1		location ⇒	6:63601622-63602074	CR956424,PigE-234J24,6:63579214-63695944 (No clone quality info on bT234J24)
POU3F1		location ⇒	6:63711236-63710784		FP102603,CH242-181G10,6:63708865-63716089 (Clone quality: bE181G10 on chr=6; Num_of_Contigs=12; )
POU3F1		location ⇒	6:63711404-63711291		FP102603,CH242-181G10,6:63708865-63716089 (Clone quality: bE181G10 on chr=6; Num_of_Contigs=12; )
POU3F2		ENSSSCG00000004346	1:69227153-69228481		CU210878,CH242-212K4,1:69227011-69237774 (Clone quality: bE212K4 on chr=1; Num_of_Contigs=4; )
POU3F3		location ⇒	1:69227813-69227741		CU210878,CH242-212K4,1:69227011-69237774 (Clone quality: bE212K4 on chr=1; Num_of_Contigs=4; )
POU3F3		location ⇒	1:69228609-69227927		CU210878,CH242-212K4,1:69227011-69237774 (Clone quality: bE212K4 on chr=1; Num_of_Contigs=4; )
POU3F4		ENSSSCG00000012454	X:65918824-65919909	CU570742,CH242-347F19,X:65773938-65937119 (Clone quality: bE347F19 on chr=X; Num_of_Contigs=2; )
POU4F2		ENSSSCG00000009034	8:70669364-70670341		CU861643,CH242-82F18,8:70668976-70728788 (Clone quality: bE82F18 on chr=8; Num_of_Contigs=9; )
POU4F3		ENSSSCG00000014412	2:133822190-133823522		FP236569,CH242-244C12,2:133816282-133826039 (Clone quality: bE244C12 on chr=2; Num_of_Contigs=5; )
POU5F1		ENSSSCG00000001393	7:27522888-27528681	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
POU6F1		ENSSSCG00000000220	5:15176248-15197625
POU6F2		ENSSSCG00000016770	18:53342179-53395054
PPA1		ENSSSCG00000010261	14:76072390-76091726		CU468481,CH242-304F15,14:76046170-76093978 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
PPA1		location ⇒	14:76072734-76072676		CU468481,CH242-304F15,14:76046170-76093978 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
PPA1		location ⇒	14:76074497-76074427		CU468481,CH242-304F15,14:76046170-76093978 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
PPA1		location ⇒	14:76089609-76089488		CU468481,CH242-304F15,14:76046170-76093978 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
PPA1		location ⇒	14:76091565-76091510		CU468481,CH242-304F15,14:76046170-76093978 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
PPAP2A		ENSSSCG00000016912	16:32232371-32330560
PPAP2B		ENSSSCG00000003839	6:110702440-110780173
PPAP2C		ENSSSCG00000014004	2:67170969-67182491	CU984591,CH242-288L4,2:67138955-67197804 (Clone quality: bE288L4 on chr=2; Num_of_Contigs=6; )
PPAPDC1A		ENSSSCG00000010691	14:136290730-136440683

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).