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)

PATZ1		ENSSSCG00000010027	14:48961261-48978020
PAWR		ENSSSCG00000000947	5:96160284-96205182
PAX2		ENSSSCG00000010557	14:116881618-116903070		CT737251,CH242-61D9,14:116829687-116905803 (Clone quality: bE61D9 on chr=14; Num_of_Contigs=5; )
PAX3		ENSSSCG00000016229	15:115564634-115567687		CU469322,CH242-212J4,15:115564264-115568806 (Clone quality: bE212J4 on chr=15; Num_of_Contigs=23; )
PAX3		location ⇒	15:115603122-115602996		CU469322,CH242-212J4,15:115602697-115609515 (Clone quality: bE212J4 on chr=15; Num_of_Contigs=23; )
PAX4		ENSSSCG00000016591	18:18800949-18805170		CU861978,CH242-2M6,18:18763764-18883603 (Clone quality: bE2M6 on chr=18; Num_of_Contigs=4; )
PAX5		ENSSSCG00000005345	1:248884989-249152155
PAX5		location ⇒	1:1776883-1776794		FP085422,CH242-242M8,1:1773943-1812577 (Clone quality: bE242M8 on chr=1; Num_of_Contigs=3; )
PAX5		location ⇒	1:1869185-1869274		FP015881,CH242-116L21,1:1862551-1871755 (Clone quality: bE116L21 on chr=1; Num_of_Contigs=12; )
PAX5		location ⇒	1:2216103-2216010		FP102285,CH242-108O7,1:2191552-2223629 (Clone quality: bE108O7 on chr=1; Num_of_Contigs=12; )
PAX5		location ⇒	1:2591798-2591887		FP089482,CH242-213J15,1:2579035-2630305 (Clone quality: bE213J15 on chr=1; Num_of_Contigs=5; )
PAX6		ENSSSCG00000013320	2:26933326-26955190
PAX7		location ⇒	15:115567612-115567447		CU469322,CH242-212J4,15:115564264-115568806 (Clone quality: bE212J4 on chr=15; Num_of_Contigs=23; )
PAX9		ENSSSCG00000001943	7:69403390-69416839
PB1_PIG		ENSSSCG00000003053	6:34884420-34886452		FP102750,CH242-80G20,6:34865935-34887494 (Clone quality: bE80G20 on chr=6; Num_of_Contigs=9; )
PBD-4		location ⇒	7:51216948-51216629		CU041392,CH242-299J7,7:51188966-51286068 (Clone quality: bE299J7 on chr=7; Num_of_Contigs=2; )
PBD-4		location ⇒	7:51221244-51221164		CU041392,CH242-299J7,7:51188966-51286068 (Clone quality: bE299J7 on chr=7; Num_of_Contigs=2; )
PBEF1		location ⇒	9:99199765-99199153		CU914712,CH242-32M2,9:99079483-99256886 (Clone quality: bE32M2 on chr=9; Num_of_Contigs=2; )
PBEF1		location ⇒	9:99215253-99215024		CU914712,CH242-32M2,9:99079483-99256886 (Clone quality: bE32M2 on chr=9; Num_of_Contigs=2; )
PBEF1		location ⇒	9:99220813-99220653		CU914712,CH242-32M2,9:99079483-99256886 (Clone quality: bE32M2 on chr=9; Num_of_Contigs=2; )
PBEF1		location ⇒	9:99230473-99230312		CU914712,CH242-32M2,9:99079483-99256886 (Clone quality: bE32M2 on chr=9; Num_of_Contigs=2; )
PBK		ENSSSCG00000009671	14:11573505-11578813		CU656007,CH242-32D13,14:11512232-11583414 (Clone quality: bE32D13 on chr=14; Num_of_Contigs=2; )
PBRM1		ENSSSCG00000011445	13:29300894-29388582
PBX1		ENSSSCG00000000881	5:80003131-80017378
PBX1		ENSSSCG00000006331	4:89472001-89943215
PBX1		location ⇒	4:89472487-89472273	CU462949,CH242-344D21,4:89403101-89565703 (Clone quality: bE344D21 on chr=4; Num_of_Contigs=1; )
PBX1		location ⇒	4:89500791-89500676	CU462949,CH242-344D21,4:89403101-89565703 (Clone quality: bE344D21 on chr=4; Num_of_Contigs=1; )
PBX1		location ⇒	4:89508379-89508215	CU462949,CH242-344D21,4:89403101-89565703 (Clone quality: bE344D21 on chr=4; Num_of_Contigs=1; )
PBX1		location ⇒	4:89513603-89513475	CU462949,CH242-344D21,4:89403101-89565703 (Clone quality: bE344D21 on chr=4; Num_of_Contigs=1; )
PBX2		ENSSSCG00000001438	7:28060959-28066345	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
PBX3		ENSSSCG00000005604	1:281081050-281136530		CU582819,CH242-6D18,1:280969881-281144863 (Clone quality: bE6D18 on chr=1; Num_of_Contigs=1; )
PBX3		location ⇒	1:281081049-281081293		CU582819,CH242-6D18,1:280969881-281144863 (Clone quality: bE6D18 on chr=1; Num_of_Contigs=1; )
PBX3		location ⇒	1:281094362-281094556		CU582819,CH242-6D18,1:280969881-281144863 (Clone quality: bE6D18 on chr=1; Num_of_Contigs=1; )
PBX3		location ⇒	1:281101861-281102001		CU582819,CH242-6D18,1:280969881-281144863 (Clone quality: bE6D18 on chr=1; Num_of_Contigs=1; )
PBX4		ENSSSCG00000013933	2:63443777-63452452		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
PBX4		location ⇒	2:63443875-63444035		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
PBX4		location ⇒	2:63444309-63444503		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
PBX4		location ⇒	2:63444747-63444886		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
PBX4		location ⇒	2:63452135-63452361		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
PBXIP1		ENSSSCG00000006536	4:98883525-98886001		CU207227,CH242-365J2,4:98865848-98886544 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
PBXIP1		location ⇒	4:98885218-98884696		CU207227,CH242-365J2,4:98865848-98886544 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
PC		ENSSSCG00000012926	2:3943363-3948616		FP089559,CH242-217L14,2:3940112-3995454 (Clone quality: bE217L14 on chr=2; Num_of_Contigs=11; )
PCBD1		ENSSSCG00000010275	14:76952143-76958632	CT737289,CH242-133B3,14:76783692-76995335 (Clone quality: bE133B3 on chr=14; Num_of_Contigs=4; )
PCCA		ENSSSCG00000009522	11:69981944-70161872
PCCB		ENSSSCG00000011651	13:63348974-63383844
PCDH12		ENSSSCG00000014395	2:130462272-130474962		FP102264,CH242-59H11,2:130351429-130495395 (Clone quality: bE59H11 on chr=2; Num_of_Contigs=3; )
PCDH12		location ⇒	2:130461955-130462494		FP102264,CH242-59H11,2:130351429-130495395 (Clone quality: bE59H11 on chr=2; Num_of_Contigs=3; )
PCDH15		ENSSSCG00000010426	14:100197944-100670231
PCDH15		location ⇒	14:100638747-100638923	CT737214,CH242-116N18,14:100458229-100652258 (Clone quality: bE116N18 on chr=14; Num_of_Contigs=1; )
PCDH15		location ⇒	14:100644973-100645193	CT737214,CH242-116N18,14:100458229-100652258 (Clone quality: bE116N18 on chr=14; Num_of_Contigs=1; )

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).