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)

CRHR1		ENSSSCG00000017313	12:15222412-15275558		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRHR1		location ⇒	12:15222490-15222612		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRHR1		location ⇒	12:15222665-15222753		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRHR1		location ⇒	12:15255292-15255412		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRHR1		location ⇒	12:15261213-15261288		CU929493,CH242-263L7,12:15220972-15314231 (Clone quality: bE263L7 on chr=12; Num_of_Contigs=5; )
CRHR2		ENSSSCG00000016675	18:40664309-40683406
CRIM1		ENSSSCG00000008504	3:97029493-97111939
CRIP1		ENSSSCG00000004609	1:121067415-121067645		CU570857,CH242-45M3,1:121035192-121118131 (Clone quality: bE45M3 on chr=1; Num_of_Contigs=5; )
CRIP1		ENSSSCG00000008349	3:67914323-67938436
CRIP3		ENSSSCG00000001666	7:44182155-44184652	CR974479,PigE-150P18,7:44038129-44188858 (Clone quality: bT150P18 on chr=7; Num_of_Contigs=4; )
CRIPT		ENSSSCG00000008438	3:87326373-87332508		CU855724,CH242-31C18,3:87289676-87333438 (Clone quality: bE31C18 on chr=3; Num_of_Contigs=5; )
CRISP1		ENSSSCG00000001739	7:51082166-51110416		CT757477,CH242-199E6,7:51040368-51150414 (Clone quality: bE199E6 on chr=7; Num_of_Contigs=1; )
CRISP1		location ⇒	7:51088991-51088882		CT757477,CH242-199E6,7:51040368-51150414 (Clone quality: bE199E6 on chr=7; Num_of_Contigs=1; )
CRISP1		location ⇒	7:51090249-51090165		CT757477,CH242-199E6,7:51040368-51150414 (Clone quality: bE199E6 on chr=7; Num_of_Contigs=1; )
CRISP1		location ⇒	7:51095679-51095626		CT757477,CH242-199E6,7:51040368-51150414 (Clone quality: bE199E6 on chr=7; Num_of_Contigs=1; )
CRISP2		ENSSSCG00000001736	7:50949716-50969586		CU655813,CH242-388J22,7:50876348-50973828 (Clone quality: bE388J22 on chr=7; Num_of_Contigs=3; )
CRISP3		ENSSSCG00000001737	7:50977103-50982725		CT757477,CH242-199E6,7:50973829-51040267 (Clone quality: bE199E6 on chr=7; Num_of_Contigs=1; )
CRISP3		location ⇒	7:50950306-50950124		CU655813,CH242-388J22,7:50876348-50973828 (Clone quality: bE388J22 on chr=7; Num_of_Contigs=3; )
CRISP3		location ⇒	7:50955620-50955521		CU655813,CH242-388J22,7:50876348-50973828 (Clone quality: bE388J22 on chr=7; Num_of_Contigs=3; )
CRISP3		location ⇒	7:50956379-50956234		CU655813,CH242-388J22,7:50876348-50973828 (Clone quality: bE388J22 on chr=7; Num_of_Contigs=3; )
CRISP3		location ⇒	7:50982735-50982639		CT757477,CH242-199E6,7:50973829-51040267 (Clone quality: bE199E6 on chr=7; Num_of_Contigs=1; )
CRISPLD1		ENSSSCG00000006171	4:63074087-63122685		CU467056,CH242-246D24,4:63048115-63176081 (Clone quality: bE246D24 on chr=4; Num_of_Contigs=2; )
CRISPLD2		ENSSSCG00000002669	6:2460526-2488611
CRKL		ENSSSCG00000010095	14:51625285-51651739		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
CRKL		location ⇒	14:51625752-51625372		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
CRKL		location ⇒	14:51637433-51637107		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
CRKRS		ENSSSCG00000017504	12:20737886-20792069
CRLF1		ENSSSCG00000013909	2:62555575-62559137		FP102402,CH242-83K20,2:62552912-62559166 (Clone quality: bE83K20 on chr=2; Num_of_Contigs=3; )
CRLF1		location ⇒	2:62559136-62558966		FP102402,CH242-83K20,2:62552912-62559166 (Clone quality: bE83K20 on chr=2; Num_of_Contigs=3; )
CRLF3		ENSSSCG00000017743	12:40737406-40763580		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
CRLF3		location ⇒	12:40659745-40659536		CU915522,CH242-75P19,12:40629158-40664039 (Clone quality: bE75P19 on chr=12; Num_of_Contigs=8; )
CRLF3		location ⇒	12:40660990-40659769		CU915522,CH242-75P19,12:40629158-40664039 (Clone quality: bE75P19 on chr=12; Num_of_Contigs=8; )
CRLF3		location ⇒	12:40763066-40764287		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
CRLF3		location ⇒	12:40764311-40764520		FP089481,CH242-212P22,12:40732922-40899579 (Clone quality: bE212P22 on chr=12; Num_of_Contigs=1; )
CRLS1		ENSSSCG00000007048	17:14003758-14034942
CRMP1		ENSSSCG00000008708	8:2086410-2099065
CRNKL1		ENSSSCG00000007102	17:29013875-29084128
CRNN		ENSSSCG00000006604	4:100792229-100797178	CU076058,CH242-126J8,4:100634937-100826648 (Clone quality: bE126J8 on chr=4; Num_of_Contigs=7; )
CROCC		ENSSSCG00000003478	6:52027411-52073582
CROT		ENSSSCG00000015391	9:86944447-86988993		CU915624,CH242-101D9,9:86873884-86992742 (Clone quality: bE101D9 on chr=9; Num_of_Contigs=2; )
CROT		location ⇒	9:86985418-86985341		CU915624,CH242-101D9,9:86873884-86992742 (Clone quality: bE101D9 on chr=9; Num_of_Contigs=2; )
CRP		ENSSSCG00000006403	4:94315127-94322791		CU302295,CH242-214I7,4:94228857-94322950 (Clone quality: bE214I7 on chr=4; Num_of_Contigs=4; )
CRP		location ⇒	4:2800262-2800189		CU179737,CH242-191A9,4:2742906-2877084 (Clone quality: bE191A9 on chr=4; Num_of_Contigs=2; )
CRP		location ⇒	4:3036284-3036401		CU861599,CH242-1G3,4:2882085-3037908 (Clone quality: bE1G3 on chr=4; Num_of_Contigs=2; )
CRP		location ⇒	4:3100634-3100739		CU550666,CH242-232I20,4:3099747-3243509 (Clone quality: bE232I20 on chr=4; Num_of_Contigs=3; )
CRP		location ⇒	4:4493834-4493717		CU686708,CH242-202I13,4:4468138-4544716 (Clone quality: bE202I13 on chr=4; Num_of_Contigs=4; )
CRSP		ENSSSCG00000004196	1:33301523-33339032		CU633754,CH242-254O2,1:33299154-33340304 (Clone quality: bE254O2 on chr=1; Num_of_Contigs=9; )
CRSP		ENSSSCG00000005720	1:287164826-287368710
CRSP		ENSSSCG00000013386	2:41163705-41168787		CU928260,CH242-273B21,2:41162604-41257476 (Clone quality: bE273B21 on chr=2; Num_of_Contigs=3; )
CRSP		ENSSSCG00000014949	9:26566364-26588641		CU464153,CH242-27K5,9:26560904-26638658 (Clone quality: bE27K5 on chr=9; 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, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).