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)

CLCN6		ENSSSCG00000003429	6:48754476-48785463		CU695168,CH242-2E14,6:48744157-48789117 (Clone quality: bE2E14 on chr=6; Num_of_Contigs=4; )
CLCN7		ENSSSCG00000008024	3:36088238-36109007		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
CLCNKA		location ⇒	6:51591079-51591167		FP103064,CH242-117J7,6:51590844-51611098 (Clone quality: bE117J7 on chr=6; Num_of_Contigs=6; )
CLCNKA		location ⇒	6:51591085-51591167		FP103064,CH242-117J7,6:51590844-51611098 (Clone quality: bE117J7 on chr=6; Num_of_Contigs=6; )
CLCNKA		location ⇒	6:51592426-51592516		FP103064,CH242-117J7,6:51590844-51611098 (Clone quality: bE117J7 on chr=6; Num_of_Contigs=6; )
CLDN1		location ⇒	8:80587854-80588154		CU914180,CH242-177J9,8:80577781-80599482 (Clone quality: bE177J9 on chr=8; Num_of_Contigs=7; )
CLDN10		ENSSSCG00000009500	11:65908586-65930973		CT971578,CH242-277H1,11:65901467-65931486 (Clone quality: bE277H1 on chr=11; Num_of_Contigs=5; )
CLDN10		location ⇒	11:65908645-65908887		CT971578,CH242-277H1,11:65901467-65931486 (Clone quality: bE277H1 on chr=11; Num_of_Contigs=5; )
CLDN10		location ⇒	11:65915397-65915560		CT971578,CH242-277H1,11:65901467-65931486 (Clone quality: bE277H1 on chr=11; Num_of_Contigs=5; )
CLDN10		location ⇒	11:65915646-65915711		CT971578,CH242-277H1,11:65901467-65931486 (Clone quality: bE277H1 on chr=11; Num_of_Contigs=5; )
CLDN10		location ⇒	11:65930862-65930969		CT971578,CH242-277H1,11:65901467-65931486 (Clone quality: bE277H1 on chr=11; Num_of_Contigs=5; )
CLDN11		ENSSSCG00000011747	13:83118367-83132179		CU928383,CH242-276A6,13:83083702-83144614 (Clone quality: bE276A6 on chr=13; Num_of_Contigs=3; )
CLDN11		location ⇒	13:83118564-83118855		CU928383,CH242-276A6,13:83083702-83144614 (Clone quality: bE276A6 on chr=13; Num_of_Contigs=3; )
CLDN11		location ⇒	13:83122183-83122348		CU928383,CH242-276A6,13:83083702-83144614 (Clone quality: bE276A6 on chr=13; Num_of_Contigs=3; )
CLDN11		location ⇒	13:83131729-83132227		CU928383,CH242-276A6,13:83083702-83144614 (Clone quality: bE276A6 on chr=13; Num_of_Contigs=3; )
CLDN11		location ⇒	13:83132275-83133186		CU928383,CH242-276A6,13:83083702-83144614 (Clone quality: bE276A6 on chr=13; Num_of_Contigs=3; )
CLDN12		ENSSSCG00000015306	9:65997122-65997856		CU927938,CH242-141B4,9:65965902-66127467 (Clone quality: bE141B4 on chr=9; Num_of_Contigs=2; )
CLDN12		location ⇒	9:65997914-65997089		CU927938,CH242-141B4,9:65965902-66127467 (Clone quality: bE141B4 on chr=9; Num_of_Contigs=2; )
CLDN14		location ⇒	13:140559236-140559908		CU638724,CH242-250N17,13:140500369-140570626 (Clone quality: bE250N17 on chr=13; Num_of_Contigs=2; )
CLDN14		location ⇒	13:140585267-140584595		CU928021,CH242-178H7,13:140575627-140587218 (Clone quality: bE178H7 on chr=13; Num_of_Contigs=3; )
CLDN17		ENSSSCG00000012031	13:137640202-137640879		CU855716,CH242-265B12,13:137593107-137722921 (Clone quality: bE265B12 on chr=13; Num_of_Contigs=4; )
CLDN18		ENSSSCG00000011657	13:64634096-64649933		CU633683,CH242-262P13,13:64625696-64724030 (Clone quality: bE262P13 on chr=13; Num_of_Contigs=2; )
CLDN18		location ⇒	13:64637816-64637669		CU633683,CH242-262P13,13:64625696-64724030 (Clone quality: bE262P13 on chr=13; Num_of_Contigs=2; )
CLDN18		location ⇒	13:64649850-64649571		CU633683,CH242-262P13,13:64625696-64724030 (Clone quality: bE262P13 on chr=13; Num_of_Contigs=2; )
CLDN2		ENSSSCG00000012554	X:85381576-85382268		FP085526,CH242-364E15,X:85378647-85389864 (Clone quality: bE364E15 on chr=X; Num_of_Contigs=12; )
CLDN2		location ⇒	X:85381414-85383919		FP085526,CH242-364E15,X:85378647-85389864 (Clone quality: bE364E15 on chr=X; Num_of_Contigs=12; )
CLDN2		location ⇒	X:85383988-85384193		FP085526,CH242-364E15,X:85378647-85389864 (Clone quality: bE364E15 on chr=X; Num_of_Contigs=12; )
CLDN20		ENSSSCG00000004067	1:12448463-12449122		CU407142,CH242-147K17,1:12392747-12483375 (Clone quality: bE147K17 on chr=1; Num_of_Contigs=2; )
CLDN20		location ⇒	1:12448463-12449121		CU407142,CH242-147K17,1:12392747-12483375 (Clone quality: bE147K17 on chr=1; Num_of_Contigs=2; )
CLDN23		ENSSSCG00000006966	17:190512-191189		CU606846,CH242-119B19,17:149649-213464 (Clone quality: bE119B19 on chr=17; Num_of_Contigs=11; )
CLDN23		location ⇒	17:190306-189511		CU606846,CH242-119B19,17:149649-213464 (Clone quality: bE119B19 on chr=17; Num_of_Contigs=11; )
CLDN25		ENSSSCG00000015051	9:40369288-40369932		CU929720,CH242-221O2,9:40363883-40373575 (Clone quality: bE221O2 on chr=9; Num_of_Contigs=7; )
CLDN3		location ⇒	3:9383489-9383382		CU915481,CH242-313A3,3:9380772-9389508 (Clone quality: bE313A3 on chr=3; Num_of_Contigs=10; )
CLDN4		ENSSSCG00000007718	3:9383007-9383636		CU915481,CH242-313A3,3:9380772-9389508 (Clone quality: bE313A3 on chr=3; Num_of_Contigs=10; )
CLDN4		location ⇒	3:9383856-9382148		CU915481,CH242-313A3,3:9380772-9389508 (Clone quality: bE313A3 on chr=3; Num_of_Contigs=10; )
CLDN5		ENSSSCG00000010123	14:52272771-52273427		CU468637,CH242-526M15,14:52233729-52290922 (Clone quality: bE526M15 on chr=14; Num_of_Contigs=13; )
CLDN5		location ⇒	14:52273530-52272180		CU468637,CH242-526M15,14:52233729-52290922 (Clone quality: bE526M15 on chr=14; Num_of_Contigs=13; )
CLDN6		location ⇒	3:9383500-9383388		CU915481,CH242-313A3,3:9380772-9389508 (Clone quality: bE313A3 on chr=3; Num_of_Contigs=10; )
CLDN7		ENSSSCG00000017934	12:49740495-49742792		CU681851,CH242-516E15,12:49735598-49749353 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
CLDN7		location ⇒	12:49740829-49741112		CU681851,CH242-516E15,12:49735598-49749353 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
CLDN7		location ⇒	12:49741948-49742115		CU681851,CH242-516E15,12:49735598-49749353 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
CLDN7		location ⇒	12:49742238-49742328		CU681851,CH242-516E15,12:49735598-49749353 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
CLDN7		location ⇒	12:49742411-49742698		CU681851,CH242-516E15,12:49735598-49749353 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
CLDN8		ENSSSCG00000012030	13:137593514-137594191		CU855716,CH242-265B12,13:137593107-137722921 (Clone quality: bE265B12 on chr=13; Num_of_Contigs=4; )
CLDN8		location ⇒	13:137593381-137594219		CU855716,CH242-265B12,13:137593107-137722921 (Clone quality: bE265B12 on chr=13; Num_of_Contigs=4; )
CLDN9		location ⇒	3:9383500-9383388		CU915481,CH242-313A3,3:9380772-9389508 (Clone quality: bE313A3 on chr=3; Num_of_Contigs=10; )
CLDND1		ENSSSCG00000011980	13:118617372-118624795		CU467089,CH242-73L22,13:118570025-118679109 (Clone quality: bE73L22 on chr=13; Num_of_Contigs=3; )
CLDND1		location ⇒	13:118617352-118617443		CU467089,CH242-73L22,13:118570025-118679109 (Clone quality: bE73L22 on chr=13; Num_of_Contigs=3; )
CLDND1		location ⇒	13:118623468-118623607		CU467089,CH242-73L22,13:118570025-118679109 (Clone quality: bE73L22 on chr=13; Num_of_Contigs=3; )
CLDND1		location ⇒	13:118623741-118623964		CU467089,CH242-73L22,13:118570025-118679109 (Clone quality: bE73L22 on chr=13; 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).