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)

AP1B1		ENSSSCG00000009978	14:47023885-47074199
AP1G1		ENSSSCG00000002740	6:10438865-10492307
AP1G1		location ⇒	6:10468832-10468887		CU467029,CH242-364E21,6:10448098-10471846 (Clone quality: bE364E21 on chr=6; Num_of_Contigs=16; )
AP1G1		location ⇒	6:10473906-10473961		CU467029,CH242-364E21,6:10471947-10473967 (Clone quality: bE364E21 on chr=6; Num_of_Contigs=16; )
AP1G1		location ⇒	6:10491716-10492784		CU467029,CH242-364E21,6:10474068-10508834 (Clone quality: bE364E21 on chr=6; Num_of_Contigs=16; )
AP1G1		location ⇒	6:10495497-10495868		CU467029,CH242-364E21,6:10474068-10508834 (Clone quality: bE364E21 on chr=6; Num_of_Contigs=16; )
AP1G2		ENSSSCG00000002015	7:81868597-81883284
AP1M1		ENSSSCG00000013856	2:60744351-60773736		CU463900,CH242-7B6,2:60719428-60778346 (Clone quality: bE7B6 on chr=2; Num_of_Contigs=11; )
AP1M2		ENSSSCG00000013636	2:52786185-52792362
AP1S2		ENSSSCG00000012142	X:11869330-11897792
AP2		ENSSSCG00000012836	2:43742-73952
AP2		ENSSSCG00000017712	12:37605804-37730282
AP2		ENSSSCG00000009305	11:3974744-3981791
AP2		ENSSSCG00000008337	3:66805405-66889135
AP2		ENSSSCG00000001922	7:65974641-66013214		CU571030,CH242-26L13,7:65973790-66032617 (Clone quality: bE26L13 on chr=7; Num_of_Contigs=6; )
AP2		ENSSSCG00000001744	7:51793918-51856199	CT961054,CH242-15K4,7:51679957-51884764 (Clone quality: bE15K4 on chr=7; Num_of_Contigs=1; )
AP2		ENSSSCG00000001036	7:7630425-7648184
AP2		ENSSSCG00000003199	6:38543474-38579195
AP2		location ⇒	7:51829771-51829823	CT961054,CH242-15K4,7:51679957-51884764 (Clone quality: bE15K4 on chr=7; Num_of_Contigs=1; )
AP2A1		ENSSSCG00000003199	6:38543474-38579195
AP2A2		ENSSSCG00000012836	2:43742-73952
AP2B1		ENSSSCG00000017712	12:37605804-37730282
AP2S1		ENSSSCG00000003106	6:36435638-36443262		FP102520,CH242-105K10,6:36431480-36450414 (Clone quality: bE105K10 on chr=6; Num_of_Contigs=11; )
AP3B1		ENSSSCG00000014101	2:75875882-76143669
AP3B2		ENSSSCG00000001807	7:58299532-58336612
AP3M1		ENSSSCG00000010314	14:80116662-80137469
AP3M2		ENSSSCG00000007033	17:11951912-11971899		CU855981,CH242-160M5,17:11940558-11980196 (Clone quality: bE160M5 on chr=17; Num_of_Contigs=14; )
AP4B1		ENSSSCG00000006762	4:111013294-111024217		CU651648,CH242-226J22,4:110972280-111079200 (Clone quality: bE226J22 on chr=4; Num_of_Contigs=4; )
AP4E1		ENSSSCG00000004634	1:125845814-125908478
AP4S1		ENSSSCG00000001972	7:74812416-74833645		CT967321,CH242-123A22,7:74790958-74854829 (Clone quality: bE123A22 on chr=7; Num_of_Contigs=3; )
APAF1		ENSSSCG00000014561	2:139895169-139900818		CU928488,CH242-163I11,2:139819049-139956868 (Clone quality: bE163I11 on chr=2; Num_of_Contigs=2; )
APAF1		ENSSSCG00000003312	6:41801395-41870667
APAF1		ENSSSCG00000000884	5:80665781-80772954
APAF1		ENSSSCG00000013940	2:63853146-63860552		CU694944,CH242-8E21,2:63851105-63883829 (Clone quality: bE8E21 on chr=2; Num_of_Contigs=5; )
APAF1		ENSSSCG00000013299	2:24519570-24540119	CU914647,CH242-254M19,2:24500034-24689730 (Clone quality: bE254M19 on chr=2; Num_of_Contigs=3; )
APAF1		ENSSSCG00000003314	6:41912292-41914574		FP236123,CH242-107C1,6:41907891-41917012 (Clone quality: bE107C1 on chr=6; Num_of_Contigs=14; )
APAF1		location ⇒	5:80717261-80717023		CU633605,CH242-89H11,5:80709247-80717579 (Clone quality: bE89H11 on chr=5; Num_of_Contigs=8; )
APAF1		location ⇒	5:80754375-80754137		FP102239,CH242-207O15,5:80752195-80758470 (Clone quality: bE207O15 on chr=5; Num_of_Contigs=5; )
APAF1		location ⇒	5:81985161-81985106		FP102267,CH242-81I11,5:81855271-82016430 (Clone quality: bE81I11 on chr=5; Num_of_Contigs=1; )
APAF1		location ⇒	5:82105593-82105538		CU457471,CH242-277A17,5:82103159-82108485 (Clone quality: bE277A17 on chr=5; Num_of_Contigs=4; )
APBA1		ENSSSCG00000005250	1:233074242-233150277
APBA1		location ⇒	1:233104837-233104690		CU407274,CH242-482L1,1:232970429-233107951 (Clone quality: bE482L1 on chr=1; Num_of_Contigs=3; )
APBA1		location ⇒	1:233113241-233113146		CU062599,CH242-81D19,1:233107952-233134399 (Clone quality: bE81D19 on chr=1; Num_of_Contigs=3; )
APBA1		location ⇒	1:233149273-233149078		CU062599,CH242-81D19,1:233134500-233190983 (Clone quality: bE81D19 on chr=1; Num_of_Contigs=3; )
APBA2		ENSSSCG00000004851	1:152027161-152042692
APBA2		ENSSSCG00000004849	1:151915124-151983488
APBA2		location ⇒	1:151915306-151915127		CU861945,CH242-211I22,1:151914373-151917206 (Clone quality: bE211I22 on chr=1; Num_of_Contigs=9; )
APBA3		ENSSSCG00000013492	2:48258231-48266210		FP102497,CH242-307J7,2:48199823-48346436 (Clone quality: bE307J7 on chr=2; Num_of_Contigs=2; )
APBB1		ENSSSCG00000014628	9:2615634-2627370
APBB2		ENSSSCG00000008797	8:27241641-27242636		CU407111,CH242-192B10,8:27130213-27281684 (Clone quality: bE192B10 on chr=8; Num_of_Contigs=2; )

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, 1751-32

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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).