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)

CASQ1		ENSSSCG00000006390	4:93723965-93733955	CU138477,CH242-105O19,4:93708821-93889364 (Clone quality: bE105O19 on chr=4; Num_of_Contigs=5; )
CASQ2		ENSSSCG00000006745	4:109235600-109298140		CU407089,CH242-512E9,4:109180674-109298819 (Clone quality: bE512E9 on chr=4; Num_of_Contigs=2; )
CASR		ENSSSCG00000011878	13:104117834-104144972		CU694886,CH242-322E12,13:103947006-104157780 (Clone quality: bE322E12 on chr=13; Num_of_Contigs=1; )
CASS4		ENSSSCG00000007495	17:59525908-59565760	CR956640,CH242-155M9,17:59463698-59643740 (No clone quality info on bE155M9)
CAST		ENSSSCG00000014170	2:92291501-92435874
CAST		location ⇒	2:92386464-92386522		CU467752,CH242-401F7,2:92377575-92391580 (Clone quality: bE401F7 on chr=2; Num_of_Contigs=11; )
CAST		location ⇒	2:92386903-92387019		CU467752,CH242-401F7,2:92377575-92391580 (Clone quality: bE401F7 on chr=2; Num_of_Contigs=11; )
CAST		location ⇒	2:92398458-92398562		CU467752,CH242-401F7,2:92391681-92402488 (Clone quality: bE401F7 on chr=2; Num_of_Contigs=11; )
CAST		location ⇒	2:92420274-92420385		CU469214,CH242-375N8,2:92406880-92429951 (Clone quality: bE375N8 on chr=2; Num_of_Contigs=13; )
CASZ1		location ⇒	6:47689259-47688611		FP015938,CH242-383C12,6:47604393-47704550 (Clone quality: bE383C12 on chr=6; Num_of_Contigs=6; )
CASZ1		location ⇒	6:47703676-47702810		FP015938,CH242-383C12,6:47604393-47704550 (Clone quality: bE383C12 on chr=6; Num_of_Contigs=6; )
CASZ1		location ⇒	6:47726571-47727063		FP015938,CH242-383C12,6:47720743-47733513 (Clone quality: bE383C12 on chr=6; Num_of_Contigs=6; )
CASZ1		location ⇒	6:47730004-47730665		FP015938,CH242-383C12,6:47720743-47733513 (Clone quality: bE383C12 on chr=6; Num_of_Contigs=6; )
CAT		ENSSSCG00000010102	14:51729892-51989336
CAT		ENSSSCG00000000764	5:65172375-65180689
CAT		ENSSSCG00000000766	5:65417079-65432963		CU467800,CH242-7B3,5:65416584-65439865 (Clone quality: bE7B3 on chr=5; Num_of_Contigs=13; )
CAT		ENSSSCG00000006987	17:5032161-5053065		CU682348,CH242-166L11,17:5021825-5054296 (Clone quality: bE166L11 on chr=17; Num_of_Contigs=5; )
CAT		ENSSSCG00000009324	11:6079920-6092468
CAT		ENSSSCG00000013302	2:24918178-24957775
CAT		ENSSSCG00000009925	14:41158158-41210960		CU640887,CH242-377K8,14:41152094-41308016 (Clone quality: bE377K8 on chr=14; Num_of_Contigs=2; )
CAT		location ⇒	2:24918908-24918182	CU928984,CH242-19I4,2:24795764-24927206 (Clone quality: bE19I4 on chr=2; Num_of_Contigs=2; )
CAT		location ⇒	2:24935303-24935108	CU928984,CH242-19I4,2:24927307-24941566 (Clone quality: bE19I4 on chr=2; Num_of_Contigs=2; )
CAT		location ⇒	2:24943802-24943628	CU582930,CH242-51J22,2:24941567-24946421 (Clone quality: bE51J22 on chr=2; Num_of_Contigs=20; )
CAT		location ⇒	2:25069264-25069069	CU582930,CH242-51J22,2:25068648-25075527 (Clone quality: bE51J22 on chr=2; Num_of_Contigs=20; )
CAT4		ENSSSCG00000010102	14:51729892-51989336
CAT4		location ⇒	2:57072211-57071837		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
CAT4		location ⇒	2:57072588-57072238		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
CAT4		location ⇒	2:57073109-57072682		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
CAT4		location ⇒	2:57073891-57073721		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
CATHL1		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL1		location ⇒	13:26045596-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL10		location ⇒	13:26044715-26044685		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL10		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL10		location ⇒	13:26045592-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL10		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CATHL11		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CATHL2		location ⇒	13:26044715-26044641		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL2		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL2		location ⇒	13:26045579-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL4		location ⇒	13:26044715-26044680		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL4		location ⇒	13:26044953-26044874		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL4		location ⇒	13:26045579-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL4		location ⇒	13:26045588-26045396		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL5		location ⇒	13:26044715-26044642		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL5		location ⇒	13:26044977-26044870		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL5		location ⇒	13:26045581-26045381		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL6		location ⇒	13:26044960-26044877		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL6		location ⇒	13:26045588-26045396		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )
CATHL8		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CATHL9		location ⇒	13:26044715-26044685		FP102065,CH242-145E9,13:26011061-26058464 (Clone quality: bE145E9 on chr=13; Num_of_Contigs=12; )

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).