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)

SPTAN1		location ⇒	1:283682425-283682575		CU862000,CH242-4D17,1:283660123-283729806 (Clone quality: bE4D17 on chr=1; Num_of_Contigs=2; )
SPTAN1		location ⇒	1:283682989-283683470		CU862000,CH242-4D17,1:283660123-283729806 (Clone quality: bE4D17 on chr=1; Num_of_Contigs=2; )
SPTB		ENSSSCG00000002277	7:97296536-97373896		CT737370,CH242-45A22,7:97273887-97416999 (Clone quality: bE45A22 on chr=7; Num_of_Contigs=1; )
SPTB		location ⇒	7:97309469-97309824		CT737370,CH242-45A22,7:97273887-97416999 (Clone quality: bE45A22 on chr=7; Num_of_Contigs=1; )
SPTB		location ⇒	7:97310931-97311127		CT737370,CH242-45A22,7:97273887-97416999 (Clone quality: bE45A22 on chr=7; Num_of_Contigs=1; )
SPTB		location ⇒	7:97312053-97312139		CT737370,CH242-45A22,7:97273887-97416999 (Clone quality: bE45A22 on chr=7; Num_of_Contigs=1; )
SPTB		location ⇒	7:97312595-97312704		CT737370,CH242-45A22,7:97273887-97416999 (Clone quality: bE45A22 on chr=7; Num_of_Contigs=1; )
SPTBN2		ENSSSCG00000012928	2:4043508-4051227		CU928093,CH242-168G1,2:4042694-4052323 (Clone quality: bE168G1 on chr=2; Num_of_Contigs=25; )
SPTBN2		location ⇒	3:80739712-80739595		CU467030,CH242-372O10,3:80729645-80744468 (Clone quality: bE372O10 on chr=3; Num_of_Contigs=6; )
SPTBN2		location ⇒	3:80746485-80746311		CU467030,CH242-372O10,3:80744569-80763839 (Clone quality: bE372O10 on chr=3; Num_of_Contigs=6; )
SPTBN2		location ⇒	3:80758384-80758229		CU467030,CH242-372O10,3:80744569-80763839 (Clone quality: bE372O10 on chr=3; Num_of_Contigs=6; )
SPTBN2		location ⇒	3:80831876-80831680		FP245491,CH242-293O23,3:80825696-80836060 (Clone quality: bE293O23 on chr=3; Num_of_Contigs=3; )
SPTBN5		ENSSSCG00000004736	1:135808513-135858068		CU468106,CH242-259N12,1:135806545-135912956 (Clone quality: bE259N12 on chr=1; Num_of_Contigs=8; )
SPTLC1		ENSSSCG00000009594	14:3487545-3583668
SPTLC2		ENSSSCG00000002404	7:108673810-108724874
SPTLC3		ENSSSCG00000007072	17:22080913-22182455
SPTY2D1		ENSSSCG00000013361	2:37768979-37774111		CU915335,CH242-299H5,2:37768972-37817128 (Clone quality: bE299H5 on chr=2; Num_of_Contigs=5; )
SPZ1		ENSSSCG00000014122	2:78392438-78393586		CU896535,CH242-174M6,2:78383909-78395477 (Clone quality: bE174M6 on chr=2; Num_of_Contigs=16; )
SQLE		ENSSSCG00000005970	4:14332677-14365215
SQRDL		ENSSSCG00000004665	1:131676579-131732409
SQSTM1		ENSSSCG00000014016	2:68101464-68112459	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
SQSTM1		location ⇒	2:68102170-68101949	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
SQSTM1		location ⇒	2:68103360-68103163	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
SQSTM1		location ⇒	2:68103852-68103636	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
SQSTM1		location ⇒	2:68109165-68109022	CU639394,CH242-198P20,2:67907486-68117033 (Clone quality: bE198P20 on chr=2; Num_of_Contigs=3; )
SR-PSOX		location ⇒	12:49356357-49355936		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
SR-PSOX		location ⇒	12:49358317-49358232		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
SR-PSOX		location ⇒	12:49358740-49358597		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
SR-PSOX		location ⇒	12:49359112-49359036		CU929524,CH242-164N17,12:49336210-49359359 (Clone quality: bE164N17 on chr=12; Num_of_Contigs=22; )
SR140		ENSSSCG00000011684	13:68255017-68300465		CU914238,CH242-182G22,13:68254760-68335472 (Clone quality: bE182G22 on chr=13; Num_of_Contigs=5; )
SRA1		ENSSSCG00000014365	2:129315328-129321316		CU459055,CH242-430O11,2:129241445-129341031 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
SRBD1		ENSSSCG00000008445	3:88353435-88549518
SRC		ENSSSCG00000007334	17:42850894-42870771
SRC		location ⇒	17:42869398-42869510		CU024884,CH242-24B10,17:42858765-42877566 (Clone quality: bE24B10 on chr=17; Num_of_Contigs=8; )
SRC		location ⇒	17:42869666-42869800		CU024884,CH242-24B10,17:42858765-42877566 (Clone quality: bE24B10 on chr=17; Num_of_Contigs=8; )
SRC		location ⇒	17:42870108-42870325		CU024884,CH242-24B10,17:42858765-42877566 (Clone quality: bE24B10 on chr=17; Num_of_Contigs=8; )
SRCAP		ENSSSCG00000007789	3:16296731-16332652
SRCIN1		ENSSSCG00000018056	12:57185825-57230312		FP067348,CH242-54E8,12:57159732-57237745 (Clone quality: bE54E8 on chr=12; Num_of_Contigs=10; )
SRCRB4D		ENSSSCG00000007694	3:8534477-8544502
SRCRB4D		location ⇒	3:8542250-8542326		FP102934,CH242-518K19,3:8540189-8542518 (Clone quality: bE518K19 on chr=3; Num_of_Contigs=10; )
SRCRB4D		location ⇒	3:8543422-8543491		FP102934,CH242-518K19,3:8542619-8553946 (Clone quality: bE518K19 on chr=3; Num_of_Contigs=10; )
SRCRB4D		location ⇒	3:8544120-8544502		FP102934,CH242-518K19,3:8542619-8553946 (Clone quality: bE518K19 on chr=3; Num_of_Contigs=10; )
SRD5A1		ENSSSCG00000017103	16:72686319-72709458
SRD5A2		ENSSSCG00000008521	3:101177771-101189231
SRD5A3		ENSSSCG00000008845	8:36367267-36384530		FP016165,CH242-16E23,8:36348269-36392852 (Clone quality: bE16E23 on chr=8; Num_of_Contigs=5; )
SREBP-1C		location ⇒	12:17948453-17948384		CU914191,CH242-236G5,12:17933540-17951807 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
SREBP-1C		location ⇒	12:17949674-17949612		CU914191,CH242-236G5,12:17933540-17951807 (Clone quality: bE236G5 on chr=12; Num_of_Contigs=14; )
SREBP-1C		location ⇒	12:18244992-18244923		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
SREBP-1C		location ⇒	12:18246213-18246151		CU570902,CH242-109J6,12:18227104-18319905 (Clone quality: bE109J6 on chr=12; Num_of_Contigs=7; )
SRF		ENSSSCG00000001661	7:44060665-44068357	CR974479,PigE-150P18,7:44038129-44188858 (Clone quality: bT150P18 on chr=7; Num_of_Contigs=4; )

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, 2601-16

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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).