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)

SAA3		location ⇒	2:38237850-38237953		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAA3		location ⇒	2:38238731-38238784		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAA4		ENSSSCG00000013370	2:38216373-38262478		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAA4		location ⇒	2:38205207-38205154		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAA4		location ⇒	2:38218588-38218646		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAA4		location ⇒	2:38238728-38238798		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAA4		location ⇒	2:38261846-38261904		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAAL1		ENSSSCG00000013371	2:38265384-38288481		CU633234,CH242-198M22,2:38149421-38299309 (Clone quality: bE198M22 on chr=2; Num_of_Contigs=1; )
SAC3D1		ENSSSCG00000013011	2:5538883-5542375	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
SACM1L		ENSSSCG00000005722	1:287565226-287567303		CU914799,CH242-187I21,1:287564996-287567510 (Clone quality: bE187I21 on chr=1; Num_of_Contigs=19; )
SACS		ENSSSCG00000009280	11:1218525-1220444		CU638824,CH242-139H14,11:1214671-1237399 (Clone quality: bE139H14 on chr=11; Num_of_Contigs=21; )
SAE1		ENSSSCG00000003111	6:36696319-36765843		FP102474,CH242-104M2,6:36670130-36777370 (Clone quality: bE104M2 on chr=6; Num_of_Contigs=1; )
SAFB		ENSSSCG00000004592	1:117200713-117244180		CU606929,CH242-39M13,1:117198722-117245361 (Clone quality: bE39M13 on chr=1; Num_of_Contigs=15; )
SAFB		ENSSSCG00000004591	1:117047112-117080996
SAFB		ENSSSCG00000013522	2:49311703-49329434		CU928983,CH242-130K15,2:49310500-49340340 (Clone quality: bE130K15 on chr=2; Num_of_Contigs=8; )
SAFB		location ⇒	2:49261056-49261568		CU928983,CH242-130K15,2:49260405-49262407 (Clone quality: bE130K15 on chr=2; Num_of_Contigs=8; )
SAFB		location ⇒	2:49304619-49304672		CU928983,CH242-130K15,2:49304588-49310399 (Clone quality: bE130K15 on chr=2; Num_of_Contigs=8; )
SAFB		location ⇒	2:49310917-49310500		CU928983,CH242-130K15,2:49310500-49340340 (Clone quality: bE130K15 on chr=2; Num_of_Contigs=8; )
SAFB		location ⇒	2:49340257-49340308		CU928983,CH242-130K15,2:49310500-49340340 (Clone quality: bE130K15 on chr=2; Num_of_Contigs=8; )
SAFB2		ENSSSCG00000013523	2:49329776-49377318
SAG		ENSSSCG00000011674	13:67333892-67340309		CU914638,CH242-182J3,13:67262584-67431184 (Clone quality: bE182J3 on chr=13; Num_of_Contigs=1; )
SAG		location ⇒	15:126161589-126161394		FP102656,CH242-26J3,15:126159392-126162286 (Clone quality: bE26J3 on chr=15; Num_of_Contigs=12; )
SAG		location ⇒	15:126172182-126172053		FP102656,CH242-26J3,15:126162387-126184947 (Clone quality: bE26J3 on chr=15; Num_of_Contigs=12; )
SAG		location ⇒	15:126294337-126294474		CU914742,CH242-379G11,15:126286654-126295034 (Clone quality: bE379G11 on chr=15; Num_of_Contigs=12; )
SAG		location ⇒	15:126305032-126305226		CU914742,CH242-379G11,15:126301787-126305842 (Clone quality: bE379G11 on chr=15; Num_of_Contigs=12; )
SAGE1		ENSSSCG00000012696	X:109230551-109247286		CU856395,CH242-127I21,X:109218984-109313326 (Clone quality: bE127I21 on chr=X; Num_of_Contigs=5; )
SAHH_PIG		ENSSSCG00000007278	17:39808805-39821501		CU606946,CH242-245E11,17:39642724-39823287 (Clone quality: bE245E11 on chr=17; Num_of_Contigs=2; )
SALL1		ENSSSCG00000002836	6:23418305-23432742		CU862046,CH242-25I9,6:23404524-23581909 (Clone quality: bE25I9 on chr=6; Num_of_Contigs=2; )
SALL3		ENSSSCG00000004858	1:153761428-153766445		FP089466,CH242-515H23,1:153735535-153776922 (Clone quality: bE515H23 on chr=1; Num_of_Contigs=4; )
SALL4		ENSSSCG00000007479	17:55278360-55297073
SAL_PIG		ENSSSCG00000005474	1:266548070-266552930		CU041260,CH242-55A14,1:266438281-266562122 (Clone quality: bE55A14 on chr=1; Num_of_Contigs=9; )
SAMD12		ENSSSCG00000006007	4:19899321-20086556
SAMD14		ENSSSCG00000017585	12:24759158-24764661
SAMD3		ENSSSCG00000004202	1:34301978-34484851
SAMD4A		ENSSSCG00000005050	1:192618998-192693488
SAMD4B		ENSSSCG00000010706	14:138631259-138656610
SAMD5		ENSSSCG00000004112	1:19154786-19155253		CU633947,CH242-282B14,1:19122981-19218327 (Clone quality: bE282B14 on chr=1; Num_of_Contigs=3; )
Samd8		ENSSSCG00000010319	14:80897338-80950958		CT737343,CH242-176H24,14:80877150-80974625 (Clone quality: bE176H24 on chr=14; Num_of_Contigs=2; )
SAMD8		ENSSSCG00000010319	14:80897338-80950958		CT737343,CH242-176H24,14:80877150-80974625 (Clone quality: bE176H24 on chr=14; Num_of_Contigs=2; )
Samd8		location ⇒	14:29399284-29399120		CU468658,CH242-245F7,14:29355652-29557150 (Clone quality: bE245F7 on chr=14; Num_of_Contigs=1; )
Samd8		location ⇒	14:80924094-80924674		CT737343,CH242-176H24,14:80877150-80974625 (Clone quality: bE176H24 on chr=14; Num_of_Contigs=2; )
Samd8		location ⇒	14:80943134-80943256		CT737343,CH242-176H24,14:80877150-80974625 (Clone quality: bE176H24 on chr=14; Num_of_Contigs=2; )
Samd8		location ⇒	14:80950639-80950947		CT737343,CH242-176H24,14:80877150-80974625 (Clone quality: bE176H24 on chr=14; Num_of_Contigs=2; )
SAMD9		location ⇒	9:68430531-68426934		FP101868,CH242-199M2,9:68426126-68451832 (Clone quality: bE199M2 on chr=9; Num_of_Contigs=3; )
SAMD9		location ⇒	9:68431382-68430612		FP101868,CH242-199M2,9:68426126-68451832 (Clone quality: bE199M2 on chr=9; Num_of_Contigs=3; )
SAMD9		location ⇒	9:68431697-68431561		FP101868,CH242-199M2,9:68426126-68451832 (Clone quality: bE199M2 on chr=9; Num_of_Contigs=3; )
SAMHD1		ENSSSCG00000007327	17:42465490-42480949		CU606915,CH242-133O2,17:42464913-42481089 (Clone quality: bE133O2 on chr=17; Num_of_Contigs=6; )
SAMHD1		location ⇒	17:42469949-42470111		CU606915,CH242-133O2,17:42464913-42481089 (Clone quality: bE133O2 on chr=17; Num_of_Contigs=6; )
SAMHD1		location ⇒	17:42472338-42472456		CU606915,CH242-133O2,17:42464913-42481089 (Clone quality: bE133O2 on chr=17; Num_of_Contigs=6; )
SAMHD1		location ⇒	17:42479175-42479259		CU606915,CH242-133O2,17:42464913-42481089 (Clone quality: bE133O2 on chr=17; Num_of_Contigs=6; )

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).