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)

C1orf114		ENSSSCG00000006293	4:84741300-84742889		CU469440,CH242-25G4,4:84740591-84744347 (Clone quality: bE25G4 on chr=4; Num_of_Contigs=20; )
C1orf115		ENSSSCG00000010827	10:10169506-10179258		CU927960,CH242-271G13,10:10129820-10201660 (Clone quality: bE271G13 on chr=10; Num_of_Contigs=7; )
C1orf123		ENSSSCG00000003850	6:112890483-112905937
C1orf124		ENSSSCG00000010173	14:61514246-61525033		CU407164,CH242-225K19,14:61489340-61536852 (Clone quality: bE225K19 on chr=14; Num_of_Contigs=10; )
C1orf125		ENSSSCG00000015528	9:113671897-113689113
C1orf127		ENSSSCG00000003408	6:47966851-47969186		CU929651,CH242-470O2,6:47950411-47976346 (Clone quality: bE470O2 on chr=6; Num_of_Contigs=4; )
C1orf130		ENSSSCG00000003547	6:56854840-56878977		FP102651,CH242-25G13,6:56816566-56894671 (Clone quality: bE25G13 on chr=6; Num_of_Contigs=5; )
C1orf131		ENSSSCG00000010176	14:61568678-61583256		CU407164,CH242-225K19,14:61559652-61608217 (Clone quality: bE225K19 on chr=14; Num_of_Contigs=10; )
C1orf133		ENSSSCG00000015609	9:125042512-125042857		CU467690,CH242-213K18,9:125041753-125043680 (Clone quality: bE213K18 on chr=9; Num_of_Contigs=3; )
C1orf135		ENSSSCG00000003552	6:57423155-57425870		CU457419,CH242-59A10,6:57413955-57437902 (Clone quality: bE59A10 on chr=6; Num_of_Contigs=10; )
C1orf141		ENSSSCG00000003803	6:102495969-102550371
C1orf146		ENSSSCG00000006905	4:129039483-129113675
C1orf150		ENSSSCG00000013943	2:64155617-64155850		CU855971,CH242-151P5,2:64154849-64164178 (Clone quality: bE151P5 on chr=2; Num_of_Contigs=10; )
C1orf156		ENSSSCG00000006285	4:84308030-84308581		CU407291,CH242-513E17,4:84284256-84310405 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
C1orf158		ENSSSCG00000003442	6:49855706-49867752
C1orf161		ENSSSCG00000006742	4:108918708-108943891		CT967312,CH242-17J23,4:108879453-108961805 (Clone quality: bE17J23 on chr=4; Num_of_Contigs=2; )
C1orf167		ENSSSCG00000003427	6:48731122-48738997
C1orf168		ENSSSCG00000003836	6:110542143-110591803
C1orf170		ENSSSCG00000005741	1:288503909-289541265
C1orf172		ENSSSCG00000003567	6:57922999-57926781		FP015947,CH242-485K18,6:57822585-57995160 (Clone quality: bE485K18 on chr=6; Num_of_Contigs=2; )
C1orf173		ENSSSCG00000003781	6:97120736-97181080		CU424470,CH242-163B16,6:97085861-97250883 (Clone quality: bE163B16 on chr=6; Num_of_Contigs=3; )
C1orf174		ENSSSCG00000003363	6:43995005-44001921		FP102728,CH242-526K10,6:43988680-44003984 (Clone quality: bE526K10 on chr=6; Num_of_Contigs=5; )
C1orf175		ENSSSCG00000003845	6:112297426-112344018		CU929610,CH242-266G21,6:112292153-112375996 (Clone quality: bE266G21 on chr=6; Num_of_Contigs=3; )
C1orf182		ENSSSCG00000006486	4:97593171-97601118		CU468311,CH242-144L15,4:97593053-97608994 (Clone quality: bE144L15 on chr=4; Num_of_Contigs=16; )
C1orf183		ENSSSCG00000006784	4:113055854-113068510		FP085509,CH242-232B23,4:113036619-113185587 (Clone quality: bE232B23 on chr=4; Num_of_Contigs=1; )
C1orf186		ENSSSCG00000015638	9:131011439-131017061		CU855983,CH242-166L15,9:130999751-131128008 (Clone quality: bE166L15 on chr=9; Num_of_Contigs=2; )
C1orf187		ENSSSCG00000003423	6:48673635-48685032		CU855519,CH242-273H12,6:48662691-48694639 (Clone quality: bE273H12 on chr=6; Num_of_Contigs=13; )
C1orf189		ENSSSCG00000006555	4:99575048-99578669		CU856218,CH242-277E7,4:99509313-99581754 (Clone quality: bE277E7 on chr=4; Num_of_Contigs=4; )
C1orf194		ENSSSCG00000006837	4:115456728-115463511		CU207233,CH242-432M23,4:115446550-115504367 (Clone quality: bE432M23 on chr=4; Num_of_Contigs=7; )
C1orf196		ENSSSCG00000003452	6:50442636-50442734		CU694706,CH242-284G6,6:50407186-50444543 (Clone quality: bE284G6 on chr=6; Num_of_Contigs=12; )
C1orf198		ENSSSCG00000010181	14:61845981-61879993		CU468327,CH242-210F14,14:61823679-61924870 (Clone quality: bE210F14 on chr=14; Num_of_Contigs=4; )
C1orf2		ENSSSCG00000006521	4:98654722-98659472
C1orf201		ENSSSCG00000003541	6:56526163-56547760
C1orf21		ENSSSCG00000015565	9:117958770-118220689
C1orf210		location ⇒	6:120217373-120217054		CU694684,CH242-210N13,6:120172350-120225775 (Clone quality: bE210N13 on chr=6; Num_of_Contigs=11; )
C1orf210		location ⇒	6:120302720-120303039		FP102012,CH242-136J24,6:120277096-120383099 (Clone quality: bE136J24 on chr=6; Num_of_Contigs=3; )
C1orf227		ENSSSCG00000015591	9:123067030-123068062		CU657946,CH242-238G6,9:122996435-123111475 (Clone quality: bE238G6 on chr=9; Num_of_Contigs=3; )
C1orf228		ENSSSCG00000003932	6:119416492-119474208
C1orf230		ENSSSCG00000006617	4:101453691-101461952	CU457723,CH242-28L6,4:101441264-101656496 (Clone quality: bE28L6 on chr=4; Num_of_Contigs=25; )
C1orf24		ENSSSCG00000015567	9:118396857-118558753
C1orf25		location ⇒	9:118649713-118649921		CU915492,CH242-37F23,9:118647499-118655502 (Clone quality: bE37F23 on chr=9; Num_of_Contigs=8; )
C1orf25		location ⇒	9:118750459-118749892		CU915492,CH242-37F23,9:118743057-118752867 (Clone quality: bE37F23 on chr=9; Num_of_Contigs=8; )
C1orf25		location ⇒	9:118772906-118772698		CU972398,CH242-133N16,9:118752868-118830369 (Clone quality: bE133N16 on chr=9; Num_of_Contigs=2; )
C1orf25		location ⇒	9:118794775-118794414		CU972398,CH242-133N16,9:118752868-118830369 (Clone quality: bE133N16 on chr=9; Num_of_Contigs=2; )
C1orf26		ENSSSCG00000015569	9:118798751-118902143
C1orf27		ENSSSCG00000015577	9:119884695-119923362		CU657929,CH242-301H1,9:119854087-120036038 (Clone quality: bE301H1 on chr=9; Num_of_Contigs=1; )
C1ORF2910964		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C1orf31		ENSSSCG00000010161	14:57950938-57958720		CT737201,CH242-14B12,14:57877790-57960629 (Clone quality: bE14B12 on chr=14; Num_of_Contigs=8; )
C1orf35		ENSSSCG00000013991	2:66560425-66562731	FP085478,CH242-132B19,2:66476472-66645587 (Clone quality: bE132B19 on chr=2; Num_of_Contigs=3; )
C1orf38		ENSSSCG00000003584	6:58586811-58600128

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).