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)

AAAS		ENSSSCG00000000268	5:17065522-17077274		CU570852,CH242-3N12,5:17057869-17089247 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
AACS		ENSSSCG00000009755	14:28056494-28095262
AADACL1		ENSSSCG00000011755	13:84529790-84546739		CU463167,CH242-393A19,13:84415923-84573669 (Clone quality: bE393A19 on chr=13; Num_of_Contigs=1; )
AADACL3		ENSSSCG00000003441	6:49831992-49836197
AADACL4		ENSSSCG00000003440	6:49784723-49799577		FP103049,CH242-116I16,6:49765010-49832358 (Clone quality: bE116I16 on chr=6; Num_of_Contigs=3; )
AADAT		ENSSSCG00000009708	14:19523625-19546705		CU468423,CH242-384M2,14:19517521-19581529 (Clone quality: bE384M2 on chr=14; Num_of_Contigs=3; )
AAGAB		ENSSSCG00000004951	1:172292133-172329373		FP236622,CH242-20C24,1:172287897-172330881 (Clone quality: bE20C24 on chr=1; Num_of_Contigs=3; )
AAK1		ENSSSCG00000008337	3:66805405-66889135
AAMP		ENSSSCG00000016189	15:113553539-113558290
AAMP		location ⇒	15:113555202-113555117		CU550681,CH242-392C2,15:113553662-113557604 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
AAMP		location ⇒	15:113555610-113555463		CU550681,CH242-392C2,15:113553662-113557604 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
AAMP		location ⇒	15:113556007-113555863		CU550681,CH242-392C2,15:113553662-113557604 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
AAMP		location ⇒	15:113556566-113556443		CU550681,CH242-392C2,15:113553662-113557604 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
AANAT		ENSSSCG00000017176	12:3263364-3264545		CU928356,CH242-33I18,12:3255856-3269726 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
AARS		ENSSSCG00000002723	6:9727150-9747183		CU929739,CH242-254K22,6:9727133-9749687 (Clone quality: bE254K22 on chr=6; Num_of_Contigs=9; )
AARS2		ENSSSCG00000001706	7:45822827-45835219	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
AASDH		ENSSSCG00000008906	8:47339179-47347656
AASDHPPT		ENSSSCG00000014998	9:35338209-35480815
AASS		ENSSSCG00000016613	18:23149414-23194976
AATF		ENSSSCG00000017693	12:36781687-36883430
AATF		location ⇒	12:36783328-36783526		CU929499,CH242-167B14,12:36768780-36783717 (Clone quality: bE167B14 on chr=12; Num_of_Contigs=5; )
AATF		location ⇒	12:36786529-36786599		CU468157,CH242-399I10,12:36783718-36983768 (Clone quality: bE399I10 on chr=12; Num_of_Contigs=1; )
AATF		location ⇒	12:36824570-36824726		CU468157,CH242-399I10,12:36783718-36983768 (Clone quality: bE399I10 on chr=12; Num_of_Contigs=1; )
AATF		location ⇒	12:36860542-36860613		CU468157,CH242-399I10,12:36783718-36983768 (Clone quality: bE399I10 on chr=12; Num_of_Contigs=1; )
AATK		ENSSSCG00000017141	12:778874-783621		CU993801,CH242-26A11,12:778298-786106 (Clone quality: bE26A11 on chr=12; Num_of_Contigs=7; )
AATK		location ⇒	12:784262-784457		CU993801,CH242-26A11,12:778298-786106 (Clone quality: bE26A11 on chr=12; Num_of_Contigs=7; )
AATK		location ⇒	12:784484-784678		CU993801,CH242-26A11,12:778298-786106 (Clone quality: bE26A11 on chr=12; Num_of_Contigs=7; )
ABAT		ENSSSCG00000007909	3:29888769-30048895
ABCA1		ENSSSCG00000005423	1:258101320-258262611
ABCA1		location ⇒	1:258114291-258114198		CU571367,CH242-482F3,1:257999449-258131842 (Clone quality: bE482F3 on chr=1; Num_of_Contigs=2; )
ABCA1		location ⇒	1:258115273-258115134		CU571367,CH242-482F3,1:257999449-258131842 (Clone quality: bE482F3 on chr=1; Num_of_Contigs=2; )
ABCA1		location ⇒	1:258117702-258117525		CU571367,CH242-482F3,1:257999449-258131842 (Clone quality: bE482F3 on chr=1; Num_of_Contigs=2; )
ABCA1		location ⇒	1:258119248-258119076		CU571367,CH242-482F3,1:257999449-258131842 (Clone quality: bE482F3 on chr=1; Num_of_Contigs=2; )
ABCA12		ENSSSCG00000016171	15:110389153-110468709
ABCA13		ENSSSCG00000015625	9:127213946-127317931
ABCA3		ENSSSCG00000008051	3:36658058-36830863
ABCA4		ENSSSCG00000006890	4:127482869-127628484
ABCA5		ENSSSCG00000017255	12:9472185-9541075
ABCA6		ENSSSCG00000017256	12:9577504-9619013
ABCA7		location ⇒	1:258113444-258113374		CU571367,CH242-482F3,1:257999449-258131842 (Clone quality: bE482F3 on chr=1; Num_of_Contigs=2; )
ABCA7		location ⇒	1:258117692-258117631		CU571367,CH242-482F3,1:257999449-258131842 (Clone quality: bE482F3 on chr=1; Num_of_Contigs=2; )
ABCA7		location ⇒	1:258137258-258137132		CU914248,CH242-220O11,1:258131843-258180962 (Clone quality: bE220O11 on chr=1; Num_of_Contigs=6; )
ABCA7		location ⇒	1:258139703-258139653		CU914248,CH242-220O11,1:258131843-258180962 (Clone quality: bE220O11 on chr=1; Num_of_Contigs=6; )
ABCA9		ENSSSCG00000017257	12:9654474-9709707		CU655864,CH242-170C16,12:9594640-9727750 (Clone quality: bE170C16 on chr=12; Num_of_Contigs=4; )
ABCB1		location ⇒	9:86488797-86489001		CU927983,CH242-78H2,9:86478072-86494384 (Clone quality: bE78H2 on chr=9; Num_of_Contigs=4; )
ABCB1		location ⇒	9:86608235-86608442		CU855672,CH242-67M19,9:86606171-86618962 (Clone quality: bE67M19 on chr=9; Num_of_Contigs=3; )
ABCB1		location ⇒	9:86760843-86761047		CU855672,CH242-67M19,9:86645212-86777014 (Clone quality: bE67M19 on chr=9; Num_of_Contigs=3; )
ABCB1		location ⇒	9:86861107-86861314		CU929528,CH242-211D13,9:86859389-86873883 (Clone quality: bE211D13 on chr=9; Num_of_Contigs=6; )
ABCB10		ENSSSCG00000010188	14:62619004-62644400		CU468504,CH242-54G23,14:62610152-62667791 (Clone quality: bE54G23 on chr=14; Num_of_Contigs=3; )
ABCB4		location ⇒	9:86771764-86771876		CU855672,CH242-67M19,9:86645212-86777014 (Clone quality: bE67M19 on chr=9; Num_of_Contigs=3; )

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).