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)

ADFP		ENSSSCG00000005171	1:212534018-212544645
ADH4		ENSSSCG00000009184	8:103894886-103916227
ADH5		ENSSSCG00000009185	8:103933564-103948707
ADH7		ENSSSCG00000009182	8:103678942-103690557
ADHFE1		ENSSSCG00000006213	4:70841559-70874911		CU855750,CH242-30I10,4:70739858-70897572 (Clone quality: bE30I10 on chr=4; Num_of_Contigs=1; )
ADIG		ENSSSCG00000007346	17:43838159-43843681
ADIPOQ		ENSSSCG00000007578	3:3410621-3627142
ADIPOQ		ENSSSCG00000004968	1:174793754-174816782
ADIPOQ		ENSSSCG00000003551	6:57374753-57385654
ADIPOQ		ENSSSCG00000002619	7:135358830-135359894		CU468948,CH242-272F22,7:135358647-135391402 (Clone quality: bE272F22 on chr=7; Num_of_Contigs=11; )
ADIPOQ		ENSSSCG00000001750	7:53320437-53367073
ADIPOR1		ENSSSCG00000010930	10:24933601-24949589		CU986276,CH242-319L9,10:24925344-24954025 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
ADIPOR1		location ⇒	10:24944237-24944412		CU986276,CH242-319L9,10:24925344-24954025 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
ADIPOR1		location ⇒	10:24946587-24946775		CU986276,CH242-319L9,10:24925344-24954025 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
ADIPOR1		location ⇒	10:24947977-24948173		CU986276,CH242-319L9,10:24925344-24954025 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
ADIPOR1		location ⇒	10:24948718-24948924		CU986276,CH242-319L9,10:24925344-24954025 (Clone quality: bE319L9 on chr=10; Num_of_Contigs=6; )
ADIPOR2		ENSSSCG00000000761	5:64623508-64623940		CU855585,CH242-72B19,5:64622959-64625697 (No clone quality info on )
ADIPOR2		location ⇒	5:64486939-64487128		FP102363,CH242-96D13,5:64481864-64487852 (Clone quality: bE96D13 on chr=5; Num_of_Contigs=18; )
ADIPOR2		location ⇒	5:64487293-64487486		FP102363,CH242-96D13,5:64481864-64487852 (Clone quality: bE96D13 on chr=5; Num_of_Contigs=18; )
ADIPOR2		location ⇒	5:64489316-64489511		FP102363,CH242-96D13,5:64487953-64493908 (Clone quality: bE96D13 on chr=5; Num_of_Contigs=18; )
ADIPOR2		location ⇒	5:64623699-64623506		CU855585,CH242-72B19,5:64622959-64625697 (No clone quality info on )
ADK		ENSSSCG00000010315	14:80215283-80533486
ADK		location ⇒	14:80298253-80298364		CU424485,CH242-474J18,14:80290908-80320902 (Clone quality: bE474J18 on chr=14; Num_of_Contigs=7; )
ADK		location ⇒	14:80387460-80387631		CT971496,CH242-302O2,14:80382977-80401636 (Clone quality: bE302O2 on chr=14; Num_of_Contigs=12; )
ADK		location ⇒	14:80448656-80448772		CT737245,CH242-213O14,14:80420441-80495130 (Clone quality: bE213O14 on chr=14; Num_of_Contigs=2; )
ADK		location ⇒	14:80532672-80532945		CT737245,CH242-213O14,14:80495231-80586220 (Clone quality: bE213O14 on chr=14; Num_of_Contigs=2; )
ADM		ENSSSCG00000013408	2:45375345-45377567
ADM		location ⇒	2:45376450-45375349		CU466333,CH242-418D21,2:45373006-45377567 (Clone quality: bE418D21 on chr=2; Num_of_Contigs=4; )
ADM		location ⇒	2:45376450-45375349		CU466333,CH242-418D21,2:45373006-45377567 (Clone quality: bE418D21 on chr=2; Num_of_Contigs=4; )
ADM		location ⇒	2:45376802-45376653		CU466333,CH242-418D21,2:45373006-45377567 (Clone quality: bE418D21 on chr=2; Num_of_Contigs=4; )
ADM		location ⇒	2:45376802-45376653		CU466333,CH242-418D21,2:45373006-45377567 (Clone quality: bE418D21 on chr=2; Num_of_Contigs=4; )
ADNP		ENSSSCG00000007473	17:54511982-54545053	CT009560,CH242-4C12,17:54397384-54561501 (No clone quality info on bE4C12)
ADNP2		ENSSSCG00000005774	1:290863346-290888776
ADO		ENSSSCG00000010223	14:68948048-68948860		CU424480,CH242-10L6,14:68823357-68962394 (Clone quality: bE10L6 on chr=14; Num_of_Contigs=2; )
ADO		location ⇒	14:68947732-68948903		CU424480,CH242-10L6,14:68823357-68962394 (Clone quality: bE10L6 on chr=14; Num_of_Contigs=2; )
ADO		location ⇒	14:68949321-68949884		CU424480,CH242-10L6,14:68823357-68962394 (Clone quality: bE10L6 on chr=14; Num_of_Contigs=2; )
ADO		location ⇒	14:68950142-68950416		CU424480,CH242-10L6,14:68823357-68962394 (Clone quality: bE10L6 on chr=14; Num_of_Contigs=2; )
ADO		location ⇒	14:68951048-68951206		CU424480,CH242-10L6,14:68823357-68962394 (Clone quality: bE10L6 on chr=14; Num_of_Contigs=2; )
ADORA1		ENSSSCG00000015479	9:107019155-107019793		CU928698,CH242-36A5,9:107014452-107027718 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
ADORA1		location ⇒	9:106853688-106854058		CU694815,CH242-126M16,9:106837475-106857411 (Clone quality: bE126M16 on chr=9; Num_of_Contigs=9; )
ADORA1		location ⇒	9:107019794-107018882		CU928698,CH242-36A5,9:107014452-107027718 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
ADORA2A		ENSSSCG00000010054	14:50520133-50528229		CU468367,CH242-50J10,14:50497776-50552589 (Clone quality: bE50J10 on chr=14; Num_of_Contigs=14; )
ADORA2A		location ⇒	14:50520187-50520466		CU468367,CH242-50J10,14:50497776-50552589 (Clone quality: bE50J10 on chr=14; Num_of_Contigs=14; )
ADORA2A		location ⇒	14:50527323-50527809		CU468367,CH242-50J10,14:50497776-50552589 (Clone quality: bE50J10 on chr=14; Num_of_Contigs=14; )
ADORA2A135		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
ADORA2B		location ⇒	14:50520252-50520416		CU468367,CH242-50J10,14:50497776-50552589 (Clone quality: bE50J10 on chr=14; Num_of_Contigs=14; )
ADORA2B		location ⇒	14:50527487-50527539		CU468367,CH242-50J10,14:50497776-50552589 (Clone quality: bE50J10 on chr=14; Num_of_Contigs=14; )
ADORA2B		location ⇒	14:50527672-50527729		CU468367,CH242-50J10,14:50497776-50552589 (Clone quality: bE50J10 on chr=14; Num_of_Contigs=14; )
ADORA3		ENSSSCG00000006787	4:113211961-113219215		CU311186,CH242-230C12,4:113204230-113251493 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
ADORA3		location ⇒	4:113213152-113213080		CU311186,CH242-230C12,4:113204230-113251493 (Clone quality: bE230C12 on chr=4; 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).