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)

RALYL		location ⇒	4:54305798-54305524		CU462924,CH242-287I18,4:54187359-54381773 (Clone quality: bE287I18 on chr=4; Num_of_Contigs=1; )
RALYL		location ⇒	4:54643307-54642548		CU234139,CH242-101I23,4:54563679-54684981 (Clone quality: bE101I23 on chr=4; Num_of_Contigs=2; )
RALYL		location ⇒	4:54643633-54643374		CU234139,CH242-101I23,4:54563679-54684981 (Clone quality: bE101I23 on chr=4; Num_of_Contigs=2; )
RAMP1		ENSSSCG00000016331	15:129966458-129997166
RAMP2		ENSSSCG00000017389	12:17691204-17693476		CU928483,CH242-17I6,12:17682845-17706351 (Clone quality: bE17I6 on chr=12; Num_of_Contigs=8; )
RAN		ENSSSCG00000009746	14:24358350-24361422		CU468532,CH242-32J1,14:24332288-24361510 (Clone quality: bE32J1 on chr=14; Num_of_Contigs=7; )
RANBP1		ENSSSCG00000010137	14:52748488-52754653		CT737345,CH242-178J1,14:52723116-52857619 (Clone quality: bE178J1 on chr=14; Num_of_Contigs=3; )
RANBP10		ENSSSCG00000002773	6:12947957-12961996
RANBP17		ENSSSCG00000017000	16:49915586-50378853
RANBP2		ENSSSCG00000008139	3:43038989-43042374		FP102256,CH242-427M21,3:43026663-43044768 (Clone quality: bE427M21 on chr=3; Num_of_Contigs=5; )
RANBP3		ENSSSCG00000013533	2:49555615-49563142		FP089464,CH242-231P22,2:49500853-49563374 (Clone quality: bE231P22 on chr=2; Num_of_Contigs=4; )
RANBP3L		ENSSSCG00000016838	16:18968670-19016951
RANBP6		ENSSSCG00000005204	1:226007781-226011098		CU640420,CH242-37P4,1:226002179-226013154 (Clone quality: bE37P4 on chr=1; Num_of_Contigs=8; )
RANBP9		ENSSSCG00000001056	7:10143401-10261724
RAP1A		ENSSSCG00000006785	4:113081795-113156162		FP085509,CH242-232B23,4:113036619-113185587 (Clone quality: bE232B23 on chr=4; Num_of_Contigs=1; )
RAP1A		location ⇒	4:113082570-113082469		FP085509,CH242-232B23,4:113036619-113185587 (Clone quality: bE232B23 on chr=4; Num_of_Contigs=1; )
RAP1A		location ⇒	4:113085746-113085629		FP085509,CH242-232B23,4:113036619-113185587 (Clone quality: bE232B23 on chr=4; Num_of_Contigs=1; )
RAP1A		location ⇒	4:113091328-113091185		FP085509,CH242-232B23,4:113036619-113185587 (Clone quality: bE232B23 on chr=4; Num_of_Contigs=1; )
RAP1A		location ⇒	4:113093159-113093016		FP085509,CH242-232B23,4:113036619-113185587 (Clone quality: bE232B23 on chr=4; Num_of_Contigs=1; )
RAP1GAP2		ENSSSCG00000017847	12:46629051-46638183		CU655851,CH242-162H14,12:46626857-46639709 (Clone quality: bE162H14 on chr=12; Num_of_Contigs=7; )
RAP2A		ENSSSCG00000009506	11:67570524-67570841		CU633821,CH242-247J23,11:67570348-67574152 (Clone quality: bE247J23 on chr=11; Num_of_Contigs=15; )
RAP2B		ENSSSCG00000011722	13:75379457-75464466
RAP2B		location ⇒	13:75379433-75379749
RAP2B		location ⇒	13:75464311-75464746
RAP2C		ENSSSCG00000012675	X:106222525-106234883
RAPGEF1		ENSSSCG00000005719	1:286923581-287082755
RAPGEF2		ENSSSCG00000008881	8:41879436-41935459
RAPGEF4		ENSSSCG00000015959	15:73959399-74091846
RAPGEF5		ENSSSCG00000015383	9:85232546-85428559
RAPGEF5		location ⇒	9:85229155-85228781		CU633345,CH242-152E19,9:85196281-85299712 (Clone quality: bE152E19 on chr=9; Num_of_Contigs=4; )
RAPGEF5		location ⇒	9:85236055-85236000		CU633345,CH242-152E19,9:85196281-85299712 (Clone quality: bE152E19 on chr=9; Num_of_Contigs=4; )
RAPGEF5		location ⇒	9:85249542-85249489		CU633345,CH242-152E19,9:85196281-85299712 (Clone quality: bE152E19 on chr=9; Num_of_Contigs=4; )
RAPGEF5		location ⇒	9:85399744-85399677		CU914219,CH242-110J12,9:85392865-85513942 (Clone quality: bE110J12 on chr=9; Num_of_Contigs=2; )
RAPGEF6		ENSSSCG00000014268	2:121741990-121784332
RAPGEFL1		ENSSSCG00000017478	12:19975310-19988087		FP015991,CH242-327H5,12:19955642-20001670 (Clone quality: bE327H5 on chr=12; Num_of_Contigs=8; )
RAPH1		ENSSSCG00000016119	15:100342788-100382114
RAPSN		ENSSSCG00000013240	2:13301643-13305456		CU856312,CH242-38I7,2:13257671-13307229 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
RARA		ENSSSCG00000017475	12:19878875-19903141
RARA		location ⇒	12:19883487-19883382		CU928542,CH242-522D8,12:19861422-19883922 (Clone quality: bE522D8 on chr=12; Num_of_Contigs=11; )
RARA		location ⇒	12:19883796-19883636		CU928542,CH242-522D8,12:19861422-19883922 (Clone quality: bE522D8 on chr=12; Num_of_Contigs=11; )
RARA		location ⇒	12:19886063-19885938		CU928542,CH242-522D8,12:19884023-19929816 (Clone quality: bE522D8 on chr=12; Num_of_Contigs=11; )
RARB		ENSSSCG00000011212	13:10322340-10341417		CU582923,CH242-318I8,13:10302635-10467629 (Clone quality: bE318I8 on chr=13; Num_of_Contigs=1; )
RARG		ENSSSCG00000000258	5:16894183-16899254
RARRES15918		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
RARS		ENSSSCG00000017015	16:52695965-52734427
RARS2		location ⇒	1:58516458-58516553		CU929873,CH242-16I3,1:58514304-58519354 (Clone quality: bE16I3 on chr=1; Num_of_Contigs=5; )
RARS2		location ⇒	1:58521584-58521642		CU929873,CH242-16I3,1:58519455-58523199 (Clone quality: bE16I3 on chr=1; Num_of_Contigs=5; )
RARS2		location ⇒	1:58577473-58577568		CU861919,CH242-138I19,1:58565530-58592955 (Clone quality: bE138I19 on chr=1; Num_of_Contigs=5; )
RARS2		location ⇒	1:58582773-58582831		CU861919,CH242-138I19,1:58565530-58592955 (Clone quality: bE138I19 on chr=1; Num_of_Contigs=5; )
RAS		location ⇒	12:49993656-49993723	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; 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, 1001-16

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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).