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)

R2		ENSSSCG00000000233	5:16023608-16057075		CU606912,CH242-90A20,5:16023396-16077450 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
R2		ENSSSCG00000005229	1:229342181-229362574		CU467086,CH242-311M15,1:229299527-229373820 (Clone quality: bE311M15 on chr=1; Num_of_Contigs=4; )
R2		ENSSSCG00000005377	1:251656031-251915759
R2		ENSSSCG00000009657	14:10337015-10424743
R2		ENSSSCG00000010989	10:31508071-31523087		CU633320,CH242-86P2,10:31485466-31523504 (Clone quality: bE86P2 on chr=10; Num_of_Contigs=12; )
R3HDM1		ENSSSCG00000015692	15:14531850-14666814
R3HDML		ENSSSCG00000007370	17:48477364-48486996
RAB10		ENSSSCG00000008573	3:105388346-105468269		CU571288,CH242-32P1,3:105305392-105483350 (Clone quality: bE32P1 on chr=3; Num_of_Contigs=1; )
RAB11A		ENSSSCG00000004940	1:170984851-170998658
RAB11A		location ⇒	1:170958221-170959362		CU915365,CH242-487M8,1:170956847-170959366 (Clone quality: bE487M8 on chr=1; Num_of_Contigs=15; )
RAB11A		location ⇒	1:170959499-170959693		CU915365,CH242-487M8,1:170959467-170967231 (Clone quality: bE487M8 on chr=1; Num_of_Contigs=15; )
RAB11A		location ⇒	1:170992338-170992535		CU915365,CH242-487M8,1:170987714-171005136 (Clone quality: bE487M8 on chr=1; Num_of_Contigs=15; )
RAB11A		location ⇒	1:170992773-170992962		CU915365,CH242-487M8,1:170987714-171005136 (Clone quality: bE487M8 on chr=1; Num_of_Contigs=15; )
RAB11B		ENSSSCG00000013600	2:51678226-51689604		FP090904,CH242-212F1,2:51608045-51700090 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
RAB11FIP1		ENSSSCG00000015823	15:46024628-46055647
RAB11FIP2		ENSSSCG00000010672	14:133950706-133989057		CU062550,CH242-292M14,14:133889135-134049376 (Clone quality: bE292M14 on chr=14; Num_of_Contigs=1; )
RAB11FIP3		ENSSSCG00000007994	3:35607368-35662467
RAB11FIP4		ENSSSCG00000017747	12:41149764-41187475
RAB13		ENSSSCG00000006564	4:99933215-99938033		CU407290,CH242-513B13,4:99899068-99941551 (Clone quality: bE513B13 on chr=4; Num_of_Contigs=7; )
RAB13		ENSSSCG00000000118	5:6481483-6507276
RAB13		location ⇒	4:99750326-99750524		CU468620,CH242-99G21,4:99706339-99812454 (Clone quality: bE99G21 on chr=4; Num_of_Contigs=4; )
RAB13		location ⇒	4:99750691-99750881		CU468620,CH242-99G21,4:99706339-99812454 (Clone quality: bE99G21 on chr=4; Num_of_Contigs=4; )
RAB13		location ⇒	4:99937475-99937673		CU407290,CH242-513B13,4:99899068-99941551 (Clone quality: bE513B13 on chr=4; Num_of_Contigs=7; )
RAB13		location ⇒	4:99937840-99938030		CU407290,CH242-513B13,4:99899068-99941551 (Clone quality: bE513B13 on chr=4; Num_of_Contigs=7; )
RAB14		ENSSSCG00000005514	1:274928809-274955608
RAB15		ENSSSCG00000002280	7:97559082-97563430		FP236589,CH242-419H20,7:97557190-97566264 (Clone quality: bE419H20 on chr=7; Num_of_Contigs=10; )
RAB17		ENSSSCG00000016328	15:129652446-129663911
RAB18		ENSSSCG00000009897	14:40272495-40287691		CU062612,CH242-93C5,14:40150672-40322842 (Clone quality: bE93C5 on chr=14; Num_of_Contigs=2; )
RAB18		location ⇒	9:7772341-7772470		CU638671,CH242-188E8,9:7745474-7773512 (Clone quality: bE188E8 on chr=9; Num_of_Contigs=8; )
RAB19		ENSSSCG00000016499	18:7783366-7786848		CU655865,CH242-334M24,18:7775821-7788399 (Clone quality: bE334M24 on chr=18; Num_of_Contigs=7; )
RAB1A		ENSSSCG00000008359	3:70732426-70763760		CU928819,CH242-253B13,3:70717646-70769112 (Clone quality: bE253B13 on chr=3; Num_of_Contigs=2; )
RAB20		ENSSSCG00000009546	11:77468650-77468946		CU041289,CH242-99E18,11:77465892-77469064 (Clone quality: bE99E18 on chr=11; Num_of_Contigs=10; )
RAB21		ENSSSCG00000000511	5:34829275-34858125		CU457452,CH242-42A3,5:34825075-34887860 (Clone quality: bE42A3 on chr=5; Num_of_Contigs=4; )
RAB22A		ENSSSCG00000007513	17:61117820-61168310	CT009685,CH242-172A22,17:61076185-61204463 (Clone quality: bE172A22 on chr=17; Num_of_Contigs=3; )
RAB23		ENSSSCG00000001495	7:33056076-33072116
RAB24		ENSSSCG00000014043	2:69752584-69754802	CU915382,CH242-167E23,2:69697156-69852996 (Clone quality: bE167E23 on chr=2; Num_of_Contigs=8; )
RAB25		ENSSSCG00000006498	4:97907394-97916970		CU302298,CH242-261P14,4:97896859-97936068 (Clone quality: bE261P14 on chr=4; Num_of_Contigs=4; )
RAB26		ENSSSCG00000008042	3:36513934-36518615		FP102350,CH242-207G4,3:36503076-36556623 (Clone quality: bE207G4 on chr=3; Num_of_Contigs=8; )
RAB27A		ENSSSCG00000004612	1:121265136-121337539
RAB27B		ENSSSCG00000004533	1:107249691-107261492		CU469481,CH242-280O12,1:107132216-107314734 (Clone quality: bE280O12 on chr=1; Num_of_Contigs=1; )
RAB28		ENSSSCG00000008733	8:4701096-4716939		FP085464,CH242-222K13,8:4634524-4724824 (Clone quality: bE222K13 on chr=8; Num_of_Contigs=3; )
RAB2A		ENSSSCG00000006232	4:75390466-75474542
RAB30		ENSSSCG00000014900	9:17201549-17291140
RAB31		location ⇒	6:66995682-66995762		CU694765,CH242-143B24,6:66975765-67012805 (Clone quality: bE143B24 on chr=6; Num_of_Contigs=15; )
RAB31		location ⇒	6:67023219-67023328		CU694765,CH242-143B24,6:67012906-67027772 (Clone quality: bE143B24 on chr=6; Num_of_Contigs=15; )
RAB31		location ⇒	6:67038261-67038181		CU694765,CH242-143B24,6:67033318-67049060 (Clone quality: bE143B24 on chr=6; Num_of_Contigs=15; )
RAB31		location ⇒	6:67039203-67039151		CU694765,CH242-143B24,6:67033318-67049060 (Clone quality: bE143B24 on chr=6; Num_of_Contigs=15; )
RAB32		ENSSSCG00000004117	1:19986491-20008415
RAB33A		ENSSSCG00000012658	X:104880782-104891790

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).