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)

RAD23B		ENSSSCG00000005436	1:261064428-261108974		CU463059,CH242-243J20,1:261022081-261154690 (Clone quality: bE243J20 on chr=1; Num_of_Contigs=3; )
RAD50		ENSSSCG00000014280	2:122720889-122848994
RAD51		ENSSSCG00000004766	1:137090000-137137217		CU633257,CH242-257P7,1:137003112-137140964 (Clone quality: bE257P7 on chr=1; Num_of_Contigs=3; )
RAD51		ENSSSCG00000002299	7:99998793-100042480		CT797462,CH242-97L17,7:99890302-100098604 (Clone quality: bE97L17 on chr=7; Num_of_Contigs=2; )
RAD51		ENSSSCG00000000722	5:61615870-61640464		CU915392,CH242-243A6,5:61597036-61647534 (Clone quality: bE243A6 on chr=5; Num_of_Contigs=1; )
RAD51		location ⇒	1:137090522-137090013		CU633257,CH242-257P7,1:137003112-137140964 (Clone quality: bE257P7 on chr=1; Num_of_Contigs=3; )
RAD51		location ⇒	1:137091677-137091546		CU633257,CH242-257P7,1:137003112-137140964 (Clone quality: bE257P7 on chr=1; Num_of_Contigs=3; )
RAD51		location ⇒	1:137178971-137179102		CU469090,CH242-416D6,1:137176175-137185091 (Clone quality: bE416D6 on chr=1; Num_of_Contigs=22; )
RAD51		location ⇒	1:137180126-137180635		CU469090,CH242-416D6,1:137176175-137185091 (Clone quality: bE416D6 on chr=1; Num_of_Contigs=22; )
RAD51AP1		ENSSSCG00000000722	5:61615870-61640464		CU915392,CH242-243A6,5:61597036-61647534 (Clone quality: bE243A6 on chr=5; Num_of_Contigs=1; )
RAD51AP2		ENSSSCG00000008616	3:111698216-111698650		CU856226,CH242-192F21,3:111679440-111698670 (Clone quality: bE192F21 on chr=3; Num_of_Contigs=9; )
RAD51C		ENSSSCG00000017646	12:32981853-33014598
RAD51L1		ENSSSCG00000002299	7:99998793-100042480		CT797462,CH242-97L17,7:99890302-100098604 (Clone quality: bE97L17 on chr=7; Num_of_Contigs=2; )
RAD52		ENSSSCG00000000754	5:63902432-63925856		CU463193,CH242-251B18,5:63844856-63945660 (Clone quality: bE251B18 on chr=5; Num_of_Contigs=3; )
RAD54L		ENSSSCG00000003905	6:118215230-118243066		CU694667,CH242-117A15,6:118158784-118247648 (Clone quality: bE117A15 on chr=6; Num_of_Contigs=3; )
RAD54L2		ENSSSCG00000011425	13:28716979-28731168
RAD9A		ENSSSCG00000012914	2:3504881-3510934		CU633429,CH242-6G2,2:3486771-3519792 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
RAD9B		ENSSSCG00000009824	14:31896749-31930523
RADIL		ENSSSCG00000007575	3:2628919-3393079
RAE1		ENSSSCG00000007503	17:60287281-60303373	CR956362,CH242-98D1,17:60206269-60416771 (No clone quality info on bE98D1)
RAF1		location ⇒	13:85844418-85844331		CU655988,CH242-249O8,13:85834232-85845881 (Clone quality: bE249O8 on chr=13; Num_of_Contigs=8; )
RAG1		ENSSSCG00000006529	4:98742216-98744330		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )
RAG1		ENSSSCG00000013289	2:23145858-23146631	FP102503,CH242-427N16,2:23115394-23146726 (Clone quality: bE427N16 on chr=2; Num_of_Contigs=4; )
RAG1		location ⇒	2:23146324-23145691	FP102503,CH242-427N16,2:23115394-23146726 (Clone quality: bE427N16 on chr=2; Num_of_Contigs=4; )
RAG1AP1		ENSSSCG00000006529	4:98742216-98744330		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )
RAG2		ENSSSCG00000013287	2:23131149-23132732	FP102503,CH242-427N16,2:23115394-23146726 (Clone quality: bE427N16 on chr=2; Num_of_Contigs=4; )
RAG2		location ⇒	2:1425545-1425684		CU469203,CH242-236K15,2:1423279-1429974 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )
RAG2		location ⇒	2:1545628-1545737		FP085516,CH242-270C7,2:1536877-1576893 (Clone quality: bE270C7 on chr=2; Num_of_Contigs=5; )
RAG2		location ⇒	2:1828238-1828316		FP102526,CH242-47B2,2:1818369-1840710 (Clone quality: bE47B2 on chr=2; Num_of_Contigs=9; )
RAG2		location ⇒	2:210993-211125		FP015900,CH242-40P17,2:201823-266668 (Clone quality: bE40P17 on chr=2; Num_of_Contigs=6; )
RAGE		ENSSSCG00000002531	7:131508878-131681515
RAI		ENSSSCG00000004655	1:128073308-128235567
RAI		ENSSSCG00000003313	6:41814425-41815804		FP236123,CH242-107C1,6:41810249-41839566 (Clone quality: bE107C1 on chr=6; Num_of_Contigs=14; )
RAI		ENSSSCG00000009581	14:768928-935245
RAI14		ENSSSCG00000016824	16:17858299-17972970
RAI2		ENSSSCG00000012153	X:13782736-13784331	CU207277,CH242-186H22,X:13637952-13829937 (Clone quality: bE186H22 on chr=X; Num_of_Contigs=1; )
RALBP1		ENSSSCG00000004146	1:26816114-26897029
RALBP1		ENSSSCG00000003680	6:67201402-67247419
RALBP1		ENSSSCG00000012150	X:12872405-13122217
RALGAPA1		ENSSSCG00000001948	7:70183479-70242124	CT797476,CH242-73E24,7:70069396-70242489 (Clone quality: bE73E24 on chr=7; Num_of_Contigs=2; )
RALGPS1		ENSSSCG00000005607	1:281880030-282119599
RALGPS2		ENSSSCG00000015523	9:113397661-113432052
RALY		ENSSSCG00000006149	4:53818628-54005841
RALY		ENSSSCG00000007275	17:39589418-39625176
RALY		location ⇒	17:39423162-39422815		CU062552,CH242-30M15,17:39420687-39425289 (Clone quality: bE30M15 on chr=17; Num_of_Contigs=4; )
RALY		location ⇒	17:39431258-39430993		CU062552,CH242-30M15,17:39428859-39437405 (Clone quality: bE30M15 on chr=17; Num_of_Contigs=4; )
RALY		location ⇒	17:39616552-39616817		CU855967,CH242-138N13,17:39606039-39642723 (Clone quality: bE138N13 on chr=17; Num_of_Contigs=11; )
RALY		location ⇒	17:39624827-39625174		CU855967,CH242-138N13,17:39606039-39642723 (Clone quality: bE138N13 on chr=17; Num_of_Contigs=11; )
RALYL		ENSSSCG00000006149	4:53818628-54005841
RALYL		location ⇒	4:53792074-53791433		CU571221,CH242-28C2,4:53783832-53806522 (Clone quality: bE28C2 on chr=4; Num_of_Contigs=6; )

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).