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)

INTS7		ENSSSCG00000015602	9:123784455-123805672
INTS8		ENSSSCG00000006096	4:42166915-42224309
INTS9		ENSSSCG00000009681	14:12602835-12679066
INTU		ENSSSCG00000009079	8:83739350-83802383
INVS		ENSSSCG00000005388	1:253626854-253708443		CU570650,CH242-257L4,1:253624740-253721417 (Clone quality: bE257L4 on chr=1; Num_of_Contigs=4; )
IP6K1		ENSSSCG00000011390	13:27015884-27035952		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
IP6K2		ENSSSCG00000011365	13:26403022-26411099		CU861514,CH242-101J13,13:26400427-26417073 (Clone quality: bE101J13 on chr=13; Num_of_Contigs=18; )
IPCEF1		ENSSSCG00000004072	1:13308055-13361382
IPMK		ENSSSCG00000010420	14:96960892-96986116
IPO11		ENSSSCG00000016937	16:38964190-38997215		CU928415,CH242-96F6,16:38944729-39006442 (Clone quality: bE96F6 on chr=16; Num_of_Contigs=1; )
IPO4		ENSSSCG00000002000	7:81451210-81459574		CT961055,CH242-32K2,7:81442434-81553552 (Clone quality: bE32K2 on chr=7; Num_of_Contigs=2; )
IPO5		ENSSSCG00000009509	11:67997892-68127863
IPO8		ENSSSCG00000000534	5:42293942-42369897
IPO9		ENSSSCG00000010916	10:24268829-24296273		CU896694,CH242-111D22,10:24267978-24372745 (Clone quality: bE111D22 on chr=10; Num_of_Contigs=6; )
IPPK		ENSSSCG00000008076	3:37680437-37715420		FP016002,CH242-245P15,3:37670882-37732166 (Clone quality: bE245P15 on chr=3; Num_of_Contigs=9; )
IQCA1		ENSSSCG00000016321	15:128575755-128743094
IQCB1		ENSSSCG00000011881	13:104224695-104276371		CU694714,CH242-321J16,13:104205510-104351881 (Clone quality: bE321J16 on chr=13; Num_of_Contigs=1; )
IQCC		ENSSSCG00000003610	6:60828960-60831341		FP102820,CH242-217B19,6:60828632-60839730 (Clone quality: bE217B19 on chr=6; Num_of_Contigs=18; )
IQCD		ENSSSCG00000009877	14:39062494-39069827
IQCE		ENSSSCG00000007568	3:1573074-1610378
IQCG		ENSSSCG00000011855	13:101294827-101342620	CU694544,CH242-123C16,13:101156837-101363233 (Clone quality: bE123C16 on chr=13; Num_of_Contigs=6; )
IQCH		ENSSSCG00000004953	1:172527891-172706294
IQCK		ENSSSCG00000007863	3:23577500-23625945
IQGAP1		ENSSSCG00000001814	7:58750347-58775745
IQGAP1		location ⇒	7:58777313-58777104		CU467044,CH242-111G6,7:58758766-58780100 (Clone quality: bE111G6 on chr=7; Num_of_Contigs=11; )
IQGAP1		location ⇒	7:58778951-58778778		CU467044,CH242-111G6,7:58758766-58780100 (Clone quality: bE111G6 on chr=7; Num_of_Contigs=11; )
IQGAP1		location ⇒	7:58789539-58789375		CU467044,CH242-111G6,7:58780201-58833725 (Clone quality: bE111G6 on chr=7; Num_of_Contigs=11; )
IQGAP1		location ⇒	7:58801756-58801578		CU467044,CH242-111G6,7:58780201-58833725 (Clone quality: bE111G6 on chr=7; Num_of_Contigs=11; )
IQGAP2		ENSSSCG00000014088	2:74411210-74453628
IQGAP2		location ⇒	2:114089470-114089394		FP102025,CH242-171C14,2:114082323-114098438 (Clone quality: bE171C14 on chr=2; Num_of_Contigs=14; )
IQGAP2		location ⇒	2:43965392-43965490		CU462938,CH242-316F6,2:43957138-44080347 (Clone quality: bE316F6 on chr=2; Num_of_Contigs=2; )
IQGAP2		location ⇒	2:56851524-56851603		FP016000,CH242-10C10,2:56824783-56952713 (Clone quality: bE10C10 on chr=2; Num_of_Contigs=2; )
IQGAP2		location ⇒	2:57197377-57197294		FP103015,CH242-135B13,2:57191025-57197413 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )
IQSEC2		ENSSSCG00000012324	X:45430705-45512688
IQSEC3		ENSSSCG00000000748	5:63339727-63404765		FP102700,CH242-407J15,5:63335661-63418162 (Clone quality: bE407J15 on chr=5; Num_of_Contigs=1; )
IQUB		ENSSSCG00000016608	18:22063004-22112561	CU463288,CH242-205B13,18:21975793-22134892 (Clone quality: bE205B13 on chr=18; Num_of_Contigs=4; )
IQWD1		ENSSSCG00000006303	4:86199465-86374629
IRAK1		ENSSSCG00000012795	X:122830457-122837020	CU914490,CH242-115P19,X:122810839-122896667 (Clone quality: bE115P19 on chr=X; Num_of_Contigs=7; )
IRAK1		location ⇒	X:122836157-122836051	CU914490,CH242-115P19,X:122810839-122896667 (Clone quality: bE115P19 on chr=X; Num_of_Contigs=7; )
IRAK1		location ⇒	X:122836407-122836276	CU914490,CH242-115P19,X:122810839-122896667 (Clone quality: bE115P19 on chr=X; Num_of_Contigs=7; )
IRAK1		location ⇒	X:122836708-122836539	CU914490,CH242-115P19,X:122810839-122896667 (Clone quality: bE115P19 on chr=X; Num_of_Contigs=7; )
IRAK1		location ⇒	X:122836847-122836795	CU914490,CH242-115P19,X:122810839-122896667 (Clone quality: bE115P19 on chr=X; Num_of_Contigs=7; )
IRAK1BP1		ENSSSCG00000004472	1:92067224-92207468
IRAK1BP1		location ⇒	1:92067152-92067306		CU582852,CH242-297D20,1:92049811-92074248 (Clone quality: bE297D20 on chr=1; Num_of_Contigs=16; )
IRAK1BP1		location ⇒	1:92067366-92067650		CU582852,CH242-297D20,1:92049811-92074248 (Clone quality: bE297D20 on chr=1; Num_of_Contigs=16; )
IRAK1BP1		location ⇒	1:92133367-92133083		FP102490,CH242-23A2,1:92129147-92144017 (Clone quality: bE23A2 on chr=1; Num_of_Contigs=2; )
IRAK1BP1		location ⇒	1:92133581-92133427		FP102490,CH242-23A2,1:92129147-92144017 (Clone quality: bE23A2 on chr=1; Num_of_Contigs=2; )
IRAK2		ENSSSCG00000011570	13:55640311-55806692
IRAK2		location ⇒	13:55534455-55534588		CU655990,CH242-268L7,13:55512556-55562333 (Clone quality: bE268L7 on chr=13; Num_of_Contigs=5; )
IRAK2		location ⇒	13:55544968-55545152		CU655990,CH242-268L7,13:55512556-55562333 (Clone quality: bE268L7 on chr=13; Num_of_Contigs=5; )

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, 1101-33

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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).