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)

CINP		ENSSSCG00000002530	7:131456242-131587586
CIRBP		ENSSSCG00000013427	2:46400461-46403609		CU929580,CH242-161G11,2:46394239-46415602 (Clone quality: bE161G11 on chr=2; Num_of_Contigs=11; )
CIRH1A		ENSSSCG00000009450	11:32683059-32683301		CU638857,CH242-392G6,11:32672471-32694168 (Clone quality: bE392G6 on chr=11; Num_of_Contigs=10; )
CISD2		ENSSSCG00000009164	8:101178233-101180799		FP090890,CH242-268L17,8:101170315-101187350 (Clone quality: bE268L17 on chr=8; Num_of_Contigs=2; )
CISH		ENSSSCG00000011414	13:27759122-27761741		CU467603,CH242-65F21,13:27740802-27761783 (Clone quality: bE65F21 on chr=13; Num_of_Contigs=9; )
CIT		ENSSSCG00000009837	14:33038433-33074999
CITED1		ENSSSCG00000012409	X:57492675-57498371		CU469343,CH242-396K9,X:57477356-57499842 (Clone quality: bE396K9 on chr=X; Num_of_Contigs=18; )
CITED2		ENSSSCG00000004142	1:26499015-26499836		CU302363,CH242-187O14,1:26498270-26530532 (Clone quality: bE187O14 on chr=1; Num_of_Contigs=5; )
CITED4		ENSSSCG00000003974	6:121720158-121721248		FP016067,CH242-126M8,6:121677068-121736023 (Clone quality: bE126M8 on chr=6; Num_of_Contigs=2; )
CIZ1		ENSSSCG00000005640	1:283255579-283275705
CKAP2		ENSSSCG00000009378	11:15769449-15783023		CU856639,CH242-171M18,11:15766368-15830462 (Clone quality: bE171M18 on chr=11; Num_of_Contigs=3; )
CKAP2L		ENSSSCG00000008089	3:39033924-39039727		CU855588,CH242-108K8,3:39033723-39081464 (Clone quality: bE108K8 on chr=3; Num_of_Contigs=4; )
CKAP4		ENSSSCG00000000171	5:12381941-12389594
CKB		location ⇒	X:71917827-71917579	CU234148,CH242-442M8,X:71836687-71999708 (Clone quality: bE442M8 on chr=X; Num_of_Contigs=1; )
CKLF		ENSSSCG00000011234	13:16094008-16105509		CU695035,CH242-232M3,13:16074613-16112727 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CKLF		ENSSSCG00000011232	13:15989159-16011778
CKLF		ENSSSCG00000002028	7:82104640-82107317		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
CKLF		ENSSSCG00000009462	11:44596280-44731528
CKLFSF7		ENSSSCG00000011234	13:16094008-16105509		CU695035,CH242-232M3,13:16074613-16112727 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CKLFSF7		location ⇒	13:16094610-16094010		CU695035,CH242-232M3,13:16074613-16112727 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CKLFSF7		location ⇒	13:16100206-16100107		CU695035,CH242-232M3,13:16074613-16112727 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CKLFSF7		location ⇒	13:16105504-16105329		CU695035,CH242-232M3,13:16074613-16112727 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CKLFSF7		location ⇒	13:16164530-16164743		CU695035,CH242-232M3,13:16139966-16170288 (Clone quality: bE232M3 on chr=13; Num_of_Contigs=6; )
CKMT2		ENSSSCG00000014128	2:79105664-79148276
CKS2		ENSSSCG00000009582	14:1102193-1107817		CU407020,CH242-127G5,14:1013971-1134837 (Clone quality: bE127G5 on chr=14; Num_of_Contigs=2; )
CLASP1		ENSSSCG00000015731	15:28251019-28282428		CU570904,CH242-119O22,15:28249508-28369816 (Clone quality: bE119O22 on chr=15; Num_of_Contigs=7; )
CLASP2		ENSSSCG00000011236	13:16284448-16407111
CLC		ENSSSCG00000008024	3:36088238-36109007		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
CLC		ENSSSCG00000009713	14:19954625-20042016
CLC		ENSSSCG00000003429	6:48754476-48785463		CU695168,CH242-2E14,6:48744157-48789117 (Clone quality: bE2E14 on chr=6; Num_of_Contigs=4; )
CLC-2		location ⇒	11:46512144-46512177		CU928033,CH242-408E22,11:46496971-46530486 (Clone quality: bE408E22 on chr=11; Num_of_Contigs=3; )
CLC-2		location ⇒	11:46512384-46512425		CU928033,CH242-408E22,11:46496971-46530486 (Clone quality: bE408E22 on chr=11; Num_of_Contigs=3; )
CLC-2		location ⇒	11:46545592-46545625		CU914606,CH242-212M22,11:46531187-46550506 (Clone quality: bE212M22 on chr=11; Num_of_Contigs=13; )
CLC-2		location ⇒	11:46545832-46545873		CU914606,CH242-212M22,11:46531187-46550506 (Clone quality: bE212M22 on chr=11; Num_of_Contigs=13; )
CLC-2		location ⇒	2:69715815-69715582	CU915382,CH242-167E23,2:69697156-69852996 (Clone quality: bE167E23 on chr=2; Num_of_Contigs=8; )
CLC-2		location ⇒	2:69715861-69715582	CU915382,CH242-167E23,2:69697156-69852996 (Clone quality: bE167E23 on chr=2; Num_of_Contigs=8; )
CLC-2		location ⇒	7:131807880-131808154		CU633632,CH242-139M12,7:131807603-131831335 (Clone quality: bE139M12 on chr=7; Num_of_Contigs=22; )
CLC-2		location ⇒	7:131808426-131808764		CU633632,CH242-139M12,7:131807603-131831335 (Clone quality: bE139M12 on chr=7; Num_of_Contigs=22; )
CLC-2		location ⇒	7:45768289-45768410	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
CLC-2		location ⇒	7:45769101-45769222	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
CLC-2		location ⇒	7:45771330-45771421	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
CLC-5		location ⇒	14:19796044-19795952		CU633253,CH242-248E6,14:19744713-19834358 (Clone quality: bE248E6 on chr=14; Num_of_Contigs=2; )
CLC-5		location ⇒	14:19960830-19960738		CU407040,CH242-197C3,14:19839359-19990350 (Clone quality: bE197C3 on chr=14; Num_of_Contigs=1; )
CLCA1		ENSSSCG00000006933	4:134581304-134613011
CLCA2		ENSSSCG00000006935	4:134628323-134662611
CLCC1		ENSSSCG00000006841	4:115583761-115606521
CLCF1		ENSSSCG00000012915	2:3549191-3551617		CU633429,CH242-6G2,2:3540925-3556381 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CLCF1		location ⇒	2:3548720-3548405		CU633429,CH242-6G2,2:3540925-3556381 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CLCN1		ENSSSCG00000016462	18:5793530-5828823
CLCN3		ENSSSCG00000009713	14:19954625-20042016

Go to records:
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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).