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)

C3		ENSSSCG00000004485	1:97276232-97430354
C3		ENSSSCG00000006691	4:103565894-103577132		CU606940,CH242-153I6,4:103564526-103582920 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
C3		ENSSSCG00000009581	14:768928-935245
C3		ENSSSCG00000013551	2:50094164-50127406
C3		location ⇒	2:50094376-50094179		CU694937,CH242-71B7,2:50092213-50102355 (Clone quality: bE71B7 on chr=2; Num_of_Contigs=4; )
C3		location ⇒	2:50109130-50108924		CU681822,CH242-171H11,2:50108713-50118107 (Clone quality: bE171H11 on chr=2; Num_of_Contigs=13; )
C3		location ⇒	2:50113666-50113452		CU681822,CH242-171H11,2:50108713-50118107 (Clone quality: bE171H11 on chr=2; Num_of_Contigs=13; )
C3		location ⇒	2:50126531-50126339		CU681822,CH242-171H11,2:50121631-50133880 (Clone quality: bE171H11 on chr=2; Num_of_Contigs=13; )
C3AR1		location ⇒	17:1671938-1672043		CU672274,CH242-509G10,17:1667284-1680930 (Clone quality: bE509G10 on chr=17; Num_of_Contigs=17; )
C3AR1		location ⇒	17:3760190-3760271		CU856052,CH242-457I4,17:3750337-3763232 (Clone quality: bE457I4 on chr=17; Num_of_Contigs=3; )
C3AR1		location ⇒	17:5474714-5474791		CU467683,CH242-191D4,17:5462149-5487727 (Clone quality: bE191D4 on chr=17; Num_of_Contigs=16; )
C3AR1		location ⇒	17:6879660-6879765		CU861958,CH242-252F14,17:6864603-6915949 (Clone quality: bE252F14 on chr=17; Num_of_Contigs=5; )
C3orf1		ENSSSCG00000011900	13:105512070-105524170
C3orf10		location ⇒	13:55499298-55499466		CU464019,CH242-82C2,13:55495223-55512555 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
C3orf10		location ⇒	13:55507136-55507215		CU464019,CH242-82C2,13:55495223-55512555 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
C3orf10		location ⇒	13:55507485-55507630		CU464019,CH242-82C2,13:55495223-55512555 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
C3orf10		location ⇒	13:55507858-55508176		CU464019,CH242-82C2,13:55495223-55512555 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
C3orf14		ENSSSCG00000011486	13:37125685-37142048
C3orf15		ENSSSCG00000011892	13:105205784-105329997
C3orf16		ENSSSCG00000011706	13:73294808-73331017
C3orf17		ENSSSCG00000011923	13:109513400-109524631		CU633650,CH242-194M8,13:109451377-109534158 (Clone quality: bE194M8 on chr=13; Num_of_Contigs=3; )
C3orf18		ENSSSCG00000011413	13:27697148-27702413
C3orf22		ENSSSCG00000011626	13:60210116-60216584		CU856309,CH242-278B22,13:60136689-60224349 (Clone quality: bE278B22 on chr=13; Num_of_Contigs=6; )
C3orf25		ENSSSCG00000011587	13:57217123-57236318
C3orf26		ENSSSCG00000011970	13:116802345-116894237
C3orf30		ENSSSCG00000011905	13:105803375-105807150		CU928677,CH242-71E1,13:105796469-105849718 (Clone quality: bE71E1 on chr=13; Num_of_Contigs=4; )
C3orf31		ENSSSCG00000011578	13:56454847-56515832
C3orf37		ENSSSCG00000011611	13:59196108-59279101
C3orf39		ENSSSCG00000011293	13:22362303-22364045		CU855990,CH242-180A2,13:22354558-22384803 (Clone quality: bE180A2 on chr=13; Num_of_Contigs=10; )
C3orf45		ENSSSCG00000011401	13:27414228-27417248		CU468071,CH242-427D1,13:27397872-27424038 (Clone quality: bE427D1 on chr=13; Num_of_Contigs=7; )
C3orf49		ENSSSCG00000011490	13:38119067-38130836		FP102046,CH242-468J9,13:38116116-38147063 (Clone quality: bE468J9 on chr=13; Num_of_Contigs=11; )
C3orf54		ENSSSCG00000011392	13:27089889-27091615		CU914539,CH242-222N14,13:27078304-27105846 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
C3orf58		ENSSSCG00000011687	13:69170772-69188672
C3orf59		ENSSSCG00000011819	13:98182106-98183392		CU633267,CH242-281O8,13:98148722-98185206 (Clone quality: bE281O8 on chr=13; Num_of_Contigs=4; )
C3orf62		ENSSSCG00000011381	13:26792144-26795521		CU856115,CH242-45E6,13:26786505-26808358 (Clone quality: bE45E6 on chr=13; Num_of_Contigs=7; )
C3orf64		ENSSSCG00000011504	13:42215547-42249381		CU464138,CH242-109C12,13:42202753-42258663 (Clone quality: bE109C12 on chr=13; Num_of_Contigs=5; )
C3orf67		ENSSSCG00000011482	13:34070941-34119019
C3orf70		ENSSSCG00000011789	13:93000242-93116126
C3orf75		ENSSSCG00000011336	13:25225237-25241878
C3P1		ENSSSCG00000013665	2:53439860-53470300
C3U2T0_PIG		ENSSSCG00000004283	1:55397780-55398896		CU468562,CH242-237C6,1:55385514-55409408 (Clone quality: bE237C6 on chr=1; Num_of_Contigs=16; )
C3VMK2_PIG		ENSSSCG00000012058	13:140584267-140584986		CU928021,CH242-178H7,13:140575627-140587218 (Clone quality: bE178H7 on chr=13; Num_of_Contigs=3; )
C3VMK2_PIG		ENSSSCG00000012057	13:140559517-140560236		CU638724,CH242-250N17,13:140500369-140570626 (Clone quality: bE250N17 on chr=13; Num_of_Contigs=2; )
C4A		location ⇒	7:27898304-27898392	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C4A		location ⇒	7:27900821-27900910	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C4A		location ⇒	7:27903828-27903911	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C4A		location ⇒	7:27903996-27904093	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C4B		ENSSSCG00000015661	9:132246494-132255986
C4B		ENSSSCG00000009138	8:96596051-96633160		CU463265,CH242-237G17,8:96455649-96640359 (Clone quality: bE237G17 on chr=8; Num_of_Contigs=1; )
C4B		location ⇒	7:128401-128514		CU657920,CH242-367F14,7:128181-155380 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )

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).