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)

ZSCAN12		ENSSSCG00000001209	7:23749244-23768550	CU062578,CH242-485A8,7:23636539-23857828 (Clone quality: bE485A8 on chr=7; Num_of_Contigs=2; )
ZSCAN20		ENSSSCG00000003621	6:61226831-61238890		CU466408,CH242-496L23,6:61180243-61284656 (Clone quality: bE496L23 on chr=6; Num_of_Contigs=3; )
ZSCAN21		ENSSSCG00000009866	14:38049340-38050749		CU468473,CH242-266G24,14:38018002-38082673 (Clone quality: bE266G24 on chr=14; Num_of_Contigs=4; )
ZSCAN23		ENSSSCG00000001210	7:23783272-23785402	CU062578,CH242-485A8,7:23636539-23857828 (Clone quality: bE485A8 on chr=7; Num_of_Contigs=2; )
ZSCAN29		ENSSSCG00000004709	1:134176671-134186378	CU210852,CH242-452O20,1:134123075-134309699 (Clone quality: bE452O20 on chr=1; Num_of_Contigs=4; )
ZSCAN4		ENSSSCG00000003987	6:122450122-122451688		CU929502,CH242-221H21,6:122418560-122496106 (Clone quality: bE221H21 on chr=6; Num_of_Contigs=5; )
ZSWIM1		ENSSSCG00000007428	17:50140162-50141636
ZSWIM2		ENSSSCG00000016030	15:86091164-86101076
ZSWIM3		ENSSSCG00000007427	17:50119329-50137248		CU076086,CH242-56C16,17:50115290-50140393 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
ZSWIM4		ENSSSCG00000013758	2:56833996-56857014		FP016000,CH242-10C10,2:56824783-56952713 (Clone quality: bE10C10 on chr=2; Num_of_Contigs=2; )
ZSWIM5		ENSSSCG00000003921	6:119127042-119157804		FP102605,CH242-186A16,6:119120152-119190598 (Clone quality: bE186A16 on chr=6; Num_of_Contigs=3; )
ZSWIM6		location ⇒	16:38280045-38279847		CU640406,CH242-276E13,16:38279783-38283128 (Clone quality: bE276E13 on chr=16; Num_of_Contigs=11; )
ZSWIM7		ENSSSCG00000018036	12:56357522-56367778		CU467081,CH242-221I17,12:56357492-56370467 (Clone quality: bE221I17 on chr=12; Num_of_Contigs=15; )
ZUFSP		ENSSSCG00000004263	1:46922801-46943234		CU407116,CH242-348P6,1:46909506-46943602 (Clone quality: bE348P6 on chr=1; Num_of_Contigs=11; )
ZW10		ENSSSCG00000015050	9:40322867-40362147
ZWILCH		ENSSSCG00000004946	1:171677492-171701612
ZXDC		ENSSSCG00000001824	7:59181434-59212781	CT868688,CH242-510G16,7:59026976-59242142 (Clone quality: bE510G16 on chr=7; Num_of_Contigs=3; )
ZYG11A		ENSSSCG00000003855	6:113236291-113270989
ZYG11B		ENSSSCG00000003857	6:113319918-113346491
ZYX		location ⇒	18:5780997-5780818		CU929961,CH242-59I9,18:5712406-5783203 (Clone quality: bE59I9 on chr=18; Num_of_Contigs=6; )
ZYX		location ⇒	18:5781282-5781111		CU929961,CH242-59I9,18:5712406-5783203 (Clone quality: bE59I9 on chr=18; Num_of_Contigs=6; )
ZYX		location ⇒	18:6051961-6052132		CU928380,CH242-107B19,18:6050676-6053603 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
ZYX		location ⇒	18:6052246-6052425		CU928380,CH242-107B19,18:6050676-6053603 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
ZZEF1		ENSSSCG00000017875	12:47327565-47365443
ZZZ3		ENSSSCG00000003772	6:94674055-94806892

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-25

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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).