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)

DPH5		ENSSSCG00000006859	4:122141852-122176528	CU151856,CH242-234M18,4:122090631-122264880 (Clone quality: bE234M18 on chr=4; Num_of_Contigs=1; )
DPM1		ENSSSCG00000007474	17:54548053-54571391
DPM2		ENSSSCG00000005632	1:283013153-283016201		CU638853,CH242-308I15,1:282900893-283022455 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
DPM3		ENSSSCG00000006528	4:98740743-98741021		CU179666,CH242-242M24,4:98705913-98751478 (Clone quality: bE242M24 on chr=4; Num_of_Contigs=7; )
DPP10		ENSSSCG00000015711	15:20356327-20697445
DPP3		ENSSSCG00000012945	2:4331535-4371006		CU928034,CH242-426E24,2:4300015-4401092 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
DPP4		ENSSSCG00000015894	15:63908071-63990308
DPP4		location ⇒	15:63945221-63945384		FP236295,CH242-307K18,15:63904195-63969139 (Clone quality: bE307K18 on chr=15; Num_of_Contigs=3; )
DPP4		location ⇒	15:63954757-63954894		FP236295,CH242-307K18,15:63904195-63969139 (Clone quality: bE307K18 on chr=15; Num_of_Contigs=3; )
DPP4		location ⇒	15:63971277-63971471		FP236295,CH242-307K18,15:63969240-63990308 (Clone quality: bE307K18 on chr=15; Num_of_Contigs=3; )
DPP4		location ⇒	15:63989903-63990093		FP236295,CH242-307K18,15:63969240-63990308 (Clone quality: bE307K18 on chr=15; Num_of_Contigs=3; )
DPP6		ENSSSCG00000016423	18:2430867-2591941
DPP8		ENSSSCG00000004934	1:170554218-170620653
DPP8		location ⇒	1:170554355-170554218		CU463002,CH242-312G12,1:170539505-170566121 (Clone quality: bE312G12 on chr=1; Num_of_Contigs=4; )
DPP8		location ⇒	1:170558050-170557939		CU463002,CH242-312G12,1:170539505-170566121 (Clone quality: bE312G12 on chr=1; Num_of_Contigs=4; )
DPP8		location ⇒	1:170559044-170558901		CU463002,CH242-312G12,1:170539505-170566121 (Clone quality: bE312G12 on chr=1; Num_of_Contigs=4; )
DPP8		location ⇒	1:170560944-170560789		CU463002,CH242-312G12,1:170539505-170566121 (Clone quality: bE312G12 on chr=1; Num_of_Contigs=4; )
DPPIV		ENSSSCG00000015896	15:64095733-64166537
DPT		ENSSSCG00000006297	4:85586984-85618631		CU896685,CH242-323B11,4:85575374-85619644 (Clone quality: bE323B11 on chr=4; Num_of_Contigs=2; )
DPT		location ⇒	4:85586984-85587317		CU896685,CH242-323B11,4:85575374-85619644 (Clone quality: bE323B11 on chr=4; Num_of_Contigs=2; )
DPT		location ⇒	4:85603739-85603866		CU896685,CH242-323B11,4:85575374-85619644 (Clone quality: bE323B11 on chr=4; Num_of_Contigs=2; )
DPT		location ⇒	4:85613411-85613520		CU896685,CH242-323B11,4:85575374-85619644 (Clone quality: bE323B11 on chr=4; Num_of_Contigs=2; )
DPT		location ⇒	4:85617480-85617801		CU896685,CH242-323B11,4:85575374-85619644 (Clone quality: bE323B11 on chr=4; Num_of_Contigs=2; )
DPY19L2		ENSSSCG00000016663	18:37858693-37928981
DPY30		ENSSSCG00000008516	3:100925440-100938425
DPYD		ENSSSCG00000006878	4:125046399-125483759
DPYS		ENSSSCG00000006040	4:33020194-33107518
DPYSL2		ENSSSCG00000009660	14:10609850-10685028		CU468375,CH242-98K7,14:10595442-10698963 (Clone quality: bE98K7 on chr=14; Num_of_Contigs=4; )
DPYSL2		location ⇒	14:10656329-10656391		CU468375,CH242-98K7,14:10595442-10698963 (Clone quality: bE98K7 on chr=14; Num_of_Contigs=4; )
DPYSL2		location ⇒	14:10685383-10685435		CU468375,CH242-98K7,14:10595442-10698963 (Clone quality: bE98K7 on chr=14; Num_of_Contigs=4; )
DPYSL2		location ⇒	14:147178930-147178851		CU640371,CH242-130L11,14:147178341-147192788 (Clone quality: bE130L11 on chr=14; Num_of_Contigs=20; )
DPYSL2		location ⇒	14:147179523-147179465		CU640371,CH242-130L11,14:147178341-147192788 (Clone quality: bE130L11 on chr=14; Num_of_Contigs=20; )
DPYSL3		ENSSSCG00000014419	2:134508374-134538817
DPYSL4		ENSSSCG00000010762	14:147175505-147188721
DPYSL5		ENSSSCG00000008560	3:104620544-104674723
DQX1		ENSSSCG00000008269	3:62912873-62914328		CU468647,CH242-164C3,3:62911000-62914387 (Clone quality: bE164C3 on chr=3; Num_of_Contigs=12; )
DR1		ENSSSCG00000006895	4:128146388-128164900
DRAM1		ENSSSCG00000000861	5:77645610-77663463		CU896609,CH242-347A3,5:77643302-77664475 (Clone quality: bE347A3 on chr=5; Num_of_Contigs=12; )
DRAM2		ENSSSCG00000006798	4:113604028-113624088		CU468595,CH242-175A23,4:113589234-113631532 (Clone quality: bE175A23 on chr=4; Num_of_Contigs=4; )
DRAP1		ENSSSCG00000012965	2:4786821-4789104		CU928325,CH242-208C18,2:4762275-4805765 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
DRD2		ENSSSCG00000015048	9:40051843-40065065
DRD3		ENSSSCG00000011911	13:108720032-108757835
DRD4		ENSSSCG00000012851	2:264884-267989
DRD5		ENSSSCG00000008730	8:4553547-4554962		FP015995,CH242-51I6,8:4535754-4587696 (Clone quality: bE51I6 on chr=8; Num_of_Contigs=6; )
DRG1		ENSSSCG00000010029	14:49011480-49037635	CT573021,XX-BE155F1,14:48970333-49086748 (Clone quality: bE155F1 on chr=13; Num_of_Contigs=18; )
DRGX		ENSSSCG00000010390	14:93783813-93816474
DRP2		ENSSSCG00000012492	X:76237626-76272227
DSC1		ENSSSCG00000003726	6:79809463-79842495		CU467049,CH242-141H18,6:79684808-79873049 (Clone quality: bE141H18 on chr=6; Num_of_Contigs=2; )
DSC2		location ⇒	6:79596411-79596498		CU914455,CH242-81E19,6:79595319-79597592 (Clone quality: bE81E19 on chr=6; Num_of_Contigs=29; )
DSC2		location ⇒	6:79677243-79677420		CU914455,CH242-81E19,6:79676241-79678044 (Clone quality: bE81E19 on chr=6; Num_of_Contigs=29; )

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, 751-16

Report problems to zhu

iastate.edu

$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).