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)

Q9GMA7_PIG		ENSSSCG00000002486	7:124534585-124543258		CU302448,CH242-17C18,7:124533478-124548661 (Clone quality: bE17C18 on chr=7; Num_of_Contigs=5; )
Q9GMZ3_PIG		ENSSSCG00000000715	5:61177442-61177765		CU582813,CH242-426K5,5:61175186-61178004 (Clone quality: bE426K5 on chr=5; Num_of_Contigs=10; )
Q9H0N3		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
Q9MZA8_PIG		ENSSSCG00000017695	12:37029878-37030102		CU466977,CH242-506H19,12:37029322-37037310 (Clone quality: bE506H19 on chr=12; Num_of_Contigs=13; )
Q9N0Y9_PIG		ENSSSCG00000004626	1:124728464-124773384
Q9N1D2_PIG		ENSSSCG00000000089	5:5237948-5303945
Q9N1Y1_PIG		ENSSSCG00000012322	X:45371154-45421544
Q9N1Y1_PIG		ENSSSCG00000012322	X:45371154-45421544
Q9NPM1		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
Q9NVL6		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
Q9TRG6_PIG		ENSSSCG00000005213	1:226680900-226687262		CU302244,CH242-254J19,1:226615674-226772700 (Clone quality: bE254J19 on chr=1; Num_of_Contigs=1; )
Q9TSJ2_PIG		ENSSSCG00000001007	7:2837181-2849640
Q9TSV9_PIG		ENSSSCG00000001232	7:24551875-24563032	CU311184,CH242-196B23,7:24509864-24676459 (Clone quality: bE196B23 on chr=7; Num_of_Contigs=3; )
Q9TSX0_PIG		ENSSSCG00000013317	2:26596563-26598709
Q9TTN8_PIG		ENSSSCG00000006517	4:98621708-98622488		CU469433,CH242-42F16,4:98620833-98627354 (Clone quality: bE42F16 on chr=4; Num_of_Contigs=13; )
Q9TTN9_PIG		ENSSSCG00000014333	2:127433066-127434397		CU856219,CH242-295G13,2:127416432-127434522 (Clone quality: bE295G13 on chr=2; Num_of_Contigs=12; )
Q9TTN9_PIG		ENSSSCG00000014336	2:127526032-127528371		FP102255,CH242-413P24,2:127510301-127565540 (Clone quality: bE413P24 on chr=2; Num_of_Contigs=3; )
Q9TTZ4_PIG		ENSSSCG00000008154	3:47183056-47201127
Q9TUK2_PIG		ENSSSCG00000012478	X:75146986-75148300		FP102041,CH242-189G21,X:75145280-75148424 (Clone quality: bE189G21 on chr=X; Num_of_Contigs=14; )
Q9TUP1_PIG		ENSSSCG00000016710	18:45005813-45011827
Q9TUP6_PIG		ENSSSCG00000003597	6:60233361-60265104
Q9XSE5_PIG		ENSSSCG00000013563	2:50600116-50609142		FP102248,CH242-295L18,2:50597874-50637371 (Clone quality: bE295L18 on chr=2; Num_of_Contigs=7; )
Q9XT08_PIG		ENSSSCG00000015663	9:132324204-132358249		CU633410,CH242-391L17,9:132252384-132466044 (Clone quality: bE391L17 on chr=9; Num_of_Contigs=2; )
Q9XT34_PIG		ENSSSCG00000013530	2:49506685-49507770		FP089464,CH242-231P22,2:49500853-49563374 (Clone quality: bE231P22 on chr=2; Num_of_Contigs=4; )
QARS		ENSSSCG00000011374	13:26666151-26673660		CU856115,CH242-45E6,13:26664108-26688116 (Clone quality: bE45E6 on chr=13; Num_of_Contigs=7; )
QKI		ENSSSCG00000004029	1:5590141-5695970
QPCT		ENSSSCG00000008491	3:95934715-95960054
QRFP		ENSSSCG00000005705	1:285996931-285997335	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
QRFPR		ENSSSCG00000009098	8:88401685-88412290		FP067390,CH242-65L9,8:88389348-88422597 (Clone quality: bE65L9 on chr=8; Num_of_Contigs=15; )
QRICH1		ENSSSCG00000011373	13:26614083-26664957
QRSL1		ENSSSCG00000004374	1:76217431-76246690
QSER1		ENSSSCG00000013314	2:26292906-26334078	CU928434,CH242-212M21,2:26147327-26334640 (Clone quality: bE212M21 on chr=2; Num_of_Contigs=7; )
QSOX1		ENSSSCG00000015535	9:114246490-114289285
QTRT1		ENSSSCG00000013637	2:52796936-52817795
QTRTD1		ENSSSCG00000011912	13:108808713-108846483

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-35

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).