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)

ATP6V1D		ENSSSCG00000002288	7:99474673-99493431		CT967298,CH242-176H11,7:99387011-99569801 (Clone quality: bE176H11 on chr=7; Num_of_Contigs=1; )
ATP6V1E1		ENSSSCG00000000767	5:65444700-65464650
ATP6V1E1		location ⇒	5:561898-563072		CU856016,CH242-237J19,5:555726-564846 (Clone quality: bE237J19 on chr=5; Num_of_Contigs=7; )
ATP6V1E1		location ⇒	5:65445330-65444703		CU929579,CH242-160B15,5:65439866-65460340 (Clone quality: bE160B15 on chr=5; Num_of_Contigs=9; )
ATP6V1E1		location ⇒	5:65464644-65464498		CU929579,CH242-160B15,5:65462557-65477894 (Clone quality: bE160B15 on chr=5; Num_of_Contigs=9; )
ATP6V1E1		location ⇒	5:759516-760210		CU694738,CH242-504C4,5:759497-761967 (Clone quality: bE504C4 on chr=5; Num_of_Contigs=10; )
ATP6V1E2		ENSSSCG00000008441	3:87441099-87441779		CU855724,CH242-31C18,3:87438278-87446148 (Clone quality: bE31C18 on chr=3; Num_of_Contigs=5; )
ATP6V1G1		location ⇒	4:46128795-46129160		FP089561,CH242-272E5,4:46107198-46131123 (Clone quality: bE272E5 on chr=4; Num_of_Contigs=5; )
ATP6V1G1		location ⇒	4:46129529-46129735		FP089561,CH242-272E5,4:46107198-46131123 (Clone quality: bE272E5 on chr=4; Num_of_Contigs=5; )
ATP6V1G2		ENSSSCG00000001401	7:27630405-27632063	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
ATP6V1G3		ENSSSCG00000010905	10:22499730-22522663
ATP6V1H		ENSSSCG00000006263	4:80311864-80370177
ATP6_PIG		ENSSSCG00000018081	MT:9120-9800
ATP7A		ENSSSCG00000012437	X:61503350-61559001		CU638862,CH242-477H4,X:61460262-61598813 (Clone quality: bE477H4 on chr=X; Num_of_Contigs=10; )
ATP7B		ENSSSCG00000009382	11:15970505-15991591
ATP8A1		ENSSSCG00000008803	8:28268621-28397410		CU694821,CH242-147I10,8:28261291-28427575 (Clone quality: bE147I10 on chr=8; Num_of_Contigs=1; )
ATP8B1		ENSSSCG00000004921	1:169967760-170093696
ATP8B2		ENSSSCG00000006550	4:99455658-99474350		CU856218,CH242-277E7,4:99454245-99496470 (Clone quality: bE277E7 on chr=4; Num_of_Contigs=4; )
ATP8B3		ENSSSCG00000013440	2:46750854-46771652
ATP8B4		ENSSSCG00000004646	1:126930123-127186765
ATP8_PIG		ENSSSCG00000018080	MT:8959-9162
ATP9A		ENSSSCG00000007478	17:55130213-55266427	CR956386,CH242-152A8,17:55100652-55296226 (No clone quality info on bE152A8)
ATPAF1		ENSSSCG00000003896	6:117900015-117930641
ATPBD4		ENSSSCG00000004798	1:142987385-142998128
ATPDase		ENSSSCG00000010497	14:112352301-112444933
ATPGD1		ENSSSCG00000012911	2:3478706-3484319		CU633429,CH242-6G2,2:3468458-3486670 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
ATPK_PIG		ENSSSCG00000007621	3:5809518-5817070		FP102617,CH242-199P18,3:5759765-5834782 (Clone quality: bE199P18 on chr=3; Num_of_Contigs=6; )
ATR		ENSSSCG00000008340	3:67221163-67472877
ATR		ENSSSCG00000011679	13:67779632-67893995
ATR		ENSSSCG00000011359	13:26222012-26276478
ATRIP		ENSSSCG00000011359	13:26222012-26276478
ATRN		ENSSSCG00000007153	17:33644913-33827182
ATRN		location ⇒	17:33731796-33731656		CU468397,CH242-208K2,17:33707807-33793840 (Clone quality: bE208K2 on chr=17; Num_of_Contigs=2; )
ATRN		location ⇒	17:33732735-33732642		CU468397,CH242-208K2,17:33707807-33793840 (Clone quality: bE208K2 on chr=17; Num_of_Contigs=2; )
ATRNL1		ENSSSCG00000010654	14:131290888-131394587
ATRNL1		location ⇒	14:131501330-131501424		CU915583,CH242-144E8,14:131458912-131652329 (Clone quality: bE144E8 on chr=14; Num_of_Contigs=1; )
ATRNL1		location ⇒	14:131507780-131507860		CU915583,CH242-144E8,14:131458912-131652329 (Clone quality: bE144E8 on chr=14; Num_of_Contigs=1; )
ATRNL1		location ⇒	14:131509808-131509967		CU915583,CH242-144E8,14:131458912-131652329 (Clone quality: bE144E8 on chr=14; Num_of_Contigs=1; )
ATRNL1		location ⇒	14:131580495-131580575		CU915583,CH242-144E8,14:131458912-131652329 (Clone quality: bE144E8 on chr=14; Num_of_Contigs=1; )
ATRX		ENSSSCG00000012434	X:61253243-61288334
ATRX		location ⇒	X:61193880-61193746		CU928840,CH242-486G13,X:61192812-61204218 (Clone quality: bE486G13 on chr=X; Num_of_Contigs=11; )
ATRX		location ⇒	X:61275308-61275442		FP102832,CH242-27L23,X:61271649-61277301 (Clone quality: bE27L23 on chr=X; Num_of_Contigs=12; )
ATRX		location ⇒	X:61286397-61287814		FP102832,CH242-27L23,X:61277402-61288337 (Clone quality: bE27L23 on chr=X; Num_of_Contigs=12; )
ATRX		location ⇒	X:61351255-61351015		CU928419,CH242-185D21,X:61350864-61356990 (Clone quality: bE185D21 on chr=X; Num_of_Contigs=9; )
ATXN1		ENSSSCG00000001065	7:12735377-12753517		CU468874,CH242-275A4,7:12717108-12821991 (Clone quality: bE275A4 on chr=7; Num_of_Contigs=3; )
ATXN10		ENSSSCG00000000008	5:259205-283748
ATXN1L		ENSSSCG00000002742	6:10521385-10523127		CU467029,CH242-364E21,6:10516296-10523128 (Clone quality: bE364E21 on chr=6; Num_of_Contigs=16; )
ATXN2		ENSSSCG00000009834	14:32715334-32822512
ATXN3L		ENSSSCG00000002446	7:121629762-121662799
ATXN7		ENSSSCG00000011493	13:38259487-38347868

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, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-32

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).