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)

ATXN7L1		ENSSSCG00000015432	9:98552552-98821154
ATXN7L2		ENSSSCG00000006828	4:115153903-115161433		CU633714,CH242-413N19,4:115147581-115211057 (Clone quality: bE413N19 on chr=4; Num_of_Contigs=4; )
ATXN7L3		ENSSSCG00000017362	12:16962534-16966022		CU469063,CH242-86P22,12:16960337-16967826 (Clone quality: bE86P22 on chr=12; Num_of_Contigs=21; )
AUH		ENSSSCG00000009590	14:2911107-2922187
AUP1		ENSSSCG00000008268	3:62908683-62911497
AUTS2		ENSSSCG00000007727	3:13043061-13068644
AVEN		ENSSSCG00000002247	7:88195236-88229559		CU633891,CH242-195C13,7:88161233-88310281 (Clone quality: bE195C13 on chr=7; Num_of_Contigs=3; )
AVEN		location ⇒	7:16386370-16386313		CU013508,CH242-266P14,7:16342873-16391656 (Clone quality: bE266P14 on chr=7; Num_of_Contigs=4; )
AVEN		location ⇒	7:20868033-20868090		CT757509,CH242-59J23,7:20849612-20971392 (Clone quality: bE59J23 on chr=7; Num_of_Contigs=2; )
AVEN		location ⇒	7:73950385-73950328		CU468143,CH242-103J4,7:73942821-73955374 (Clone quality: bE103J4 on chr=7; Num_of_Contigs=3; )
AVEN		location ⇒	7:97360125-97360182		CT737370,CH242-45A22,7:97273887-97416999 (Clone quality: bE45A22 on chr=7; Num_of_Contigs=1; )
AVP		ENSSSCG00000007163	17:34153617-34155563		CU302217,CH242-196N9,17:34148660-34159474 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )
AVPR1A		ENSSSCG00000000459	5:27413378-27500016
AVPR1B		ENSSSCG00000015639	9:131030250-131034023		CU855983,CH242-166L15,9:130999751-131128008 (Clone quality: bE166L15 on chr=9; Num_of_Contigs=2; )
AVPR2		ENSSSCG00000012789	X:122750024-122752424		CU915581,CH242-139K22,X:122729751-122810838 (Clone quality: bE139K22 on chr=X; Num_of_Contigs=13; )
AWN_PIG		ENSSSCG00000002980	6:33177691-33179053		FP236607,CH242-159H19,6:33151690-33180802 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AXIN2		ENSSSCG00000017265	12:10334242-10337719
AXL		ENSSSCG00000003005	6:33860521-33914906
AXL		location ⇒	6:33860872-33859786		CU915811,CH242-275M5,6:33859786-33862912 (Clone quality: bE275M5 on chr=6; Num_of_Contigs=27; )
AXL		location ⇒	6:33908993-33908871		CU915811,CH242-275M5,6:33908483-33916263 (Clone quality: bE275M5 on chr=6; Num_of_Contigs=27; )
AXL		location ⇒	6:33909461-33909368		CU915811,CH242-275M5,6:33908483-33916263 (Clone quality: bE275M5 on chr=6; Num_of_Contigs=27; )
AXL		location ⇒	6:33911535-33911434		CU915811,CH242-275M5,6:33908483-33916263 (Clone quality: bE275M5 on chr=6; Num_of_Contigs=27; )
AZGP1		ENSSSCG00000007642	3:6241086-6248437		FP102393,CH242-6M17,3:6222987-6313567 (Clone quality: bE6M17 on chr=3; Num_of_Contigs=3; )
AZGP1		location ⇒	3:6247135-6247204		FP102393,CH242-6M17,3:6222987-6313567 (Clone quality: bE6M17 on chr=3; Num_of_Contigs=3; )
AZGP1		location ⇒	3:6247903-6248426		FP102393,CH242-6M17,3:6222987-6313567 (Clone quality: bE6M17 on chr=3; Num_of_Contigs=3; )
AZI1		ENSSSCG00000017143	12:857667-860904		CU993801,CH242-26A11,12:857666-865196 (Clone quality: bE26A11 on chr=12; Num_of_Contigs=7; )
AZI2		ENSSSCG00000011220	13:12455576-12464784		CU856671,CH242-489B14,13:12454758-12470463 (Clone quality: bE489B14 on chr=13; Num_of_Contigs=16; )
AZU1		ENSSSCG00000013415	2:46124133-46126990		FP015903,CH242-504E7,2:46123296-46128259 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
AZU1		location ⇒	2:46124429-46124587		FP015903,CH242-504E7,2:46123296-46128259 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
AZU1		location ⇒	2:46125012-46125153		FP015903,CH242-504E7,2:46123296-46128259 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
AZU1		location ⇒	2:46125785-46126019		FP015903,CH242-504E7,2:46123296-46128259 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
AZU1		location ⇒	2:46126705-46126830		FP015903,CH242-504E7,2:46123296-46128259 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )

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

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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).