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)

ARL4A		location ⇒	9:77038723-77040169		CU972383,CH242-147M18,9:77036567-77045078 (Clone quality: bE147M18 on chr=9; Num_of_Contigs=11; )
ARL4A		location ⇒	9:77040283-77040657		CU972383,CH242-147M18,9:77036567-77045078 (Clone quality: bE147M18 on chr=9; Num_of_Contigs=11; )
ARL4A		location ⇒	9:77040855-77041068		CU972383,CH242-147M18,9:77036567-77045078 (Clone quality: bE147M18 on chr=9; Num_of_Contigs=11; )
ARL4A		location ⇒	9:77041222-77041262		CU972383,CH242-147M18,9:77036567-77045078 (Clone quality: bE147M18 on chr=9; Num_of_Contigs=11; )
ARL4C		ENSSSCG00000016316	15:127293829-127294407		CU861897,CH242-118I22,15:127196368-127294813 (Clone quality: bE118I22 on chr=15; Num_of_Contigs=2; )
ARL4D		ENSSSCG00000017380	12:17527832-17528434		FP102477,CH242-134N6,12:17523781-17558173 (Clone quality: bE134N6 on chr=12; Num_of_Contigs=2; )
ARL6IP2		ENSSSCG00000008487	3:94935004-95028975
ARL6IP2		location ⇒	3:94935003-94935123		CU929798,CH242-422N20,3:94823407-94935247 (Clone quality: bE422N20 on chr=3; Num_of_Contigs=6; )
ARL6IP2		location ⇒	3:94991152-94991401		CU914221,CH242-115E10,3:94987054-95129120 (Clone quality: bE115E10 on chr=3; Num_of_Contigs=2; )
ARL6IP2		location ⇒	3:95012533-95012671		CU914221,CH242-115E10,3:94987054-95129120 (Clone quality: bE115E10 on chr=3; Num_of_Contigs=2; )
ARL6IP2		location ⇒	3:95017015-95017260		CU914221,CH242-115E10,3:94987054-95129120 (Clone quality: bE115E10 on chr=3; Num_of_Contigs=2; )
ARL6IP4		ENSSSCG00000009782	14:29961436-29963862		CU467951,CH242-194A1,14:29956356-29993852 (Clone quality: bE194A1 on chr=14; Num_of_Contigs=2; )
ARL6IP5		ENSSSCG00000011507	13:42325329-42358671
ARL6IP6		ENSSSCG00000015868	15:56490709-56522096		CU571020,CH242-207L23,15:56451427-56532529 (Clone quality: bE207L23 on chr=15; Num_of_Contigs=2; )
ARL8B		ENSSSCG00000011535	13:51406313-51460676
ARL9		ENSSSCG00000008899	8:47095675-47107943		CU606852,CH242-220F7,8:47084665-47178142 (Clone quality: bE220F7 on chr=8; Num_of_Contigs=9; )
ARMC1		ENSSSCG00000006220	4:71562950-71593964		CU207226,CH242-348A19,4:71544804-71642206 (Clone quality: bE348A19 on chr=4; Num_of_Contigs=2; )
ARMC2		ENSSSCG00000004388	1:78517539-78622619
ARMC3		ENSSSCG00000011078	10:49477929-49567345
ARMC4		ENSSSCG00000011069	10:47425951-47671171
ARMC6		ENSSSCG00000013927	2:63225931-63246324
ARMC7		ENSSSCG00000017214	12:4346497-4364312	CU928896,CH242-521B23,12:4294467-4388657 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
ARMC8		ENSSSCG00000011658	13:64925838-64956102		CU915328,CH242-252D2,13:64912315-64972199 (Clone quality: bE252D2 on chr=13; Num_of_Contigs=10; )
ARMC9		ENSSSCG00000016271	15:124210069-124279521
ARMCX2		ENSSSCG00000012510	X:80998482-81000416	CU856396,CH242-129F20,X:80923600-81096541 (Clone quality: bE129F20 on chr=X; Num_of_Contigs=6; )
ARMCX3		ENSSSCG00000012509	X:80974172-80975308	CU856396,CH242-129F20,X:80923600-81096541 (Clone quality: bE129F20 on chr=X; Num_of_Contigs=6; )
ARMCX5		ENSSSCG00000012518	X:81589532-81591079	FP102262,CH242-56M13,X:81498967-81645707 (Clone quality: bE56M13 on chr=X; Num_of_Contigs=1; )
ARMCX6		ENSSSCG00000012508	X:80964714-80965622	CU856396,CH242-129F20,X:80923600-81096541 (Clone quality: bE129F20 on chr=X; Num_of_Contigs=6; )
ARMET		ENSSSCG00000011421	13:28523284-28527271		CU633548,CH242-178K10,13:28496828-28528245 (Clone quality: bE178K10 on chr=13; Num_of_Contigs=3; )
ARNT		ENSSSCG00000006646	4:102300527-102337717
ARNT		ENSSSCG00000001781	7:55310116-55451812
ARNT		ENSSSCG00000000551	5:44821595-44852621
ARNT		location ⇒	4:102300912-102300968		CU463875,CH242-217B6,4:102294033-102302784 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
ARNT		location ⇒	4:102316187-102316396		CU463875,CH242-217B6,4:102305952-102327368 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
ARNT2		ENSSSCG00000001781	7:55310116-55451812
ARNTL		ENSSSCG00000013396	2:42869799-42945016
ARNTL2		ENSSSCG00000000551	5:44821595-44852621
ARPC1A		ENSSSCG00000007609	3:5453886-5613296
ARPC1B		ENSSSCG00000007610	3:5466046-5472201
ARPC1B		location ⇒	3:5467317-5467548		FP103031,CH242-519M18,3:5461129-5467599 (Clone quality: bE519M18 on chr=3; Num_of_Contigs=12; )
ARPC1B		location ⇒	3:5469409-5469616		FP103031,CH242-519M18,3:5467700-5472870 (Clone quality: bE519M18 on chr=3; Num_of_Contigs=12; )
ARPC1B		location ⇒	3:5866953-5866746		FP102617,CH242-199P18,3:5866556-5870160 (Clone quality: bE199P18 on chr=3; Num_of_Contigs=6; )
ARPC1B		location ⇒	3:5869057-5868826		FP102617,CH242-199P18,3:5866556-5870160 (Clone quality: bE199P18 on chr=3; Num_of_Contigs=6; )
ARPC2		ENSSSCG00000016185	15:113464998-113517043
ARPC3		ENSSSCG00000009821	14:31856349-31868731
ARPC4		ENSSSCG00000011552	13:55270515-55279072		CU633418,CH242-443E24,13:55267897-55295654 (Clone quality: bE443E24 on chr=13; Num_of_Contigs=9; )
ARPC5		ENSSSCG00000015560	9:117168774-117178530		CU570827,CH242-238C10,9:117082384-117181431 (Clone quality: bE238C10 on chr=9; Num_of_Contigs=5; )
ARPC5L		ENSSSCG00000005596	1:280482559-280490906		CU468031,CH242-524N14,1:280318183-280492192 (Clone quality: bE524N14 on chr=1; Num_of_Contigs=1; )
ARPP-19		ENSSSCG00000004618	1:123932964-123952385
ARPP-19		location ⇒	1:110049029-110049205		CU651598,CH242-205J9,1:110025549-110049683 (Clone quality: bE205J9 on chr=1; Num_of_Contigs=12; )

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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).