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)

LAMB3		location ⇒	9:125849919-125849540		CU856114,CH242-415I14,9:125842463-125851158 (Clone quality: bE415I14 on chr=9; Num_of_Contigs=22; )
LAMC1		ENSSSCG00000015555	9:116580488-116700320
LAMC1		location ⇒	9:116580732-116580903		CU914232,CH242-156L24,9:116541439-116611650 (Clone quality: bE156L24 on chr=9; Num_of_Contigs=4; )
LAMC1		location ⇒	9:116656122-116656428		CU914232,CH242-156L24,9:116636595-116740024 (Clone quality: bE156L24 on chr=9; Num_of_Contigs=4; )
LAMC1		location ⇒	9:116661243-116661379		CU914232,CH242-156L24,9:116636595-116740024 (Clone quality: bE156L24 on chr=9; Num_of_Contigs=4; )
LAMC1		location ⇒	9:116663642-116663769		CU914232,CH242-156L24,9:116636595-116740024 (Clone quality: bE156L24 on chr=9; Num_of_Contigs=4; )
LAMC2		ENSSSCG00000015556	9:116768429-116808413
LAMC2		location ⇒	9:116798873-116798964		CU984578,CH242-212D15,9:116778945-116820374 (Clone quality: bE212D15 on chr=9; Num_of_Contigs=8; )
LAMC2		location ⇒	9:116801307-116801509		CU984578,CH242-212D15,9:116778945-116820374 (Clone quality: bE212D15 on chr=9; Num_of_Contigs=8; )
LAMC2		location ⇒	9:116803651-116803814		CU984578,CH242-212D15,9:116778945-116820374 (Clone quality: bE212D15 on chr=9; Num_of_Contigs=8; )
LAMC2		location ⇒	9:116803903-116803990		CU984578,CH242-212D15,9:116778945-116820374 (Clone quality: bE212D15 on chr=9; Num_of_Contigs=8; )
LAMC3		ENSSSCG00000005710	1:286273578-286338495
LAMC3		location ⇒	1:286316449-286316588		CU407178,CH242-255P5,1:286289047-286316688 (Clone quality: bE255P5 on chr=1; Num_of_Contigs=12; )
LAMC3		location ⇒	1:286316789-286317253
LAMC3		location ⇒	1:286397124-286396476	FP236754,CH242-296P20,1:286369892-286398150 (Clone quality: bE296P20 on chr=1; Num_of_Contigs=12; )
LAMP1		ENSSSCG00000009555	11:78810578-78827352		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
LAMP1		location ⇒	11:78813407-78813316		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
LAMP1		location ⇒	11:78815939-78815780		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
LAMP1		location ⇒	11:78816273-78816054		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
LAMP1		location ⇒	11:78818344-78818262		FP236214,CH242-266L11,11:78807891-78889241 (Clone quality: bE266L11 on chr=11; Num_of_Contigs=10; )
LAMP2		ENSSSCG00000012604	X:95827889-95864680
LAMP2		location ⇒	X:95827923-95828131	CU468368,CH242-64G23,X:95803160-95832085 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
LAMP2		location ⇒	X:95841408-95841611	CU468368,CH242-64G23,X:95832186-95842039 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
LAMP2		location ⇒	X:95846144-95846335	CU468368,CH242-64G23,X:95842140-95870590 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
LAMP2		location ⇒	X:95861460-95862878	CU468368,CH242-64G23,X:95842140-95870590 (Clone quality: bE64G23 on chr=X; Num_of_Contigs=10; )
LANCL1		ENSSSCG00000016158	15:106340959-106352733
langerin		ENSSSCG00000008319	3:65820549-65827189		CU855593,CH242-53L10,3:65814892-65863091 (Clone quality: bE53L10 on chr=3; Num_of_Contigs=46; )
LAP1		ENSSSCG00000002525	7:130944988-130993025		CT998550,CH242-445C19,7:130928637-130997560 (Clone quality: bE445C19 on chr=7; Num_of_Contigs=6; )
LAP1		ENSSSCG00000003793	6:100505356-100631067
LAP3		ENSSSCG00000010642	14:129889934-129921308		CU012038,CH242-328H13,14:129818796-130012065 (Clone quality: bE328H13 on chr=14; Num_of_Contigs=2; )
LAPTM4A		ENSSSCG00000008602	3:109743419-109761206
LAPTM4B		ENSSSCG00000006083	4:39263751-39346138
LARGE		ENSSSCG00000000959	5:99566747-99627766		CU928557,CH242-260H14,5:99566358-99629951 (Clone quality: bE260H14 on chr=5; Num_of_Contigs=4; )
LARP1		ENSSSCG00000017069	16:65752255-65773579		CU633659,CH242-20B14,16:65750551-65782929 (Clone quality: bE20B14 on chr=16; Num_of_Contigs=6; )
LARP1B		ENSSSCG00000009073	8:83314531-83402429
LARP4		ENSSSCG00000000219	5:14998721-15027719
LARP4B		ENSSSCG00000011162	10:64414963-64449290
LARP6		ENSSSCG00000004974	1:176276416-176296626
LARP7		ENSSSCG00000009119	8:92246263-92265955
LARS		ENSSSCG00000014411	2:133660235-133733874
LARS2		ENSSSCG00000011312	13:24189843-24289441
LAS1L		ENSSSCG00000012366	X:51581099-51586626		CU468312,CH242-149K13,X:51559586-51588166 (Clone quality: bE149K13 on chr=X; Num_of_Contigs=13; )
LASS1		ENSSSCG00000013922	2:63048881-63068333
LASS1		location ⇒	2:62859726-62859562		CU928669,CH242-407A11,2:62858565-62861762 (Clone quality: bE407A11 on chr=2; Num_of_Contigs=14; )
LASS1		location ⇒	2:62869383-62869130		CU928669,CH242-407A11,2:62861863-62869383 (Clone quality: bE407A11 on chr=2; Num_of_Contigs=14; )
LASS1		location ⇒	2:63048885-63049244		CU640483,CH242-64G8,2:63048545-63053142 (Clone quality: bE64G8 on chr=2; Num_of_Contigs=8; )
LASS1		location ⇒	2:63058262-63058426		CU640483,CH242-64G8,2:63053243-63184458 (Clone quality: bE64G8 on chr=2; Num_of_Contigs=8; )
LASS2		ENSSSCG00000006644	4:102206169-102215878
LASS3		ENSSSCG00000004819	1:146698977-146855681
LASS4		ENSSSCG00000013595	2:51539246-51582385		FP102075,CH242-165I11,2:51517048-51603044 (Clone quality: bE165I11 on chr=2; Num_of_Contigs=3; )

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, 851-45

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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).