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)

SYAP1		ENSSSCG00000012148	X:12694894-12719654
SYCE1		ENSSSCG00000010779	14:148105589-148108724
SYCE1L		ENSSSCG00000002700	6:7786541-7792690		FP085416,CH242-260P4,6:7763653-7801275 (Clone quality: bE260P4 on chr=6; Num_of_Contigs=4; )
SYCE2		ENSSSCG00000013740	2:56113769-56115760		CU914382,CH242-275M24,2:56111569-56116284 (Clone quality: bE275M24 on chr=2; Num_of_Contigs=7; )
SYCN		ENSSSCG00000010710	14:138696776-138697183		FP236263,CH242-159G20,14:138694973-138703067 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
SYCP1		ENSSSCG00000006750	4:109854947-109992603
SYCP2		ENSSSCG00000007529	17:62493409-62573095
SYCP2L		ENSSSCG00000001044	7:7993408-7996762		CU407176,CH242-253P8,7:7972581-8004189 (Clone quality: bE253P8 on chr=7; Num_of_Contigs=5; )
SYCP3		ENSSSCG00000000863	5:77869294-77877570		CU928944,CH242-147F20,5:77866870-77879539 (Clone quality: bE147F20 on chr=5; Num_of_Contigs=9; )
SYDE1		ENSSSCG00000013829	2:60052027-60057996		CU915718,CH242-156C19,2:60006607-60065169 (Clone quality: bE156C19 on chr=2; Num_of_Contigs=6; )
SYDE2		ENSSSCG00000006947	4:135693944-135739124		CU595636,CH242-517I9,4:135693355-135754140 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
SYK		ENSSSCG00000008193	3:51825880-51842062
SYK		ENSSSCG00000009589	14:2618466-2676342		CU329688,CH242-307C4,14:2610978-2700701 (Clone quality: bE307C4 on chr=14; Num_of_Contigs=6; )
SYK		location ⇒	14:2618447-2618880		CU329688,CH242-307C4,14:2610978-2700701 (Clone quality: bE307C4 on chr=14; Num_of_Contigs=6; )
SYK		location ⇒	14:2660422-2660632		CU329688,CH242-307C4,14:2610978-2700701 (Clone quality: bE307C4 on chr=14; Num_of_Contigs=6; )
SYK		location ⇒	14:2662335-2662528		CU329688,CH242-307C4,14:2610978-2700701 (Clone quality: bE307C4 on chr=14; Num_of_Contigs=6; )
SYK		location ⇒	14:2675623-2676089		CU329688,CH242-307C4,14:2610978-2700701 (Clone quality: bE307C4 on chr=14; Num_of_Contigs=6; )
SYMPK		ENSSSCG00000003093	6:36001320-36035868		FP102597,CH242-173N22,6:35989500-36043367 (Clone quality: bE173N22 on chr=6; Num_of_Contigs=4; )
SYMPK		location ⇒	6:36028854-36028760		FP102597,CH242-173N22,6:35989500-36043367 (Clone quality: bE173N22 on chr=6; Num_of_Contigs=4; )
SYMPK		location ⇒	6:36030090-36029988		FP102597,CH242-173N22,6:35989500-36043367 (Clone quality: bE173N22 on chr=6; Num_of_Contigs=4; )
SYMPK		location ⇒	6:36033802-36033611		FP102597,CH242-173N22,6:35989500-36043367 (Clone quality: bE173N22 on chr=6; Num_of_Contigs=4; )
SYMPK		location ⇒	6:36034741-36034567		FP102597,CH242-173N22,6:35989500-36043367 (Clone quality: bE173N22 on chr=6; Num_of_Contigs=4; )
SYN1		ENSSSCG00000012276	X:42058789-42110182
SYN3		ENSSSCG00000000154	5:10230975-10680952
SYNCRIP		ENSSSCG00000004294	1:57013611-57043212
SYNE1		ENSSSCG00000004082	1:15004138-15163032
SYNE2		ENSSSCG00000005110	1:202841045-203109516
SYNE2		location ⇒	1:202841631-202840747		CU686778,CH242-58A17,1:202816885-202857200 (Clone quality: bE58A17 on chr=1; Num_of_Contigs=8; )
SYNE2		location ⇒	1:202843779-202843587		CU686778,CH242-58A17,1:202816885-202857200 (Clone quality: bE58A17 on chr=1; Num_of_Contigs=8; )
SYNE2		location ⇒	1:202846418-202846215		CU686778,CH242-58A17,1:202816885-202857200 (Clone quality: bE58A17 on chr=1; Num_of_Contigs=8; )
SYNE2		location ⇒	1:202847598-202847392		CU686778,CH242-58A17,1:202816885-202857200 (Clone quality: bE58A17 on chr=1; Num_of_Contigs=8; )
SYNGAP1		ENSSSCG00000001513	7:34129201-34159851
SYNGR1		ENSSSCG00000000088	5:5188767-5194577
SYNGR3		ENSSSCG00000008036	3:36370434-36373210		FP102350,CH242-207G4,3:36359565-36381485 (Clone quality: bE207G4 on chr=3; Num_of_Contigs=8; )
SYNGR4		ENSSSCG00000003131	6:37420477-37422438		FP102301,CH242-20J11,6:37418263-37433567 (Clone quality: bE20J11 on chr=6; Note=In Finishing;)
SYNJ1		ENSSSCG00000012035	13:138639603-138712660
SYNJ2		ENSSSCG00000012315	X:44294650-44362435
SYNJ2BP		ENSSSCG00000002318	7:102299770-102319698		CU695063,CH242-376L7,7:102238342-102373323 (Clone quality: bE376L7 on chr=7; Num_of_Contigs=1; )
SYNM		location ⇒	13:70346668-70346778		CU468880,CH242-513O5,13:70307780-70349104 (Clone quality: bE513O5 on chr=13; Num_of_Contigs=4; )
SYNPO2		ENSSSCG00000009111	8:90208385-90293945
SYNPO2L		ENSSSCG00000010303	14:79699240-79706115		CT827821,CH242-151I16,14:79697766-79768615 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
SYP		location ⇒	X:42669883-42669934		FP067404,CH242-247J8,X:42641466-42673583 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
SYP		location ⇒	X:42675458-42675657		FP067404,CH242-247J8,X:42673684-42680665 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
SYP		location ⇒	X:42677763-42678102		FP067404,CH242-247J8,X:42673684-42680665 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
SYP		location ⇒	X:42798714-42798765		FP067430,CH242-266D21,X:42786366-42803395 (Clone quality: bE266D21 on chr=X; Num_of_Contigs=12; )
SYPL2		ENSSSCG00000006829	4:115165965-115178469		CU633714,CH242-413N19,4:115147581-115211057 (Clone quality: bE413N19 on chr=4; Num_of_Contigs=4; )
SYS1		ENSSSCG00000007395	17:49515190-49699686
SYT1		ENSSSCG00000000948	5:96283973-96812569
SYT10		ENSSSCG00000000527	5:40127198-40212502
SYT11		ENSSSCG00000006506	4:98089212-98114716

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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).