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)

SPACA3		location ⇒	12:39648666-39648543		FP017292,CH242-263E12,12:39622307-39714413 (Clone quality: bE263E12 on chr=12; Num_of_Contigs=2; )
SPAG1		ENSSSCG00000006067	4:37192336-37278775
SPAG17		ENSSSCG00000006726	4:106687256-106887233
SPAG4		ENSSSCG00000007305	17:41082074-41086637		CU914282,CH242-434B21,17:41068548-41118158 (Clone quality: bE434B21 on chr=17; Num_of_Contigs=4; )
SPAG4L		ENSSSCG00000007256	17:38513294-38524933		CU179704,CH242-134M1,17:38326500-38527268 (Clone quality: bE134M1 on chr=17; Num_of_Contigs=1; )
SPAG5		ENSSSCG00000017758	12:42436324-42451441
SPAG6		ENSSSCG00000011080	10:50014090-50089109
SPAG7		ENSSSCG00000017903	12:49144672-49149406		FP015831,CH242-271O18,12:49076321-49169107 (Clone quality: bE271O18 on chr=12; Num_of_Contigs=4; )
SPAM-1		location ⇒	18:12311857-12311926		FP236477,CH242-106A2,18:12287895-12332688 (Clone quality: bE106A2 on chr=18; Num_of_Contigs=4; )
SPAM-1		location ⇒	18:31526164-31526112		FP016082,CH242-96C1,18:31524683-31544958 (Clone quality: bE96C1 on chr=18; Num_of_Contigs=8; )
SPAM-1		location ⇒	18:31692354-31692406		CU655857,CH242-129N18,18:31691267-31695845 (Clone quality: bE129N18 on chr=18; Num_of_Contigs=19; )
SPAM-1		location ⇒	18:48863901-48863972		FP085442,CH242-169J21,18:48862045-48865534 (Clone quality: bE169J21 on chr=18; Num_of_Contigs=4; )
SPAM1		ENSSSCG00000016601	18:21743205-21752002	CU467663,CH242-113A4,18:21660168-21802380 (Clone quality: bE113A4 on chr=18; Num_of_Contigs=6; )
SPARC		ENSSSCG00000017083	16:68695277-68708070		CU896612,CH242-127G9,16:68686564-68784061 (Clone quality: bE127G9 on chr=16; Num_of_Contigs=5; )
SPARC		ENSSSCG00000010283	14:78123712-78133143		CU469117,CH242-331I9,14:78120132-78134401 (Clone quality: bE331I9 on chr=14; Num_of_Contigs=11; )
SPARC		ENSSSCG00000009722	14:21490946-21857061
SPARC		ENSSSCG00000009222	8:112884827-112929202
SPARC		ENSSSCG00000004013	1:1240205-1711059
SPARC		ENSSSCG00000002314	7:101933488-102011490		CT943645,CH242-235L8,7:101928117-102040051 (Clone quality: bE235L8 on chr=7; Num_of_Contigs=2; )
SPARC		location ⇒	16:68639873-68639749		CU856189,CH242-157P14,16:68639449-68645964 (Clone quality: bE157P14 on chr=16; Num_of_Contigs=8; )
SPARC		location ⇒	16:68704319-68704470		CU896612,CH242-127G9,16:68686564-68784061 (Clone quality: bE127G9 on chr=16; Num_of_Contigs=5; )
SPARC		location ⇒	16:68706474-68706623		CU896612,CH242-127G9,16:68686564-68784061 (Clone quality: bE127G9 on chr=16; Num_of_Contigs=5; )
SPARC		location ⇒	16:68707189-68708070		CU896612,CH242-127G9,16:68686564-68784061 (Clone quality: bE127G9 on chr=16; Num_of_Contigs=5; )
SPARCL1		ENSSSCG00000009222	8:112884827-112929202
SPAST		ENSSSCG00000008517	3:100951823-101019095
SPATA13		ENSSSCG00000009293	11:2098010-2138043
SPATA18		ENSSSCG00000008834	8:33725629-33756090
SPATA20		ENSSSCG00000017565	12:24171778-24181644
SPATA21		ENSSSCG00000003476	6:51955433-51987172
SPATA22		ENSSSCG00000017857	12:46814974-46822200
SPATA24		ENSSSCG00000014348	2:128349129-128355452		FP101965,CH242-45H7,2:128263088-128357212 (Clone quality: bE45H7 on chr=2; Num_of_Contigs=5; )
SPATA3		ENSSSCG00000016269	15:124130663-124139388
SPATA4		ENSSSCG00000015767	15:35663541-35670373		CU929806,CH242-45C6,15:35610411-35680760 (Clone quality: bE45C6 on chr=15; Num_of_Contigs=7; )
SPATA5		ENSSSCG00000009084	8:86751395-86811881
SPATA5L1		ENSSSCG00000004671	1:131962071-131982676		CU457441,CH242-247F23,1:131950006-132050038 (Clone quality: bE247F23 on chr=1; Num_of_Contigs=7; )
SPATA6		ENSSSCG00000003881	6:116750667-116836008
SPATA7		ENSSSCG00000002424	7:118178168-118232788		CT757500,CH242-29G23,7:118096292-118255857 (Clone quality: bE29G23 on chr=7; Num_of_Contigs=2; )
SPATA9		ENSSSCG00000014142	2:82863498-82877247		FP016071,CH242-117B6,2:82845314-82879561 (Clone quality: bE117B6 on chr=2; Num_of_Contigs=5; )
SPATC1		ENSSSCG00000005923	4:750190-755055
SPATS2L		ENSSSCG00000016090	15:97626846-97803033
SPC25		ENSSSCG00000015924	15:70844089-70855030
SPCS1		ENSSSCG00000011447	13:29433476-29435672		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
SPCS1		location ⇒	13:29433963-29433478		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
SPCS1		location ⇒	13:29434532-29434446		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
SPCS1		location ⇒	13:29434679-29434619		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
SPCS1		location ⇒	13:29435160-29435041		CU469164,CH242-456I18,13:29421147-29460847 (Clone quality: bE456I18 on chr=13; Num_of_Contigs=15; )
SPCS2		ENSSSCG00000014850	9:9030926-9054949
SPCS3		ENSSSCG00000015769	15:35744840-35753951		FP102103,CH242-76K8,15:35682403-35757598 (Clone quality: bE76K8 on chr=15; Num_of_Contigs=1; )
SPDYA		ENSSSCG00000008538	3:103414469-103438581		CU915333,CH242-291B11,3:103412187-103440125 (Clone quality: bE291B11 on chr=3; Num_of_Contigs=4; )
SPDYC		ENSSSCG00000013000	2:5432442-5459350	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )

Go to records:
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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).