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)

SAMHD1		location ⇒	17:42525269-42525008		CU607009,CH242-275L23,17:42524970-42535424 (Clone quality: bE275L23 on chr=17; Num_of_Contigs=17; )
SAMSN1		ENSSSCG00000012008	13:129176607-129223219
SAMSN1		location ⇒	13:129194273-129194115		CU466325,CH242-227D14,13:129152733-129199798 (Clone quality: bE227D14 on chr=13; Num_of_Contigs=8; )
SAMSN1		location ⇒	13:129196642-129196508		CU466325,CH242-227D14,13:129152733-129199798 (Clone quality: bE227D14 on chr=13; Num_of_Contigs=8; )
SAMSN1		location ⇒	13:129198853-129198702		CU466325,CH242-227D14,13:129152733-129199798 (Clone quality: bE227D14 on chr=13; Num_of_Contigs=8; )
SAMSN1		location ⇒	13:129223131-129223019		CU467992,CH242-28D20,13:129199799-129227363 (Clone quality: bE28D20 on chr=13; Num_of_Contigs=8; )
SAP130		ENSSSCG00000015859	15:55597935-55657213
SAP30BP		ENSSSCG00000017205	12:4046984-4059524	CU928968,CH242-19M24,12:4017937-4068721 (Clone quality: bE19M24 on chr=12; Num_of_Contigs=4; )
SAP30L		ENSSSCG00000017071	16:66076976-66085929		FP102668,CH242-292L19,16:66063645-66087050 (Clone quality: bE292L19 on chr=16; Num_of_Contigs=7; )
SAPS1		ENSSSCG00000003301	6:41442634-41456183		FP245423,CH242-507H20,6:41440341-41468144 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
SAPS2		ENSSSCG00000000970	5:99747673-99804069
SAPS3		ENSSSCG00000012884	2:2697212-2875651
SAR1A_PIG		ENSSSCG00000010260	14:76032227-76048157
SAR1B		ENSSSCG00000014305	2:124650368-124675802		CU862042,CH242-222J18,2:124579543-124681819 (Clone quality: bE222J18 on chr=2; Num_of_Contigs=7; )
SARDH		ENSSSCG00000005740	1:288422911-288467034
SARNP		ENSSSCG00000000364	5:20157789-20203838	CU606916,CH242-141C7,5:20096881-20252808 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
SARS		ENSSSCG00000006835	4:115358082-115375689		CU207229,CH242-373I13,4:115346120-115398613 (Clone quality: bE373I13 on chr=4; Num_of_Contigs=14; )
SARS2		ENSSSCG00000002972	6:32958096-32958368		FP236339,CH242-31J9,6:32956103-32971338 (Clone quality: bE31J9 on chr=6; Num_of_Contigs=14; )
SART1		ENSSSCG00000012963	2:4732734-4750366		CU928325,CH242-208C18,2:4726433-4762174 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
SART3		ENSSSCG00000009946	14:42621537-42635768		CT955994,CH242-510E14,14:42585637-42637905 (Clone quality: bE510E14 on chr=14; Num_of_Contigs=6; )
SART3		location ⇒	14:42622287-42621355		CT955994,CH242-510E14,14:42585637-42637905 (Clone quality: bE510E14 on chr=14; Num_of_Contigs=6; )
SART3		location ⇒	14:42623054-42622861		CT955994,CH242-510E14,14:42585637-42637905 (Clone quality: bE510E14 on chr=14; Num_of_Contigs=6; )
SART3		location ⇒	14:42624010-42623855		CT955994,CH242-510E14,14:42585637-42637905 (Clone quality: bE510E14 on chr=14; Num_of_Contigs=6; )
SART3		location ⇒	14:42625158-42624715		CT955994,CH242-510E14,14:42585637-42637905 (Clone quality: bE510E14 on chr=14; Num_of_Contigs=6; )
SASH3		ENSSSCG00000012652	X:104537896-104549372
SAT		ENSSSCG00000010437	14:104637431-104663609
SAT		location ⇒	7:131973198-131972632		CT827828,CH242-222B17,7:131956656-132005324 (Clone quality: bE222B17 on chr=7; Num_of_Contigs=5; )
SAT1_PIG		ENSSSCG00000012173	X:18735356-18738387		CU855499,CH242-206C22,X:18734944-18752333 (Clone quality: bE206C22 on chr=X; Num_of_Contigs=6; )
SAT2		ENSSSCG00000017952	12:50024654-50026327	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
SATB1		ENSSSCG00000011201	13:4234402-4328152
SATB2		ENSSSCG00000016084	15:96508875-96582823
SATB2		location ⇒	15:96507150-96506137		CU466539,CH242-419M2,15:96503936-96514752 (Clone quality: bE419M2 on chr=15; Num_of_Contigs=1; )
SATB2		location ⇒	15:96509336-96508831		CU466539,CH242-419M2,15:96503936-96514752 (Clone quality: bE419M2 on chr=15; Num_of_Contigs=1; )
SATB2		location ⇒	15:96569263-96569738		CU571124,CH242-277D16,15:96555028-96569750 (Clone quality: bE277D16 on chr=15; Num_of_Contigs=8; )
SATB2		location ⇒	15:96648832-96649063		CU571124,CH242-277D16,15:96644208-96692025 (Clone quality: bE277D16 on chr=15; Num_of_Contigs=8; )
SATL1		ENSSSCG00000012460	X:67449161-67463423
SAV1		ENSSSCG00000005021	1:188671293-188711532		CU074392,CH242-137I1,1:188633939-188748299 (Clone quality: bE137I1 on chr=1; Num_of_Contigs=3; )
SBDS		ENSSSCG00000007732	3:14466464-14472957
SBF1		ENSSSCG00000000968	5:99729580-99746866		CU929756,CH242-288F8,5:99727875-99746962 (Clone quality: bE288F8 on chr=5; Num_of_Contigs=8; )
SBF2		ENSSSCG00000013409	2:45389097-45848941
SBK1		ENSSSCG00000007810	3:16789816-16793749		CU928476,CH242-24P1,3:16769332-16803748 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
SBNO1		ENSSSCG00000009776	14:29613340-29669235
SC4MOL		ENSSSCG00000008857	8:37778020-37844323
SC5A1_PIG		ENSSSCG00000010036	14:49513275-49664648
SC5DL		ENSSSCG00000015134	9:46918844-46923299		CU633338,CH242-137B6,9:46914143-46959056 (Clone quality: bE137B6 on chr=9; Num_of_Contigs=4; )
SCAF1		ENSSSCG00000003182	6:38262443-38273375
SCAMP1		ENSSSCG00000014103	2:76310779-76338860		CU467790,CH242-520F21,2:76299276-76401251 (Clone quality: bE520F21 on chr=2; Num_of_Contigs=6; )
SCAMP2		ENSSSCG00000001892	7:63934411-64198467
SCAMP4		ENSSSCG00000013446	2:46930156-46939708		FP236669,CH242-487E14,2:46923330-46939836 (Clone quality: bE487E14 on chr=2; Num_of_Contigs=9; )
SCAMP5		ENSSSCG00000001887	7:63810844-63816720		CT971477,CH242-112H24,7:63781048-63818100 (Clone quality: bE112H24 on chr=7; Num_of_Contigs=4; )

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).