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)

SDR39U1		ENSSSCG00000001983	7:81192117-81194765		CT997804,CH242-280B15,7:81187212-81281808 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
SDR42E2		ENSSSCG00000007842	3:21765227-21791458
SDR9C7		ENSSSCG00000000415	5:21288817-21293734		FP236389,CH242-191L18,5:21283790-21294860 (Clone quality: bE191L18 on chr=5; Num_of_Contigs=7; )
SDS		ENSSSCG00000007732	3:14466464-14472957
SDS		ENSSSCG00000009870	14:38829379-38842345		CU468670,CH242-408G16,14:38815431-38894429 (Clone quality: bE408G16 on chr=14; Num_of_Contigs=3; )
SDS		ENSSSCG00000009871	14:38859065-38869026		CU468670,CH242-408G16,14:38815431-38894429 (Clone quality: bE408G16 on chr=14; Num_of_Contigs=3; )
SDS		location ⇒	7:23685342-23683959	CU062578,CH242-485A8,7:23636539-23857828 (Clone quality: bE485A8 on chr=7; Num_of_Contigs=2; )
SDSL		ENSSSCG00000009870	14:38829379-38842345		CU468670,CH242-408G16,14:38815431-38894429 (Clone quality: bE408G16 on chr=14; Num_of_Contigs=3; )
SEC11C		ENSSSCG00000004912	1:168694607-168709165
SEC13		ENSSSCG00000011572	13:55724725-55732990
SEC14L1		ENSSSCG00000017169	12:2795045-2843691	CU655873,CH242-326F7,12:2701845-2922206 (Clone quality: bE326F7 on chr=12; Num_of_Contigs=17; )
SEC14L2		ENSSSCG00000010006	14:48179234-48199044		CT956025,CH242-69C12,14:48142322-48239134 (Clone quality: bE69C12 on chr=14; Num_of_Contigs=15; )
SEC14L3		ENSSSCG00000010008	14:48216507-48227116		CT956025,CH242-69C12,14:48142322-48239134 (Clone quality: bE69C12 on chr=14; Num_of_Contigs=15; )
SEC14L5		ENSSSCG00000007926	3:33427339-33468709
SEC16B		ENSSSCG00000015517	9:112316481-112416119
SEC22A		ENSSSCG00000011869	13:103228425-103248063		CU466991,CH242-220A1,13:103212548-103309325 (Clone quality: bE220A1 on chr=13; Num_of_Contigs=5; )
SEC22C		ENSSSCG00000011282	13:21958255-21977849
SEC23A		ENSSSCG00000001934	7:66480361-66548766
SEC23B		ENSSSCG00000007097	17:27502558-27592491
SEC23IP		ENSSSCG00000010690	14:135744484-135782643
SEC24A		ENSSSCG00000014304	2:124581289-124640599		CU862042,CH242-222J18,2:124579543-124681819 (Clone quality: bE222J18 on chr=2; Num_of_Contigs=7; )
SEC24B		ENSSSCG00000009142	8:96788595-96820608		CU694741,CH242-514C2,8:96788111-96820948 (Clone quality: bE514C2 on chr=8; Num_of_Contigs=10; )
SEC24C		ENSSSCG00000010306	14:79778202-79801010		CT827821,CH242-151I16,14:79768716-79822020 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
SEC24D		ENSSSCG00000009112	8:90507160-90522303		CU856577,CH242-217F22,8:90502439-90526363 (Clone quality: bE217F22 on chr=8; Num_of_Contigs=8; )
SEC31A		ENSSSCG00000009244	8:116586687-116636903
SEC31B		ENSSSCG00000006165	4:60660004-60689354		FP236645,CH242-456M6,4:60652237-60698249 (No clone quality info on )
SEC61A1		ENSSSCG00000011621	13:59787051-59801331		CU633391,CH242-298L24,13:59768847-59869888 (Clone quality: bE298L24 on chr=13; Num_of_Contigs=9; )
SEC61A2		ENSSSCG00000011114	10:56716723-56743109		CU929734,CH242-242C1,10:56703179-56747603 (Clone quality: bE242C1 on chr=10; Num_of_Contigs=3; )
SEC61B		ENSSSCG00000005384	1:252557609-252564363		CU861555,CH242-297P22,1:252535523-252612502 (Clone quality: bE297P22 on chr=1; Num_of_Contigs=1; )
SEC61G		ENSSSCG00000015637	9:130853151-130860568		FP016192,CH242-155J13,9:130817076-130861660 (Clone quality: bE155J13 on chr=9; Num_of_Contigs=3; )
SEC61G		ENSSSCG00000015637	9:130853151-130860568		FP016192,CH242-155J13,9:130817076-130861660 (Clone quality: bE155J13 on chr=9; Num_of_Contigs=3; )
SEC61G		location ⇒	9:130856840-130856740		FP016192,CH242-155J13,9:130817076-130861660 (Clone quality: bE155J13 on chr=9; Num_of_Contigs=3; )
SEC61G		location ⇒	9:130858679-130858584		FP016192,CH242-155J13,9:130817076-130861660 (Clone quality: bE155J13 on chr=9; Num_of_Contigs=3; )
SEC63		ENSSSCG00000004382	1:77584156-77658872	CU207397,CH242-240D13,1:77563184-77792541 (Clone quality: bE240D13 on chr=1; Num_of_Contigs=11; )
SECISBP2		ENSSSCG00000009583	14:1109426-1152891
SECISBP2L		ENSSSCG00000004653	1:127980053-128031526
SEL1L		ENSSSCG00000002414	7:111689451-111750395
SEL1L2		ENSSSCG00000007078	17:22801018-22818854		CU459111,CH242-291K5,17:22790454-22824341 (Clone quality: bE291K5 on chr=17; Num_of_Contigs=3; )
SEL1L3		ENSSSCG00000008759	8:15729616-15762591
SELE		ENSSSCG00000006286	4:84377739-84387530		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELE		location ⇒	4:84320812-84321199		CU407291,CH242-513E17,4:84310506-84324751 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELE		location ⇒	4:84378770-84379157		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELE		location ⇒	4:84381462-84381652		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELE		location ⇒	4:84385927-84387530		CU407291,CH242-513E17,4:84329694-84430611 (Clone quality: bE513E17 on chr=4; Num_of_Contigs=7; )
SELENBP1		ENSSSCG00000006624	4:101839726-101848590	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
SELENBP1		ENSSSCG00000006624	4:101839726-101848590	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
SELENBP1		location ⇒	4:101842695-101842811	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
SELENBP1		location ⇒	4:101843088-101843276	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
SELENBP1		location ⇒	4:101845438-101845611	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
SELENBP1		location ⇒	4:101847877-101848032	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )

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, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

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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).