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)

CLECSF13		location ⇒	12:49695628-49695471		CU914703,CH242-254H21,12:49691319-49717351 (Clone quality: bE254H21 on chr=12; Num_of_Contigs=9; )
CLECSF13		location ⇒	12:49859995-49860152		CU681851,CH242-516E15,12:49859371-49861656 (Clone quality: bE516E15 on chr=12; Num_of_Contigs=27; )
CLECSF29976		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CLECSF8		location ⇒	X:41022050-41022002		FP067429,CH242-220D22,X:41014620-41024428 (Clone quality: bE220D22 on chr=X; Num_of_Contigs=6; )
CLECSF8		location ⇒	X:55691768-55691716		CU929942,CH242-488P24,X:55691654-55705221 (Clone quality: bE488P24 on chr=X; Num_of_Contigs=8; )
CLECSF8		location ⇒	X:87171150-87171099		CU468324,CH242-206D8,X:87160905-87178070 (Clone quality: bE206D8 on chr=X; Num_of_Contigs=8; )
CLECSF8		location ⇒	X:89694194-89694136		CU862025,CH242-121D17,X:89681966-89701632 (Clone quality: bE121D17 on chr=X; Num_of_Contigs=8; )
CLIC1		location ⇒	6:113791119-113792076		CU466988,CH242-11L21,6:113658667-113818538 (Clone quality: bE11L21 on chr=6; Num_of_Contigs=2; )
CLIC1		location ⇒	6:113872142-113873099		CU896569,CH242-102E3,6:113871595-113879541 (Clone quality: bE102E3 on chr=6; Num_of_Contigs=25; )
CLIC2		ENSSSCG00000012808	X:123297243-123311031		FP102234,CH242-131F14,X:123279613-123318272 (Clone quality: bE131F14 on chr=X; Num_of_Contigs=12; )
CLIC5		ENSSSCG00000001711	7:47714573-47837291
CLINT1		ENSSSCG00000017047	16:63206842-63234679
CLIP1		ENSSSCG00000009793	14:30378835-30504101		CT827829,CH242-223D18,14:30359194-30510705 (Clone quality: bE223D18 on chr=14; Num_of_Contigs=3; )
CLIP2		ENSSSCG00000007719	3:9514099-9550606		CU914415,CH242-263E18,3:9513248-9552353 (Clone quality: bE263E18 on chr=3; Num_of_Contigs=9; )
CLIP3		ENSSSCG00000002921	6:30486053-30498919
CLIP4		ENSSSCG00000008535	3:103196370-103249101
CLK1		ENSSSCG00000016095	15:98241882-98250545		CU468511,CH242-98M12,15:98176186-98278835 (Clone quality: bE98M12 on chr=15; Num_of_Contigs=5; )
CLK3		ENSSSCG00000001904	7:64395775-64410241		CU469022,CH242-37P17,7:64332302-64422082 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CLK3		location ⇒	7:64396195-64395708		CU469022,CH242-37P17,7:64332302-64422082 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CLK3		location ⇒	7:64397157-64397074		CU469022,CH242-37P17,7:64332302-64422082 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CLK3		location ⇒	7:64400418-64400252		CU469022,CH242-37P17,7:64332302-64422082 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CLK3		location ⇒	7:64405937-64405722		CU469022,CH242-37P17,7:64332302-64422082 (Clone quality: bE37P17 on chr=7; Num_of_Contigs=3; )
CLK4		ENSSSCG00000014028	2:68892405-68915560	FP085445,CH242-191I1,2:68882349-69082246 (Clone quality: bE191I1 on chr=2; Num_of_Contigs=1; )
CLN5		ENSSSCG00000009471	11:48051903-48072745		CU457401,CH242-185J22,11:48004963-48075214 (Clone quality: bE185J22 on chr=11; Num_of_Contigs=2; )
CLN6		ENSSSCG00000004957	1:173254236-173260062
CLN6		location ⇒	1:173254717-173254392		CU929738,CH242-251L9,1:173246278-173258052 (Clone quality: bE251L9 on chr=1; Num_of_Contigs=5; )
CLN6		location ⇒	1:173258701-173258511		CU929738,CH242-251L9,1:173258153-173262303 (Clone quality: bE251L9 on chr=1; Num_of_Contigs=5; )
CLN6		location ⇒	1:173471964-173471906		CU468716,CH242-496M3,1:173470465-173474124 (Clone quality: bE496M3 on chr=1; Num_of_Contigs=17; )
CLN6		location ⇒	1:173472468-173472278		CU468716,CH242-496M3,1:173470465-173474124 (Clone quality: bE496M3 on chr=1; Num_of_Contigs=17; )
CLNS1A		ENSSSCG00000014881	9:11970670-11990732
CLNS1A		location ⇒	9:11971237-11970953		CU915366,CH242-505I16,9:11970439-11978225 (Clone quality: bE505I16 on chr=9; Num_of_Contigs=7; )
CLNS1A		location ⇒	9:11975054-11974963		CU915366,CH242-505I16,9:11970439-11978225 (Clone quality: bE505I16 on chr=9; Num_of_Contigs=7; )
CLNS1A		location ⇒	9:11980488-11980314		CU915366,CH242-505I16,9:11978326-11983446 (Clone quality: bE505I16 on chr=9; Num_of_Contigs=7; )
CLNS1A		location ⇒	9:11981606-11981499		CU915366,CH242-505I16,9:11978326-11983446 (Clone quality: bE505I16 on chr=9; Num_of_Contigs=7; )
CLOCK		ENSSSCG00000008911	8:47922112-47932289		CU693432,CH242-81G7,8:47915614-47976118 (Clone quality: bE81G7 on chr=8; Num_of_Contigs=7; )
CLP1		ENSSSCG00000013179	2:11287780-11290332		CU914175,CH242-140O21,2:11248278-11317852 (Clone quality: bE140O21 on chr=2; Num_of_Contigs=3; )
CLPB		ENSSSCG00000014814	9:6357863-6360032		FP090889,CH242-166B16,9:6323247-6365214 (Clone quality: bE166B16 on chr=9; Num_of_Contigs=3; )
CLPP		ENSSSCG00000013542	2:49841849-49847914		CU929921,CH242-352E11,2:49825944-49850143 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
CLPS		ENSSSCG00000001552	7:36239777-36241997		CT868716,CH242-516I1,7:36091251-36290487 (Clone quality: bE516I1 on chr=7; Num_of_Contigs=1; )
CLPTM1		ENSSSCG00000003085	6:35841670-35871491
CLPTM1L		ENSSSCG00000017119	16:76772553-76774861		FP236205,CH242-148J9,16:76762632-76774908 (Clone quality: bE148J9 on chr=16; Num_of_Contigs=7; )
CLPX		ENSSSCG00000004927	1:170207699-170255355
CLRN1		ENSSSCG00000011711	13:73858766-73883790		CU927942,CH242-182E13,13:73849869-73909752 (Clone quality: bE182E13 on chr=13; Num_of_Contigs=7; )
CLSPN		ENSSSCG00000003628	6:62244904-62267194		CU929817,CH242-484C10,6:62244702-62311674 (Clone quality: bE484C10 on chr=6; Num_of_Contigs=3; )
CLSTN1		ENSSSCG00000003396	6:47161005-47201204
CLSTN1		location ⇒	6:47163546-47163394		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
CLSTN1		location ⇒	6:47163986-47163812		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
CLSTN1		location ⇒	6:47164730-47164504		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
CLSTN2		ENSSSCG00000011666	13:66135315-66280571
CLSTN2		location ⇒	13:66194382-66193749		CU463158,CH242-222K3,13:66117443-66207413 (Clone quality: bE222K3 on chr=13; 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, 851-900, 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, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).