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)

CBX3		location ⇒	14:86025661-86026146		CT827849,CH242-277H6,14:85946850-86127993 (Clone quality: bE277H6 on chr=14; Num_of_Contigs=1; )
CBX3		location ⇒	14:86027207-86027262		CT827849,CH242-277H6,14:85946850-86127993 (Clone quality: bE277H6 on chr=14; Num_of_Contigs=1; )
CBX4		ENSSSCG00000017160	12:1631211-1636644	CU464073,CH242-396G1,12:1427255-1662757 (Clone quality: bE396G1 on chr=3; Num_of_Contigs=9; )
CBX5		ENSSSCG00000000282	5:17804056-17815030
CBX7		ENSSSCG00000000090	5:5348860-5377673
CBX8		ENSSSCG00000017161	12:1769595-1771952		FP236795,CH242-62A6,12:1768960-1772450 (Clone quality: bE62A6 on chr=12; Num_of_Contigs=13; )
CBY3		ENSSSCG00000014021	2:68279165-68279566		CU915704,CH242-394M22,2:68275757-68351064 (Clone quality: bE394M22 on chr=2; Num_of_Contigs=5; )
CC2D1A		ENSSSCG00000013761	2:56916863-56933585		FP016000,CH242-10C10,2:56824783-56952713 (Clone quality: bE10C10 on chr=2; Num_of_Contigs=2; )
CC2D1B		ENSSSCG00000003862	6:113635952-113649304
CC2D2A		ENSSSCG00000008738	8:7983627-8131883
CC2D2A		location ⇒	8:7991111-7991199		CU928759,CH242-80M6,8:7978732-7995608 (Clone quality: bE80M6 on chr=8; Num_of_Contigs=5; )
CC2D2A		location ⇒	8:8041717-8041799		FP089472,CH242-122C5,8:8040243-8118614 (Clone quality: bE122C5 on chr=8; Num_of_Contigs=3; )
CC2D2A		location ⇒	8:8049919-8050007		FP089472,CH242-122C5,8:8040243-8118614 (Clone quality: bE122C5 on chr=8; Num_of_Contigs=3; )
CC2D2A		location ⇒	8:8103496-8103580		FP089472,CH242-122C5,8:8040243-8118614 (Clone quality: bE122C5 on chr=8; Num_of_Contigs=3; )
CC2D2B		ENSSSCG00000010501	14:112529740-112560616		CT827825,CH242-216D24,14:112519668-112654753 (Clone quality: bE216D24 on chr=14; Num_of_Contigs=2; )
CCAR1		location ⇒	14:74843711-74843770		CT990630,CH242-252D18,14:74823718-74858719 (Clone quality: bE252D18 on chr=14; Num_of_Contigs=6; )
CCAR1		location ⇒	14:74909551-74909899		CT990630,CH242-252D18,14:74871228-74924418 (Clone quality: bE252D18 on chr=14; Num_of_Contigs=6; )
CCAR1		location ⇒	14:74952944-74952596		CU407004,CH242-94B14,14:74933928-74989402 (Clone quality: bE94B14 on chr=14; Num_of_Contigs=6; )
CCAR1		location ⇒	14:75039880-75040228		CU468175,CH242-355K2,14:75014394-75098751 (Clone quality: bE355K2 on chr=14; Num_of_Contigs=4; )
CCBE1		ENSSSCG00000004907	1:168405537-168442891
CCBL1		ENSSSCG00000005663	1:283846900-283883788
CCBL2		ENSSSCG00000006925	4:132106877-132163150		CU151869,CH242-289B10,4:132020285-132181322 (Clone quality: bE289B10 on chr=4; Num_of_Contigs=2; )
CCBP2		ENSSSCG00000011289	13:22127196-22128347		CU466505,CH242-515M14,13:22123386-22182273 (Clone quality: bE515M14 on chr=13; Num_of_Contigs=3; )
CCBP2		location ⇒	13:22126039-22126089		CU466505,CH242-515M14,13:22123386-22182273 (Clone quality: bE515M14 on chr=13; Num_of_Contigs=3; )
CCBP2		location ⇒	13:22127647-22128078		CU466505,CH242-515M14,13:22123386-22182273 (Clone quality: bE515M14 on chr=13; Num_of_Contigs=3; )
CCDC102B		ENSSSCG00000004883	1:160889427-160901494		CU915525,CH242-7L4,1:160884005-160919579 (Clone quality: bE7L4 on chr=1; Num_of_Contigs=10; )
CCDC103		ENSSSCG00000017345	12:16332412-16336502		CU896578,CH242-101E18,12:16315123-16339681 (Clone quality: bE101E18 on chr=12; Num_of_Contigs=7; )
CCDC104		ENSSSCG00000008400	3:79737733-79763154
CCDC105		ENSSSCG00000013834	2:60134107-60145192		CU915718,CH242-156C19,2:60080233-60146626 (Clone quality: bE156C19 on chr=2; Num_of_Contigs=6; )
CCDC107		ENSSSCG00000005313	1:247472968-247476009		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CCDC109A		ENSSSCG00000010290	14:78779843-79116317
CCDC109B		ENSSSCG00000009141	8:96737112-96753889
CCDC11		ENSSSCG00000004515	1:102905469-102928901		CU914451,CH242-152J17,1:102889373-103019647 (Clone quality: bE152J17 on chr=1; Num_of_Contigs=3; )
CCDC110		ENSSSCG00000015795	15:43743435-43751271		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
CCDC110		location ⇒	15:43743380-43742805		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
CCDC110		location ⇒	15:43744825-43743463		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
CCDC110		location ⇒	15:43747948-43747889		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
CCDC110		location ⇒	15:43750904-43750818		CU571359,CH242-312E7,15:43699298-43786916 (Clone quality: bE312E7 on chr=15; Num_of_Contigs=3; )
CCDC111		ENSSSCG00000015786	15:43028193-43074054
CCDC113		ENSSSCG00000002803	6:19510434-19519941		FP102099,CH242-149H9,6:19510295-19556098 (Clone quality: bE149H9 on chr=6; Num_of_Contigs=10; )
CCDC115		ENSSSCG00000015737	15:29172998-29176420		CU606932,CH242-515L21,15:29170199-29176525 (Clone quality: bE515L21 on chr=15; Num_of_Contigs=27; )
CCDC116		ENSSSCG00000010086	14:51330256-51333544		CU633431,CH242-79C11,14:51180713-51414471 (Clone quality: bE79C11 on chr=14; Num_of_Contigs=4; )
CCDC120		ENSSSCG00000012288	X:42573795-42582129
CCDC121		ENSSSCG00000008547	3:104191041-104192024		CU972435,CH242-399O12,3:104165318-104194695 (Clone quality: bE399O12 on chr=3; Num_of_Contigs=8; )
CCDC122		ENSSSCG00000009426	11:22289352-22479921
CCDC124		ENSSSCG00000013891	2:62179572-62189501		CU463003,CH242-317A24,2:62151810-62279750 (Clone quality: bE317A24 on chr=2; Num_of_Contigs=2; )
CCDC126		ENSSSCG00000015703	15:16162633-16178675		FP085441,CH242-167G2,15:16156798-16191371 (Clone quality: bE167G2 on chr=15; Num_of_Contigs=4; )
CCDC129		ENSSSCG00000016671	18:39976741-40056956
CCDC130		ENSSSCG00000013755	2:56797201-56813176		CU855962,CH242-129F14,2:56772208-56824782 (Clone quality: bE129F14 on chr=2; Num_of_Contigs=2; )
CCDC132		ENSSSCG00000015321	9:68590255-68596067		CU915449,CH242-148H14,9:68588974-68600714 (Clone quality: bE148H14 on chr=9; Num_of_Contigs=6; )

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).