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)

CD1b		ENSSSCG00000006451	4:95668388-95673909		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1B		ENSSSCG00000006451	4:95668388-95673909		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1B		location ⇒	4:95670884-95670603		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1B		location ⇒	4:95671379-95671101		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1B		location ⇒	4:95673548-95673281		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1B		location ⇒	4:95700963-95700877		CU570749,CH242-3I5,4:95680815-95725403 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1C		location ⇒	4:21652-21745		CU914810,CH242-87G5,4:8785-61312 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
CD1C		location ⇒	4:54597-54717		CU914810,CH242-87G5,4:8785-61312 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
CD1C		location ⇒	4:54716-54627		CU914810,CH242-87G5,4:8785-61312 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
CD1C		location ⇒	4:71410-71349		CU914810,CH242-87G5,4:61413-80075 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
CD1D		ENSSSCG00000006452	4:95727872-95732173		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1d		ENSSSCG00000006452	4:95727872-95732173		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1D		location ⇒	4:95700963-95700877		CU570749,CH242-3I5,4:95680815-95725403 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1D		location ⇒	4:95730130-95729850		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1D		location ⇒	4:95731226-95730948		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1D		location ⇒	4:95731820-95731526		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1E		ENSSSCG00000006450	4:95648271-95651805
CD1e		ENSSSCG00000006450	4:95648271-95651805
CD1E		location ⇒	4:95649231-95648949		CU570749,CH242-3I5,4:95632910-95650891 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1E		location ⇒	4:95649749-95649471		CU570749,CH242-3I5,4:95632910-95650891 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1E		location ⇒	4:95651469-95651172		CU570749,CH242-3I5,4:95650992-95680714 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD1E		location ⇒	4:95730130-95729848		CU570749,CH242-3I5,4:95725504-95735613 (Clone quality: bE3I5 on chr=4; Num_of_Contigs=11; )
CD2		ENSSSCG00000007791	3:16405822-16544539
CD2		ENSSSCG00000006736	4:108091395-108105900		CU861521,CH242-137N11,4:108073224-108106811 (Clone quality: bE137N11 on chr=4; Num_of_Contigs=13; )
CD2		ENSSSCG00000001728	7:49649644-49692739
CD2		ENSSSCG00000001867	7:62397796-62440268		CT868718,CH242-524I20,7:62378964-62491858 (Clone quality: bE524I20 on chr=7; Num_of_Contigs=2; )
CD2		ENSSSCG00000006378	4:93220455-93235041		CU606866,CH242-143J3,4:93072841-93235164 (Clone quality: bE143J3 on chr=4; Num_of_Contigs=1; )
CD2		ENSSSCG00000006400	4:94052098-94054645		CU856127,CH242-86L20,4:94027417-94074463 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
CD2		location ⇒	4:108092973-108092674		CU861521,CH242-137N11,4:108073224-108106811 (Clone quality: bE137N11 on chr=4; Num_of_Contigs=13; )
CD2		location ⇒	4:108097125-108097002		CU861521,CH242-137N11,4:108073224-108106811 (Clone quality: bE137N11 on chr=4; Num_of_Contigs=13; )
CD2		location ⇒	4:108101278-108101042		CU861521,CH242-137N11,4:108073224-108106811 (Clone quality: bE137N11 on chr=4; Num_of_Contigs=13; )
CD2		location ⇒	4:108105657-108105350		CU861521,CH242-137N11,4:108073224-108106811 (Clone quality: bE137N11 on chr=4; Num_of_Contigs=13; )
CD20		ENSSSCG00000013102	2:9017992-9032881		CU861944,CH242-210E8,2:8884557-9032900 (Clone quality: bE210E8 on chr=2; Num_of_Contigs=1; )
CD20		ENSSSCG00000013101	2:8963401-8984819		CU861944,CH242-210E8,2:8884557-9032900 (Clone quality: bE210E8 on chr=2; Num_of_Contigs=1; )
CD200		ENSSSCG00000011925	13:109591738-109602863		CU466425,CH242-101P22,13:109590350-109605580 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD200R1		location ⇒	13:109591746-109592065		CU466425,CH242-101P22,13:109590350-109605580 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD200R1		location ⇒	13:109592185-109592440		CU466425,CH242-101P22,13:109590350-109605580 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD200R1		location ⇒	13:109655339-109655658		CU466425,CH242-101P22,13:109631854-109698317 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD200R1		location ⇒	13:109675609-109676017		CU466425,CH242-101P22,13:109631854-109698317 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD200R1L		location ⇒	13:109591909-109592065		CU466425,CH242-101P22,13:109590350-109605580 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD200R1L		location ⇒	13:109655502-109655658		CU466425,CH242-101P22,13:109631854-109698317 (Clone quality: bE101P22 on chr=13; Num_of_Contigs=8; )
CD203c		ENSSSCG00000004194	1:33281351-33390761
CD204		ENSSSCG00000006979	17:3672614-3753871
CD207		ENSSSCG00000008319	3:65820549-65827189		CU855593,CH242-53L10,3:65814892-65863091 (Clone quality: bE53L10 on chr=3; Num_of_Contigs=46; )
CD207		location ⇒	3:65826994-65827189		CU855593,CH242-53L10,3:65814892-65863091 (Clone quality: bE53L10 on chr=3; Num_of_Contigs=46; )
CD209		location ⇒	X:11564502-11564159		CU463006,CH242-416I16,X:11549591-11568867 (Clone quality: bE416I16 on chr=X; Num_of_Contigs=8; )
CD209		location ⇒	X:11664865-11664984		CU463006,CH242-416I16,X:11612262-11674199 (Clone quality: bE416I16 on chr=X; Num_of_Contigs=8; )
CD209		location ⇒	X:11673055-11673272		CU463006,CH242-416I16,X:11612262-11674199 (Clone quality: bE416I16 on chr=X; Num_of_Contigs=8; )
CD209		location ⇒	X:11864671-11865014		FP102132,CH242-155E24,X:11859162-11890796 (Clone quality: bE155E24 on chr=X; Num_of_Contigs=10; )
CD213a2		ENSSSCG00000012594	X:92327870-92364246	CU468335,CH242-247D14,X:92311862-92443789 (Clone quality: bE247D14 on chr=X; Num_of_Contigs=4; )

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

Report problems to zhu

iastate.edu

$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).