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)

SNX13		ENSSSCG00000015365	9:81513431-81543975
SNX13		location ⇒	9:81512184-81510804		CU915622,CH242-512I4,9:81510743-81522941 (Clone quality: bE512I4 on chr=9; Num_of_Contigs=8; )
SNX13		location ⇒	9:81513680-81512430		CU915622,CH242-512I4,9:81510743-81522941 (Clone quality: bE512I4 on chr=9; Num_of_Contigs=8; )
SNX13		location ⇒	9:81519639-81519563		CU915622,CH242-512I4,9:81510743-81522941 (Clone quality: bE512I4 on chr=9; Num_of_Contigs=8; )
SNX13		location ⇒	9:81730504-81730279		CU694722,CH242-364C16,9:81719669-81742001 (Clone quality: bE364C16 on chr=9; Num_of_Contigs=20; )
SNX14		ENSSSCG00000004293	1:56907308-56993302
SNX15		ENSSSCG00000013012	2:5543548-5555660	CU457406,CH242-284K16,2:5352106-5575890 (Clone quality: bE284K16 on chr=2; Num_of_Contigs=20; )
SNX16		ENSSSCG00000006151	4:56555803-56590104		CU633211,CH242-12D19,4:56513740-56598488 (Clone quality: bE12D19 on chr=4; Num_of_Contigs=3; )
SNX18		ENSSSCG00000016897	16:31167245-31169360		CU633347,CH242-158G2,16:31159370-31174801 (Clone quality: bE158G2 on chr=16; Num_of_Contigs=9; )
SNX19		ENSSSCG00000015252	9:55934379-55973562
SNX21		ENSSSCG00000007425	17:50098033-50103408		CU076086,CH242-56C16,17:49960216-50115189 (Clone quality: bE56C16 on chr=17; Num_of_Contigs=2; )
SNX24		location ⇒	2:114344578-114344676		CU929833,CH242-55A15,2:114343471-114370232 (Clone quality: bE55A15 on chr=2; Num_of_Contigs=8; )
SNX24		location ⇒	2:114379247-114379317		CU929833,CH242-55A15,2:114370333-114399095 (Clone quality: bE55A15 on chr=2; Num_of_Contigs=8; )
SNX24		location ⇒	2:114432119-114432203		CU929833,CH242-55A15,2:114428776-114455243 (Clone quality: bE55A15 on chr=2; Num_of_Contigs=8; )
SNX24		location ⇒	2:114451521-114451620		CU929833,CH242-55A15,2:114428776-114455243 (Clone quality: bE55A15 on chr=2; Num_of_Contigs=8; )
SNX25		ENSSSCG00000015789	15:43427369-43628381
SNX26		ENSSSCG00000002909	6:30362464-30374095		CU466979,CH242-510C11,6:30348318-30377094 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
SNX27		ENSSSCG00000006619	4:101491726-101574918	CU457723,CH242-28L6,4:101441264-101656496 (Clone quality: bE28L6 on chr=4; Num_of_Contigs=25; )
SNX29		ENSSSCG00000007885	3:27457810-27491279
SNX3		ENSSSCG00000004385	1:77886324-77895209
SNX30		ENSSSCG00000005471	1:266390018-266459700
SNX31		ENSSSCG00000006064	4:36694058-36742254
SNX32		ENSSSCG00000012975	2:4878367-4890663		CU856129,CH242-95H3,2:4866849-4898129 (Clone quality: bE95H3 on chr=2; Num_of_Contigs=5; )
SNX33		ENSSSCG00000001875	7:63228903-63238222		CU582918,CH242-27K6,7:63199750-63260944 (Clone quality: bE27K6 on chr=7; Num_of_Contigs=5; )
SNX6		ENSSSCG00000001961	7:71000026-71042602		CT867954,CH242-216K6,7:70958499-71046494 (Clone quality: bE216K6 on chr=7; Num_of_Contigs=4; )
SNX7		ENSSSCG00000006877	4:123997517-124064481
SOAT2		ENSSSCG00000000260	5:16937704-16949895
SOBP		ENSSSCG00000004379	1:77135195-77288213
SOCS1		location ⇒	5:125-202		FP016092,CH242-185O3,5:1-16341 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
SOCS1		location ⇒	5:190-125		FP016092,CH242-185O3,5:1-16341 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
SOCS1		location ⇒	5:6354-6439		FP016092,CH242-185O3,5:1-16341 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
SOCS1		location ⇒	5:6425-6320		FP016092,CH242-185O3,5:1-16341 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
SOCS2		ENSSSCG00000000910	5:84086013-84090321		CU915373,CH242-67L15,5:84083925-84090330 (Clone quality: bE67L15 on chr=5; Num_of_Contigs=3; )
SOCS2		location ⇒	5:84086658-84086072		CU915373,CH242-67L15,5:84083925-84090330 (Clone quality: bE67L15 on chr=5; Num_of_Contigs=3; )
SOCS2		location ⇒	5:84088567-84088328		CU915373,CH242-67L15,5:84083925-84090330 (Clone quality: bE67L15 on chr=5; Num_of_Contigs=3; )
SOCS3		location ⇒	1:135043257-135043631		FP015979,CH242-120L15,1:135033363-135056764 (Clone quality: bE120L15 on chr=1; Num_of_Contigs=4; )
SOCS3		location ⇒	1:135043817-135043906		FP015979,CH242-120L15,1:135033363-135056764 (Clone quality: bE120L15 on chr=1; Num_of_Contigs=4; )
SOCS3		location ⇒	1:135043817-135044390		FP015979,CH242-120L15,1:135033363-135056764 (Clone quality: bE120L15 on chr=1; Num_of_Contigs=4; )
SOCS3		location ⇒	1:135045067-135045197		FP015979,CH242-120L15,1:135033363-135056764 (Clone quality: bE120L15 on chr=1; Num_of_Contigs=4; )
SOCS4		ENSSSCG00000004878	1:159702244-159703851		CU062492,CH242-25B22,1:159618913-159740703 (Clone quality: bE25B22 on chr=1; Num_of_Contigs=4; )
SOCS4		ENSSSCG00000005053	1:193023177-193024502		CU855754,CH242-58I7,1:193004056-193034238 (Clone quality: bE58I7 on chr=1; Num_of_Contigs=12; )
SOCS4		location ⇒	1:193009398-193009699		CU855754,CH242-58I7,1:193004056-193034238 (Clone quality: bE58I7 on chr=1; Num_of_Contigs=12; )
SOCS4		location ⇒	1:193023085-193025020		CU855754,CH242-58I7,1:193004056-193034238 (Clone quality: bE58I7 on chr=1; Num_of_Contigs=12; )
SOCS5		ENSSSCG00000008437	3:87196381-87197991		CU856453,CH242-426I21,3:87152554-87198631 (Clone quality: bE426I21 on chr=3; Num_of_Contigs=2; )
SOCS5		location ⇒	3:87197639-87196827		CU856453,CH242-426I21,3:87152554-87198631 (Clone quality: bE426I21 on chr=3; Num_of_Contigs=2; )
SOCS6		ENSSSCG00000004878	1:159702244-159703851		CU062492,CH242-25B22,1:159618913-159740703 (Clone quality: bE25B22 on chr=1; Num_of_Contigs=4; )
SOCS6		location ⇒	1:159702386-159701519		CU062492,CH242-25B22,1:159618913-159740703 (Clone quality: bE25B22 on chr=1; Num_of_Contigs=4; )
SOCS7		ENSSSCG00000005053	1:193023177-193024502		CU855754,CH242-58I7,1:193004056-193034238 (Clone quality: bE58I7 on chr=1; Num_of_Contigs=12; )
SOCS7		ENSSSCG00000018057	12:57289765-57315983		CU929736,CH242-246D8,12:57289656-57329714 (Clone quality: bE246D8 on chr=12; Num_of_Contigs=8; )
SOD2		ENSSSCG00000004051	1:8803672-8813898		CU469098,CH242-59I11,1:8788287-8824605 (Clone quality: bE59I11 on chr=1; Num_of_Contigs=7; )

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

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).