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)

CSRNP3		ENSSSCG00000015906	15:67371232-67459906
CSRP2		ENSSSCG00000000951	5:97345390-97367476
CSRP2BP		ENSSSCG00000007092	17:27226775-27263179
CSRP3		location ⇒	2:37465787-37465471		CU929970,CH242-88H14,2:37460475-37487234 (Clone quality: bE88H14 on chr=2; Num_of_Contigs=9; )
CSRP3		location ⇒	2:37471764-37471594		CU929970,CH242-88H14,2:37460475-37487234 (Clone quality: bE88H14 on chr=2; Num_of_Contigs=9; )
CSRP3		location ⇒	2:37550660-37550830		CU929490,CH242-88D19,2:37544950-37556367 (Clone quality: bE88D19 on chr=2; Num_of_Contigs=15; )
CSRP3		location ⇒	2:58620872-58620556		CU972360,CH242-151N21,2:58618903-58621032 (Clone quality: bE151N21 on chr=2; Num_of_Contigs=28; )
CST11		ENSSSCG00000007122	17:32006857-32009878		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST2		location ⇒	17:32064035-32063846		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST2		location ⇒	17:32067383-32067107		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST2		location ⇒	17:32217004-32217280		CU855486,CH242-118N5,17:32216750-32231251 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
CST2		location ⇒	17:32220352-32220541		CU855486,CH242-118N5,17:32216750-32231251 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
CST3		location ⇒	17:32064767-32064651		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST3		location ⇒	17:32067284-32067107		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST3		location ⇒	17:32217103-32217280		CU855486,CH242-118N5,17:32216750-32231251 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
CST3		location ⇒	17:32219620-32219736		CU855486,CH242-118N5,17:32216750-32231251 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
CST4		location ⇒	17:32064035-32063750		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST4		location ⇒	17:32067238-32067107		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST4		location ⇒	17:32217149-32217280		CU855486,CH242-118N5,17:32216750-32231251 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
CST4		location ⇒	17:32220352-32220637		CU855486,CH242-118N5,17:32216750-32231251 (Clone quality: bE118N5 on chr=17; Num_of_Contigs=6; )
CST6		ENSSSCG00000012960	2:4696311-4698228		CU694743,CH242-58A13,2:4689745-4721432 (Clone quality: bE58A13 on chr=2; Num_of_Contigs=2; )
CST7		ENSSSCG00000007131	17:32358920-32367539		CU633263,CH242-272K17,17:32349266-32389163 (Clone quality: bE272K17 on chr=17; Num_of_Contigs=9; )
CST7		location ⇒	17:32358940-32359013		CU633263,CH242-272K17,17:32349266-32389163 (Clone quality: bE272K17 on chr=17; Num_of_Contigs=9; )
CST7		location ⇒	17:32365491-32365665		CU633263,CH242-272K17,17:32349266-32389163 (Clone quality: bE272K17 on chr=17; Num_of_Contigs=9; )
CST7		location ⇒	17:32366447-32366569		CU633263,CH242-272K17,17:32349266-32389163 (Clone quality: bE272K17 on chr=17; Num_of_Contigs=9; )
CST7		location ⇒	17:32367178-32367536		CU633263,CH242-272K17,17:32349266-32389163 (Clone quality: bE272K17 on chr=17; Num_of_Contigs=9; )
CST8		ENSSSCG00000007124	17:32023664-32028500		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST8		location ⇒	17:32024087-32024203		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST8		location ⇒	17:32024895-32025012		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CST8		location ⇒	17:32028331-32028500		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CSTF1		ENSSSCG00000007494	17:59507260-59518798	CR956640,CH242-155M9,17:59463698-59643740 (No clone quality info on bE155M9)
CSTF2		ENSSSCG00000012486	X:75805025-75834515		CU861981,CH242-34M18,X:75781114-75888901 (Clone quality: bE34M18 on chr=X; Num_of_Contigs=4; )
CSTF2		location ⇒	14:102550849-102551030		CT737328,CH242-97N16,14:102429109-102576581 (Clone quality: bE97N16 on chr=14; Num_of_Contigs=2; )
CSTF2		location ⇒	14:39428654-39428473		CT954338,CH242-92C5,14:39428244-39430439 (Clone quality: bE92C5 on chr=14; Num_of_Contigs=25; )
CSTF2T		ENSSSCG00000009884	14:39428466-39430310		CT954338,CH242-92C5,14:39428244-39430439 (Clone quality: bE92C5 on chr=14; Num_of_Contigs=25; )
CSTL1		ENSSSCG00000007121	17:31996639-32000314		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
CTAGE5		location ⇒	1:177521632-177521773		CU639454,CH242-168O7,1:177493143-177594002 (Clone quality: bE168O7 on chr=1; Num_of_Contigs=4; )
CTAGE5		location ⇒	1:177539862-177540023		CU639454,CH242-168O7,1:177493143-177594002 (Clone quality: bE168O7 on chr=1; Num_of_Contigs=4; )
CTAGE5		location ⇒	1:177756902-177757043		CU582949,CH242-31P23,1:177726070-177824602 (Clone quality: bE31P23 on chr=1; Num_of_Contigs=2; )
CTAGE5		location ⇒	1:177775131-177775292		CU582949,CH242-31P23,1:177726070-177824602 (Clone quality: bE31P23 on chr=1; Num_of_Contigs=2; )
CTAPIII		location ⇒	8:59486235-59486133		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CTAPIII		location ⇒	8:59486502-59486365		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CTAPIII		location ⇒	8:59486948-59486783		CU928337,CH242-266F15,8:59474833-59511571 (Clone quality: bE266F15 on chr=8; Num_of_Contigs=10; )
CTBS		ENSSSCG00000003758	6:89205167-89219755
CTCFL		ENSSSCG00000007505	17:60397216-60426514
CTDP1		ENSSSCG00000005787	1:292406993-292431302		CU633378,CH242-250D17,1:292365925-292431399 (Clone quality: bE250D17 on chr=1; Num_of_Contigs=11; )
CTDSPL		ENSSSCG00000011247	13:18742098-18751158
CTDSPL2		ENSSSCG00000004690	1:133101196-133126786
CTF1		ENSSSCG00000003396	6:47161005-47201204
CTF1		ENSSSCG00000007774	3:16040475-16044704		FP102303,CH242-232B18,3:16040061-16090011 (Clone quality: bE232B18 on chr=3; 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, 2601-2650, 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).