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)

PTCD1		ENSSSCG00000007622	3:5836439-5846668		FP102617,CH242-199P18,3:5834883-5866455 (Clone quality: bE199P18 on chr=3; Num_of_Contigs=6; )
PTCD2		ENSSSCG00000016975	16:46039843-46092746
PTCD3		ENSSSCG00000008225	3:53542683-53578492		CU570839,CH242-286N20,3:53540211-53717808 (Clone quality: bE286N20 on chr=3; Num_of_Contigs=1; )
PTCH		location ⇒	18:17609120-17609012		CU638846,CH242-272C14,18:17604734-17699485 (Clone quality: bE272C14 on chr=18; Num_of_Contigs=4; )
PTCH		location ⇒	18:17636578-17636506		CU638846,CH242-272C14,18:17604734-17699485 (Clone quality: bE272C14 on chr=18; Num_of_Contigs=4; )
PTCHD1		ENSSSCG00000012170	X:18312969-18364243
PTCHD2		ENSSSCG00000003417	6:48397874-48489261
PTCRA		ENSSSCG00000001650	7:43853027-43859109	CR956379,CH242-196P11,7:43779717-43958428 (No clone quality info on bE196P11)
PTDSS1		ENSSSCG00000006089	4:40685100-40693748		CU463146,CH242-381B20,4:40683877-40696118 (Clone quality: bE381B20 on chr=4; Num_of_Contigs=11; )
PTEN		ENSSSCG00000003506	6:54215030-54329215
PTEN		ENSSSCG00000010440	14:104786815-104878376
PTEN		ENSSSCG00000013226	2:13068848-13074399		CU856103,CH242-271O6,2:12985573-13119992 (Clone quality: bE271O6 on chr=2; Num_of_Contigs=3; )
PTEN		location ⇒	10:66407013-66406216		CT956084,PigE-149L18,10:66256961-66421506 (Clone quality: bT149L18 on chr=10; Num_of_Contigs=4; )
PTEN		location ⇒	10:66518031-66517234		CT841523,CH242-158A13,10:66421507-66520400 (Clone quality: bE158A13 on chr=10; Num_of_Contigs=4; )
PTEN		location ⇒	10:66671744-66670947		CU928902,CH242-223D20,10:66623280-66721750 (Clone quality: bE223D20 on chr=10; Num_of_Contigs=4; )
PTER		ENSSSCG00000011044	10:43512198-43519179
PTF-BETA		ENSSSCG00000016522	18:10629256-10718361
PTF-BETA		location ⇒	18:10629281-10629527		CU856469,CH242-395I4,18:10602596-10663955 (Clone quality: bE395I4 on chr=18; Num_of_Contigs=3; )
PTF-BETA		location ⇒	18:10698155-10698321		CU856469,CH242-395I4,18:10667157-10728997 (Clone quality: bE395I4 on chr=18; Num_of_Contigs=3; )
PTF-BETA		location ⇒	18:10717605-10717797		CU856469,CH242-395I4,18:10667157-10728997 (Clone quality: bE395I4 on chr=18; Num_of_Contigs=3; )
PTF-BETA		location ⇒	18:10770012-10769820		CU638822,CH242-106K14,18:10769689-10771768 (Clone quality: bE106K14 on chr=18; Num_of_Contigs=20; )
PTGDR		ENSSSCG00000005031	1:190214029-190221736		CU571369,CH242-523L1,1:190155010-190315370 (Clone quality: bE523L1 on chr=1; Num_of_Contigs=2; )
PTGDR		location ⇒	1:190213929-190214576		CU571369,CH242-523L1,1:190155010-190315370 (Clone quality: bE523L1 on chr=1; Num_of_Contigs=2; )
PTGDR		location ⇒	1:190408041-190408688		CU651561,CH242-138M14,1:190406686-190445303 (Clone quality: bE138M14 on chr=1; Num_of_Contigs=15; )
PTGER1		ENSSSCG00000013782	2:57305113-57306333		FP103015,CH242-135B13,2:57305111-57311746 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )
PTGER3		ENSSSCG00000003788	6:99719587-99802331
PTGES3		ENSSSCG00000000406	5:21082002-21102681		CU468457,CH242-203P23,5:21058663-21129178 (Clone quality: bE203P23 on chr=5; Num_of_Contigs=4; )
PTGES3		location ⇒	5:21081581-21081299		CU468457,CH242-203P23,5:21058663-21129178 (Clone quality: bE203P23 on chr=5; Num_of_Contigs=4; )
PTGES3		location ⇒	5:21081665-21081613		CU468457,CH242-203P23,5:21058663-21129178 (Clone quality: bE203P23 on chr=5; Num_of_Contigs=4; )
PTGES3		location ⇒	5:21082465-21081692		CU468457,CH242-203P23,5:21058663-21129178 (Clone quality: bE203P23 on chr=5; Num_of_Contigs=4; )
PTGES3		location ⇒	5:21102641-21102345		CU468457,CH242-203P23,5:21058663-21129178 (Clone quality: bE203P23 on chr=5; Num_of_Contigs=4; )
PTGFR		ENSSSCG00000003764	6:93814979-93858324
PTGFR		location ⇒	6:93815508-93814983		CU442727,CH242-106J21,6:93808181-93817146 (Clone quality: bE106J21 on chr=6; Num_of_Contigs=6; )
PTGFR		location ⇒	6:93858324-93857488		CU442727,CH242-106J21,6:93852451-93892359 (Clone quality: bE106J21 on chr=6; Num_of_Contigs=6; )
PTGFRN		ENSSSCG00000006735	4:107859868-107904918
PTGIR		location ⇒	1:190254967-190254142		CU571369,CH242-523L1,1:190155010-190315370 (Clone quality: bE523L1 on chr=1; Num_of_Contigs=2; )
PTGIR		location ⇒	1:190321346-190320521		CU651561,CH242-138M14,1:190319425-190343071 (Clone quality: bE138M14 on chr=1; Num_of_Contigs=15; )
PTGIS		ENSSSCG00000007463	17:53354140-53397753
PTGR1		ENSSSCG00000005461	1:265325397-265327678		CU928768,CH242-206J15,1:265322512-265329305 (Clone quality: bE206J15 on chr=1; Num_of_Contigs=17; )
PTGR1		location ⇒	1:265254941-265254771		CU928768,CH242-206J15,1:265253734-265259775 (Clone quality: bE206J15 on chr=1; Num_of_Contigs=17; )
PTGR1		location ⇒	1:265256477-265256419		CU928768,CH242-206J15,1:265253734-265259775 (Clone quality: bE206J15 on chr=1; Num_of_Contigs=17; )
PTGR1		location ⇒	1:265325560-265325401		CU928768,CH242-206J15,1:265322512-265329305 (Clone quality: bE206J15 on chr=1; Num_of_Contigs=17; )
PTGR1		location ⇒	1:265327677-265327558		CU928768,CH242-206J15,1:265322512-265329305 (Clone quality: bE206J15 on chr=1; Num_of_Contigs=17; )
PTGR2		ENSSSCG00000002351	7:105188719-105210057
PTGS1		ENSSSCG00000005533	1:276223853-276249153		CU210908,CH242-184P19,1:276194297-276251264 (Clone quality: bE184P19 on chr=1; Num_of_Contigs=5; )
PTGS1		ENSSSCG00000005533	1:276223853-276249153		CU210908,CH242-184P19,1:276194297-276251264 (Clone quality: bE184P19 on chr=1; Num_of_Contigs=5; )
PTGS1		location ⇒	1:104640824-104640773		CU041339,CH242-8K19,1:104633010-104681317 (Clone quality: bE8K19 on chr=1; Num_of_Contigs=4; )
PTGS1		location ⇒	1:117674285-117674197		CU633518,CH242-477B4,1:117667613-117756572 (Clone quality: bE477B4 on chr=1; Num_of_Contigs=5; )
PTGS1		location ⇒	1:192716751-192716654		CU062414,CH242-96C10,1:192642735-192764991 (Clone quality: bE96C10 on chr=1; Num_of_Contigs=3; )
PTGS1		location ⇒	1:276250391-276250465		CU210908,CH242-184P19,1:276194297-276251264 (Clone quality: bE184P19 on chr=1; Num_of_Contigs=5; )

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, 2201-21

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).