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)

AQN-1		ENSSSCG00000002979	6:33144491-33166421
AQN-1		location ⇒	6:33107884-33107960		FP236607,CH242-159H19,6:33106086-33108160 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-1		location ⇒	6:33159730-33159454		FP236607,CH242-159H19,6:33151690-33180802 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-1		location ⇒	6:33160960-33160773		FP236607,CH242-159H19,6:33151690-33180802 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-1		location ⇒	6:33162889-33162752		FP236607,CH242-159H19,6:33151690-33180802 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-3		ENSSSCG00000002977	6:33107915-33111962
AQN-3		location ⇒	6:33107886-33107960		FP236607,CH242-159H19,6:33106086-33108160 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-3		location ⇒	6:33109459-33109596		FP236607,CH242-159H19,6:33108261-33119731 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-3		location ⇒	6:33111443-33111631		FP236607,CH242-159H19,6:33108261-33119731 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQN-3		location ⇒	6:33112304-33112585		FP236607,CH242-159H19,6:33108261-33119731 (Clone quality: bE159H19 on chr=6; Num_of_Contigs=6; )
AQP10		ENSSSCG00000006551	4:99497924-99501015		CU856218,CH242-277E7,4:99496571-99509212 (Clone quality: bE277E7 on chr=4; Num_of_Contigs=4; )
AQP11		ENSSSCG00000014880	9:11943020-11953570
AQP2		ENSSSCG00000000210	5:14543046-14612790
AQP3		ENSSSCG00000010991	10:31577116-31582878		CU856468,CH242-364H6,10:31568942-31633500 (Clone quality: bE364H6 on chr=10; Num_of_Contigs=8; )
AQP4		ENSSSCG00000003720	6:76987944-76998242
AQP5_PIG		ENSSSCG00000000211	5:14555840-14559134
AQP6		ENSSSCG00000000212	5:14566595-14569114		CU633424,CH242-4O24,5:14564670-14570649 (Clone quality: bE4O24 on chr=5; Num_of_Contigs=4; )
AQP7		ENSSSCG00000010992	10:31630934-31646078
AQP8		ENSSSCG00000007825	3:19662475-19673262		FP236419,CH242-58N20,3:19658528-19750192 (Clone quality: bE58N20 on chr=3; Num_of_Contigs=7; )
AQP9		ENSSSCG00000004597	1:117866259-117917833
AQP9		location ⇒	1:117879391-117879187		CU302241,CH242-214O17,1:117835555-117880891 (Clone quality: bE214O17 on chr=1; Num_of_Contigs=4; )
AQP9		location ⇒	1:117884259-117884121		CU302241,CH242-214O17,1:117880992-117925321 (Clone quality: bE214O17 on chr=1; Num_of_Contigs=4; )
AQP9		location ⇒	1:117889497-117889369		CU302241,CH242-214O17,1:117880992-117925321 (Clone quality: bE214O17 on chr=1; Num_of_Contigs=4; )
AQP9		location ⇒	1:117917534-117917361		CU302241,CH242-214O17,1:117880992-117925321 (Clone quality: bE214O17 on chr=1; Num_of_Contigs=4; )
AQR		ENSSSCG00000004802	1:143630242-143864257
AR		ENSSSCG00000016539	18:12977858-12996185		CU928709,CH242-57B10,18:12964676-13013079 (Clone quality: bE57B10 on chr=18; Num_of_Contigs=5; )
AR		ENSSSCG00000012371	X:53291744-53430261
AR		location ⇒	X:53276733-53276430		CU469176,CH242-1I1,X:53259877-53281514 (Clone quality: bE1I1 on chr=X; Num_of_Contigs=5; )
AR		location ⇒	X:53367928-53368219		CU469162,CH242-427P7,X:53359552-53377779 (Clone quality: bE427P7 on chr=X; Num_of_Contigs=18; )
AR		location ⇒	X:53477536-53477868		CU695131,CH242-263G11,X:53474428-53478259 (Clone quality: bE263G11 on chr=X; Num_of_Contigs=17; )
AR		location ⇒	X:53477934-53478244		CU695131,CH242-263G11,X:53474428-53478259 (Clone quality: bE263G11 on chr=X; Num_of_Contigs=17; )
ARAF		ENSSSCG00000012275	X:42046719-42058777		FP015952,CH242-69I19,X:42024061-42060417 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
ARAF1		location ⇒	X:42048072-42048233		FP015952,CH242-69I19,X:42024061-42060417 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
ARAF1		location ⇒	X:42052731-42052935		FP015952,CH242-69I19,X:42024061-42060417 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
ARAF1		location ⇒	X:42055519-42055698		FP015952,CH242-69I19,X:42024061-42060417 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
ARAF1		location ⇒	X:42058189-42058773		FP015952,CH242-69I19,X:42024061-42060417 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
ARAP1		ENSSSCG00000014817	9:6871425-6910802
ARAP2		ENSSSCG00000008768	8:23087629-23258955
ARAP3		ENSSSCG00000014391	2:130214738-130236145		CU463118,CH242-312A3,2:130116991-130237824 (Clone quality: bE312A3 on chr=2; Num_of_Contigs=2; )
ARAP3		location ⇒	2:130216421-130216363		CU463118,CH242-312A3,2:130116991-130237824 (Clone quality: bE312A3 on chr=2; Num_of_Contigs=2; )
ARAP3		location ⇒	2:130216775-130216702		CU463118,CH242-312A3,2:130116991-130237824 (Clone quality: bE312A3 on chr=2; Num_of_Contigs=2; )
ARAP3		location ⇒	2:130218477-130218398		CU463118,CH242-312A3,2:130116991-130237824 (Clone quality: bE312A3 on chr=2; Num_of_Contigs=2; )
ARAP3		location ⇒	2:130219457-130219396		CU463118,CH242-312A3,2:130116991-130237824 (Clone quality: bE312A3 on chr=2; Num_of_Contigs=2; )
ARD1A		ENSSSCG00000012791	X:122769968-122774250		CU915581,CH242-139K22,X:122729751-122810838 (Clone quality: bE139K22 on chr=X; Num_of_Contigs=13; )
AREG		location ⇒	8:59669330-59669588		FP236682,CH242-469E11,8:59668455-59672292 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
AREG		location ⇒	8:59689818-59689663		FP236682,CH242-469E11,8:59686247-59692235 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
AREG		location ⇒	8:59710024-59710273		FP236682,CH242-469E11,8:59708899-59712361 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
AREG		location ⇒	8:59711410-59711642		FP236682,CH242-469E11,8:59708899-59712361 (Clone quality: bE469E11 on chr=8; Num_of_Contigs=18; )
ARF1		ENSSSCG00000013987	2:66452046-66469897	FP102564,CH242-144G7,2:66452040-66471471 (Clone quality: bE144G7 on chr=2; Num_of_Contigs=6; )
ARF3		ENSSSCG00000017315	12:15322002-15324599		CU928092,CH242-153I17,12:15321386-15347761 (Clone quality: bE153I17 on chr=12; Num_of_Contigs=9; )

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, 1751-32

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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).