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)

NUP43		ENSSSCG00000004105	1:17234332-17248548		CU571230,CH242-42L8,1:17232467-17263259 (Clone quality: bE42L8 on chr=1; Num_of_Contigs=10; )
NUP54		ENSSSCG00000008375	3:73307894-73309404		CU856445,CH242-9L3,3:73296463-73329290 (Clone quality: bE9L3 on chr=3; Num_of_Contigs=3; )
NUP62		ENSSSCG00000003200	6:38600113-38601716
NUP62CL		ENSSSCG00000012557	X:85734317-85791631		FP236674,CH242-495N5,X:85707853-85814600 (Clone quality: bE495N5 on chr=X; Num_of_Contigs=2; )
NUP85		ENSSSCG00000017207	12:4188884-4285059
NUP85		location ⇒	12:4266915-4266782	CU928896,CH242-521B23,12:4242297-4294366 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
NUP85		location ⇒	12:4267246-4267124	CU928896,CH242-521B23,12:4242297-4294366 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
NUP85		location ⇒	12:4267485-4267350	CU928896,CH242-521B23,12:4242297-4294366 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
NUP85		location ⇒	12:4270307-4270179	CU928896,CH242-521B23,12:4242297-4294366 (Clone quality: bE521B23 on chr=12; Num_of_Contigs=4; )
NUP98		ENSSSCG00000014794	9:5682301-5824335
NUPL1		ENSSSCG00000009295	11:2402138-2404941		CU469293,CH242-40N5,11:2399075-2405229 (Clone quality: bE40N5 on chr=11; Num_of_Contigs=14; )
NUS1		ENSSSCG00000004251	1:46100868-46127994		CU463113,CH242-216M8,1:45998574-46130403 (Clone quality: bE216M8 on chr=1; Num_of_Contigs=4; )
NUSAP1		ENSSSCG00000004749	1:136429272-136468524
NUTF2		ENSSSCG00000002770	6:12896485-12915247
NUTF2		location ⇒	3:88201564-88202243		CU582919,CH242-292A3,3:88197040-88215506 (Clone quality: bE292A3 on chr=3; Num_of_Contigs=13; )
NUTF2		location ⇒	3:88202258-88202384		CU582919,CH242-292A3,3:88197040-88215506 (Clone quality: bE292A3 on chr=3; Num_of_Contigs=13; )
NUTF2		location ⇒	3:96340163-96340079		CU571019,CH242-203O20,3:96331591-96413289 (Clone quality: bE203O20 on chr=3; Num_of_Contigs=4; )
NWD1		ENSSSCG00000013865	2:61259826-61298384
NXN		ENSSSCG00000017805	12:44982547-44987092		CU928997,CH242-26C19,12:44982217-45011842 (Clone quality: bE26C19 on chr=12; Num_of_Contigs=2; )
NXNL1		ENSSSCG00000013881	2:61835444-61839951		CU861959,CH242-254K17,2:61834641-61845581 (Clone quality: bE254K17 on chr=2; Num_of_Contigs=9; )
NXPH1		ENSSSCG00000015348	9:74495003-74496755		CU640437,CH242-149B19,9:74468869-74603609 (Clone quality: bE149B19 on chr=9; Num_of_Contigs=2; )
NXPH2		ENSSSCG00000015682	15:11601183-11601996		CU469208,CH242-29C3,15:11595150-11602619 (Clone quality: bE29C3 on chr=15; Num_of_Contigs=6; )
NXPH3		ENSSSCG00000017552	12:23315318-23318719		CU466971,CH242-449D17,12:23302117-23323430 (Clone quality: bE449D17 on chr=12; Num_of_Contigs=9; )
NXPH4		ENSSSCG00000000422	5:21386000-21393790
NXT1		ENSSSCG00000007119	17:31933714-31934136		CU606898,CH242-256N2,17:31905701-32110440 (Clone quality: bE256N2 on chr=17; Num_of_Contigs=3; )
NXT2		ENSSSCG00000012581	X:88783545-88788536		FP102602,CH242-17O13,X:88721438-88793803 (Clone quality: bE17O13 on chr=X; Num_of_Contigs=3; )
NXT2		location ⇒	X:88785700-88785788		FP102602,CH242-17O13,X:88721438-88793803 (Clone quality: bE17O13 on chr=X; Num_of_Contigs=3; )
NXT2		location ⇒	X:88787326-88787471		FP102602,CH242-17O13,X:88721438-88793803 (Clone quality: bE17O13 on chr=X; Num_of_Contigs=3; )
NXT2		location ⇒	X:88790416-88790539		FP102602,CH242-17O13,X:88721438-88793803 (Clone quality: bE17O13 on chr=X; Num_of_Contigs=3; )

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, 951-29

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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).