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)

C7H6orf134		ENSSSCG00000001367	7:27007755-27019780	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
C7H6orf134		ENSSSCG00000001374	7:27130130-27142459	CU480634,CH242-391N4,7:27128408-27216112 (Clone quality: bE391N4 on chr=7; Num_of_Contigs=11; )
C7H6orf136		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7H6orf15		location ⇒	7:27474273-27473627	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
C7H6orf15		location ⇒	7:27474569-27474502	CT737281,CH242-102G9,7:27394698-27581746 (Clone quality: bE102G9 on chr=7; Num_of_Contigs=3; )
C7H6orf205		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7H6orf25		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7H6orf26		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7H6orf27		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7H6orf29		ENSSSCG00000001419	7:27780863-27799469	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C7H6orf31		ENSSSCG00000001432	7:28022923-28026258	CT954269,CH242-404E7,7:27953077-28153182 (Clone quality: bE404E7 on chr=7; Num_of_Contigs=12; )
C7H6orf47		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7H6orf48		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
C7orf10		ENSSSCG00000016767	18:52725556-53151715
C7orf11		ENSSSCG00000016768	18:53152102-53154305		CU862010,CH242-80D20,18:53118722-53191615 (Clone quality: bE80D20 on chr=18; Num_of_Contigs=4; )
C7orf16		ENSSSCG00000016670	18:39924478-39940881		FP103018,CH242-223A3,18:39907552-39967173 (Clone quality: bE223A3 on chr=18; Num_of_Contigs=1; )
C7orf20		ENSSSCG00000007545	3:307525-317681
C7orf23		ENSSSCG00000015392	9:87074539-87097481		CU464022,CH242-96H15,9:87068725-87124706 (Clone quality: bE96H15 on chr=9; Num_of_Contigs=4; )
C7orf23		ENSSSCG00000015392	9:87074539-87097481		CU464022,CH242-96H15,9:87068725-87124706 (Clone quality: bE96H15 on chr=9; Num_of_Contigs=4; )
C7orf23		location ⇒	9:87075424-87075533		CU464022,CH242-96H15,9:87068725-87124706 (Clone quality: bE96H15 on chr=9; Num_of_Contigs=4; )
C7orf23		location ⇒	9:87094046-87094102		CU464022,CH242-96H15,9:87068725-87124706 (Clone quality: bE96H15 on chr=9; Num_of_Contigs=4; )
C7orf23		location ⇒	9:87095103-87095207		CU464022,CH242-96H15,9:87068725-87124706 (Clone quality: bE96H15 on chr=9; Num_of_Contigs=4; )
C7orf23		location ⇒	9:87096874-87097479		CU464022,CH242-96H15,9:87068725-87124706 (Clone quality: bE96H15 on chr=9; Num_of_Contigs=4; )
C7orf25		ENSSSCG00000016760	18:50539046-50540311		CU915549,CH242-245G12,18:50525956-50543096 (Clone quality: bE245G12 on chr=18; Num_of_Contigs=11; )
C7orf27		ENSSSCG00000007563	3:1365237-1448858
C7orf31		ENSSSCG00000016713	18:45997362-45998168		FP236676,CH242-236O10,18:45995820-46011919 (Clone quality: bE236O10 on chr=18; Num_of_Contigs=8; )
C7orf34		ENSSSCG00000016471	18:6124827-6126356		CU928245,CH242-100K20,18:6102984-6180022 (Clone quality: bE100K20 on chr=18; Num_of_Contigs=3; )
C7orf41		ENSSSCG00000016681	18:41133118-41162880		CU694612,CH242-369I21,18:41102122-41184105 (Clone quality: bE369I21 on chr=18; Num_of_Contigs=4; )
C7orf42		ENSSSCG00000007736	3:14680997-14769244
C7orf42		location ⇒	3:14708078-14708423		CU467678,CH242-176C17,3:14673683-14714118 (Clone quality: bE176C17 on chr=3; Num_of_Contigs=8; )
C7orf42		location ⇒	3:14764050-14764124		FP102662,CH242-281O12,3:14764025-14790436 (Clone quality: bE281O12 on chr=3; Num_of_Contigs=5; )
C7orf42		location ⇒	3:14771424-14771769		FP102662,CH242-281O12,3:14764025-14790436 (Clone quality: bE281O12 on chr=3; Num_of_Contigs=5; )
C7orf42		location ⇒	3:93758304-93758362		CU463885,CH242-321C14,3:93758119-93776601 (Clone quality: bE321C14 on chr=3; Num_of_Contigs=7; )
C7orf43		ENSSSCG00000007647	3:6408169-6411795		CU694680,CH242-187A15,3:6349164-6471889 (Clone quality: bE187A15 on chr=3; Num_of_Contigs=2; )
C7orf44		ENSSSCG00000016757	18:49886945-49896318
C7orf45		ENSSSCG00000016562	18:16871211-16880213		CU655939,CH242-371G20,18:16845786-16901352 (Clone quality: bE371G20 on chr=18; Num_of_Contigs=7; )
C7orf47		ENSSSCG00000007652	3:6477282-6478538		CU464007,CH242-351O3,3:6471890-6520364 (Clone quality: bE351O3 on chr=3; Num_of_Contigs=5; )
C7orf49		ENSSSCG00000016531	18:12374390-12378712		FP236477,CH242-106A2,18:12349582-12433361 (Clone quality: bE106A2 on chr=18; Num_of_Contigs=4; )
C7orf50		ENSSSCG00000007546	3:311371-423235
C7orf53		ENSSSCG00000016645	18:31926735-31932179		CU928378,CH242-57L18,18:31908994-32026468 (Clone quality: bE57L18 on chr=18; Num_of_Contigs=7; )
C7orf55		ENSSSCG00000016508	18:8453934-8458448		CU928606,CH242-43O4,18:8449152-8508589 (Clone quality: bE43O4 on chr=18; Num_of_Contigs=8; )
C7orf58		ENSSSCG00000016618	18:23815760-24094665
C7orf59		ENSSSCG00000007646	3:6404794-6407416		CU694680,CH242-187A15,3:6349164-6471889 (Clone quality: bE187A15 on chr=3; Num_of_Contigs=2; )
C7orf63		ENSSSCG00000015303	9:65871801-65928508
C7orf72		ENSSSCG00000015628	9:128109071-128116560		CU655938,CH242-370K12,9:128089275-128121046 (Clone quality: bE370K12 on chr=9; Num_of_Contigs=11; )
C8A		ENSSSCG00000003835	6:110311107-110360077		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8A		location ⇒	6:110311586-110311242		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8A		location ⇒	6:110315475-110315250		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8A		location ⇒	6:110343376-110343132		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8A		location ⇒	6:110348236-110348045		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )

Go to records:
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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).