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)

ABCB4		location ⇒	9:86829759-86829647		CU929528,CH242-211D13,9:86824597-86859288 (Clone quality: bE211D13 on chr=9; Num_of_Contigs=6; )
ABCB4		location ⇒	9:86928049-86928246		CU915624,CH242-101D9,9:86873884-86992742 (Clone quality: bE101D9 on chr=9; Num_of_Contigs=2; )
ABCB4		location ⇒	9:86929716-86929922		CU915624,CH242-101D9,9:86873884-86992742 (Clone quality: bE101D9 on chr=9; Num_of_Contigs=2; )
ABCB5		ENSSSCG00000015377	9:84109317-84137158		CU928331,CH242-65P8,9:84104934-84138527 (Clone quality: bE65P8 on chr=9; Num_of_Contigs=5; )
ABCB6		ENSSSCG00000016210	15:114242170-114250020		CU457453,CH242-470M7,15:114242050-114256523 (Clone quality: bE470M7 on chr=15; Num_of_Contigs=11; )
ABCB7		ENSSSCG00000012424	X:59586167-59712452
ABCB7		location ⇒	X:59599084-59598909	CU406979,CH242-222D13,X:59573238-59629300 (Clone quality: bE222D13 on chr=X; Num_of_Contigs=6; )
ABCB7		location ⇒	X:59606649-59606470	CU406979,CH242-222D13,X:59573238-59629300 (Clone quality: bE222D13 on chr=X; Num_of_Contigs=6; )
ABCB7		location ⇒	X:59608577-59608309	CU406979,CH242-222D13,X:59573238-59629300 (Clone quality: bE222D13 on chr=X; Num_of_Contigs=6; )
ABCB7		location ⇒	X:59712446-59712265	CU406979,CH242-222D13,X:59629401-59728011 (Clone quality: bE222D13 on chr=X; Num_of_Contigs=6; )
ABCB9		ENSSSCG00000009784	14:29985305-30010304
ABCB9		location ⇒	14:142092082-142092155		CT841550,CH242-252A14,14:142089742-142117350 (Clone quality: bE252A14 on chr=14; Num_of_Contigs=5; )
ABCB9		location ⇒	14:24318722-24318625		CU468532,CH242-32J1,14:24253662-24329849 (Clone quality: bE32J1 on chr=14; Num_of_Contigs=7; )
ABCB9		location ⇒	14:49501328-49501243	CT827879,CH242-298L14,14:49419558-49570938 (Clone quality: bE298L14 on chr=14; Num_of_Contigs=1; )
ABCB9		location ⇒	14:59069552-59069459		CU407011,CH242-111K11,14:59044843-59098748 (Clone quality: bE111K11 on chr=14; Num_of_Contigs=5; )
ABCC1		ENSSSCG00000007874	3:25657262-25744405
ABCC1		location ⇒	3:25646968-25647100		FP103089,CH242-68P10,3:25645483-25652054 (Clone quality: bE68P10 on chr=3; Num_of_Contigs=10; )
ABCC1		location ⇒	3:25819411-25819520		FP103089,CH242-68P10,3:25817427-25821122 (Clone quality: bE68P10 on chr=3; Num_of_Contigs=10; )
ABCC1		location ⇒	3:25820337-25820442		FP103089,CH242-68P10,3:25817427-25821122 (Clone quality: bE68P10 on chr=3; Num_of_Contigs=10; )
ABCC10		ENSSSCG00000001680	7:44661255-44816825
ABCC2		ENSSSCG00000010543	14:115716020-115793964
ABCC2		location ⇒	14:115778395-115778550		CU407002,CH242-427K14,14:115736639-115822002 (Clone quality: bE427K14 on chr=14; Num_of_Contigs=2; )
ABCC2		location ⇒	14:115780355-115780560		CU407002,CH242-427K14,14:115736639-115822002 (Clone quality: bE427K14 on chr=14; Num_of_Contigs=2; )
ABCC2		location ⇒	14:115786978-115787139		CU407002,CH242-427K14,14:115736639-115822002 (Clone quality: bE427K14 on chr=14; Num_of_Contigs=2; )
ABCC2		location ⇒	14:115788604-115788773		CU407002,CH242-427K14,14:115736639-115822002 (Clone quality: bE427K14 on chr=14; Num_of_Contigs=2; )
ABCC4		ENSSSCG00000009495	11:64507825-64604664
ABCC5		ENSSSCG00000011782	13:92341956-92485222
ABCC8		ENSSSCG00000013378	2:38991417-39078510
ABCC9		ENSSSCG00000000571	5:49451970-49495319
ABCD2		ENSSSCG00000000781	5:66991160-67127430
ABCE1		ENSSSCG00000009043	8:71941578-71990160
ABCE1		location ⇒	8:71951419-71951330		CU914231,CH242-155D23,8:71946688-71958074 (Clone quality: bE155D23 on chr=8; Num_of_Contigs=4; )
ABCE1		location ⇒	8:71952412-71952315		CU914231,CH242-155D23,8:71946688-71958074 (Clone quality: bE155D23 on chr=8; Num_of_Contigs=4; )
ABCE1		location ⇒	8:71987435-71987240		CU914231,CH242-155D23,8:71984718-71990981 (Clone quality: bE155D23 on chr=8; Num_of_Contigs=4; )
ABCE1		location ⇒	8:71990160-71990036		CU914231,CH242-155D23,8:71984718-71990981 (Clone quality: bE155D23 on chr=8; Num_of_Contigs=4; )
ABCF1		ENSSSCG00000001346	7:26680608-26697722	CU498826,CH242-119D24,7:26553813-26728014 (Clone quality: bE119D24 on chr=7; Num_of_Contigs=31; )
ABCF1		ENSSSCG00000001370	7:27049238-27066960	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
ABCF2		ENSSSCG00000016441	18:5212154-5217819		FP102583,CH242-165F21,18:5207145-5218026 (Clone quality: bE165F21 on chr=18; Num_of_Contigs=16; )
ABCG1		location ⇒	9:44984117-44984195		CU639481,CH242-263G17,9:44899832-45096295 (Clone quality: bE263G17 on chr=9; Num_of_Contigs=2; )
ABCG1		location ⇒	9:44985078-44985145		CU639481,CH242-263G17,9:44899832-45096295 (Clone quality: bE263G17 on chr=9; Num_of_Contigs=2; )
ABCG1		location ⇒	9:44988902-44988975		CU639481,CH242-263G17,9:44899832-45096295 (Clone quality: bE263G17 on chr=9; Num_of_Contigs=2; )
ABCG1		location ⇒	9:44990859-44990987		CU639481,CH242-263G17,9:44899832-45096295 (Clone quality: bE263G17 on chr=9; Num_of_Contigs=2; )
ABCG2		ENSSSCG00000009213	8:112296288-112514103
ABCG2		ENSSSCG00000009215	8:112366445-112459036
ABCG4		ENSSSCG00000015113	9:44978279-44991351		CU639481,CH242-263G17,9:44899832-45096295 (Clone quality: bE263G17 on chr=9; Num_of_Contigs=2; )
ABHD1		ENSSSCG00000008554	3:104432464-104438369		CU896571,CH242-143O19,3:104398046-104492436 (Clone quality: bE143O19 on chr=3; Num_of_Contigs=6; )
ABHD11		ENSSSCG00000007715	3:9321979-9324894
ABHD12B		ENSSSCG00000005023	1:188912051-188937708
ABHD13		ENSSSCG00000009541	11:76012439-76013449		CU019584,CH242-370B14,11:75986969-76035774 (Clone quality: bE370B14 on chr=11; Num_of_Contigs=3; )
ABHD15		ENSSSCG00000017789	12:43481311-43485261		CU463822,CH242-488A20,12:43480158-43486368 (Clone quality: bE488A20 on chr=12; Num_of_Contigs=10; )

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).