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)

MMP8		location ⇒	9:33016232-33016077		CU972438,CH242-43B10,9:32968828-33020634 (Clone quality: bE43B10 on chr=9; Num_of_Contigs=1; )
MMP8		location ⇒	9:33018359-33018242		CU972438,CH242-43B10,9:32968828-33020634 (Clone quality: bE43B10 on chr=9; Num_of_Contigs=1; )
MMP8		location ⇒	9:33019805-33019643		CU972438,CH242-43B10,9:32968828-33020634 (Clone quality: bE43B10 on chr=9; Num_of_Contigs=1; )
MMP8		location ⇒	9:33022747-33022624		CU972438,CH242-43B10,9:33020735-33037750 (Clone quality: bE43B10 on chr=9; Num_of_Contigs=1; )
MMP9		ENSSSCG00000007436	17:50241605-50248663
MMP9		location ⇒	17:50243240-50243369		CU407252,CH242-441N18,17:50243141-50261548 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
MMP9		location ⇒	17:50243888-50243977		CU407252,CH242-441N18,17:50243141-50261548 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
MMP9		location ⇒	17:50244409-50244588		CU407252,CH242-441N18,17:50243141-50261548 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
MMP9		location ⇒	17:50246684-50246751		CU407252,CH242-441N18,17:50243141-50261548 (Clone quality: bE441N18 on chr=17; Num_of_Contigs=7; )
MMRN1		ENSSSCG00000009202	8:110920156-110977414
MMRN1		location ⇒	8:110920580-110920063		CU861567,CH242-60L18,8:110919679-110923665 (Clone quality: bE60L18 on chr=8; Num_of_Contigs=6; )
MMRN1		location ⇒	8:110921928-110921811		CU861567,CH242-60L18,8:110919679-110923665 (Clone quality: bE60L18 on chr=8; Num_of_Contigs=6; )
MMRN1		location ⇒	8:110941002-110940835		CU861567,CH242-60L18,8:110938021-110941863 (Clone quality: bE60L18 on chr=8; Num_of_Contigs=6; )
MMRN1		location ⇒	8:110951125-110951020		CU861567,CH242-60L18,8:110941964-110952047 (Clone quality: bE60L18 on chr=8; Num_of_Contigs=6; )
MMS19		ENSSSCG00000010520	14:113695817-113729395		CU407093,CH242-523G22,14:113665116-113843304 (Clone quality: bE523G22 on chr=14; Num_of_Contigs=4; )
MN1		ENSSSCG00000009966	14:45641698-45733632
MNAT1		ENSSSCG00000005090	1:198435585-198751937
MND1		ENSSSCG00000009009	8:64856053-65018234
MNDA		ENSSSCG00000006419	4:94976120-95034103
MNDA		location ⇒	4:94976311-94976121		CU138566,CH242-255O6,4:94956939-95026169 (Clone quality: bE255O6 on chr=4; Num_of_Contigs=2; )
MNDA		location ⇒	4:94977959-94977535		CU138566,CH242-255O6,4:94956939-95026169 (Clone quality: bE255O6 on chr=4; Num_of_Contigs=2; )
MNS1		ENSSSCG00000004601	1:119932156-120067311
MNT		ENSSSCG00000017830	12:45921764-45936087		CU640470,CH242-300A22,12:45898923-45939129 (Clone quality: bE300A22 on chr=12; Num_of_Contigs=5; )
MNX1		ENSSSCG00000016410	18:836518-841444		CU928638,CH242-402N9,18:819646-860056 (Clone quality: bE402N9 on chr=18; Num_of_Contigs=6; )
MOBKL1A		ENSSSCG00000008941	8:57468776-57517006
MOBKL1B		ENSSSCG00000008290	3:63374263-63385089		CU929887,CH242-215C22,3:63373310-63423045 (Clone quality: bE215C22 on chr=3; Num_of_Contigs=7; )
MOBKL2A		ENSSSCG00000013458	2:47090385-47095888
MOBKL2B		ENSSSCG00000011012	10:37668939-37951607
MOBKL2C		ENSSSCG00000003897	6:117933930-117937520		FP236153,CH242-65E2,6:117932715-117959989 (Clone quality: bE65E2 on chr=6; Num_of_Contigs=7; )
MOBKL3		ENSSSCG00000016079	15:94930691-94956685
MOBP		ENSSSCG00000011267	13:19895867-19896070		CU466503,CH242-513H20,13:19865758-19907598 (Clone quality: bE513H20 on chr=13; Num_of_Contigs=12; )
MOCOS		ENSSSCG00000003744	6:83371943-83488370
MOCS1		ENSSSCG00000001596	7:40358393-40391959	CT737355,CH242-117B8,7:40336981-40518356 (Clone quality: bE117B8 on chr=7; Num_of_Contigs=1; )
MOCS1		location ⇒	7:40356471-40356404	CT737355,CH242-117B8,7:40336981-40518356 (Clone quality: bE117B8 on chr=7; Num_of_Contigs=1; )
MOCS1		location ⇒	7:40356939-40356843	CT737355,CH242-117B8,7:40336981-40518356 (Clone quality: bE117B8 on chr=7; Num_of_Contigs=1; )
MOCS1		location ⇒	7:40359135-40358403	CT737355,CH242-117B8,7:40336981-40518356 (Clone quality: bE117B8 on chr=7; Num_of_Contigs=1; )
MOCS1		location ⇒	7:40361103-40361053	CT737355,CH242-117B8,7:40336981-40518356 (Clone quality: bE117B8 on chr=7; Num_of_Contigs=1; )
MOCS2		ENSSSCG00000016888	16:29508066-29527665		CU928375,CH242-425K19,16:29401619-29534620 (Clone quality: bE425K19 on chr=16; Num_of_Contigs=1; )
MOCS3		ENSSSCG00000007475	17:54571666-54574034	CR974565,CH242-123M10,17:54561502-54579305 (Clone quality: bE123M10 on chr=17; Num_of_Contigs=7; )
MOESIN		ENSSSCG00000012365	X:51389669-51452622		CU633325,CH242-9L4,X:51371292-51511308 (Clone quality: bE9L4 on chr=X; Num_of_Contigs=2; )
MOESIN		ENSSSCG00000015013	9:37246242-37286547
MOESIN		location ⇒	X:51390311-51389628		CU633325,CH242-9L4,X:51371292-51511308 (Clone quality: bE9L4 on chr=X; Num_of_Contigs=2; )
MOESIN		location ⇒	X:51391111-51390884		CU633325,CH242-9L4,X:51371292-51511308 (Clone quality: bE9L4 on chr=X; Num_of_Contigs=2; )
MOESIN		location ⇒	X:51396148-51395984		CU633325,CH242-9L4,X:51371292-51511308 (Clone quality: bE9L4 on chr=X; Num_of_Contigs=2; )
MOESIN		location ⇒	X:51401701-51401424		CU633325,CH242-9L4,X:51371292-51511308 (Clone quality: bE9L4 on chr=X; Num_of_Contigs=2; )
MOG		ENSSSCG00000001248	7:24862783-24873807	CT737425,CH242-47O8,7:24783186-24956885 (Clone quality: bE47O8 on chr=7; Num_of_Contigs=3; )
MOGAT1		ENSSSCG00000016225	15:115135473-115151214
MON1B		ENSSSCG00000002701	6:7802619-7809869
MON2		ENSSSCG00000000458	5:26680855-26795617
MORC1		ENSSSCG00000011937	13:111799878-111959723

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, 1401-46

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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).