Schema for IKMC Genes Mapped - International Knockout Mouse Consortium Genes Mapped to Human Genome
  Database: hg38    Primary Table: hgIkmc    Row Count: 46,316   Data last updated: 2015-03-31
Format description: Browser extensible data
fieldexampleSQL type info description
bin 592smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 960586int(10) unsigned range Start position in chromosome
chromEnd 965715int(10) unsigned range End position in chromosome
name Klhl17_VG16928varchar(255) values Name of item
score 0int(10) unsigned range Optional score, nominal range 0-1000
strand .char(1) values + or -
thickStart 960586int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 960586int(10) unsigned range End of where display should be thick (stop codon)
itemRgb 0int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 1int(10) unsigned range Number of blocks
blockSizes 5129,longblob   Comma separated list of block sizes
chromStarts 0,longblob   Start positions relative to chromStart

Connected Tables and Joining Fields
        hg38.hgIkmcExtra.name (via hgIkmc.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgbblockCountblockSizeschromStarts
592chr1960586965715Klhl17_VG169280.9605869605860,0,015129,0,
592chr1966496975108Plekhn1_680740.9664969664960,240,018612,0,
592chr110134661014540Isg15_695170.10134661013466255,215,011074,0,
592chr110134661014540Isg15_777210.10134661013466255,215,011074,0,
9chr110201221056112Agrn_657480.102012210201220,240,0135990,0,
9chr110201221056112Agrn_812300.102012210201220,240,0135990,0,
593chr1108181711163569430015G10Rik_315880.108181710818170,240,0134539,0,
593chr1108181711163569430015G10Rik_315890.108181710818170,240,0134539,0,
593chr1108181711163569430015G10Rik_315900.108181710818170,240,0134539,0,
593chr1108181711163569430015G10Rik_315910.108181710818170,240,0134539,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

IKMC Genes Mapped (hgIkmc) Track Description
 

Description

This track shows genes targeted by International Knockout Mouse Consortium (IKMC) mapped to the human genome. IKMC is a collaboration to generate a public resource of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome. Gene targets are color-coded by status:

  • Green: Reagent(s) Available
  • Yellow: In Progress
  • Blue: Not Started/On Hold
  • Black: Withdrawn/Problematic

The KnockOut Mouse Project Data Coordination Center (KOMP DCC) is the central database resource for coordinating mouse gene targeting within IKMC and provides web-based query and display tools for IKMC data. In addition, the KOMP DCC website provides a tool for the scientific community to nominate genes of interest to be knocked out by the KOMP initiative.

IKMC members include

KOMP includes two production centers: CSD, a collaborative team at the Children's Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine, and a team at the VelociGene division of Regeneron Pharmaceuticals, Inc. EUCOMM includes 9 participating institutions. NorCOMM includes several participating institutions.

Methods

Using complementary targeting strategies, the IKMC centers design and create targeting vectors, mutant ES cell lines and, to some extent, mutant mice, embryos or sperm. Materials are distributed to the research community.

The KOMP Repository archives, maintains, and distributes IKMC products. Researchers can order products and get product information from the Repository. Researchers can also express interest in products that are still in the pipeline. They will then receive email notification as soon as KOMP generated products are available for distribution.

The process for ordering EUCOMM materials can be found here.

The process for ordering TIGM materials can be found here.

Information on NorCOMM products and services can be found here.

Genes were mapped to the human genome by IKMC.

Credits

Thanks to the International Knockout Mouse Consortium, and Carol Bult in particular, for providing these data.

References

Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT et al. The knockout mouse project. Nat Genet. 2004 Sep;36(9):921-4. PMID: 15340423; PMC: PMC2716027

Collins FS, Finnell RH, Rossant J, Wurst W. A new partner for the international knockout mouse consortium. Cell. 2007 Apr 20;129(2):235. PMID: 17448981

International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W. A mouse for all reasons. Cell. 2007 Jan 12;128(1):9-13. PMID: 17218247