Mouse Gene Hnrnpk (uc007qty.1) Description and Page Index
  Description: heterogeneous nuclear ribonucleoprotein K
RefSeq Summary (NM_025279): The protein encoded by this gene is a component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex, and is a poly-cytosine binding protein (PCBP). It is found in multiple subcellular compartments including the nucleus, cytoplasm and mitochondria. This gene product is thought to interact with RNA, DNA, and protein, and is involved in multiple cellular processes, including transcription, chromatin remodeling, DNA damage response, signal transduction, mRNA splicing, export, and translation. Multiple transcript variants and protein isoforms exist, with some isoforms containing a unique C-terminus. There are four pseudogenes of this gene, found on chromosomes 2, 3, 7 and 13. [provided by RefSeq, Aug 2014].
Transcript (Including UTRs)
   Position: mm9 chr13:58,493,312-58,503,873 Size: 10,562 Total Exon Count: 15 Strand: -
Coding Region
   Position: mm9 chr13:58,493,747-58,501,751 Size: 8,005 Coding Exon Count: 14 

Page IndexSequence and LinksCTDMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2011-03-02

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:58,493,312-58,503,873)mRNA (may differ from genome)Protein (439 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAllen Brain Atlas
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkPubMedReactomeStanford SOURCEUniProtKB

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from GNF1M Mouse Chip

    
     
      
       
     
    
   
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Rinn et. al Sex Gene Expression Data on MOE430A Chip

        
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GNF Expression Atlas Data from U74a Mouse Chip

        
     
    
    
    
   
    
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Affymetrix All Exon Microarrays

           
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.60147-0.371 Picture PostScript Text
3' UTR -114.71435-0.264 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00013 - KH domain
PF08067 - ROKNT (NUC014) domain

SCOP Domains:
54791 - Eukaryotic type KH-domain (KH-domain type I)
54814 - Prokaryotic type KH domain (KH-domain type II)

ModBase Predicted Comparative 3D Structure on P61979-3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
GenBankRGDEnsemblFlyBaseWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  Descriptions from all associated GenBank mRNAs
  AK160887 - Mus musculus 12 days embryo embryonic body below diaphragm region cDNA, RIKEN full-length enriched library, clone:3732412G03 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
BC089328 - Mus musculus heterogeneous nuclear ribonucleoprotein K, mRNA (cDNA clone MGC:102032 IMAGE:6402614), complete cds.
AK135519 - Mus musculus 12 days embryo female mullerian duct includes surrounding region cDNA, RIKEN full-length enriched library, clone:6820441P15 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK166656 - Mus musculus 5 days embryo whole body cDNA, RIKEN full-length enriched library, clone:I0C0047C10 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK168918 - Mus musculus 17 days pregnant adult female amnion cDNA, RIKEN full-length enriched library, clone:I920065D03 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK166927 - Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0023F17 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK151689 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830034A09 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK152927 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830091E20 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK169064 - Mus musculus 17 days embryo stomach cDNA, RIKEN full-length enriched library, clone:I920078E05 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK167600 - Mus musculus 12 days pregnant adult female placenta cDNA, RIKEN full-length enriched library, clone:I530024J07 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK128891 - Mus musculus cDNA fis, clone TRACH2004251, moderately similar to Heterogeneous nuclear ribonucleoprotein K.
AK150848 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830015P21 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK088462 - Mus musculus 2 days neonate thymus thymic cells cDNA, RIKEN full-length enriched library, clone:E430018E05 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
BC006694 - Mus musculus heterogeneous nuclear ribonucleoprotein K, mRNA (cDNA clone MGC:6388 IMAGE:3583037), complete cds.
AK051313 - Mus musculus 12 days embryo spinal ganglion cDNA, RIKEN full-length enriched library, clone:D130033C09 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK011428 - Mus musculus 10 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2610016P11 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK078777 - Mus musculus 15 days embryo male testis cDNA, RIKEN full-length enriched library, clone:8030474M07 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK160615 - Mus musculus 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2700025J10 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.
AK206192 - Mus musculus cDNA, clone:Y2G0104A20, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058619, based on BLAT search.
AK196607 - Mus musculus cDNA, clone:Y1G0122F22, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058619, based on BLAT search.
AK192668 - Mus musculus cDNA, clone:Y1G0109J04, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058619, based on BLAT search.
AK186860 - Mus musculus cDNA, clone:Y0G0139A13, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058619, based on BLAT search.
AK211652 - Mus musculus cDNA, clone:Y2G0122G23, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058184, based on BLAT search.
AK215933 - Mus musculus cDNA, clone:Y2G0136K16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058184, based on BLAT search.
AK203272 - Mus musculus cDNA, clone:Y1G0144F16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058184, based on BLAT search.
AK207611 - Mus musculus cDNA, clone:Y2G0108I22, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058184, based on BLAT search.
AK204979 - Mus musculus cDNA, clone:Y1G0150E03, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058184, based on BLAT search.
EU604547 - Mus musculus heterogeneous nuclear ribonucleoprotein K (Hnrpk) mRNA, complete cds.
AK208657 - Mus musculus cDNA, clone:Y2G0112F13, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000043269, based on BLAT search.
AK205281 - Mus musculus cDNA, clone:Y2G0101D13, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000043269, based on BLAT search.
AK179362 - Mus musculus cDNA, clone:Y0G0110B16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058619, based on BLAT search.
AK197677 - Mus musculus cDNA, clone:Y1G0125M24, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000058619, based on BLAT search.
AK191331 - Mus musculus cDNA, clone:Y1G0105I18, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000051522, based on BLAT search.
AK201722 - Mus musculus cDNA, clone:Y1G0139C16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000051522, based on BLAT search.
AK204853 - Mus musculus cDNA, clone:Y1G0149N07, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000051522, based on BLAT search.
AK220023 - Mus musculus cDNA, clone:Y2G0150I10, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000051522, based on BLAT search.
AK194621 - Mus musculus cDNA, clone:Y1G0115O18, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000051522, based on BLAT search.
AK028023 - Mus musculus 18-day embryo whole body cDNA, RIKEN full-length enriched library, clone:1190020K22 product:heterogeneous nuclear ribonucleoprotein K, full insert sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein P61979 (Reactome details) participates in the following event(s):

R-MMU-72127 Formation of the Spliceosomal B Complex
R-MMU-72139 Formation of the active Spliceosomal C (B*) complex
R-MMU-72143 Lariat Formation and 5'-Splice Site Cleavage
R-MMU-156661 Formation of Exon Junction Complex
R-MMU-72163 mRNA Splicing - Major Pathway
R-MMU-72172 mRNA Splicing
R-MMU-72203 Processing of Capped Intron-Containing Pre-mRNA
R-MMU-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: AK051313, Hnrpk, NM_025279, NP_079555, P61979-3
UCSC ID: uc007qty.1
RefSeq Accession: NM_025279
Protein: P61979-3, splice isoform of P61979

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK051313.1
exon count: 15CDS single in 3' UTR: no RNA size: 1896
ORF size: 1320CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2840.00frame shift in genome: no % Coverage: 99.95
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.