Human Gene HNRNPK (uc004anl.4)
  Description: Homo sapiens heterogeneous nuclear ribonucleoprotein K (HNRNPK), transcript variant 1, mRNA.
RefSeq Summary (NM_002140): This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene is located in the nucleoplasm and has three repeats of KH domains that binds to RNAs. It is distinct among other hnRNP proteins in its binding preference; it binds tenaciously to poly(C). This protein is also thought to have a role during cell cycle progession. Several alternatively spliced transcript variants have been described for this gene, however, not all of them are fully characterized. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr9:86,582,998-86,595,569 Size: 12,572 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr9:86,584,322-86,593,167 Size: 8,846 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:86,582,998-86,595,569)mRNA (may differ from genome)Protein (464 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIOMIMPubMedTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: Q6IBN1_HUMAN
DESCRIPTION: SubName: Full=HNRPK protein; SubName: Full=Heterogeneous nuclear ribonucleoprotein K; SubName: Full=Heterogeneous nuclear ribonucleoprotein K isoform a; SubName: Full=Heterogeneous nuclear ribonucleoprotein K, isoform CRA_c; SubName: Full=cDNA FLJ77137, highly similar to Homo sapiens heterogeneous nuclear ribonucleoprotein K (HNRPK), transcript variant 1, mRNA;
SIMILARITY: Contains 3 KH domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HNRNPK
Diseases sorted by gene-association score: au-kline syndrome* (1269), neurodevelopmental disorder-craniofacial dysmorphism-cardiac defect-hip dysplasia syndrome due to 9q21 microdeletion* (25), spinocerebellar ataxia 10 (17), stomatitis (8), hepatitis c virus (2), lymphocytic choriomeningitis (2), intellectual disability (2)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 229.02 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 5891.12 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -94.30259-0.364 Picture PostScript Text
3' UTR -334.441324-0.253 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
  InterPro Domains: Graphical view of domain structure
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1
IPR012987 - ROK_N

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 Q6IBN1
FrontTopSide
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  X72727 - H.sapiens tunp mRNA for transformation upregulated nuclear protein.
AB209562 - Homo sapiens mRNA for heterogeneous nuclear ribonucleoprotein K isoform a variant protein.
BC013220 - Homo sapiens heterogeneous nuclear ribonucleoprotein K, mRNA (cDNA clone IMAGE:4149675).
AK096385 - Homo sapiens cDNA FLJ39066 fis, clone NT2RP7014743, highly similar to HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K.
S74678 - heterogeneous nuclear ribonucleoprotein complex K [human, mRNA, 2302 nt].
JD548770 - Sequence 529794 from Patent EP1572962.
JD262561 - Sequence 243585 from Patent EP1572962.
BC063540 - Homo sapiens cDNA clone IMAGE:4523373, **** WARNING: chimeric clone ****.
BC000355 - Homo sapiens heterogeneous nuclear ribonucleoprotein K, mRNA (cDNA clone MGC:8660 IMAGE:2964383), complete cds.
BC025321 - Homo sapiens heterogeneous nuclear ribonucleoprotein K, mRNA (cDNA clone IMAGE:5421682).
BC014980 - Homo sapiens heterogeneous nuclear ribonucleoprotein K, mRNA (cDNA clone MGC:23171 IMAGE:4906241), complete cds.
AK123117 - Homo sapiens cDNA FLJ41122 fis, clone BRACE2013911, highly similar to HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K.
AK300744 - Homo sapiens cDNA FLJ54552 complete cds, highly similar to Heterogeneous nuclear ribonucleoprotein K.
JD469161 - Sequence 450185 from Patent EP1572962.
AY911506 - Homo sapiens heterogeneous nuclear ribonucleoprotein K transcript variant (HNRPK) mRNA, complete cds, alternatively spliced.
AK294067 - Homo sapiens cDNA FLJ53312 complete cds, highly similar to Heterogeneous nuclear ribonucleoprotein K.
JD036591 - Sequence 17615 from Patent EP1572962.
AK291336 - Homo sapiens cDNA FLJ77137 complete cds, highly similar to Homo sapiens heterogeneous nuclear ribonucleoprotein K (HNRPK), transcript variant 1, mRNA.
KJ896997 - Synthetic construct Homo sapiens clone ccsbBroadEn_06391 HNRNPK gene, encodes complete protein.
AB451263 - Homo sapiens HNRNPK mRNA for heterogeneous nuclear ribonucleoprotein K isoform a, complete cds, clone: FLJ08080AAAN.
CR456771 - Homo sapiens full open reading frame cDNA clone RZPDo834E024D for gene HNRPK, heterogeneous nuclear ribonucleoprotein K; complete cds, incl. stopcodon.
DQ890727 - Synthetic construct clone IMAGE:100003357; FLH165506.01X; RZPDo839D03160D heterogeneous nuclear ribonucleoprotein K (HNRPK) gene, encodes complete protein.
KJ891374 - Synthetic construct Homo sapiens clone ccsbBroadEn_00768 HNRNPK gene, encodes complete protein.
DQ893902 - Synthetic construct Homo sapiens clone IMAGE:100008362; FLH165502.01L; RZPDo839D03159D heterogeneous nuclear ribonucleoprotein K (HNRPK) gene, encodes complete protein.
AB384978 - Synthetic construct DNA, clone: pF1KB4689, Homo sapiens HNRPK gene for heterogeneous nuclear ribonucleoprotein K, complete cds, without stop codon, in Flexi system.
AB451390 - Homo sapiens HNRNPK mRNA for heterogeneous nuclear ribonucleoprotein K isoform a, partial cds, clone: FLJ08080AAAF.
AK307962 - Homo sapiens cDNA, FLJ97910.
CU674174 - Synthetic construct Homo sapiens gateway clone IMAGE:100018317 5' read HNRPK mRNA.
JD534300 - Sequence 515324 from Patent EP1572962.
JD525400 - Sequence 506424 from Patent EP1572962.
JD364953 - Sequence 345977 from Patent EP1572962.
JD342559 - Sequence 323583 from Patent EP1572962.
JD173827 - Sequence 154851 from Patent EP1572962.
JD313790 - Sequence 294814 from Patent EP1572962.
JD033875 - Sequence 14899 from Patent EP1572962.
JD027145 - Sequence 8169 from Patent EP1572962.
JD520201 - Sequence 501225 from Patent EP1572962.
JD475386 - Sequence 456410 from Patent EP1572962.
JD272439 - Sequence 253463 from Patent EP1572962.
JD119965 - Sequence 100989 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

-  Other Names for This Gene
  Alternate Gene Symbols: hCG_1985922, HNRPK, NM_002140, NP_112553, Q6IBN1, Q6IBN1_HUMAN, RP11-575L7.1-003
UCSC ID: uc004anl.4
RefSeq Accession: NM_002140
Protein: Q6IBN1 CCDS: CCDS6668.1, CCDS6667.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene HNRNPK:
au-kline (Au-Kline Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002140.3
exon count: 17CDS single in 3' UTR: no RNA size: 2995
ORF size: 1395CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2990.00frame shift in genome: no % Coverage: 99.43
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.