Human Gene HNRNPK (ENST00000376281.8) from GENCODE V43
  Description: Homo sapiens heterogeneous nuclear ribonucleoprotein K (HNRNPK), transcript variant 1, mRNA. (from RefSeq NM_002140)
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].
Gencode Transcript: ENST00000376281.8
Gencode Gene: ENSG00000165119.22
Transcript (Including UTRs)
   Position: hg38 chr9:83,968,083-83,980,604 Size: 12,522 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg38 chr9:83,969,407-83,978,252 Size: 8,846 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-02-17 13:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:83,968,083-83,980,604)mRNA (may differ from genome)Protein (464 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Heterogeneous nuclear ribonucleoprotein K; Short=hnRNP K; AltName: Full=Transformation up-regulated nuclear protein; Short=TUNP;
FUNCTION: One of the major pre-mRNA-binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. Can also bind poly(C) single- stranded DNA. Plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. When sumoylated, acts as a transcriptional coactivator of p53/TP53, playing a role in p21/CDKN1A and 14-3-3 sigma/SFN induction (By similarity). As far as transcription repression is concerned, acts by interacting with long intergenic RNA p21 (lincRNA-p21), a non-coding RNA induced by p53/TP53. This interaction is necessary for the induction of apoptosis, but not cell cycle arrest.
SUBUNIT: Interacts with RBM42 and ZIK1. Interacts with BRDT (By similarity). Identified in the spliceosome C complex. Interacts with ANKRD28. Interacts with HCV core protein. Interacts with ASFV p30 protein. Interacts with DDX1. Interacts with MDM2; this interaction leads to ubiquitination and proteasomal degradation. Interacts with p53/TP53.
INTERACTION: Q96PU8:QKI; NbExp=3; IntAct=EBI-304185, EBI-945792; Q9H3D4:TP63; NbExp=2; IntAct=EBI-304185, EBI-2337775;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleoplasm. Note=Recruited to p53/TP53-responsive promoters, in the presence of functional p53/TP53. In case of ASFV infection, there is a shift in the localization which becomes predominantly nuclear.
INDUCTION: By DNA damage, including ionizing radiations and phleomycin treatment or UV irradiation. This induction requires ATM kinase activity (ionizing radiations and phleomycin) or ATR activity (UV irradiation). Up-regulation is due to protein stabilization. Constitutive protein levels are controlled by MDM2- mediated ubiquitination and degradation via the proteasome pathway.
PTM: Arg-296 and Arg-299 are dimethylated, probably to asymmetric dimethylarginine.
PTM: Sumoylated by CBX4. Sumoylation is increased upon DNA damage, such as that produced by doxorubicin, etoposide, UV light and camptothecin, due to enhanced CBX4 phosphorylation by HIPK2 under these conditions.
PTM: Ubiquitinated by MDM2. Doxorubicin treatment does not affect monoubiquitination, but slightly decreases HNRNPK poly- ubiquitination.
MASS SPECTROMETRY: Mass=50976.25; Method=MALDI; Range=1-463 (P61978-1); Source=PubMed:11840567;
SIMILARITY: Contains 3 KH domains.
SEQUENCE CAUTION: Sequence=BAD92799.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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

-  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 -67.10209-0.321 Picture PostScript Text
3' UTR -317.001324-0.239 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1J5K - NMR MuPIT 1KHM - NMR MuPIT 1ZZI - X-ray MuPIT 1ZZJ - X-ray MuPIT 1ZZK - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P61978
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0019904 protein domain specific binding
GO:0042802 identical protein binding
GO:0045296 cadherin binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0007165 signal transduction
GO:0008380 RNA splicing
GO:0010988 regulation of low-density lipoprotein particle clearance
GO:0016032 viral process
GO:0016070 RNA metabolic process
GO:0043066 negative regulation of apoptotic process
GO:0045716 positive regulation of low-density lipoprotein particle receptor biosynthetic process
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048025 negative regulation of mRNA splicing, via spliceosome
GO:0048260 positive regulation of receptor-mediated endocytosis
GO:0072369 regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter
GO:1902165 regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

Cellular Component:
GO:0000790 nuclear chromatin
GO:0002102 podosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005737 cytoplasm
GO:0005925 focal adhesion
GO:0010494 cytoplasmic stress granule
GO:0016020 membrane
GO:0030054 cell junction
GO:0042995 cell projection
GO:0070062 extracellular exosome
GO:0071013 catalytic step 2 spliceosome

-  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.
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

Reactome (by CSHL, EBI, and GO)

Protein P61978 (Reactome details) participates in the following event(s):

R-HSA-72103 Formation of pre-mRNPs
R-HSA-4570499 CBX4 (Pc2) SUMOylates HNRNPK with SUMO2
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-72172 mRNA Splicing
R-HSA-2990846 SUMOylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000376281.1, ENST00000376281.2, ENST00000376281.3, ENST00000376281.4, ENST00000376281.5, ENST00000376281.6, ENST00000376281.7, HNRPK, HNRPK_HUMAN, NM_002140, P61978, Q07244, Q15671, Q59F98, Q5T6W4, Q60577, Q922Y7, Q96J62, uc004anl.1, uc004anl.2, uc004anl.3, uc004anl.4, uc004anl.5
UCSC ID: ENST00000376281.8
RefSeq Accession: NM_002140
Protein: P61978 (aka HNRPK_HUMAN)
CCDS: CCDS6668.1, CCDS6667.1

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

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