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HNRNPU heterogeneous nuclear ribonucleoprotein U [ Homo sapiens (human) ]

Gene ID: 3192, updated on 9-Dec-2018

Summary

Official Symbol
HNRNPUprovided by HGNC
Official Full Name
heterogeneous nuclear ribonucleoprotein Uprovided by HGNC
Primary source
HGNC:HGNC:5048
See related
Ensembl:ENSG00000153187 MIM:602869
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SAFA; HNRPU; SAF-A; U21.1; pp120; EIEE54; GRIP120; hnRNP U; HNRNPU-AS1
Summary
This gene encodes a member of a family of proteins that bind nucleic acids and function in the formation of ribonucleoprotein complexes in the nucleus with heterogeneous nuclear RNA (hnRNA). The encoded protein has affinity for both RNA and DNA, and binds scaffold-attached region (SAR) DNA. Mutations in this gene have been associated with epileptic encephalopathy, early infantile, 54. A pseudogene of this gene has been identified on chromosome 14. [provided by RefSeq, Jun 2017]
Expression
Ubiquitous expression in bone marrow (RPKM 31.0), lymph node (RPKM 28.0) and 25 other tissues See more
Orthologs

Genomic context

See HNRNPU in Genome Data Viewer
Location:
1q44
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (244850300..244864525, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (245013602..245027827, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268258 Neighboring gene cytochrome c oxidase assembly factor COX20 Neighboring gene small nucleolar RNA, H/ACA box 100 Neighboring gene RNA, 7SK small nuclear pseudogene 55 Neighboring gene RNA, U6 small nuclear 947, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Epileptic encephalopathy, early infantile, 54
MedGen: C4479319 OMIM: 617391 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2016-09-14)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2016-09-14)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A; HNRNPU) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein U (HNRNPU), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein U (HNRNPU), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein U (HNRNPU), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify heterogeneous nuclear ribonucleoprotein U (HNRNPU), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Rev rev HIV-1 Rev interacting protein, heterogeneous nuclear ribonucleoprotein U (HNRNPU), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with HNRNPU is increased by RRE PubMed
rev HIV-1 Rev interacts with the heterogeneous nuclear ribonucleoproteins (hnRNP) U. The amino acids 9-14 in Rev are required for the interaction between Rev and hnRNP U PubMed
Vpr vpr Human hnRNP U1 protein binding to splicing-incompetent U1 snRNA binding sites suffices to augment cross-exon interactions and spicing at 3'ssA2, leading to modulate HIV-1 vpr mRNA and Vpr protein expression PubMed
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human heterogeneous nuclear ribonucleoprotein U (HNRNPU: scaffold attachment factor A) at amino acid residues 255-256 and 258-259 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ30202, FLJ37978, DKFZp547G047

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA polymerase II C-terminal domain binding ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II complex binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
TFIIH-class transcription factor complex binding IDA
Inferred from Direct Assay
more info
PubMed 
actin binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(A) binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(C) RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
poly(G) binding IDA
Inferred from Direct Assay
more info
PubMed 
pre-mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
promoter-specific chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
snRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
telomerase RNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
CRD-mediated mRNA stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
RNA localization to chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA metabolic process TAS
Traceable Author Statement
more info
 
RNA processing TAS
Traceable Author Statement
more info
PubMed 
adaptive thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cardiac muscle cell development IEA
Inferred from Electronic Annotation
more info
 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
cellular response to glucocorticoid stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to leukemia inhibitory factor ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
dendritic transport of messenger ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 
dosage compensation by inactivation of X chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
mRNA stabilization IDA
Inferred from Direct Assay
more info
PubMed 
maintenance of protein location in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of telomere maintenance via telomerase IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription elongation from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
osteoblast differentiation HDA PubMed 
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of attachment of mitotic spindle microtubules to kinetochore IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of brown fat cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of stem cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization to spindle microtubule IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of alternative mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
regulation of chromatin organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
CRD-mediated mRNA stability complex IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with RNA polymerase II transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
condensed chromosome kinetochore IEA
Inferred from Electronic Annotation
more info
 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 
dendrite cytoplasm IEA
Inferred from Electronic Annotation
more info
 
inactive sex chromosome IDA
Inferred from Direct Assay
more info
PubMed 
kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
membrane HDA PubMed 
midbody IDA
Inferred from Direct Assay
more info
PubMed 
mitotic spindle IDA
Inferred from Direct Assay
more info
PubMed 
mitotic spindle microtubule IDA
Inferred from Direct Assay
more info
PubMed 
mitotic spindle midzone IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
spindle pole IEA
Inferred from Electronic Annotation
more info
 
telomerase holoenzyme complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
heterogeneous nuclear ribonucleoprotein U
Names
HNRNPU antisense RNA 1
heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)
nuclear p120 ribonucleoprotein
p120 nuclear protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042184.1 RefSeqGene

    Range
    5001..19226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004501.3NP_004492.2  heterogeneous nuclear ribonucleoprotein U isoform b

    See identical proteins and their annotated locations for NP_004492.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region compared to variant 1, and encodes a shorter protein (isoform b).
    Source sequence(s)
    AF068846, AK095525, BC003367, BX323046
    Consensus CDS
    CCDS31081.1
    UniProtKB/Swiss-Prot
    Q00839
    Related
    ENSP00000393151.2, ENST00000444376.7
    Conserved Domains (3) summary
    smart00513
    Location:842
    SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
    cd12884
    Location:269444
    SPRY_hnRNP; SPRY domain in heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1
    pfam13671
    Location:480624
    AAA_33; AAA domain
  2. NM_031844.3NP_114032.2  heterogeneous nuclear ribonucleoprotein U isoform a

    See identical proteins and their annotated locations for NP_114032.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AF068846, AK095525, BC015782, BC024767, BX323046
    Consensus CDS
    CCDS41479.1
    UniProtKB/Swiss-Prot
    Q00839
    UniProtKB/TrEMBL
    Q96BA7
    Related
    ENSP00000491215.1, ENST00000640218.1
    Conserved Domains (3) summary
    smart00513
    Location:842
    SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
    cd12884
    Location:288463
    SPRY_hnRNP; SPRY domain in heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1
    pfam13671
    Location:499643
    AAA_33; AAA domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    244850300..244864525 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_026778.1: Suppressed sequence

    Description
    NR_026778.1: This RefSeq was removed because currently there is insufficient support for the transcript.
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