U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

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

    Gene ID: 3192, updated on 20-May-2024

    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; AllianceGenome:HGNC:5048
    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; DEE54; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HNRNPU in Genome Data Viewer
    Location:
    1q44
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (244850297..244864543, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (244266602..244280849, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (245013599..245027845, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985372 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:244972422-244972922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2844 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:244978837-244979663 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:244979664-244980490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:244996871-244997630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2019 Neighboring gene cytochrome c oxidase assembly factor COX20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2020 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245027219-245028050 Neighboring gene small nucleolar RNA, H/ACA box 100 Neighboring gene UPF0764 protein C16orf89-like Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:245028051-245028881 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:245031973-245032572 Neighboring gene MPRA-validated peak809 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2023 Neighboring gene RN7SK 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ30202, FLJ37978, DKFZp547G047

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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
      4983..19229
      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/TrEMBL
      B4DLR3
      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
      O75507, Q00839, Q8N174, Q96HY9, Q9BQ09
      UniProtKB/TrEMBL
      B4DLR3
      Related
      ENSP00000491215.1, ENST00000640218.2
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      244850297..244864543 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      244266602..244280849 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.