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    HNRNPU heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) [ Homo sapiens ]

    Gene ID: 3192, updated on 13-May-2012
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    Summary

    Official Symbol
    HNRNPUprovided by HGNC
    Official Full Name
    heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)provided by HGNC
    Primary source
    HGNC:5048
    Locus tag
    RP11-11N7.3
    See related
    Ensembl:ENSG00000153187; HPRD:04185; MIM:602869; Vega:OTTHUMG00000040396
    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
    HNRPU; SAF-A; U21.1; hnRNP U
    Summary
    This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they form complexes 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 contains a RNA binding domain and scaffold-associated region (SAR)-specific bipartite DNA-binding domain. This protein is also thought to be involved in the packaging of hnRNA into large ribonucleoprotein complexes. During apoptosis, this protein is cleaved in a caspase-dependent way. Cleavage occurs at the SALD site, resulting in a loss of DNA-binding activity and a concomitant detachment of this protein from nuclear structural sites. But this cleavage does not affect the function of the encoded protein in RNA metabolism. At least two alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]
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    Genomic context

    Location :
    1q44
    Sequence :
    Chromosome: 1; NC_000001.10 (245013602..245027827, complement)
    See HNRNPU in Epigenomics, MapViewer

    Chromosome 1 - NC_000001.10Genomic Context describing neighboring genes Neighboring gene desumoylating isopeptidase 2 Neighboring gene ribosomal protein L37 pseudogene 8 Neighboring gene HNRNPU antisense RNA 1 (non-protein coding) Neighboring gene COX20 Cox2 chaperone homolog (S. cerevisiae) Neighboring gene EF-hand calcium binding domain 2 Neighboring gene kinesin family member 26B

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. Xiao R, et al. Mol Cell, 2012 Mar 9. PMID 22325991.
    2. A cohesin-RAD21 interactome. Panigrahi AK, et al. Biochem J, 2012 Mar 15. PMID 22145905.
    3. Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. Lee KA, et al. J Biol Chem, 2011 Dec 2. PMID 21987572.
    4. Global identification of modular cullin-RING ligase substrates. Emanuele MJ, et al. Cell, 2011 Oct 14. PMID 21963094.
    5. Proteomic dissection of the von Hippel-Lindau (VHL) interactome. Lai Y, et al. J Proteome Res, 2011 Nov 4. PMID 21942715.

    See all (92) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. hnRNP U is a regulator of SMN2 splicing.
      Title: Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation.
    2. The nuclear scaffold protein (SAF-A) is a novel spindle regulator that plays an essential role in kinetochore-microtubules (MT)attachment and mitotic spindle organization.
      Title: The nuclear scaffold protein SAF-A is required for kinetochore-microtubule attachment and contributes to the targeting of Aurora-A to mitotic spindles.
    3. Single nucleotide polymorphism in HNRPU gene is associated with speech delay, seizures and variable corpus callosum thickness.
      Title: Four patients with speech delay, seizures and variable corpus callosum thickness sharing a 0.440 Mb deletion in region 1q44 containing the HNRPU gene.
    4. hnRNP U/SAF-A/SP120 regulates the enzyme DNA Topoisomerase IIbeta in dual ways
      Title: Regulation of DNA Topoisomerase IIbeta through RNA-dependent association with heterogeneous nuclear ribonucleoprotein U (hnRNP U).
    5. Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation.
      Title: The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation.
    6. Data demonstrate that expression levels of hnRNP A1, Q, K, R, and U influence HIV-1 production by persistently infected astrocytes, linking these hnRNPs to HIV replication.
      Title: Identification of a heterogeneous nuclear ribonucleoprotein-recognition region in the HIV Rev protein.
    7. Data demonstrate that hnRNP U is involved in HP1alpha function, shedding new light on the mode of action of HP1alpha and on the function of hnRNP U.
      Title: Physical and functional interaction between heterochromatin protein 1alpha and the RNA-binding protein heterogeneous nuclear ribonucleoprotein U.
    8. hnRNP-U is phosphorylated at Ser59 by DNA-PK in vitro and in cells in response to DNA double-strand breaks.
      Title: hnRNP-U is a specific DNA-dependent protein kinase substrate phosphorylated in response to DNA double-strand breaks.
    9. Using shotgun mass spectrometry, we found this protein differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia.
      Title: Prefrontal cortex shotgun proteome analysis reveals altered calcium homeostasis and immune system imbalance in schizophrenia.
    10. the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1gamma, RNA polymerase II, matrin 3, and SAF-A sites
      Title: Identifying functional neighborhoods within the cell nucleus: proximity analysis of early S-phase replicating chromatin domains to sites of transcription, RNA polymerase II, HP1gamma, matrin 3 and SAF-A.
    Submit: New GeneRIF Correction See all (17)
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    NP_114032.1 NP_001092.1 ACTB    BIND  PubMed ACTB (beta-actin) interacts with HNRPU (hnRNP U). 
    NP_114032.1 NP_001868.2 CR2    BIND  PubMed p120RNP interacts with CR2. 
    Q00839 P60709 ACTB    HPRD  PubMed  
    Q00839 Q9Y297 BTRC    HPRD  PubMed  
    Q00839 P42574 CASP3    HPRD  PubMed  
    Q00839 P06127 CD5    HPRD  PubMed  
    Q00839 P20023 CR2    HPRD  PubMed  
    Q00839 P55199 ELL    HPRD  PubMed  
    Q00839 Q09472 EP300    HPRD  PubMed  
    Q00839 Q05586 GRIN1    HPRD  PubMed  
    Q00839 O15399 GRIN2D    HPRD  PubMed  
    Q00839 P32780 GTF2H1    HPRD  PubMed  
    Q00839 Q99608 NDN    HPRD  PubMed  
    Q00839 Q92597 NDRG1    HPRD  PubMed  
    Q00839 P04150 NR3C1    HPRD  PubMed  
    Q00839 P49335 POU3F4    HPRD  PubMed  
    Q00839 Q99873 PRMT1    HPRD  PubMed  
    Q00839 Q06124 PTPN11    HPRD  PubMed  
    Q00839 Q16637 SMN2    HPRD  PubMed  
    Q00839 Q8WXA9 SREK1    HPRD  PubMed  
    Q00839 O95793 STAU1    HPRD  PubMed  
    Q00839 P43405 SYK    HPRD  PubMed  
    Q00839 P46937 YAP1    HPRD  PubMed  
    Q00839 Q96CS4 ZNF689    HPRD  PubMed  
    BioGRID:109433 BioGRID:223223 AI837181    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:114457 BTRC    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:120548 C20orf20    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:107457 CDK7    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:109433 BioGRID:107459 CDK9    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:107487 CENPA    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:198624 Cdk1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:198963 Ctcf    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:119986 DGCR8    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:124082 DOT1L    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:114023 DYRK2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:971788 EBNA-LP    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:108325 EMD    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:108347 EP300    BioGRID  PubMed Affinity Capture-Western; Co-fractionation; Reconstituted Complex 
    BioGRID:109433 BioGRID:114094 GAS7    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:116452 GPN1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:109217 GTF2F1    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:109318 HDGF    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:109428 HNRNPH1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:109767 IKBKB    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:116669 KDM4B    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:110319 MAX    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:116134 MORF4L1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:115001 MORF4L2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:110694 MYC    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:110772 NDN    BioGRID  PubMed Affinity Capture-Western; Co-fractionation 
    BioGRID:109433 BioGRID:115669 NDRG1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:110811 NEDD4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:110859 NFKBIA    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:115783 NOP56    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:110929 NPM1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:109165 NR3C1    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:211904 Ndc80    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:111317 PIN1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:111384 PML    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:111426 POLR2A    BioGRID  PubMed Affinity Capture-Western; Co-localization 
    BioGRID:109433 BioGRID:111435 POLR2J    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:111452 POU3F4    BioGRID  PubMed Far Western 
    BioGRID:109433 BioGRID:109512 PRMT1    BioGRID  PubMed Biochemical Activity 
    BioGRID:109433 BioGRID:120792 PRPF40A    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:111822 RAD21    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:109433 BioGRID:111849 RARA    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:114952 RBM39    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:123598 RNF146    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:116067 RUVBL2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:219759 Recql4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:109072 SFN    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:121244 SMARCAD1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:116597 SNW1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:126754 SREK1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:112657 STAU1    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:109433 BioGRID:113188 SUMO1    BioGRID  PubMed Affinity Capture-MS; Reconstituted Complex 
    BioGRID:109433 BioGRID:112497 SUMO2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:116120 TCERG1    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:214351 Trim69    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS; Reconstituted Complex 
    BioGRID:109433 BioGRID:113269 VHL    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:116363 WBP4    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:109433 BioGRID:204613 Ybx1    BioGRID  PubMed Affinity Capture-MS 
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    General gene information

    Markers

    Genotypes

    Homology

    Pathways from BioSystems

    • 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 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...
    • 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...

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    CRD-mediated mRNA stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    RNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    RNA splicing TAS
    Traceable Author Statement
    more info
    		  
    gene expression TAS
    Traceable Author Statement
    more info
    		  
    nuclear mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    nuclear mRNA splicing, via spliceosome TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    CRD-mediated mRNA stability complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    heterogeneous nuclear ribonucleoprotein complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  
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    General protein information

    Preferred Names
    heterogeneous nuclear ribonucleoprotein U
    Names
    heterogeneous nuclear ribonucleoprotein U
    pp120
    p120 nuclear protein
    scaffold attachment factor A
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    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.

    mRNA and Protein(s)

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

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment in the coding region compared to variant 1. This causes isoform b to be shorter than isoform a, yet with the same reading frame.
      Source sequence(s)
      AF068846, AK095525, BC003367, BX323046
      Consensus CDS
      CCDS31081.1
      UniProtKB/Swiss-Prot
      Q00839
      Related
      ENSP00000393151, OTTHUMP00000038192, ENST00000444376, OTTHUMT00000097162
      Conserved Domains (2) summary
      pfam13671
      Location:480 – 624
      Blast Score: 309
      AAA_33; AAA domain
      cl02614
      Location:328 – 444
      Blast Score: 253
      SPRY; SPRY domain

    2. NM_031844.2 → NP_114032.2  heterogeneous nuclear ribonucleoprotein U isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the full length isoform (a).
      Source sequence(s)
      AF068846, AK095525, BC015782, BC024767, BX323046
      Consensus CDS
      CCDS41479.1
      UniProtKB/Swiss-Prot
      Q00839
      UniProtKB/TrEMBL
      Q96BA7
      Related
      ENSP00000283179, OTTHUMP00000038193, ENST00000283179, OTTHUMT00000097163
      Conserved Domains (2) summary
      pfam13671
      Location:499 – 643
      Blast Score: 308
      AAA_33; AAA domain
      cl02614
      Location:347 – 463
      Blast Score: 253
      SPRY; SPRY domain

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000001.10 Reference GRCh37.p5 Primary Assembly

      Range
      245013602..245027827, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000133.1 Alternate HuRef

      Range
      215396765..215410903, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic BX323046.3 CAI11055.1
      CAI11056.1
      CAI11057.1
      CAI11058.1
    genomic CH236957.1 (361376..361876) None
    genomic CH471148.1 EAW77126.1
      EAW77127.1
    mRNA AF068846.1 AAC19382.1
    mRNA AF461014.1 AAP97707.1
    mRNA AK095525.1 None
    mRNA AK126868.1 BAG54384.1
    mRNA AK130669.1 None
    mRNA AK297119.1 BAG59625.1
    mRNA AK307661.1 None
    mRNA BC003367.1 AAH03367.1
    mRNA BC003621.2 AAH03621.1
    mRNA BC007950.2 AAH07950.2
    mRNA BC015782.1 AAH15782.1
    mRNA BC024767.1 AAH24767.1
    mRNA BC034925.1 AAH34925.1
    mRNA X65488.1 CAA46472.1
    other-genetic DQ893316.2 ABM84242.1
    other-genetic DQ896631.2 ABM87630.1
    other-genetic EU831468.1 ACE87155.1
    other-genetic EU831555.1 ACE86474.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q00839.6 GenPept UniProtKB/Swiss-Prot:Q00839
    Q5RI17 GenPept UniProtKB/TrEMBL:Q5RI17
    Q5RI18 GenPept UniProtKB/TrEMBL:Q5RI18
    Q5RI19 GenPept UniProtKB/TrEMBL:Q5RI19
    Q7Z4Q5 GenPept UniProtKB/TrEMBL:Q7Z4Q5
    Q96BA7 GenPept UniProtKB/TrEMBL:Q96BA7
    Q9UEL2 GenPept UniProtKB/TrEMBL:Q9UEL2
    Help top of page

    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Medical
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    Research Materials
    Tools
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