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Aliases for HNRNPU Gene

Aliases for HNRNPU Gene

  • Heterogeneous Nuclear Ribonucleoprotein U (Scaffold Attachment Factor A) 2 3 5
  • HNRNPU Antisense RNA 1 2 3
  • HnRNP U 3 4
  • HNRPU 3 4
  • SAF-A 3 4
  • U21.1 3 4
  • Pp120 3 4
  • SAFA 3 4
  • HNRNPU Antisense RNA 1 (Non-Protein Coding) 2
  • Chromosome 1 Open Reading Frame 199 2
  • Scaffold Attachment Factor A 4
  • Non-Protein Coding RNA 201 2
  • P120 Nuclear Protein 3
  • HNRNPU-AS1 3
  • P120 4

External Ids for HNRNPU Gene

Previous HGNC Symbols for HNRNPU Gene

  • HNRPU
  • HNRNPU-AS1
  • C1orf199
  • NCRNA00201

Previous GeneCards Identifiers for HNRNPU Gene

  • GC01M243081
  • GC01M245013
  • GC01M215396

Summaries for HNRNPU Gene

Entrez Gene Summary for HNRNPU Gene

  • 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]

GeneCards Summary for HNRNPU Gene

HNRNPU (Heterogeneous Nuclear Ribonucleoprotein U (Scaffold Attachment Factor A)) is a Protein Coding gene. Diseases associated with HNRNPU include Diffuse Gastric Cancer. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and kinase activity. An important paralog of this gene is HNRNPUL2-BSCL2.

UniProtKB/Swiss-Prot for HNRNPU Gene

  • Component of the CRD-mediated complex that promotes MYC mRNA stabilization. Binds to pre-mRNA. Has high affinity for scaffold-attached region (SAR) DNA. Binds to double- and single-stranded DNA and RNA. Plays a role in the circadian regulation of the core clock component ARNTL/BMAL1 transcription (By similarity).

Gene Wiki entry for HNRNPU Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HNRNPU Gene

Genomics for HNRNPU Gene

Regulatory Elements for HNRNPU Gene

Enhancers for HNRNPU Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around HNRNPU on UCSC Golden Path with GeneCards custom track

Promoters for HNRNPU Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HNRNPU on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the HNRNPU gene promoter:

Genomic Location for HNRNPU Gene

Chromosome:
1
Start:
244,850,300 bp from pter
End:
244,864,542 bp from pter
Size:
14,243 bases
Orientation:
Minus strand

Genomic View for HNRNPU Gene

Genes around HNRNPU on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HNRNPU Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HNRNPU Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HNRNPU Gene

Proteins for HNRNPU Gene

  • Protein details for HNRNPU Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q00839-HNRPU_HUMAN
    Recommended name:
    Heterogeneous nuclear ribonucleoprotein U
    Protein Accession:
    Q00839
    Secondary Accessions:
    • O75507
    • Q8N174
    • Q96HY9
    • Q9BQ09

    Protein attributes for HNRNPU Gene

    Size:
    825 amino acids
    Molecular mass:
    90584 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with IGF2BP1, IGF2BP2, IGF2BP3 and ERBB4. Ligand for CR2. Interacts with CRY1 (By similarity). Interacts with UBQLN2 (PubMed:25616961).
    SequenceCaution:
    • Sequence=AAC19382.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HNRNPU Gene

    Alternative splice isoforms for HNRNPU Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HNRNPU Gene

Proteomics data for HNRNPU Gene at MOPED

Post-translational modifications for HNRNPU Gene

  • Arg-739 is dimethylated, probably to asymmetric dimethylarginine.
  • Citrullinated by PADI4.
  • Extensively phosphorylated.
  • Ubiquitination at Lys 9, Lys 186, Lys 464, Lys 516, Lys 524, Lys 536, Lys 544, Lys 565, Lys 602, Lys 635, and Lys 814
  • Modification sites at PhosphoSitePlus

Other Protein References for HNRNPU Gene

Antibody Products

No data available for DME Specific Peptides for HNRNPU Gene

Domains & Families for HNRNPU Gene

Protein Domains for HNRNPU Gene

Graphical View of Domain Structure for InterPro Entry

Q00839

UniProtKB/Swiss-Prot:

HNRPU_HUMAN :
  • Contains 1 B30.2/SPRY domain.
Domain:
  • Contains 1 B30.2/SPRY domain.
  • Contains 1 SAP domain.
genes like me logo Genes that share domains with HNRNPU: view

No data available for Gene Families for HNRNPU Gene

Function for HNRNPU Gene

Molecular function for HNRNPU Gene

UniProtKB/Swiss-Prot Function:
Component of the CRD-mediated complex that promotes MYC mRNA stabilization. Binds to pre-mRNA. Has high affinity for scaffold-attached region (SAR) DNA. Binds to double- and single-stranded DNA and RNA. Plays a role in the circadian regulation of the core clock component ARNTL/BMAL1 transcription (By similarity).

Gene Ontology (GO) - Molecular Function for HNRNPU Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 1628625
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with HNRNPU: view
genes like me logo Genes that share phenotypes with HNRNPU: view

Animal Model Products

miRNA for HNRNPU Gene

miRTarBase miRNAs that target HNRNPU

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HNRNPU Gene

Localization for HNRNPU Gene

Subcellular locations from UniProtKB/Swiss-Prot for HNRNPU Gene

Nucleus. Cytoplasm. Cell surface. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Component of ribonucleosomes. {ECO:0000269 PubMed:17289661}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HNRNPU Gene COMPARTMENTS Subcellular localization image for HNRNPU gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 2
plasma membrane 2
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for HNRNPU Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 22720776
GO:0005697 colocalizes_with telomerase holoenzyme complex IDA 18082603
GO:0016020 membrane IDA 16210410
GO:0071013 catalytic step 2 spliceosome IDA 11991638
genes like me logo Genes that share ontologies with HNRNPU: view

Pathways & Interactions for HNRNPU Gene

genes like me logo Genes that share pathways with HNRNPU: view

Pathways by source for HNRNPU Gene

1 KEGG pathway for HNRNPU Gene

SIGNOR curated interactions for HNRNPU Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HNRNPU Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010628 positive regulation of gene expression IEA --
GO:0070934 CRD-mediated mRNA stabilization IMP 19029303
GO:0071549 cellular response to dexamethasone stimulus IEA --
GO:2000373 positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IEA --
genes like me logo Genes that share ontologies with HNRNPU: view

Drugs & Compounds for HNRNPU Gene

(2) Drugs for HNRNPU Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for HNRNPU Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HNRNPU: view

Transcripts for HNRNPU Gene

Unigene Clusters for HNRNPU Gene

Heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HNRNPU Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b
SP1: - - - - -
SP2: - - - -
SP3: - - - -
SP4: -
SP5:
SP6:

Relevant External Links for HNRNPU Gene

GeneLoc Exon Structure for
HNRNPU
ECgene alternative splicing isoforms for
HNRNPU

Expression for HNRNPU Gene

mRNA expression in normal human tissues for HNRNPU Gene

Protein differential expression in normal tissues from HIPED for HNRNPU Gene

This gene is overexpressed in Lymph node (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HNRNPU Gene



SOURCE GeneReport for Unigene cluster for HNRNPU Gene Hs.106212

genes like me logo Genes that share expression patterns with HNRNPU: view

Protein tissue co-expression partners for HNRNPU Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HNRNPU Gene

Orthologs for HNRNPU Gene

This gene was present in the common ancestor of animals.

Orthologs for HNRNPU Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HNRNPU 35
  • 94.79 (n)
  • 98.55 (a)
HNRNPU 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HNRNPU 35
  • 94.37 (n)
  • 98.75 (a)
HNRNPU 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hnrnpu 35
  • 92.03 (n)
  • 96.87 (a)
Hnrnpu 16
Hnrnpu 36
  • 95 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hnrnpu 35
  • 92.31 (n)
  • 96.74 (a)
oppossum
(Monodelphis domestica)
Mammalia HNRNPU 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HNRNPU 36
  • 95 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia HNRNPU 36
  • 99 (a)
OneToOne
chicken
(Gallus gallus)
Aves HNRNPU 35
  • 85.46 (n)
  • 93.72 (a)
HNRNPU 36
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HNRNPU 36
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hnrnpu 35
  • 71.65 (n)
  • 74.67 (a)
Str.7999 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.8951 35
zebrafish
(Danio rerio)
Actinopterygii hnrnpub 35
  • 65.34 (n)
  • 65.85 (a)
hnrnpua 36
  • 53 (a)
OneToMany
hnrnpub 36
  • 54 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG30122 36
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y41E3.11 36
  • 8 (a)
OneToMany
Species with no ortholog for HNRNPU:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HNRNPU Gene

ENSEMBL:
Gene Tree for HNRNPU (if available)
TreeFam:
Gene Tree for HNRNPU (if available)

Paralogs for HNRNPU Gene

Paralogs for HNRNPU Gene

(4) SIMAP similar genes for HNRNPU Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for HNRNPU Gene

genes like me logo Genes that share paralogs with HNRNPU: view

Variants for HNRNPU Gene

Sequence variations from dbSNP and Humsavar for HNRNPU Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1052660 - 244,855,937(-) GAGGA(C/T)TCAAT reference, missense
rs877 -- 244,853,885(+) TGTTA(C/T)TTTAA utr-variant-3-prime
rs878 -- 244,853,868(+) AATTA(A/T)ACCAA utr-variant-3-prime
rs879 -- 244,853,815(+) CTACA(C/T)ACACT utr-variant-3-prime
rs880 -- 244,853,821(+) ACACT(A/C)CATCT utr-variant-3-prime

Variation tolerance for HNRNPU Gene

Residual Variation Intolerance Score: 14.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.21; 24.28% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HNRNPU Gene

Human Gene Mutation Database (HGMD)
HNRNPU

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for HNRNPU Gene

Disorders for HNRNPU Gene

MalaCards: The human disease database

(1) MalaCards diseases for HNRNPU Gene - From: GeneCards

Disorder Aliases PubMed IDs
diffuse gastric cancer
  • signet ring cell carcinoma
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for HNRNPU

Genetic Association Database (GAD)
HNRNPU
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HNRNPU
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HNRNPU
genes like me logo Genes that share disorders with HNRNPU: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HNRNPU Gene

Publications for HNRNPU Gene

  1. hnRNP-U/SAF-A is encoded by two differentially polyadenylated mRNAs in human cells. (PMID: 7509195) Fackelmayer F.O. … Richter A. (Biochim. Biophys. Acta 1994) 2 3 4 23 67
  2. Purification of two isoforms of hnRNP-U and characterization of their nucleic acid binding activity. (PMID: 8068679) Fackelmayer F.O. … Richter A. (Biochemistry 1994) 2 3 23
  3. Proteomic and genomic analysis of PITX2 interacting and regulating networks. (PMID: 19174163) Huang Y. … Zhu G.Z. (FEBS Lett. 2009) 3 23
  4. hnRNP-U is a specific DNA-dependent protein kinase substrate phosphorylated in response to DNA double-strand breaks. (PMID: 19351595) Berglund F.M. … Clarke P.R. (Biochem. Biophys. Res. Commun. 2009) 3 23
  5. hnRNP U interacts with the c-Myc-Max complex on the E-box promoter region inducing the ornithine decarboxylase gene. (PMID: 19578763) Matsuoka Y. … Tsubura A. (Oncol. Rep. 2009) 3 23

Products for HNRNPU Gene

Sources for HNRNPU Gene

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