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Aliases for HNRNPU Gene

Aliases for HNRNPU Gene

  • Heterogeneous Nuclear Ribonucleoprotein U 2 3 5
  • Heterogeneous Nuclear Ribonucleoprotein U (Scaffold Attachment Factor A) 2 3
  • Scaffold Attachment Factor A 2 4
  • 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
  • Non-Protein Coding RNA 201 2
  • P120 Nuclear Protein 3
  • HNRNPU-AS1 3
  • EIEE54 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) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Circadian rythm related genes. GO annotations related to this gene include poly(A) RNA binding and kinase activity. An important paralog of this gene is HNRNPUL1.

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 CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G244860 1.7 Ensembl ENCODE dbSUPER 0.7 +1.0 991 6.7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF548 ZNF263 SP3 NFYC COX20 ADSS HNRNPU
GH01G244855 1.9 Ensembl dbSUPER 0.4 +10.2 10160 0.4 SCRT1 PAF1 ZNF362 ZFP37 BCL11B ZNF335 CTBP1 ZSCAN16 RNU6-947P HNRNPU COX20
GH01G244832 1.5 ENCODE dbSUPER 0.3 +29.0 28962 6.4 MLX CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF143 ZNF548 ZNF263 SP3 COX20 ADSS HNRNPU
GH01G244839 1.1 ENCODE dbSUPER 0.3 +23.3 23338 2.6 YBX3 CBX3 AGO1 INSM2 ZNF121 CBX5 ZSCAN5C ZNF143 RELB ZNF280D COX20 RNU6-947P HNRNPU
GH01G244854 0.7 dbSUPER 0.4 +9.3 9276 1.1 ZNF384 BCL11B ZIC2 ZNF335 ZFHX2 POLR2A EED BCLAF1 EGR2 SCRT1 COX20 RNU6-947P HNRNPU
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000022956 1360 4001 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF548 ZNF263 SP3 SSRP1

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

Genomic Location for HNRNPU Gene

Chromosome:
1
Start:
244,840,638 bp from pter
End:
244,864,560 bp from pter
Size:
23,923 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). Interacts with GEMIN5 (PubMed:25911097).
    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

Post-translational modifications for HNRNPU Gene

  • Arg-739 is dimethylated, probably to asymmetric dimethylarginine.
  • Citrullinated by PADI4.
  • Extensively phosphorylated.
  • Ubiquitination at isoforms=29, isoforms=2186, isoforms=2464, isoforms=2516, isoforms=2524, posLast=536536, isoforms=2544, isoforms=2565, isoforms=2602, isoforms=2635, and isoforms=2814
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HNRNPU Gene

Domains & Families for HNRNPU Gene

No data available for Gene Families and UniProtKB/Swiss-Prot 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:0001047 core promoter binding ISS --
GO:0003677 DNA binding TAS 1628625
GO:0003723 RNA binding TAS,IDA 22658674
GO:0005515 protein binding IPI 17289661
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

CRISPR Products

miRNA for HNRNPU Gene

miRTarBase miRNAs that target HNRNPU

Inhibitory RNA Products

Clone Products

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HNRNPU gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 3
cytosol 2
plasma membrane 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for HNRNPU Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 22720776
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005697 colocalizes_with telomerase holoenzyme complex IDA 18082603
GO:0005737 cytoplasm IEA --
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:0000398 mRNA splicing, via spliceosome TAS --
GO:0001649 osteoblast differentiation IDA 16210410
GO:0006396 RNA processing TAS 1628625
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for HNRNPU Gene



Protein tissue co-expression partners for HNRNPU Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HNRNPU Gene:

HNRNPU

SOURCE GeneReport for Unigene cluster for HNRNPU Gene:

Hs.106212

Evidence on tissue expression from TISSUES for HNRNPU Gene

  • Nervous system(4.9)
  • Blood(4.8)
  • Skin(4.8)
  • Liver(4.7)
  • Eye(4.6)
  • Lung(4.5)
  • Kidney(3.9)
  • Intestine(3.8)
  • Muscle(2.6)
  • Spleen(2.3)
  • Bone(2.2)
  • Bone marrow(2.2)
  • Heart(2.2)
  • Pancreas(2.2)
  • Lymph node(2.1)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with HNRNPU: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia HNRNPU 35
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia HNRNPU 35
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia HNRNPU 34 35
  • 94.79 (n)
dog
(Canis familiaris)
Mammalia HNRNPU 34 35
  • 94.37 (n)
rat
(Rattus norvegicus)
Mammalia Hnrnpu 34
  • 92.31 (n)
mouse
(Mus musculus)
Mammalia Hnrnpu 34 16 35
  • 92.03 (n)
oppossum
(Monodelphis domestica)
Mammalia HNRNPU 35
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves HNRNPU 34 35
  • 85.46 (n)
lizard
(Anolis carolinensis)
Reptilia HNRNPU 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hnrnpu 34
  • 71.65 (n)
Str.7999 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.8951 34
zebrafish
(Danio rerio)
Actinopterygii hnrnpub 34 35
  • 65.34 (n)
hnrnpua 35
  • 53 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG30122 35
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y41E3.11 35
  • 8 (a)
OneToMany
Species where no ortholog for HNRNPU was found in the sources mined by GeneCards:
  • 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:

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
rs587777004 Pathogenic 244,842,055(+) TGTTC(A/C)CTAGT intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs794729648 Pathogenic 244,855,471(-) AACAG(-/AG)GGAAC upstream-variant-2KB, reference, frameshift-variant
rs886041983 Pathogenic 244,863,788(-) AGCCC(C/T)AACAG reference, stop-gained
rs147700538 Likely pathogenic 244,842,234(+) AGGGT(G/T)TATCT nc-transcript-variant, reference, missense, utr-variant-3-prime
rs373824502 Likely pathogenic 244,841,992(+) GCGCC(A/C/T)GGCAT intron-variant, nc-transcript-variant, downstream-variant-500B, reference, synonymous-codon, missense

Structural Variations from Database of Genomic Variants (DGV) for HNRNPU Gene

Variant ID Type Subtype PubMed ID
nsv549493 CNV gain 21841781
nsv549493 CNV gain 21841781

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
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HNRNPU

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HNRNPU Gene

Disorders for HNRNPU Gene

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

No disorders were found for HNRNPU Gene.

No data available for MalaCards , 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 22 64
  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 4 22 64
  3. Major cell surface-located protein substrates of an ecto-protein kinase are homologs of known nuclear proteins. (PMID: 7993898) Jordan P. … Kubler D. (Biochemistry 1994) 3 4 22 64
  4. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. (PMID: 1628625) Kiledjian M. … Dreyfuss G. (EMBO J. 1992) 3 4 22 64
  5. ALS-linked mutations in ubiquilin-2 or hnRNPA1 reduce interaction between ubiquilin-2 and hnRNPA1. (PMID: 25616961) Gilpin K.M. … Monteiro M.J. (Hum. Mol. Genet. 2015) 3 4 64

Products for HNRNPU Gene

Sources for HNRNPU Gene

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