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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

  • C1orf199
  • NCRNA00201

Previous GeneCards Identifiers for HNRNPU Gene

  • GC01M243081
  • GC01M245013
  • GC01M215396

Summaries for HNRNPU Gene

Entrez Gene Summary for HNRNPU Gene

  • 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]

GeneCards Summary for HNRNPU Gene

HNRNPU (Heterogeneous Nuclear Ribonucleoprotein U) is a Protein Coding gene. Diseases associated with HNRNPU include Epileptic Encephalopathy, Early Infantile, 54 and 1Q44 Microdeletion Syndrome. 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

Additional gene information 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
GH01H244860 1.7 Ensembl ENCODE dbSUPER 93.2 +1.0 991 6.7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF548 SP3 NFYC SSRP1 HNRNPU DESI2 COX20 ADSS CATSPERE ENSG00000240963 ENSG00000238224 RN7SKP55 LOC101928068 ENSG00000237759
GH01H244967 1.4 ENCODE dbSUPER 56.3 -105.7 -105706 4.6 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 SP3 MEF2D LOC101928068 EFCAB2 HNRNPU COX20 ADSS ENSG00000238224 ENSG00000240963 RN7SKP55 DESI2 ENSG00000237759
GH01H244318 1.9 FANTOM5 Ensembl ENCODE dbSUPER 30.5 +541.9 541853 9 PKNOX1 ATF1 ARNT SIN3A YY1 ZNF121 ZNF766 ATF7 FOS RUNX3 HNRNPU ADSS C1orf100 AKT3 LOC105373262 GC01M244263
GH01H244940 1.2 ENCODE dbSUPER 47.3 -76.4 -76414 1.4 PKNOX1 TBL1XR1 ZFP64 ZNF23 ATF7 RUNX3 CREM IKZF2 ZNF202 ZNF680 HNRNPU CATSPERE LOC101928068 COX20 DESI2 GC01P244944 ENSG00000273175
GH01H244832 1.4 ENCODE dbSUPER 37.4 +29.0 28962 6.4 MLX FEZF1 DMAP1 YY1 ZNF143 ZNF548 SP3 ZNF610 GLIS1 RCOR2 DESI2 HNRNPU COX20 ADSS ENSG00000240963 ENSG00000238224 LOC101928068 AKT3 RN7SKP55 ENSG00000237759
- 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 SP3 SSRP1 ZNF610

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

Genomic Locations for HNRNPU Gene

Genomic Locations for HNRNPU Gene
23,923 bases
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:
    Recommended name:
    Heterogeneous nuclear ribonucleoprotein U
    Protein Accession:
    Secondary Accessions:
    • O75507
    • Q8N174
    • Q96HY9
    • Q9BQ09

    Protein attributes for HNRNPU Gene

    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).
    • 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


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 posLast=99, isoforms=2186, isoforms=2464, isoforms=2516, isoforms=2524, isoforms=2536, posLast=544544, isoforms=2565, posLast=602602, isoforms=2635, and posLast=814814
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HNRNPU Gene

Domains & Families for HNRNPU Gene

Gene Families for HNRNPU Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for HNRNPU Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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).

Phenotypes From GWAS Catalog for HNRNPU Gene

Gene Ontology (GO) - Molecular Function for HNRNPU Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II core binding IDA 10490622
GO:0001047 core promoter binding ISS,IEA --
GO:0001097 TFIIH-class transcription factor binding IDA 10490622
GO:0003677 DNA binding TAS,IDA 9204873
GO:0003682 chromatin binding IDA 9405365
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

Inhibitory RNA 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

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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HNRNPU Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 11003645
GO:0005634 nucleus IEA,IDA 9353307
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005697 colocalizes_with telomerase holoenzyme complex IDA 18082603
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:0000122 negative regulation of transcription from RNA polymerase II promoter IMP 9353307
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IDA 22325991
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0001649 osteoblast differentiation IDA 16210410
GO:0006396 RNA processing TAS 1628625
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:

Inhibitory RNA 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: -

Relevant External Links for HNRNPU Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

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:


SOURCE GeneReport for Unigene cluster for HNRNPU Gene:


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

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
(Pan troglodytes)
Mammalia HNRNPU 34
  • 99 (a)
(Ornithorhynchus anatinus)
Mammalia HNRNPU 34
  • 95 (a)
(Bos Taurus)
Mammalia HNRNPU 33 34
  • 94.79 (n)
(Canis familiaris)
Mammalia HNRNPU 33 34
  • 94.37 (n)
(Rattus norvegicus)
Mammalia Hnrnpu 33
  • 92.31 (n)
(Mus musculus)
Mammalia Hnrnpu 33 16 34
  • 92.03 (n)
(Monodelphis domestica)
Mammalia HNRNPU 34
  • 90 (a)
(Gallus gallus)
Aves HNRNPU 33 34
  • 85.46 (n)
(Anolis carolinensis)
Reptilia HNRNPU 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hnrnpu 33
  • 71.65 (n)
Str.7999 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8951 33
(Danio rerio)
Actinopterygii hnrnpub 33 34
  • 65.34 (n)
hnrnpua 34
  • 53 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG30122 34
  • 17 (a)
(Caenorhabditis elegans)
Secernentea Y41E3.11 34
  • 8 (a)
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

Gene Tree for HNRNPU (if available)
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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for HNRNPU Gene

MalaCards: The human disease database

(3) MalaCards diseases for HNRNPU Gene - From: HGMD, OMIM, ClinVar, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 54
  • eiee54
1q44 microdeletion syndrome
  • chromosome 1q44 microdeletion syndrome
diffuse gastric cancer
  • signet cell adenocarcinoma
- elite association - COSMIC cancer census association via MalaCards


  • Epileptic encephalopathy, early infantile, 54 (EIEE54) [MIM:617391]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. {ECO:0000269 PubMed:23708187, ECO:0000269 PubMed:25356899}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HNRNPU

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

No data available for 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 FO … Richter A (Biochimica et biophysica acta 1994) 2 3 4 22 60
  2. Purification of two isoforms of hnRNP-U and characterization of their nucleic acid binding activity. (PMID: 8068679) Fackelmayer FO … Richter A (Biochemistry 1994) 2 3 4 22 60
  3. Major cell surface-located protein substrates of an ecto-protein kinase are homologs of known nuclear proteins. (PMID: 7993898) Jordan P … Kübler D (Biochemistry 1994) 3 4 22 60
  4. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. (PMID: 1628625) Kiledjian M … Dreyfuss G (The EMBO journal 1992) 3 4 22 60
  5. ALS-linked mutations in ubiquilin-2 or hnRNPA1 reduce interaction between ubiquilin-2 and hnRNPA1. (PMID: 25616961) Gilpin KM … Monteiro MJ (Human molecular genetics 2015) 3 4 60

Products for HNRNPU Gene

Sources for HNRNPU Gene

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