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

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: mouse all
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Genomic context

Location:: 1q44

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (244850297..244864543, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (244266602..244280849, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (245013599..245027845, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator.
Title: RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator.
Circular RNA CircSLC22A23 Promotes Gastric Cancer Progression by Activating HNRNPU Expression.
Title: Circular RNA CircSLC22A23 Promotes Gastric Cancer Progression by Activating HNRNPU Expression.
ITGA9-AS1 up-regulates ITGA9 by targeting miR-4765 and recruiting HNRNPU to affect the proliferation and apoptosis of non-small cell lung cancer cells.
Title: ITGA9-AS1 up-regulates ITGA9 by targeting miR-4765 and recruiting HNRNPU to affect the proliferation and apoptosis of non-small cell lung cancer cells.
Alternative Splicing Factor Heterogeneous Nuclear Ribonucleoprotein U as a Promising Biomarker for Gastric Cancer Risk and Prognosis with Tumor-Promoting Properties.
Title: Alternative Splicing Factor Heterogeneous Nuclear Ribonucleoprotein U as a Promising Biomarker for Gastric Cancer Risk and Prognosis with Tumor-Promoting Properties.
RNA-binding protein hnRNPU regulates multiple myeloma resistance to selinexor.
Title: RNA-binding protein hnRNPU regulates multiple myeloma resistance to selinexor.
circ-hnRNPU inhibits NONO-mediated c-Myc transactivation and mRNA stabilization essential for glycosylation and cancer progression.
Title: circ-hnRNPU inhibits NONO-mediated c-Myc transactivation and mRNA stabilization essential for glycosylation and cancer progression.
Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.
Title: Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.
Germline pathogenic variants in HNRNPU are associated with alterations in blood methylome.
Title: Germline pathogenic variants in HNRNPU are associated with alterations in blood methylome.
piRNA-1742 promotes renal cell carcinoma malignancy by regulating USP8 stability through binding to hnRNPU and thereby inhibiting MUC12 ubiquitination.
Title: piRNA-1742 promotes renal cell carcinoma malignancy by regulating USP8 stability through binding to hnRNPU and thereby inhibiting MUC12 ubiquitination.
[Clinical significance and pathogenesis analysis of heterogeneous nuclear ribonucleoprotein U in acute myeloid leukemia].
Title: [Clinical significance and pathogenesis analysis of heterogeneous nuclear ribonucleoprotein U in acute myeloid leukemia].

Submit: New GeneRIF Correction See all GeneRIFs (55)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Developmental and epileptic encephalopathy, 54 MedGen: C4479319 OMIM: 617391 GeneReviews: HNRNPU-Related Neurodevelopmental Disorder	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:546820

Hnrnpu (e-PCR), detects polymorphism
- UniSTS:546820

HNRPU (e-PCR)
- UniSTS:506402

GDB:6028664 (e-PCR)
- UniSTS:60734

HNRPU_1518 (e-PCR)
- UniSTS:277316

MARC_12257-12258:1008001094:5 (e-PCR)
- UniSTS:267386

MARC_12257-12258:1044472182:2 (e-PCR)
- UniSTS:267386

RH18125 (e-PCR)
- UniSTS:42376

RH93803 (e-PCR)
- UniSTS:84362

C86794 (e-PCR)
- UniSTS:207257

RH92446 (e-PCR)
- UniSTS:84894

MARC_20677-20678:1024509130:1 (e-PCR)
- UniSTS:268469

SHGC-76609 (e-PCR)
- UniSTS:36278

D14S1285 (e-PCR)
- UniSTS:10169

A007A33 (e-PCR)
- UniSTS:49593

MARC_26419-26420:1036768776:5 (e-PCR)
- UniSTS:268990

WI-7584 (e-PCR)
- UniSTS:31692

WI-8450 (e-PCR)
- UniSTS:79572

SHGC-76627 (e-PCR)
- UniSTS:3545

SHGC-76621 (e-PCR)
- UniSTS:46824

D1S3027 (e-PCR)
- UniSTS:72191

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 more info	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 piRNA binding	IPI Inferred from Physical Interaction 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 more info	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 random inactivation of X chromosome	IDA Inferred from Direct Assay 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
involved_in regulatory ncRNA-mediated heterochromatin formation	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	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 more info	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

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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)

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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

NG_042184.1 RefSeqGene

Range

4983..19229

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_004501.3 → NP_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:8 → 42

SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation

cd12884
Location:269 → 444

SPRY_hnRNP; SPRY domain in heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1

pfam13671
Location:480 → 624

AAA_33; AAA domain
NM_031844.3 → NP_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:8 → 42

SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation

cd12884
Location:288 → 463

SPRY_hnRNP; SPRY domain in heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1

pfam13671
Location:499 → 643

AAA_33; AAA domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

244850297..244864543 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NR_026778.1: Suppressed sequence

Description

NR_026778.1: This RefSeq was removed because currently there is insufficient support for the transcript.