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HNRNPDL heterogeneous nuclear ribonucleoprotein D like [ Homo sapiens (human) ]

Gene ID: 9987, updated on 3-Nov-2024

Summary

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Official Symbol
HNRNPDLprovided by HGNC
Official Full Name
heterogeneous nuclear ribonucleoprotein D likeprovided by HGNC
Primary source
HGNC:HGNC:5037
See related
Ensembl:ENSG00000152795 MIM:607137; AllianceGenome:HGNC:5037
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
HNRNP; JKTBP; HNRPDL; JKTBP2; LGMD1G; LGMDD3; laAUF1
Summary
This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins and they complex 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 has two RRM domains that bind to RNAs. Three alternatively spliced transcript variants have been described for this gene. One of the variants is probably not translated because the transcript is a candidate for nonsense-mediated mRNA decay. The protein isoforms encoded by this gene are similar to its family member HNRPD. [provided by RefSeq, May 2011]
Expression
Ubiquitous expression in ovary (RPKM 71.3), endometrium (RPKM 57.4) and 25 other tissues See more
Orthologs
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Genomic context

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See HNRNPDL in Genome Data Viewer
Location:
4q21.22
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (82422564..82430462, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (85752194..85760070, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (83343717..83351615, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD42 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:83332215-83333169 Neighboring gene IGBP1 pseudogene 4 Neighboring gene NANOG hESC enhancer GRCh37_chr4:83337083-83337615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15529 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:83350279-83351074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:83351075-83351870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21664 Neighboring gene enolase-phosphatase 1 Neighboring gene uncharacterized LOC105377310 Neighboring gene transmembrane protein 150C

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. hnRNPDL extensively regulates transcription and alternative splicing. Li RZ, et al. Gene, 2019 Mar 1. PMID 30447347
  2. Molecular cloning of the cDNA encoding A + U-rich element RNA binding factor. Doi A, et al. Biochim Biophys Acta, 1998 Mar 4. PMID 9524220
  3. Two forms of expression and genomic structure of the human heterogeneous nuclear ribonucleoprotein D-like JKTBP gene (HNRPDL). Kamei D, et al. Gene, 1999 Mar 4. PMID 10072754
  4. Identification of the nucleocytoplasmic shuttling sequence of heterogeneous nuclear ribonucleoprotein D-like protein JKTBP and its interaction with mRNA. Kawamura H, et al. J Biol Chem, 2002 Jan 25. PMID 11705999
  5. Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3. Garcia-Pardo J, et al. Nat Commun, 2023 Jan 16. PMID 36646699, Free PMC Article

See all (197) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3.
    Title: Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3.
  2. HNRPDL transforms hematopoietic cells and a novel HNRPDL/PBX1 axis plays an important role in human CML CD34(+) cells
    Title: Oncogenic heterogeneous nuclear ribonucleoprotein D-like modulates the growth and imatinib response of human chronic myeloid leukemia CD34(+) cells via pre-B-cell leukemia homeobox 1.
  3. High HNRNPDL expression is associated with cervical cancer.
    Title: hnRNPDL extensively regulates transcription and alternative splicing.
  4. Heterogeneous nuclear ribonucleoprotein D-like (HNRPDL) is aberrantly expressed in specimens from colorectal cancer patients.
    Title: Oncogenic heterogeneous nuclear ribonucleoprotein D-like promotes the growth of human colon cancer SW620 cells via its regulation of cell-cycle.
  5. Both hnRNP D and DL are able to control their own expression by alternative splicing of cassette exons in their 3'UTRs. Exon inclusion produces mRNAs degraded by nonsense-mediated decay. Moreover, hnRNP D and DL control the expression of one another by the same mechanism.
    Title: Auto- and cross-regulation of the hnRNPs D and DL.
  6. A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G.
    Title: A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G).
  7. hnRNP DL and CNBP are novel antigens for SLE patients
    Title: Proteomic analyses and identification of arginine methylated proteins differentially recognized by autosera from anti-Sm positive SLE patients.
  8. A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
    Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
  9. The results indicate that JKTBP1 regulates the level of NRF protein expression by binding to both NRF 5' and 3' UTRs.
    Title: JKTBP1 is involved in stabilization and IRES-dependent translation of NRF mRNAs by binding to 5' and 3' untranslated regions.
  10. Study shows that there is interaction of the intracellular domain of beta-amyloid precursor protein with JKTBP2, indicating that JKTBP2 may have an important function in AD formation.
    Title: [The interaction of the intracellular domain of beta-amyloid precursor protein with JKTBP2].
Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Autosomal dominant limb-girdle muscular dystrophy type 1G
MedGen: C1836765 OMIM: 609115 GeneReviews: Not available
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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 D-like (HNRPDL) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, heterogeneous nuclear ribonucleoprotein D-like (HNRPDL), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with HNRPDL is increased by RRE PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables poly(A) binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables poly(G) binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA processing NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
heterogeneous nuclear ribonucleoprotein D-like
Names
A+U-rich element RNA binding factor
AU-rich element RNA-binding factor
JKT41-binding protein
hnRNP D-like
hnRNP DL
limb girdle muscular dystrophy 1G (autosomal dominant)
protein laAUF1

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

  1. NG_029681.1 RefSeqGene

    Range
    4764..12657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001207000.1 → NP_001193929.1  heterogeneous nuclear ribonucleoprotein D-like isoform b

    See identical proteins and their annotated locations for NP_001193929.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AB017019, AB066484, AC124016, BC071944, CK300994
    Consensus CDS
    CCDS75153.1
    UniProtKB/TrEMBL
    A0A087WUK2
    Related
    ENSP00000478723.1, ENST00000614627.4
    Conserved Domains (2) summary
    cd12585
    Location:234 → 308
    RRM2_hnRPDL; RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins
    cd12758
    Location:149 → 224
    RRM1_hnRPDL; RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

  2. NM_031372.4 → NP_112740.1  heterogeneous nuclear ribonucleoprotein D-like isoform a

    See identical proteins and their annotated locations for NP_112740.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the longer isoform (a).
    Source sequence(s)
    AB017019, AC110787, AC124016, BC071944, CK300994
    Consensus CDS
    CCDS3593.1
    UniProtKB/Swiss-Prot
    O14979, Q6SPF2, Q7KZ74, Q7KZ75, Q96IM0, Q96S43
    Related
    ENSP00000295470.5, ENST00000295470.10
    Conserved Domains (2) summary
    cd12585
    Location:234 → 308
    RRM2_hnRPDL; RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins
    cd12758
    Location:149 → 224
    RRM1_hnRPDL; RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

RNA

  1. NR_003249.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript. However, this transcript is a candidate for nonsense-mediated mRNA decay (NMD), and so it is thought to be a noncoding transcript.
    Source sequence(s)
    AB017019, AC124016, CK300994

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

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    82422564..82430462 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    85752194..85760070 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_005463.2: Suppressed sequence

    Description
    NM_005463.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14979.3 GenPept UniProtKB/Swiss-Prot:O14979

Gene LinkOut

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