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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
    mouse all
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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 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
    		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 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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