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    MATR3 matrin 3 [ Homo sapiens (human) ]

    Gene ID: 9782, updated on 23-Nov-2023

    Summary

    Official Symbol
    MATR3provided by HGNC
    Official Full Name
    matrin 3provided by HGNC
    Primary source
    HGNC:HGNC:6912
    See related
    Ensembl:ENSG00000015479 MIM:164015; AllianceGenome:HGNC:6912
    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
    MPD2; ALS21; VCPDM
    Summary
    This gene encodes a nuclear matrix protein, which is proposed to stabilize certain messenger RNA species. Mutations of this gene are associated with distal myopathy 2, which often includes vocal cord and pharyngeal weakness. Alternatively spliced transcript variants, including read-through transcripts composed of the upstream small nucleolar RNA host gene 4 (non-protein coding) and matrin 3 gene sequence, have been identified. Pseudogenes of this gene are located on chromosomes 1 and X. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in brain (RPKM 79.2), thyroid (RPKM 60.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See MATR3 in Genome Data Viewer
    Location:
    5q31.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (139274101..139331677)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (139800176..139857743)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138609790..138667366)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene SIL1 nucleotide exchange factor Neighboring gene ribosomal protein L12 pseudogene 21 Neighboring gene MPRA-validated peak5496 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138559318-138560164 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:138567539-138568038 Neighboring gene RNA, U6 small nuclear 572, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16406 Neighboring gene uncharacterized LOC124901081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16407 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138629501-138630204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138630205-138630907 Neighboring gene small nucleolar RNA, H/ACA box 74D Neighboring gene Sharpr-MPRA regulatory region 13556 Neighboring gene small nucleolar RNA, H/ACA box 74A Neighboring gene small nucleolar RNA host gene 4 Neighboring gene RNA, 5S ribosomal pseudogene 195 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:138657767-138658966 Neighboring gene RN7SK pseudogene 64 Neighboring gene poly(A) binding protein interacting protein 2 Neighboring gene solute carrier family 23 member 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    siRNA knockdown of MATR3 improves the ZAP-induced degradation of HIV-1 transcripts; MATR3 enhances HIV-1 replication PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify matrin 3 (MATR3), 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 matrin 3 (MATR3), 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 matrin 3 (MATR3), 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 matrin 3 (MATR3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    gag Overexpression of Matrin 3 increases HIV-1 Gag expression; knockdown of Matrin 3 decreases HIV-1 Gag expression PubMed
    Rev rev Association of PSF with MATR3 is involved in nuclear retention of unspliced HIV-1 RNA and Rev activity PubMed
    rev The interaction of HIV-1 Rev and Matrin 3 specifically requires the presence of a Rev-dependent RRE-containing RNA. Two RNA recognition motifs (residues 586-612) in Matrin 3 are required for activity on Rev/RRE PubMed
    rev HIV-1 Rev interacting protein, matrin 3 (MATR3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with MATR3 is increased by RRE PubMed
    Tat tat Matrin 3 protein (MATR3) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of matrin 3 (MATR3) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed
    vpr HIV-1 Vpr is identified to have a physical interaction with matrin 3 (MATR3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC9105, KIAA0723, DKFZp686K0542, DKFZp686K23100

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables miRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural molecule activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in activation of innate immune response IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in blastocyst formation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within heart valve development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in post-transcriptional regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within ventricular septum development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 
    located_in nuclear inner membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    matrin-3
    Names
    vocal cord and pharyngeal weakness with distal myopathy

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_012846.1 RefSeqGene

      Range
      24638..62575
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001194954.2NP_001181883.1  matrin-3 isoform a

      See identical proteins and their annotated locations for NP_001181883.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform (a).
      Source sequence(s)
      AA233906, AB018266, AC011404, AK307872, BX537365
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
      Conserved Domains (3) summary
      smart00451
      Location:798833
      ZnF_U1; U1-like zinc finger
      cd12714
      Location:398473
      RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
      cd12715
      Location:496575
      RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
    2. NM_001194955.2NP_001181884.1  matrin-3 isoform a

      See identical proteins and their annotated locations for NP_001181884.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform (a).
      Source sequence(s)
      AA233906, AB018266, AC011404, AK316420, BX537365
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
      Related
      ENSP00000482895.1, ENST00000618441.5
      Conserved Domains (3) summary
      smart00451
      Location:798833
      ZnF_U1; U1-like zinc finger
      cd12714
      Location:398473
      RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
      cd12715
      Location:496575
      RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
    3. NM_001194956.2NP_001181885.1  matrin-3 isoform b

      See identical proteins and their annotated locations for NP_001181885.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
      Source sequence(s)
      AA233906, AC011404, AK316420, BX537365
      Consensus CDS
      CCDS54908.1
      UniProtKB/TrEMBL
      B4DRS1
      Related
      ENSP00000423587.1, ENST00000503811.5
      Conserved Domains (3) summary
      smart00451
      Location:510545
      ZnF_U1; U1-like zinc finger
      cd12714
      Location:110185
      RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
      cd12715
      Location:208287
      RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
    4. NM_001282278.2NP_001269207.1  matrin-3 isoform c

      See identical proteins and their annotated locations for NP_001269207.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an exon which contains a portion of the 5' UTR and 5' coding region including the start codon, compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (c) with a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      AA233906, AB018266, AC011404, AK293952, AK307872, BX537365
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
      Conserved Domains (3) summary
      smart00451
      Location:460495
      ZnF_U1; U1-like zinc finger
      cd12714
      Location:60135
      RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
      cd12715
      Location:158237
      RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
    5. NM_001400441.1NP_001387370.1  matrin-3 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      A8MXP9, Q68D11
    6. NM_001400442.1NP_001387371.1  matrin-3 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      A8MXP9, Q68D11
    7. NM_001400443.1NP_001387372.1  matrin-3 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      A8MXP9, Q68D11
    8. NM_001400444.1NP_001387373.1  matrin-3 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      A8MXP9, Q68D11
    9. NM_001400445.1NP_001387374.1  matrin-3 isoform d

      Status: REVIEWED

      Source sequence(s)
      AC011404
      Consensus CDS
      CCDS93789.1
      UniProtKB/TrEMBL
      A8MXP9, Q68D11
    10. NM_001400447.1NP_001387376.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    11. NM_001400448.1NP_001387377.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    12. NM_001400450.1NP_001387379.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    13. NM_001400451.1NP_001387380.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    14. NM_001400452.1NP_001387381.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    15. NM_001400453.1NP_001387382.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    16. NM_001400454.1NP_001387383.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    17. NM_001400455.1NP_001387384.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    18. NM_001400456.1NP_001387385.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    19. NM_001400457.1NP_001387386.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    20. NM_001400458.1NP_001387387.1  matrin-3 isoform a

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
    21. NM_001400459.1NP_001387388.1  matrin-3 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B4DRS1
    22. NM_001400460.1NP_001387389.1  matrin-3 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      Q5CZA7
    23. NM_001400461.1NP_001387390.1  matrin-3 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B4DRS1
    24. NM_001400462.1NP_001387391.1  matrin-3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
    25. NM_001400463.1NP_001387392.1  matrin-3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
    26. NM_001400464.1NP_001387393.1  matrin-3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
    27. NM_001400465.1NP_001387394.1  matrin-3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
    28. NM_001400466.1NP_001387395.1  matrin-3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
    29. NM_001400467.1NP_001387396.1  matrin-3 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC011404
      UniProtKB/TrEMBL
      B3KM87, B4DF66, Q5CZA7
      Related
      ENSP00000426030.1, ENST00000502499.5
    30. NM_018834.6NP_061322.2  matrin-3 isoform a

      See identical proteins and their annotated locations for NP_061322.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-4 encode the same isoform (a).
      Source sequence(s)
      AA233906, AC011404, AY007157, BX537365
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
      Related
      ENSP00000378284.3, ENST00000394805.8
      Conserved Domains (3) summary
      smart00451
      Location:798833
      ZnF_U1; U1-like zinc finger
      cd12714
      Location:398473
      RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
      cd12715
      Location:496575
      RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3
    31. NM_199189.3NP_954659.1  matrin-3 isoform a

      See identical proteins and their annotated locations for NP_954659.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1-4 encode the same isoform (a).
      Source sequence(s)
      AA233906, AB018266, AC011404, AK307872, BX537365
      UniProtKB/Swiss-Prot
      B7ZAV5, D3DQC3, P43243, Q9UHW0, Q9UQ27
      UniProtKB/TrEMBL
      A0A0R4J2E8, Q68D11
      Conserved Domains (3) summary
      smart00451
      Location:798833
      ZnF_U1; U1-like zinc finger
      cd12714
      Location:398473
      RRM1_MATR3; RNA recognition motif 1 in vertebrate matrin-3
      cd12715
      Location:496575
      RRM2_MATR3; RNA recognition motif 2 in vertebrate matrin-3

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      139274101..139331677
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      139800176..139857743
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)