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MATR3 matrin 3 [ Homo sapiens (human) ]

Gene ID: 9782, updated on 7-Apr-2024

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
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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
  6. NM_001400442.1NP_001387371.1  matrin-3 isoform d

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

    Source sequence(s)
    AC011404
    Consensus CDS
    CCDS93789.1
    UniProtKB/TrEMBL
    A8MXP9
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  21. NM_001400459.1NP_001387388.1  matrin-3 isoform e

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

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

    Status: REVIEWED

    Source sequence(s)
    AC011404
    UniProtKB/TrEMBL
    B3KM87
    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)