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    ZMAT5 zinc finger matrin-type 5 [ Homo sapiens (human) ]

    Gene ID: 55954, updated on 5-Mar-2024

    Summary

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    Official Symbol
    ZMAT5provided by HGNC
    Official Full Name
    zinc finger matrin-type 5provided by HGNC
    Primary source
    HGNC:HGNC:28046
    See related
    Ensembl:ENSG00000100319 MIM:619741; AllianceGenome:HGNC:28046
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZC3H19; SNRNP20; U11/U12-20K
    Summary
    Predicted to enable zinc ion binding activity. Predicted to be involved in RNA splicing. Located in nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal (RPKM 7.7), lung (RPKM 7.3) and 25 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    22q12.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (29730956..29767007, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30194319..30230905, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30126945..30162996, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30009952-30010452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30026831-30027330 Neighboring gene ribulose-5-phosphate-3-epimerase pseudogene 4 Neighboring gene NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30084213-30084714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30084715-30085214 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:30085434-30085934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30087218-30087838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30087839-30088460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30088461-30089081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30101159-30101822 Neighboring gene MPRA-validated peak4478 silencer Neighboring gene CABP7 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30117301-30118091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30133259-30134112 Neighboring gene calcium binding protein 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30143413-30144160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30144161-30144906 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30162231-30162880 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30162881-30163530 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:30179115-30179288 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit X Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30194678-30195178 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30195179-30195679 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30196571-30197566 Neighboring gene activating signal cointegrator 1 complex subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18820 Neighboring gene Sharpr-MPRA regulatory region 3108

    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. Search for chromosome rearrangements: new approaches toward discovery of novel translocations in head and neck squamous cell carcinoma. Wang VW, et al. Head Neck, 2013 Jun. PMID 22807096
    2. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. Will CL, et al. RNA, 2004 Jun. PMID 15146077, Free PMC Article
    3. Identification of genes related to Parkinson's disease using expressed sequence tags. Kim JM, et al. DNA Res, 2006 Dec 31. PMID 17213182
    4. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Adams MD, et al. Nature, 1995 Sep 28. PMID 7566098
    5. Characterizing WW domain interactions of tumor suppressor WWOX reveals its association with multiprotein networks. Abu-Odeh M, et al. J Biol Chem, 2014 Mar 28. PMID 24550385, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of U12-type spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U12-type spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger matrin-type protein 5
    Names
    U11/U12 small nuclear ribonucleoprotein 20 kDa protein
    U11/U12 snRNP 20 kDa protein
    U11/U12 snRNP 20K
    zinc finger CCCH-type containing 19

    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.

    mRNA and Protein(s)

    1. NM_001003692.2 → NP_001003692.1  zinc finger matrin-type protein 5

      See identical proteins and their annotated locations for NP_001003692.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC004882, BC009717, BU598307
      Consensus CDS
      CCDS13868.1
      UniProtKB/Swiss-Prot
      A8K9F6, Q9UDW3
      Related
      ENSP00000344241.3, ENST00000344318.4
      Conserved Domains (2) summary
      cl22907
      Location:4 → 46
      zf-U1; U1 zinc finger
      pfam00642
      Location:55 → 76
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

    2. NM_001318129.2 → NP_001305058.1  zinc finger matrin-type protein 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-3 encode the same protein.
      Source sequence(s)
      BC009717, BQ931527, DT217179
      Consensus CDS
      CCDS13868.1
      UniProtKB/Swiss-Prot
      A8K9F6, Q9UDW3
      Conserved Domains (2) summary
      cl22907
      Location:4 → 46
      zf-U1; U1 zinc finger
      pfam00642
      Location:55 → 76
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

    3. NM_019103.3 → NP_061976.1  zinc finger matrin-type protein 5

      See identical proteins and their annotated locations for NP_061976.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AA312132, AC004882, AL160311, BC009717, BG285784
      Consensus CDS
      CCDS13868.1
      UniProtKB/Swiss-Prot
      A8K9F6, Q9UDW3
      Conserved Domains (2) summary
      cl22907
      Location:4 → 46
      zf-U1; U1 zinc finger
      pfam00642
      Location:55 → 76
      zf-CCCH; Zinc finger C-x8-C-x5-C-x3-H type (and similar)

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      29730956..29767007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      30194319..30230905 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325795.1 → XP_054181770.1  zinc finger matrin-type protein 5 isoform X1

      UniProtKB/Swiss-Prot
      A8K9F6, Q9UDW3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UDW3.1 GenPept UniProtKB/Swiss-Prot:Q9UDW3

    Gene LinkOut

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

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