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    XIRP1 xin actin binding repeat containing 1 [ Homo sapiens (human) ]

    Gene ID: 165904, updated on 10-Dec-2024

    Summary

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    Official Symbol
    XIRP1provided by HGNC
    Official Full Name
    xin actin binding repeat containing 1provided by HGNC
    Primary source
    HGNC:HGNC:14301
    See related
    Ensembl:ENSG00000168334 MIM:609777; AllianceGenome:HGNC:14301
    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
    Xin; CMYA1
    Summary
    The protein encoded by this gene is a striated muscle protein and belongs to the Xin actin-binding repeat-containing protein (XIRP) family. The protein functions to protect actin filaments during depolymerization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]
    Expression
    Restricted expression toward heart (RPKM 52.8) See more
    Orthologs
    mouse all
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    Genomic context

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    See XIRP1 in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (39183215..39192595, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (39196207..39205587, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (39224706..39234086, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene cysteine and serine rich nuclear protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:39194268-39195127 Neighboring gene uncharacterized LOC101928263 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:39195907-39196406 Neighboring gene Sharpr-MPRA regulatory region 1375 Neighboring gene uncharacterized LOC105377035 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:39232857-39233846 Neighboring gene uncharacterized LOC124909366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:39251989-39252657 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:39252658-39253325 Neighboring gene DSTN pseudogene 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Cardiomyopathy-Associated Gene 1-Sensitive PKC-Dependent Connexin 43 Expression and Phosphorylation in Left Ventricular Noncompaction Cardiomyopathy. Xie Y, et al. Cell Physiol Biochem, 2017. PMID 29176328
    2. Xin is a marker of skeletal muscle damage severity in myopathies. Nilsson MI, et al. Am J Pathol, 2013 Dec. PMID 24225086
    3. Differential involvement of sarcomeric proteins in myofibrillar myopathies: a morphological and immunohistochemical study. Claeys KG, et al. Acta Neuropathol, 2009 Mar. PMID 19151983
    4. Multiple tumor-suppressor genes on chromosome 3p contribute to head and neck squamous cell carcinoma tumorigenesis. Lee DJ, et al. Cancer Biol Ther, 2010 Oct 1. PMID 20657180, Free PMC Article
    5. A combined laser microdissection and mass spectrometry approach reveals new disease relevant proteins accumulating in aggregates of filaminopathy patients. Kley RA, et al. Mol Cell Proteomics, 2013 Jan. PMID 23115302, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An interaction of heart disease-associated proteins POPDC1/2 with XIRP1 in transverse tubules and intercalated discs.
      Title: An interaction of heart disease-associated proteins POPDC1/2 with XIRP1 in transverse tubules and intercalated discs.
    2. Report pathogenic XIRP1/2 rare variants in arrhythmogenic disorders such as sudden unexplained nocturnal death syndrome and Brugada syndrome.
      Title: Critical Roles of Xirp Proteins in Cardiac Conduction and Their Rare Variants Identified in Sudden Unexplained Nocturnal Death Syndrome and Brugada Syndrome in Chinese Han Population.
    3. Abnormal CMYA1 expression affects the phosphorylation of Cx43 through the protein kinase c signaling pathway, which is involved in the regulation of gap junction intercellular communication.
      Title: Cardiomyopathy-Associated Gene 1-Sensitive PKC-Dependent Connexin 43 Expression and Phosphorylation in Left Ventricular Noncompaction Cardiomyopathy.
    4. Aciculin interacts with filamin C and Xin and is essential for myofibril assembly.
      Title: Aciculin interacts with filamin C and Xin and is essential for myofibril assembly, remodeling and maintenance.
    5. The strong correlation between the degree of muscle damage and Xin immunoreactivity suggests that Xin may be a suitable outcome measure to evaluate disease progression and treatment effects in clinical trials.
      Title: Xin is a marker of skeletal muscle damage severity in myopathies.
    6. We identify the SH3 domains of nebulin and nebulette as novel ligands of proline-rich regions of Xin and XIRP2.
      Title: Identification of Xin-repeat proteins as novel ligands of the SH3 domains of nebulin and nebulette and analysis of their interaction during myofibril formation and remodeling.
    7. Data provide further support that ALS2CL, EPHA3, and CMYA1 are bona-fide tumor-suppressor genes and contribute to the tumorigenesis of HNSCC.
      Title: Multiple tumor-suppressor genes on chromosome 3p contribute to head and neck squamous cell carcinoma tumorigenesis.
    8. Data show that in myofibrillar myopathies Xin protein exhibites significant alterations in their localization.
      Title: Differential involvement of sarcomeric proteins in myofibrillar myopathies: a morphological and immunohistochemical study.
    9. Here, we identify Xin, the protein encoded by the human gene 'cardiomyopathy associated 1'(CMYA1) as filamin c binding partner at these specialized structures where the ends of myofibrils are attached to the sarcolemma
      Title: Unusual splicing events result in distinct Xin isoforms that associate differentially with filamin c and Mena/VASP.
    10. Xin and XIRP2 define a novel actin-binding motif
      Title: Xin repeats define a novel actin-binding motif.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
    EBI GWAS Catalog

    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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    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif upregulates the expression of xin actin-binding repeat containing 1 (XIRP1) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp451D042, DKFZp779C1255, DKFZp779C1947

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in actin filament organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in myoblast differentiation involved in skeletal muscle regeneration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of protein binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in satellite cell activation involved in skeletal muscle regeneration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in adherens junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in desmosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with focal adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with focal adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    colocalizes_with stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with stress fiber IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    xin actin-binding repeat-containing protein 1
    Names
    cardiomyopathy associated 1
    cardiomyopathy-associated protein 1

    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_054927.1 RefSeqGene

      Range
      5026..14406
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001198621.4 → NP_001185550.1  xin actin-binding repeat-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001185550.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate internal segment compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC092053
      Consensus CDS
      CCDS56245.1
      UniProtKB/Swiss-Prot
      Q702N8
      Related
      ENSP00000379550.1, ENST00000396251.1
      Conserved Domains (1) summary
      pfam08043
      Location:508 → 521
      Xin; Xin repeat

    2. NM_001351377.2 → NP_001338306.1  xin actin-binding repeat-containing protein 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC092053
      Consensus CDS
      CCDS87065.1
      UniProtKB/TrEMBL
      B3KV77
      Related
      ENSP00000391645.1, ENST00000421646.1
      Conserved Domains (1) summary
      cl26247
      Location:14 → 168
      DNA_pol3_delta2; DNA polymerase III, delta subunit

    3. NM_194293.4 → NP_919269.2  xin actin-binding repeat-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_919269.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC092053
      Consensus CDS
      CCDS2683.1
      UniProtKB/Swiss-Prot
      A0JP25, A4QPE2, Q68DF2, Q6ZTR3, Q702N8, Q702N9, Q8IVN7, Q8N1N3, Q8N904, Q8TCG7
      Related
      ENSP00000343140.3, ENST00000340369.4
      Conserved Domains (1) summary
      pfam08043
      Location:508 → 521
      Xin; Xin repeat

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      39183215..39192595 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447588.1 → XP_047303544.1  xin actin-binding repeat-containing protein 1 isoform X2

    2. XM_005264909.4 → XP_005264966.1  xin actin-binding repeat-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005264966.1

      UniProtKB/Swiss-Prot
      A0JP25, A4QPE2, Q68DF2, Q6ZTR3, Q702N8, Q702N9, Q8IVN7, Q8N1N3, Q8N904, Q8TCG7
      Conserved Domains (1) summary
      pfam08043
      Location:508 → 521
      Xin; Xin repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      39196207..39205587 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345487.1 → XP_054201462.1  xin actin-binding repeat-containing protein 1 isoform X2

    2. XM_054345486.1 → XP_054201461.1  xin actin-binding repeat-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q702N8.1 GenPept UniProtKB/Swiss-Prot:Q702N8

    Gene LinkOut

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

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