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    XIRP2 xin actin binding repeat containing 2 [ Homo sapiens (human) ]

    Gene ID: 129446, updated on 28-Oct-2024

    Summary

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    Official Symbol
    XIRP2provided by HGNC
    Official Full Name
    xin actin binding repeat containing 2provided by HGNC
    Primary source
    HGNC:HGNC:14303
    See related
    Ensembl:ENSG00000163092 MIM:609778; AllianceGenome:HGNC:14303
    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
    CMYA3
    Summary
    Enables actin filament binding activity. Predicted to be involved in actin filament organization and regulation of actin filament organization. Predicted to act upstream of or within cardiac muscle tissue morphogenesis; cell-cell junction organization; and ventricular septum development. Located in focal adhesion and stress fiber. Implicated in depressive disorder. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in heart (RPKM 30.7) and prostate (RPKM 5.9) See more
    Orthologs
    mouse all
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    Genomic context

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    See XIRP2 in Genome Data Viewer
    Location:
    2q24.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (166888480..167259753)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (167346432..167717651)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (167744990..168116263)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906087 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:167367421-167367674 Neighboring gene uncharacterized LOC107985958 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:167465572-167466152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:167467227-167467749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:167485044-167485544 Neighboring gene NANOG hESC enhancer GRCh37_chr2:167817284-167817785 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:167844661-167845264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:167943626-167944126 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:167996802-167998001 Neighboring gene XIRP2 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:168131495-168132298 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:168148777-168149390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:168150619-168151231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:168187453-168188226 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:168188227-168188998 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:168188999-168189770 Neighboring gene Sharpr-MPRA regulatory region 15114 Neighboring gene beta-1,3-galactosyltransferase 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:168262488-168263041 Neighboring gene RNA, U7 small nuclear 148 pseudogene Neighboring gene CTAGE family member 14, pseudogene

    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. CCDD Phenotype Associated with a Small Chromosome 2 Deletion. Abu-Amero KK, et al. Semin Ophthalmol, 2015. PMID 24475916
    2. Sequencing, tissue distribution and physical mapping of the porcine homologue of cardiomyopathy associated 3 (CMYA3). Pan PW, et al. Anim Genet, 2003 Dec. PMID 14687087
    3. SLC25A12 and CMYA3 gene variants are not associated with autism in the IMGSAC multiplex family sample. Blasi F, et al. Eur J Hum Genet, 2006 Jan. PMID 16205742
    4. A genome-wide association study reveals 2 new susceptibility loci for atopic dermatitis. Schaarschmidt H, et al. J Allergy Clin Immunol, 2015 Sep. PMID 25865352
    5. Genome-wide association study identifies genes that may contribute to risk for developing heroin addiction. Nielsen DA, et al. Psychiatr Genet, 2010 Oct. PMID 20520587, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Genetic information from this patient implies that genes involved in development and maintenance of extraocular muscles can cause congenital ocular motility disorders as well.
      Title: CCDD Phenotype Associated with a Small Chromosome 2 Deletion.
    3. A genome-wide association study reveals 2 new susceptibility loci for atopic dermatitis, XIRP2 and DMRTA1.
      Title: A genome-wide association study reveals 2 new susceptibility loci for atopic dermatitis.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study identifies genes that may contribute to risk for developing heroin addiction.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: SLC25A12 and CMYA3 gene variants are not associated with autism in the IMGSAC multiplex family sample.
    7. 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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ39111, FLJ40200, DKFZp451G055, DKFZp779G1747

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 alpha-actinin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cardiac muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell junction organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of actin filament organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in ventricular septum development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Z disc IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell-cell junction 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 2
    Names
    beta-xin
    cardiomyopathy associated 3
    cardiomyopathy-associated protein 3
    myomaxin
    xeplin
    xin repeat protein 2

    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_001079810.4 → NP_001073278.1  xin actin-binding repeat-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001073278.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks the biggest exon in the CDS, as compared to variant 1. The resulting isoform (2) has a much shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AA665183, AC092601, AK097519, EF119720
      Consensus CDS
      CCDS42768.1
      UniProtKB/TrEMBL
      A0A5F9ZHW6
      Related
      ENSP00000386454.1, ENST00000409043.5
      Conserved Domains (1) summary
      cd09442
      Location:402 → 454
      LIM_Eplin_like; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

    2. NM_001199143.2 → NP_001186072.1  xin actin-binding repeat-containing protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001186072.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an additional in-frame exon and lacks the biggest exon in the CDS, as compared to variant 1. The resulting isoform (3) has an additional segment and a much shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AA665183, AC092601, AK097519, EF119722
      Consensus CDS
      CCDS56143.1
      UniProtKB/TrEMBL
      A0A5F9ZHW6
      Related
      ENSP00000386619.1, ENST00000409728.5
      Conserved Domains (1) summary
      cd09442
      Location:435 → 487
      LIM_Eplin_like; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

    3. NM_001199144.2 → NP_001186073.1  xin actin-binding repeat-containing protein 2 isoform 4

      See identical proteins and their annotated locations for NP_001186073.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks a few of exons from the 5' end and contains an alternate 5' exon, resulting in a downstream AUG start codon, as compared to variant 1. The resulting isoform (4) has a shorter N-terminus, as compared to isoform 1.
      Source sequence(s)
      AL832011, EF119711
      Consensus CDS
      CCDS56144.1
      UniProtKB/Swiss-Prot
      A0PJ94, A4UGR9, B2BBS0, B2BBS1, B2BBS4, B3KVH0, J3KNB1, Q53R52, Q5MJ67, Q702N7, Q86T36, Q86T38, Q86T46, Q86T51, Q86T53, Q86T55, Q86T79, Q86TB6, Q8N1M9, Q8N3R5, Q8TBV6
      Related
      ENSP00000387255.1, ENST00000409273.6
      Conserved Domains (1) summary
      pfam08043
      Location:868 → 881
      Xin; Xin repeat

    4. NM_001199145.2 → NP_001186074.1  xin actin-binding repeat-containing protein 2 isoform 5

      See identical proteins and their annotated locations for NP_001186074.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks a few of exons from the 5' end and the biggest exon in the CDS, and contains an alternate 5' exon, resulting in a downstream AUG start codon, as compared to variant 1. The resulting isoform (5) has a shorter N-terminus, and a much shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AL832011, EF119717
      Consensus CDS
      CCDS56145.1
      UniProtKB/Swiss-Prot
      A4UGR9
      Related
      ENSP00000386981.1, ENST00000409605.1
      Conserved Domains (1) summary
      cd09442
      Location:180 → 232
      LIM_Eplin_like; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

    5. NM_152381.6 → NP_689594.4  xin actin-binding repeat-containing protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC092601, AC093684, AC108494
      Consensus CDS
      CCDS42769.1
      UniProtKB/Swiss-Prot
      A0PJ94, A4UGR9, B2BBS0, B2BBS1, B2BBS4, B3KVH0, J3KNB1, Q53R52, Q5MJ67, Q702N7, Q86T36, Q86T38, Q86T46, Q86T51, Q86T53, Q86T55, Q86T79, Q86TB6, Q8N1M9, Q8N3R5, Q8TBV6
      Related
      ENSP00000386840.2, ENST00000409195.6
      Conserved Domains (1) summary
      pfam08043
      Location:1090 → 1103
      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      166888480..167259753
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003309.2 → XP_016858798.1  xin actin-binding repeat-containing protein 2 isoform X1

      UniProtKB/Swiss-Prot
      A0PJ94, A4UGR9, B2BBS0, B2BBS1, B2BBS4, B3KVH0, J3KNB1, Q53R52, Q5MJ67, Q702N7, Q86T36, Q86T38, Q86T46, Q86T51, Q86T53, Q86T55, Q86T79, Q86TB6, Q8N1M9, Q8N3R5, Q8TBV6
      Related
      ENST00000672277.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      167346432..167717651
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340473.1 → XP_054196448.1  xin actin-binding repeat-containing protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A4UGR9.2 GenPept UniProtKB/Swiss-Prot:A4UGR9

    Gene LinkOut

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

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