Human Gene XIRP1 (ENST00000340369.4_10) from GENCODE V47lift37
  Description: xin actin binding repeat containing 1, transcript variant 1 (from RefSeq NM_194293.4)
Gencode Transcript: ENST00000340369.4_10
Gencode Gene: ENSG00000168334.9_11
Transcript (Including UTRs)
   Position: hg19 chr3:39,224,706-39,234,086 Size: 9,381 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr3:39,225,405-39,230,936 Size: 5,532 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:39,224,706-39,234,086)mRNA (may differ from genome)Protein (1843 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: XIRP1_HUMAN
DESCRIPTION: RecName: Full=Xin actin-binding repeat-containing protein 1; AltName: Full=Cardiomyopathy-associated protein 1;
FUNCTION: Protects actin filaments from depolymerization.
SUBUNIT: Interacts with CTNNB1 (By similarity). Interacts with F- actin, FLNC and VASP.
SUBCELLULAR LOCATION: Cell junction. Note=Colocalizes with actin stress fibers.
TISSUE SPECIFICITY: Isoform A, isoform B and isoform C are expressed in heart.
DOMAIN: Xin repeats bind F-actin.
MISCELLANEOUS: 'Xin' means 'heart' in Chinese.
SIMILARITY: Belongs to the Xin family.
SIMILARITY: Contains 17 Xin repeats.
SEQUENCE CAUTION: Sequence=BAC86519.1; Type=Erroneous initiation; Sequence=CAC81057.1; Type=Frameshift; Positions=1594; Sequence=CAD28459.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: XIRP1
Diseases sorted by gene-association score: arrhythmogenic right ventricular dysplasia 5 (12), brachial plexus lesion (11), myopathy, myofibrillar, 5 (7), cardiomyopathy, dilated, 1e (6), brachial plexus neuropathy (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 110.64 RPKM in Heart - Left Ventricle
Total median expression: 259.94 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.50230-0.224 Picture PostScript Text
3' UTR -237.90699-0.340 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012510 - Actin-binding_Xin_repeat

Pfam Domains:
PF08043 - Xin repeat

ModBase Predicted Comparative 3D Structure on Q702N8
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003779 actin binding
GO:0005515 protein binding

Biological Process:
GO:0007507 heart development
GO:0030036 actin cytoskeleton organization
GO:0032091 negative regulation of protein binding

Cellular Component:
GO:0030054 cell junction
GO:0001725 stress fiber
GO:0005925 focal adhesion
GO:0031941 filamentous actin


-  Descriptions from all associated GenBank mRNAs
  AK126299 - Homo sapiens cDNA FLJ44319 fis, clone TRACH3000926, moderately similar to Mus musculus cardiac morphogenesis (Xin).
CR749430 - Homo sapiens mRNA; cDNA DKFZp779C1947 (from clone DKFZp779C1947).
AJ271461 - Homo sapiens partial mRNA for hypothetical protein (PD05924 gene).
AL713648 - Homo sapiens mRNA; cDNA DKFZp451D042 (from clone DKFZp451D042).
AL832459 - Homo sapiens mRNA; cDNA DKFZp451P241 (from clone DKFZp451P241).
AJ626899 - Homo sapiens mRNA for Xin B (CMYA1 gene).
AJ626900 - Homo sapiens mRNA for Xin A (CMYA1 gene).
BX648565 - Homo sapiens mRNA; cDNA DKFZp779C1255 (from clone DKFZp779C1255).
AK095941 - Homo sapiens cDNA FLJ38622 fis, clone HEART2008364, moderately similar to Mus musculus Xin mRNA.
AK122723 - Homo sapiens cDNA FLJ16222 fis, clone CTONG3002947, highly similar to Homo sapiens cardiomyopathy associated 1 (CMYA1), mRNA.
AY375160 - Homo sapiens cardiomyopathy associated protein 1 (CMYA1) mRNA, complete cds.
AK096421 - Homo sapiens cDNA FLJ39102 fis, clone NTONG2002948, moderately similar to Mus musculus Xin mRNA.
AL831956 - Homo sapiens mRNA; cDNA DKFZp451E205 (from clone DKFZp451E205).
AL832020 - Homo sapiens mRNA; cDNA DKFZp451H224 (from clone DKFZp451H224).
JD185621 - Sequence 166645 from Patent EP1572962.
JD379885 - Sequence 360909 from Patent EP1572962.
JD126456 - Sequence 107480 from Patent EP1572962.
JD251419 - Sequence 232443 from Patent EP1572962.
JD391231 - Sequence 372255 from Patent EP1572962.
JD191718 - Sequence 172742 from Patent EP1572962.
BC127119 - Homo sapiens xin actin-binding repeat containing 1, mRNA (cDNA clone IMAGE:40125445), complete cds.
BC139782 - Homo sapiens xin actin-binding repeat containing 1, mRNA (cDNA clone IMAGE:40125446), complete cds.
JD322826 - Sequence 303850 from Patent EP1572962.
JD178783 - Sequence 159807 from Patent EP1572962.
JD225559 - Sequence 206583 from Patent EP1572962.
JD356187 - Sequence 337211 from Patent EP1572962.
JD209761 - Sequence 190785 from Patent EP1572962.
JD555859 - Sequence 536883 from Patent EP1572962.
JD159451 - Sequence 140475 from Patent EP1572962.
JD216483 - Sequence 197507 from Patent EP1572962.
JD209859 - Sequence 190883 from Patent EP1572962.
BC172374 - Synthetic construct Homo sapiens clone IMAGE:100069068, MGC:199079 xin actin-binding repeat containing 1 (XIRP1) mRNA, encodes complete protein.
JD520731 - Sequence 501755 from Patent EP1572962.
JD386004 - Sequence 367028 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A0JP25, A4QPE2, CMYA1, ENST00000340369.1, ENST00000340369.2, ENST00000340369.3, NM_194293, Q68DF2, Q6ZTR3, Q702N8, Q702N9, Q8IVN7, Q8N1N3, Q8N904, Q8TCG7, uc317vqq.1, uc317vqq.2, XIN, XIRP1_HUMAN
UCSC ID: ENST00000340369.4_10
RefSeq Accession: NM_194293.4
Protein: Q702N8 (aka XIRP1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.