Human Gene PARVB (ENST00000338758.12) from GENCODE V44
  Description: Homo sapiens parvin beta (PARVB), transcript variant 2, mRNA. (from RefSeq NM_013327)
RefSeq Summary (NM_013327): This gene encodes a member of the parvin family of actin-binding proteins, which play a role in cytoskeleton organization and cell adhesion. These proteins are associated with focal contacts and contain calponin homology domains that bind to actin filaments. This family member binds to alphaPIX and alpha-actinin, and it can inhibit the activity of integrin-linked kinase. This protein also functions in tumor suppression. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011].
Gencode Transcript: ENST00000338758.12
Gencode Gene: ENSG00000188677.15
Transcript (Including UTRs)
   Position: hg38 chr22:44,024,302-44,172,939 Size: 148,638 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg38 chr22:44,024,340-44,168,678 Size: 144,339 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:44,024,302-44,172,939)mRNA (may differ from genome)Protein (364 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PARVB_HUMAN
DESCRIPTION: RecName: Full=Beta-parvin; AltName: Full=Affixin;
FUNCTION: Probably plays a role in the regulation of cell adhesion and cytoskeleton organization.
SUBUNIT: Interacts with DYSF. Interacts with integrin-linked protein kinase and actin.
SUBCELLULAR LOCATION: Cell junction, focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm, cytoskeleton. Note=Constituent of focal adhesions.
TISSUE SPECIFICITY: Expressed predominantly in heart and skeletal muscle.
SIMILARITY: Belongs to the parvin family.
SIMILARITY: Contains 2 CH (calponin-homology) domains.
SEQUENCE CAUTION: Sequence=AAD34051.1; Type=Frameshift; Positions=4, 14, 48, 58, 155, 162, 171, 327, 331, 344; Sequence=BG743702; Type=Frameshift; Positions=136, 232, 237;

-  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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.97 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 294.81 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 -14.6038-0.384 Picture PostScript Text
3' UTR -1799.904261-0.422 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
IPR001715 - CH-domain

Pfam Domains:
PF00307 - Calponin homology (CH) domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
4EDL - X-ray MuPIT 4EDM - X-ray MuPIT 4EDN - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9HBI1
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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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0005515 protein binding

Biological Process:
GO:0007155 cell adhesion
GO:0030031 cell projection assembly
GO:0030032 lamellipodium assembly
GO:0031532 actin cytoskeleton reorganization
GO:0071963 establishment or maintenance of cell polarity regulating cell shape

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030017 sarcomere
GO:0030018 Z disc
GO:0030027 lamellipodium
GO:0030054 cell junction
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AF303887 - Homo sapiens CLINT mRNA, complete cds.
LF385066 - JP 2014500723-A/192569: Polycomb-Associated Non-Coding RNAs.
MA620643 - JP 2018138019-A/192569: Polycomb-Associated Non-Coding RNAs.
BC017461 - Homo sapiens parvin, beta, mRNA (cDNA clone IMAGE:4859691).
AK309987 - Homo sapiens cDNA, FLJ17029.
AK313957 - Homo sapiens cDNA, FLJ94603, highly similar to Homo sapiens parvin, beta (PARVB), mRNA.
BC046103 - Homo sapiens parvin, beta, mRNA (cDNA clone MGC:57521 IMAGE:5763848), complete cds.
AB048276 - Homo sapiens mRNA for affixin, complete cds.
AF151814 - Homo sapiens CGI-56 protein mRNA, complete cds.
AF237769 - Homo sapiens beta-parvin (PARVB) mRNA, complete cds.
AL159142 - Novel human gene mapping to chomosome 22.
AK308443 - Homo sapiens cDNA, FLJ98391.
BC039811 - Homo sapiens, Similar to parvin, beta, clone IMAGE:5757378, mRNA.
LF337527 - JP 2014500723-A/145030: Polycomb-Associated Non-Coding RNAs.
MA573104 - JP 2018138019-A/145030: Polycomb-Associated Non-Coding RNAs.
JD061934 - Sequence 42958 from Patent EP1572962.
JD181023 - Sequence 162047 from Patent EP1572962.
JD275166 - Sequence 256190 from Patent EP1572962.
JD045035 - Sequence 26059 from Patent EP1572962.
JD126407 - Sequence 107431 from Patent EP1572962.
JD121715 - Sequence 102739 from Patent EP1572962.
JD054700 - Sequence 35724 from Patent EP1572962.
JD263153 - Sequence 244177 from Patent EP1572962.
JD442239 - Sequence 423263 from Patent EP1572962.
JD287615 - Sequence 268639 from Patent EP1572962.
JD458997 - Sequence 440021 from Patent EP1572962.
JD391686 - Sequence 372710 from Patent EP1572962.
JD395908 - Sequence 376932 from Patent EP1572962.
JD535554 - Sequence 516578 from Patent EP1572962.
LF337529 - JP 2014500723-A/145032: Polycomb-Associated Non-Coding RNAs.
MA573106 - JP 2018138019-A/145032: Polycomb-Associated Non-Coding RNAs.
LF337530 - JP 2014500723-A/145033: Polycomb-Associated Non-Coding RNAs.
MA573107 - JP 2018138019-A/145033: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion

Reactome (by CSHL, EBI, and GO)

Protein Q9HBI1 (Reactome details) participates in the following event(s):

R-HSA-430308 PARVB interacts with Alpha-actinin
R-HSA-432946 PARVB/Affixin interacts with alpha PIX
R-HSA-446391 Formation of the PINCH-ILK-parvin complex
R-HSA-446388 Regulation of cytoskeletal remodeling and cell spreading by IPP complex components
R-HSA-446353 Cell-extracellular matrix interactions
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: B0QYN1, B2R9X6, CGI-56, ENST00000338758.1, ENST00000338758.10, ENST00000338758.11, ENST00000338758.2, ENST00000338758.3, ENST00000338758.4, ENST00000338758.5, ENST00000338758.6, ENST00000338758.7, ENST00000338758.8, ENST00000338758.9, NM_013327, PARVB_HUMAN, Q5TGJ5, Q86X93, Q96PN1, Q9HBI1, Q9NSP7, Q9UGT3, Q9Y368, Q9Y3L6, Q9Y3L7, uc003ben.1, uc003ben.2, uc003ben.3, uc003ben.4, uc003ben.5
UCSC ID: ENST00000338758.12
RefSeq Accession: NM_013327
Protein: Q9HBI1 (aka PARVB_HUMAN or PARB_HUMAN)
CCDS: CCDS14056.1

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