Human Gene PARVA (uc001mki.4) Description and Page Index
  Description: Homo sapiens parvin, alpha (PARVA), mRNA.
RefSeq Summary (NM_018222): This gene encodes a member of the parvin family of actin-binding proteins. Parvins are associated with focal contacts and contain calponin homology domains that bind to actin filaments. The encoded protein is part of the integrin-linked kinase signaling complex and plays a role in cell adhesion, motility and survival. [provided by RefSeq, Dec 2010]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660803.102228.1, AF237771.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on manual assertion, conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:12,399,026-12,556,903 Size: 157,878 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr11:12,399,075-12,549,472 Size: 150,398 Coding Exon Count: 13 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:12,399,026-12,556,903)mRNA (may differ from genome)Protein (412 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PARVA
CDC HuGE Published Literature: PARVA
Positive Disease Associations: Arteries , Cardiomegaly , Forced Expiratory Volume , Iron , Mortality , Pulse , Triglycerides
Related Studies:
  1. Arteries
    , , . [PubMed 0]
  2. Cardiomegaly
    Christopher Newton-Cheh et al. BMC medical genetics 2007, Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study., BMC medical genetics. [PubMed 17903306]
    In the community-based Framingham Heart Study none of the ECG and HRV results individually attained genomewide significance. However, the presence of bona fide QT-associated SNPs among the top 117 results for QT duration supports the importance of efforts to validate top results from the reported scans. Finding genetic variants associated with ECG and HRV quantitative traits may identify novel genes and pathways implicated in arrhythmogenesis and allow for improved recognition of individuals at high risk for arrhythmias in the general population.
  3. Forced Expiratory Volume
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PARVA
Diseases sorted by gene-association score: metagonimiasis (4), adiaspiromycosis (4), breast giant fibroadenoma (2), vein disease (1)

-  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: 59.98 RPKM in Esophagus - Muscularis
Total median expression: 948.20 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 -13.1049-0.267 Picture PostScript Text
3' UTR -2261.627431-0.304 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

SCOP Domains:
47576 - Calponin-homology domain, CH-domain

ModBase Predicted Comparative 3D Structure on J3KNQ4
FrontTopSide
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

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

Biological Process:
GO:0002040 sprouting angiogenesis
GO:0003148 outflow tract septum morphogenesis
GO:0007155 cell adhesion
GO:0007163 establishment or maintenance of cell polarity
GO:0031532 actin cytoskeleton reorganization
GO:0034113 heterotypic cell-cell adhesion
GO:0034446 substrate adhesion-dependent cell spreading
GO:0070252 actin-mediated cell contraction
GO:0071670 smooth muscle cell chemotaxis

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005925 focal adhesion
GO:0015629 actin cytoskeleton
GO:0030027 lamellipodium


-  Descriptions from all associated GenBank mRNAs
  AK098504 - Homo sapiens cDNA FLJ25638 fis, clone STM04720, highly similar to Mus musculus actopaxin mRNA.
AF237771 - Homo sapiens alpha-parvin (PARVA) mRNA, complete cds.
AK022316 - Homo sapiens cDNA FLJ12254 fis, clone MAMMA1001465.
BC016713 - Homo sapiens parvin, alpha, mRNA (cDNA clone MGC:24388 IMAGE:4065758), complete cds.
AK001655 - Homo sapiens cDNA FLJ10793 fis, clone NT2RP4000588.
BC014535 - Homo sapiens parvin, alpha, mRNA (cDNA clone MGC:13400 IMAGE:4065820), complete cds.
AB464001 - Synthetic construct DNA, clone: pF1KB6555, Homo sapiens PARVA gene for parvin, alpha, without stop codon, in Flexi system.
HQ448212 - Synthetic construct Homo sapiens clone IMAGE:100071611; CCSB006276_02 parvin, alpha (PARVA) gene, encodes complete protein.
EU832601 - Synthetic construct Homo sapiens clone HAIB:100067630; DKFZo004H0430 parvin, alpha protein (PARVA) gene, encodes complete protein.
CU677693 - Synthetic construct Homo sapiens gateway clone IMAGE:100017119 5' read PARVA mRNA.
CU677039 - Synthetic construct Homo sapiens gateway clone IMAGE:100023374 5' read PARVA mRNA.
KJ894251 - Synthetic construct Homo sapiens clone ccsbBroadEn_03645 PARVA gene, encodes complete protein.
KJ899182 - Synthetic construct Homo sapiens clone ccsbBroadEn_08576 PARVA gene, encodes complete protein.
AF325830 - Homo sapiens calponin-like integrin-linked kinase binding protein mRNA, complete cds.
AK304444 - Homo sapiens cDNA FLJ54827 complete cds, highly similar to Alpha-parvin.
JD147812 - Sequence 128836 from Patent EP1572962.
JD464588 - Sequence 445612 from Patent EP1572962.
JD127592 - Sequence 108616 from Patent EP1572962.
JD406093 - Sequence 387117 from Patent EP1572962.
JD157589 - Sequence 138613 from Patent EP1572962.
JD271125 - Sequence 252149 from Patent EP1572962.
JD439805 - Sequence 420829 from Patent EP1572962.
JD362582 - Sequence 343606 from Patent EP1572962.
JD493363 - Sequence 474387 from Patent EP1572962.
JD321328 - Sequence 302352 from Patent EP1572962.
JD358993 - Sequence 340017 from Patent EP1572962.
JD208116 - Sequence 189140 from Patent EP1572962.
JD449126 - Sequence 430150 from Patent EP1572962.
JD564991 - Sequence 546015 from Patent EP1572962.
JD206104 - Sequence 187128 from Patent EP1572962.
JD351412 - Sequence 332436 from Patent EP1572962.
JD138682 - Sequence 119706 from Patent EP1572962.
JD347542 - Sequence 328566 from Patent EP1572962.
JD237545 - Sequence 218569 from Patent EP1572962.
JD485244 - Sequence 466268 from Patent EP1572962.
JD464057 - Sequence 445081 from Patent EP1572962.
JD403494 - Sequence 384518 from Patent EP1572962.
JD265804 - Sequence 246828 from Patent EP1572962.
JD493129 - Sequence 474153 from Patent EP1572962.
JD504057 - Sequence 485081 from Patent EP1572962.
JD063112 - Sequence 44136 from Patent EP1572962.
JD252587 - Sequence 233611 from Patent EP1572962.
JD194590 - Sequence 175614 from Patent EP1572962.
JD088035 - Sequence 69059 from Patent EP1572962.
JD433821 - Sequence 414845 from Patent EP1572962.
JD552815 - Sequence 533839 from Patent EP1572962.
AK128814 - Homo sapiens cDNA FLJ46049 fis, clone SYNOV2020463.
JD426697 - Sequence 407721 from Patent EP1572962.
JD135793 - Sequence 116817 from Patent EP1572962.
JD238367 - Sequence 219391 from Patent EP1572962.
JD238368 - Sequence 219392 from Patent EP1572962.
JD047609 - Sequence 28633 from Patent EP1572962.
JD047610 - Sequence 28634 from Patent EP1572962.
JD481567 - Sequence 462591 from Patent EP1572962.
JD472377 - Sequence 453401 from Patent EP1572962.
JD421419 - Sequence 402443 from Patent EP1572962.
JD220087 - Sequence 201111 from Patent EP1572962.
AK057835 - Homo sapiens cDNA FLJ25106 fis, clone CBR01467.

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

-  Other Names for This Gene
  Alternate Gene Symbols: hCG_23646, J3KNQ4, J3KNQ4_HUMAN, NM_018222, NP_060692, uc001mki.3
UCSC ID: uc001mki.4
RefSeq Accession: NM_018222
Protein: J3KNQ4 CCDS: CCDS44541.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018222.4
exon count: 13CDS single in 3' UTR: no RNA size: 8719
ORF size: 1239CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2437.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.