Human Gene AFAP1 (uc003gkg.1)
  Description: Homo sapiens actin filament associated protein 1 (AFAP1), transcript variant 2, mRNA.
RefSeq Summary (NM_198595): The protein encoded by this gene is a Src binding partner. It may represent a potential modulator of actin filament integrity in response to cellular signals, and may function as an adaptor protein by linking Src family members and/or other signaling proteins to actin filaments. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008].
Transcript (Including UTRs)
   Position: hg19 chr4:7,760,440-7,941,653 Size: 181,214 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr4:7,765,492-7,873,805 Size: 108,314 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:7,760,440-7,941,653)mRNA (may differ from genome)Protein (730 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AFAP1_HUMAN
DESCRIPTION: RecName: Full=Actin filament-associated protein 1; AltName: Full=110 kDa actin filament-associated protein; Short=AFAP-110;
FUNCTION: Can cross-link actin filaments into both network and bundle structures (By similarity). May modulate changes in actin filament integrity and induce lamellipodia formation. May function as an adapter molecule that links other proteins, such as SRC and PKC to the actin cytoskeleton. Seems to play a role in the development and progression of prostate adenocarcinoma by regulating cell-matrix adhesions and migration in the cancer cells.
SUBUNIT: Monomer and homomultimer. Interacts via its C-terminus with F-actin; probably involving AFAP1 multimers (By similarity). Interacts with activated SRC SH3-SH2 domains. Interacts via its PH 1 domain with PRKCA, PRKCB and PRKCI (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Note=Localizes with stress fibers in quiescent cells, concentrated in cell motility structures such as lamellipodia, filopodia and membrane ruffles upon their induction.
TISSUE SPECIFICITY: Low expression in normal breast epithelial cell line MCF-10A and in tumorigenic breast cancer cell lines MCF- 7, T-47D and ZR75-1. Highly expressed in the invasive breast cancer cell lines MDA-MB-231 and MDA-MB-435. Overexpressed in prostate carcinoma.
PTM: Phosphorylated on tyrosine residues by SRC.
MISCELLANEOUS: Knockdown in MDA-MB-231 cells resulted in loss of actin stress fibers, decreased adhesion and spreading on fibronectin.
SIMILARITY: Contains 2 PH domains.

-  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

+  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: 11.31 RPKM in Colon - Sigmoid
Total median expression: 259.40 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -156.50273-0.573 Picture PostScript Text
3' UTR -1739.755052-0.344 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
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology

Pfam Domains:
PF00169 - PH domain

SCOP Domains:
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on Q8N556
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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

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

Biological Process:
GO:0009966 regulation of signal transduction
GO:0051493 regulation of cytoskeleton organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005925 focal adhesion
GO:0015629 actin cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AF188700 - Homo sapiens actin filament associated protein (AFAP) mRNA, complete cds.
BC032777 - Homo sapiens actin filament associated protein 1, mRNA (cDNA clone MGC:44840 IMAGE:4914388), complete cds.
AK297631 - Homo sapiens cDNA FLJ56849 complete cds, moderately similar to Mus musculus actin filament associated protein 1 (Afap1), mRNA.
AK290807 - Homo sapiens cDNA FLJ75286 complete cds, highly similar to Homo sapiens actin filament associated protein (AFAP), transcript variant 1, mRNA.
KJ899395 - Synthetic construct Homo sapiens clone ccsbBroadEn_08789 AFAP1 gene, encodes complete protein.
AB527433 - Synthetic construct DNA, clone: pF1KE1022, Homo sapiens AFAP1 gene for actin filament associated protein 1, without stop codon, in Flexi system.
CU689530 - Synthetic construct Homo sapiens gateway clone IMAGE:100017789 5' read AFAP1 mRNA.
D25248 - Homo sapiens mRNA, clone: RES4-4.
JD059176 - Sequence 40200 from Patent EP1572962.
JD102985 - Sequence 84009 from Patent EP1572962.
JD303897 - Sequence 284921 from Patent EP1572962.
JD289395 - Sequence 270419 from Patent EP1572962.
JD165712 - Sequence 146736 from Patent EP1572962.
JD300188 - Sequence 281212 from Patent EP1572962.
JD160044 - Sequence 141068 from Patent EP1572962.
JD137910 - Sequence 118934 from Patent EP1572962.
JD449931 - Sequence 430955 from Patent EP1572962.
JD167378 - Sequence 148402 from Patent EP1572962.
JD327644 - Sequence 308668 from Patent EP1572962.
JD269435 - Sequence 250459 from Patent EP1572962.
JD189405 - Sequence 170429 from Patent EP1572962.
JD211324 - Sequence 192348 from Patent EP1572962.
JD484835 - Sequence 465859 from Patent EP1572962.
JD123842 - Sequence 104866 from Patent EP1572962.
JD486525 - Sequence 467549 from Patent EP1572962.
JD482820 - Sequence 463844 from Patent EP1572962.
JD468302 - Sequence 449326 from Patent EP1572962.
JD119651 - Sequence 100675 from Patent EP1572962.
JD301193 - Sequence 282217 from Patent EP1572962.
JD554414 - Sequence 535438 from Patent EP1572962.
JD485555 - Sequence 466579 from Patent EP1572962.
JD466113 - Sequence 447137 from Patent EP1572962.
JD471255 - Sequence 452279 from Patent EP1572962.
JD537795 - Sequence 518819 from Patent EP1572962.
JD365804 - Sequence 346828 from Patent EP1572962.
JD067695 - Sequence 48719 from Patent EP1572962.
JD460739 - Sequence 441763 from Patent EP1572962.
BC015900 - Homo sapiens, clone IMAGE:3909917, mRNA.
JD192789 - Sequence 173813 from Patent EP1572962.
DQ585763 - Homo sapiens piRNA piR-52875, complete sequence.
JD459237 - Sequence 440261 from Patent EP1572962.
JD498509 - Sequence 479533 from Patent EP1572962.
JD318588 - Sequence 299612 from Patent EP1572962.
JD176183 - Sequence 157207 from Patent EP1572962.
JD488922 - Sequence 469946 from Patent EP1572962.
JD155367 - Sequence 136391 from Patent EP1572962.
JD367126 - Sequence 348150 from Patent EP1572962.
JD036694 - Sequence 17718 from Patent EP1572962.
JD292741 - Sequence 273765 from Patent EP1572962.
JD336685 - Sequence 317709 from Patent EP1572962.
JD164265 - Sequence 145289 from Patent EP1572962.
JD183519 - Sequence 164543 from Patent EP1572962.
JD106706 - Sequence 87730 from Patent EP1572962.
JD452952 - Sequence 433976 from Patent EP1572962.
JD349580 - Sequence 330604 from Patent EP1572962.
JD133536 - Sequence 114560 from Patent EP1572962.
JD193510 - Sequence 174534 from Patent EP1572962.
JD134357 - Sequence 115381 from Patent EP1572962.
JD231213 - Sequence 212237 from Patent EP1572962.
JD278195 - Sequence 259219 from Patent EP1572962.
JD398871 - Sequence 379895 from Patent EP1572962.
JD518589 - Sequence 499613 from Patent EP1572962.
JD372768 - Sequence 353792 from Patent EP1572962.
DQ599547 - Homo sapiens piRNA piR-37613, complete sequence.
JD212052 - Sequence 193076 from Patent EP1572962.
JD415945 - Sequence 396969 from Patent EP1572962.
JD345190 - Sequence 326214 from Patent EP1572962.
JD096022 - Sequence 77046 from Patent EP1572962.
JD202462 - Sequence 183486 from Patent EP1572962.
JD380498 - Sequence 361522 from Patent EP1572962.
JD494584 - Sequence 475608 from Patent EP1572962.
JD474169 - Sequence 455193 from Patent EP1572962.
JD288758 - Sequence 269782 from Patent EP1572962.
AB209676 - Homo sapiens mRNA for actin filament associated protein variant protein.
AK127962 - Homo sapiens cDNA FLJ46074 fis, clone TESTI2001915, highly similar to Homo sapiens actin filament associated protein (AFAP).
JD179573 - Sequence 160597 from Patent EP1572962.
JD253813 - Sequence 234837 from Patent EP1572962.
JD438077 - Sequence 419101 from Patent EP1572962.
JD342909 - Sequence 323933 from Patent EP1572962.
JD242053 - Sequence 223077 from Patent EP1572962.
JD146261 - Sequence 127285 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K442, AFAP, AFAP1_HUMAN, NM_198595, NP_940997, Q59EY5, Q8N556, Q9HBY1
UCSC ID: uc003gkg.1
RefSeq Accession: NM_198595
Protein: Q8N556 (aka AFAP1_HUMAN)
CCDS: CCDS3397.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_198595.2
exon count: 17CDS single in 3' UTR: no RNA size: 7534
ORF size: 2193CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4194.00frame shift in genome: no % Coverage: 99.79
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.