Human Gene FARP1 (ENST00000319562.11_7) from GENCODE V47lift37
  Description: FERM, ARH/RhoGEF and pleckstrin domain protein 1, transcript variant 1 (from RefSeq NM_005766.4)
Gencode Transcript: ENST00000319562.11_7
Gencode Gene: ENSG00000152767.17_16
Transcript (Including UTRs)
   Position: hg19 chr13:98,795,348-99,107,430 Size: 312,083 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg19 chr13:98,865,497-99,100,571 Size: 235,075 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:98,795,348-99,107,430)mRNA (may differ from genome)Protein (1045 aa)
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-  Comments and Description Text from UniProtKB
  ID: FARP1_HUMAN
DESCRIPTION: RecName: Full=FERM, RhoGEF and pleckstrin domain-containing protein 1; AltName: Full=Chondrocyte-derived ezrin-like protein; AltName: Full=Pleckstrin homology domain-containing family C member 2; Short=PH domain-containing family C member 2;
FUNCTION: May function as Rho-guanine nucleotide exchange factor (By similarity).
TISSUE SPECIFICITY: Detected in cAMP-treated chondrocytes, but not in untreated chondrocytes. Detected in fetal brain, heart and spleen, and in adult testis, kidney and lung.
INDUCTION: Up-regulated in response to cAMP in cultured embryonic chondrocytes.
SIMILARITY: Contains 1 DH (DBL-homology) domain.
SIMILARITY: Contains 1 FERM domain.
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: 19.10 RPKM in Kidney - Cortex
Total median expression: 310.79 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 -242.10422-0.574 Picture PostScript Text
3' UTR -1948.106859-0.284 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
IPR019749 - Band_41_domain
IPR019750 - Band_41_fam
IPR000219 - DH-domain
IPR000798 - Ez/rad/moesin
IPR014847 - FERM-adjacent
IPR014352 - FERM/acyl-CoA-bd_prot_3-hlx
IPR019748 - FERM_central
IPR019747 - FERM_CS
IPR000299 - FERM_domain
IPR018979 - FERM_N
IPR018980 - FERM_PH-like_C
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology

Pfam Domains:
PF00169 - PH domain
PF00373 - FERM central domain
PF00621 - RhoGEF domain
PF08736 - FERM adjacent (FA)
PF09379 - FERM N-terminal domain
PF09380 - FERM C-terminal PH-like domain

SCOP Domains:
47031 - Second domain of FERM
63600 - Telomeric repeat binding factor (TRF) dimerisation domain
103657 - BAR/IMD domain-like
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like
54236 - Ubiquitin-like

ModBase Predicted Comparative 3D Structure on Q9Y4F1
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005089 Rho guanyl-nucleotide exchange factor activity
GO:0008092 cytoskeletal protein binding
GO:0030676 Rac guanyl-nucleotide exchange factor activity

Biological Process:
GO:0007275 multicellular organism development
GO:0007416 synapse assembly
GO:0010923 negative regulation of phosphatase activity
GO:0035023 regulation of Rho protein signal transduction
GO:0048813 dendrite morphogenesis

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030054 cell junction
GO:0030175 filopodium
GO:0030425 dendrite
GO:0031234 extrinsic component of cytoplasmic side of plasma membrane
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043197 dendritic spine
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  BC071592 - Homo sapiens FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived), mRNA (cDNA clone MGC:87400 IMAGE:30342239), complete cds.
BC041595 - Homo sapiens FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived), mRNA (cDNA clone MGC:52223 IMAGE:5443230), complete cds.
AB008430 - Homo sapiens mRNA for CDEP, complete cds.
BC065020 - Homo sapiens FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived), mRNA (cDNA clone IMAGE:6047510), with apparent retained intron.
AB385176 - Synthetic construct DNA, clone: pF1KB7011, Homo sapiens FARP1 gene for FERM, RhoGEF and pleckstrin domain-containing protein 1, complete cds, without stop codon, in Flexi system.
AM393180 - Synthetic construct Homo sapiens clone IMAGE:100002712 for hypothetical protein (FARP1 gene).
AM393217 - Synthetic construct Homo sapiens clone IMAGE:100002942 for hypothetical protein (FARP1 gene).
AM393453 - Synthetic construct Homo sapiens clone IMAGE:100002943 for hypothetical protein (FARP1 gene).
JD166730 - Sequence 147754 from Patent EP1572962.
AK123565 - Homo sapiens cDNA FLJ41571 fis, clone CTONG2009531.
AK095747 - Homo sapiens cDNA FLJ38428 fis, clone FEBRA2013274, weakly similar to Homo sapiens mRNA for CDEP.
JD520300 - Sequence 501324 from Patent EP1572962.
JD539274 - Sequence 520298 from Patent EP1572962.
JD400917 - Sequence 381941 from Patent EP1572962.
BC053593 - Homo sapiens FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived), mRNA (cDNA clone IMAGE:5727055), partial cds.
CU690113 - Synthetic construct Homo sapiens gateway clone IMAGE:100019365 3' read STK24 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: CDEP, ENST00000319562.1, ENST00000319562.10, ENST00000319562.2, ENST00000319562.3, ENST00000319562.4, ENST00000319562.5, ENST00000319562.6, ENST00000319562.7, ENST00000319562.8, ENST00000319562.9, FARP1_HUMAN, NM_005766, PLEKHC2, Q5JVI9, Q6IQ29, Q9Y4F1, uc317qrw.1, uc317qrw.2
UCSC ID: ENST00000319562.11_7
RefSeq Accession: NM_005766.4
Protein: Q9Y4F1 (aka FARP1_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.