Human Gene CCDC88A (ENST00000436346.7_11) from GENCODE V47lift37
  Description: coiled-coil domain containing 88A, transcript variant 4 (from RefSeq NM_001365480.1)
Gencode Transcript: ENST00000436346.7_11
Gencode Gene: ENSG00000115355.18_17
Transcript (Including UTRs)
   Position: hg19 chr2:55,514,978-55,646,992 Size: 132,015 Total Exon Count: 33 Strand: -
Coding Region
   Position: hg19 chr2:55,518,847-55,646,215 Size: 127,369 Coding Exon Count: 32 

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 (chr2:55,514,978-55,646,992)mRNA (may differ from genome)Protein (1871 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GRDN_HUMAN
DESCRIPTION: RecName: Full=Girdin; AltName: Full=Akt phosphorylation enhancer; Short=APE; AltName: Full=Coiled-coil domain-containing protein 88A; AltName: Full=G alpha-interacting vesicle-associated protein; Short=GIV; AltName: Full=Girders of actin filament; AltName: Full=Hook-related protein 1; Short=HkRP1;
FUNCTION: Plays a role as a key modulator of the AKT-mTOR signaling pathway controlling the tempo of the process of newborn neurons integration during adult neurogenesis, including correct neuron positioning, dendritic development and synapse formation. Enhances phosphoinositide 3-kinase (PI3K)-dependent phosphorylation and kinase activity of AKT1/PKB, but does not possess kinase activity itself. Phosphorylation of AKT1/PKB thereby induces the phosphorylation of downstream effectors GSK3 and FOXO1/FKHR, and regulates DNA replication and cell proliferation (By similarity). Essential for the integrity of the actin cytoskeleton and for cell migration. Required for formation of actin stress fibers and lamellipodia. May be involved in membrane sorting in the early endosome.
SUBUNIT: Interacts (via C-terminus) with DISC1; the interaction is direct. Interacts with AKT proteins; the interaction is inhibited in presence of DISC1 (By similarity). Homodimer. The non- phosphorylated form interacts with phosphatidylinositol 4- phosphate [PI(4)P] and weakly with phosphatidylinositol 3- phosphate [PI(3)P]. Interacts with microtubules. Interacts with actin through its C-terminal domain. Interacts with the C-terminus of AKT1/PKB.
SUBCELLULAR LOCATION: Membrane. Cell membrane. Cytoplasm, cytosol. Cytoplasmic vesicle. Cell projection, lamellipodium. Note=Localizes to the cell membrane through interaction with phosphoinositides.
TISSUE SPECIFICITY: Expressed ubiquitously.
PTM: Phosphorylation is induced by epidermal growth factor (EGF) in a phosphoinositide 3-kinase (PI3K)-dependent manner. Phosphorylation by AKT1/PKB is necessary for the delocalization from the cell membrane and for cell migration.
SIMILARITY: Belongs to the CCDC88 family.
SEQUENCE CAUTION: Sequence=AAY14932.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAD97945.1; Type=Miscellaneous discrepancy; Note=Intron retention at the C-terminus; Sequence=CAI46020.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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: CCDC88A
Diseases sorted by gene-association score: peho syndrome-like* (1300), peho syndrome* (242)
* = Manually curated disease association

-  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: 15.73 RPKM in Testis
Total median expression: 232.79 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 -322.80777-0.415 Picture PostScript Text
3' UTR -695.103358-0.207 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
IPR008636 - HOOK

Pfam Domains:
PF19047 - HOOK domain

SCOP Domains:
116907 - Hook domain

ModBase Predicted Comparative 3D Structure on Q3V6T2
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0008017 microtubule binding
GO:0035091 phosphatidylinositol binding
GO:0042803 protein homodimerization activity
GO:0043422 protein kinase B binding
GO:0051959 dynein light intermediate chain binding

Biological Process:
GO:0001932 regulation of protein phosphorylation
GO:0006260 DNA replication
GO:0006275 regulation of DNA replication
GO:0007399 nervous system development
GO:0010975 regulation of neuron projection development
GO:0016477 cell migration
GO:0030030 cell projection organization
GO:0030032 lamellipodium assembly
GO:0030705 cytoskeleton-dependent intracellular transport
GO:0031122 cytoplasmic microtubule organization
GO:0031929 TOR signaling
GO:0032148 activation of protein kinase B activity
GO:0032956 regulation of actin cytoskeleton organization
GO:0042127 regulation of cell proliferation
GO:0045724 positive regulation of cilium assembly
GO:0061024 membrane organization
GO:1903566 positive regulation of protein localization to cilium

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005813 centrosome
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030027 lamellipodium
GO:0031252 cell leading edge
GO:0031410 cytoplasmic vesicle
GO:0036064 ciliary basal body
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AB201172 - Homo sapiens GRDN mRNA for girdin, complete cds.
BC132736 - Homo sapiens coiled-coil domain containing 88A, mRNA (cDNA clone MGC:164367 IMAGE:40146758), complete cds.
BC144320 - Homo sapiens coiled-coil domain containing 88A, mRNA (cDNA clone MGC:177857 IMAGE:9052840), complete cds.
AB125644 - Homo sapiens ape mRNA for PKB/Akt-binding protein, complete cds.
BC078168 - Homo sapiens coiled-coil domain containing 88A, mRNA (cDNA clone IMAGE:6176807), partial cds.
AF112218 - Homo sapiens unknown mRNA.
D64159 - Homo sapiens mRNA for hypothetical protein, partial cds.
AK307964 - Homo sapiens cDNA, FLJ97912.
AK024717 - Homo sapiens cDNA: FLJ21064 fis, clone CAS01306, highly similar to AF112218 Homo sapiens unknown mRNA.
BC060037 - Homo sapiens coiled-coil domain containing 88A, mRNA (cDNA clone IMAGE:4108973), partial cds.
BC014905 - Homo sapiens coiled-coil domain containing 88A, mRNA (cDNA clone IMAGE:3910327), containing frame-shift errors.
BC041160 - Homo sapiens coiled-coil domain containing 88A, mRNA (cDNA clone IMAGE:3906864), partial cds.
AK025723 - Homo sapiens cDNA: FLJ22070 fis, clone HEP11687, highly similar to AF112218 Homo sapiens unknown mRNA.
BC045829 - Homo sapiens KIAA1212, mRNA (cDNA clone IMAGE:5263034).
AK124603 - Homo sapiens cDNA FLJ42612 fis, clone BRACE3013780.
BC092515 - Homo sapiens cDNA clone IMAGE:3100728, containing frame-shift errors.
BX538154 - Homo sapiens mRNA; cDNA DKFZp686P1243 (from clone DKFZp686P1243).
BX648138 - Homo sapiens mRNA; cDNA DKFZp686H0346 (from clone DKFZp686H0346).
AB033038 - Homo sapiens mRNA for KIAA1212 protein, partial cds.
BC032683 - Homo sapiens KIAA1212, mRNA (cDNA clone IMAGE:5583156).
BX647874 - Homo sapiens mRNA; cDNA DKFZp313P1821 (from clone DKFZp313P1821).
AK124761 - Homo sapiens cDNA FLJ42771 fis, clone BRAWH3003801.
AK299823 - Homo sapiens cDNA FLJ53516 complete cds.
BX537985 - Homo sapiens mRNA; cDNA DKFZp686D0630 (from clone DKFZp686D0630).
HZ473945 - WO 2016002844-A/59: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
AK001254 - Homo sapiens cDNA FLJ10392 fis, clone NT2RM4000169, weakly similar to INTRACELLULAR PROTEIN TRANSPORT PROTEIN USO1.
HZ473944 - WO 2016002844-A/58: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
BC056885 - Homo sapiens KIAA1212, mRNA (cDNA clone IMAGE:6526320).
HZ473946 - WO 2016002844-A/60: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
JD553899 - Sequence 534923 from Patent EP1572962.
JD431465 - Sequence 412489 from Patent EP1572962.
JD172192 - Sequence 153216 from Patent EP1572962.
HZ473943 - WO 2016002844-A/57: ANTI-INVASIVE/ANTI-METASTATIC DRUG FOR PANCREATIC CANCER CELL.
BC015539 - Homo sapiens KIAA1212, mRNA (cDNA clone IMAGE:3885871).
BC142646 - Homo sapiens cDNA clone IMAGE:40147956, with apparent retained intron.
BC142700 - Homo sapiens cDNA clone IMAGE:40148782, with apparent retained intron.
BC035848 - Homo sapiens, clone IMAGE:5753629, mRNA.
JD090547 - Sequence 71571 from Patent EP1572962.
DQ569996 - Homo sapiens piRNA piR-30108, complete sequence.
JD357989 - Sequence 339013 from Patent EP1572962.
JD554155 - Sequence 535179 from Patent EP1572962.
JD520033 - Sequence 501057 from Patent EP1572962.
JD166874 - Sequence 147898 from Patent EP1572962.
JD383490 - Sequence 364514 from Patent EP1572962.
JD545271 - Sequence 526295 from Patent EP1572962.
JD158318 - Sequence 139342 from Patent EP1572962.
JD406004 - Sequence 387028 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A1IGE7, APE , B7ZM78, C9JG83, ENST00000436346.1, ENST00000436346.2, ENST00000436346.3, ENST00000436346.4, ENST00000436346.5, ENST00000436346.6, GRDN, GRDN_HUMAN, KIAA1212 , NM_001365480, Q3V6T2, Q53SF1, Q581G3, Q5HYD0, Q7Z339, Q7Z3C5, uc320esg.1, uc320esg.2
UCSC ID: ENST00000436346.7_11
RefSeq Accession: NM_001365480.1
Protein: Q3V6T2 (aka GRDN_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.