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Afdn afadin, adherens junction formation factor [ Rattus norvegicus (Norway rat) ]

Gene ID: 26955, updated on 19-Apr-2019

Summary

Official Symbol
Afdnprovided by RGD
Official Full Name
afadin, adherens junction formation factorprovided by RGD
Primary source
RGD:708561
See related
Ensembl:ENSRNOG00000023753
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Af6; Mllt4
Summary
may play a role in linking the actin cytoskeleton to the plasma membrane [RGD, Feb 2006]
Annotation information
Annotation category: partial on reference assembly
Expression
Biased expression in Kidney (RPKM 376.1), Lung (RPKM 347.6) and 9 other tissues See more
Orthologs

Genomic context

See Afdn in Genome Data Viewer
Location:
1q12
Exon count:
37
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (53713873..53861918, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 1 NC_005100.3 (54955635..55043460, complement)

Chromosome 1 - NC_005100.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102548318 Neighboring gene unc-93 homolog A Neighboring gene similar to Serine/threonine-protein kinase MARK2 (MAP/microtubule affinity-regulating kinase 2) (ELKL motif kinase) (EMK1) (PAR1 homolog) Neighboring gene uncharacterized LOC103690979 Neighboring gene high mobility group protein B1 pseudogene Neighboring gene uncharacterized LOC108348488

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Adherens junction, organism-specific biosystem (from KEGG)
    Adherens junction, organism-specific biosystemCell-cell adherens junctions (AJs), the most common type of intercellular adhesions, are important for maintaining tissue architecture and cell polarity and can limit cell movement and proliferation....
  • Adherens junction, conserved biosystem (from KEGG)
    Adherens junction, conserved biosystemCell-cell adherens junctions (AJs), the most common type of intercellular adhesions, are important for maintaining tissue architecture and cell polarity and can limit cell movement and proliferation....
  • Adherens junctions interactions, organism-specific biosystem (from REACTOME)
    Adherens junctions interactions, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Cell junction organization, organism-specific biosystem (from REACTOME)
    Cell junction organization, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Cell-Cell communication, organism-specific biosystem (from REACTOME)
    Cell-Cell communication, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Cell-cell junction organization, organism-specific biosystem (from REACTOME)
    Cell-cell junction organization, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Leukocyte transendothelial migration, organism-specific biosystem (from KEGG)
    Leukocyte transendothelial migration, organism-specific biosystemLeukocyte migaration from the blood into tissues is vital for immune surveillance and inflammation. During this diapedesis of leukocytes, the leukocytes bind to endothelial cell adhesion molecules (C...
  • Leukocyte transendothelial migration, conserved biosystem (from KEGG)
    Leukocyte transendothelial migration, conserved biosystemLeukocyte migaration from the blood into tissues is vital for immune surveillance and inflammation. During this diapedesis of leukocytes, the leukocytes bind to endothelial cell adhesion molecules (C...
  • Rap1 signaling pathway, organism-specific biosystem (from KEGG)
    Rap1 signaling pathway, organism-specific biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
  • Rap1 signaling pathway, conserved biosystem (from KEGG)
    Rap1 signaling pathway, conserved biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
  • Ras signaling pathway, organism-specific biosystem (from KEGG)
    Ras signaling pathway, organism-specific biosystemThe Ras proteins are GTPases that function as molecular switches for signaling pathways regulating cell proliferation, survival, growth, migration, differentiation or cytoskeletal dynamism. Ras prote...
  • Tight junction, organism-specific biosystem (from KEGG)
    Tight junction, organism-specific biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
  • Tight junction, conserved biosystem (from KEGG)
    Tight junction, conserved biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
  • cAMP signaling pathway, organism-specific biosystem (from KEGG)
    cAMP signaling pathway, organism-specific biosystemcAMP is one of the most common and universal second messengers, and its formation is promoted by adenylyl cyclase (AC) activation after ligation of G protein-coupled receptors (GPCRs) by ligands incl...
  • cAMP signaling pathway, conserved biosystem (from KEGG)
    cAMP signaling pathway, conserved biosystemcAMP is one of the most common and universal second messengers, and its formation is promoted by adenylyl cyclase (AC) activation after ligation of G protein-coupled receptors (GPCRs) by ligands incl...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
LIM domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
Ras GTPase binding ISO
Inferred from Sequence Orthology
more info
PubMed 
actin filament binding ISO
Inferred from Sequence Orthology
more info
PubMed 
cell adhesion molecule binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion molecule binding IEA
Inferred from Electronic Annotation
more info
 
cell adhesion molecule binding ISO
Inferred from Sequence Orthology
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adherens junction maintenance IEA
Inferred from Electronic Annotation
more info
 
adherens junction maintenance ISO
Inferred from Sequence Orthology
more info
PubMed 
bicellular tight junction assembly ISO
Inferred from Sequence Orthology
more info
PubMed 
brain morphogenesis IEA
Inferred from Electronic Annotation
more info
 
brain morphogenesis ISO
Inferred from Sequence Orthology
more info
PubMed 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion mediated by cadherin IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion mediated by cadherin ISO
Inferred from Sequence Orthology
more info
PubMed 
cerebral cortex development IEA
Inferred from Electronic Annotation
more info
 
cerebral cortex development ISO
Inferred from Sequence Orthology
more info
PubMed 
dendrite arborization IMP
Inferred from Mutant Phenotype
more info
PubMed 
establishment of endothelial intestinal barrier ISO
Inferred from Sequence Orthology
more info
PubMed 
establishment of protein localization to plasma membrane IEA
Inferred from Electronic Annotation
more info
 
establishment of protein localization to plasma membrane ISO
Inferred from Sequence Orthology
more info
PubMed 
homeostasis of number of cells IEA
Inferred from Electronic Annotation
more info
 
homeostasis of number of cells ISO
Inferred from Sequence Orthology
more info
PubMed 
negative regulation of cell migration ISO
Inferred from Sequence Orthology
more info
PubMed 
neuroepithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
neuroepithelial cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of GTPase activity ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of cell-cell adhesion ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of cell-cell adhesion mediated by cadherin ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of dendrite extension IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of dendrite morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of dendritic spine morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of mini excitatory postsynaptic potential IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to cell junction IEA
Inferred from Electronic Annotation
more info
 
protein localization to cell junction ISO
Inferred from Sequence Orthology
more info
PubMed 
radial glial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
radial glial cell differentiation ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of oligodendrocyte progenitor proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of oligodendrocyte progenitor proliferation ISO
Inferred from Sequence Orthology
more info
PubMed 
regulation of protein localization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
telencephalon development ISO
Inferred from Sequence Orthology
more info
PubMed 
Component Evidence Code Pubs
adherens junction ISO
Inferred from Sequence Orthology
more info
PubMed 
apical junction complex IEA
Inferred from Electronic Annotation
more info
 
apical junction complex ISO
Inferred from Sequence Orthology
more info
PubMed 
apical part of cell IEA
Inferred from Electronic Annotation
more info
 
apical part of cell ISO
Inferred from Sequence Orthology
more info
PubMed 
axon IDA
Inferred from Direct Assay
more info
PubMed 
cell junction ISO
Inferred from Sequence Orthology
more info
PubMed 
cell-cell adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adherens junction IDA
Inferred from Direct Assay
more info
PubMed 
cell-cell adherens junction IEA
Inferred from Electronic Annotation
more info
 
cell-cell adherens junction ISO
Inferred from Sequence Orthology
more info
PubMed 
cell-cell contact zone ISO
Inferred from Sequence Orthology
more info
PubMed 
cell-cell junction ISO
Inferred from Sequence Orthology
more info
PubMed 
cytoplasm ISO
Inferred from Sequence Orthology
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
cytosol TAS
Traceable Author Statement
more info
 
colocalizes_with excitatory synapse IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IEA
Inferred from Electronic Annotation
more info
 
nuclear speck ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISO
Inferred from Sequence Orthology
more info
 
somatodendritic compartment IDA
Inferred from Direct Assay
more info
PubMed 
tight junction ISO
Inferred from Sequence Orthology
more info
PubMed 

General protein information

Preferred Names
afadin
Names
myeloid/lymphoid or mixed lineage-leukemia translocation to 4 homolog
myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)
myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4
myeloid/lymphoid or mixed-lineage leukemia; translocated to, 4
protein Af-6
translocated to, 4

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_013217.2NP_037349.1  afadin

    See identical proteins and their annotated locations for NP_037349.1

    Status: VALIDATED

    Source sequence(s)
    AA963026, CA511204, CK476731, CN542111, EV767501, U83230
    UniProtKB/Swiss-Prot
    O35889
    Related
    ENSRNOP00000029044.6, ENSRNOT00000032667.7
    Conserved Domains (6) summary
    cd01781
    Location:247346
    AF6_RA_repeat2; Ubiquitin domain of AT-6, second repeat
    cd00060
    Location:417499
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd15471
    Location:611939
    Myo5p-like_CBD_afadin; cargo binding domain of myosin 5-like of afadin
    pfam00595
    Location:10151097
    PDZ; PDZ domain (Also known as DHR or GLGF)
    pfam03064
    Location:15991685
    U79_P34; HSV U79 / HCMV P34
    cl00155
    Location:20131
    UBQ; Ubiquitin-like proteins

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005100.4 Reference Rnor_6.0 Primary Assembly

    Range
    53713873..53861918 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Rn_Celera

Genomic

  1. AC_000069.1 Alternate Rn_Celera

    Range
    50355039..50445230 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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