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

Summary

Official Symbol: Afdnprovided by RGD
Official Full Name: afadin, adherens junction formation factorprovided by RGD
Primary source: RGD:708561
See related: Ensembl:ENSRNOG00000023753 AllianceGenome:RGD:708561
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: Enables LIM domain binding activity. Involved in dendrite arborization; positive regulation of mini excitatory postsynaptic potential; and regulation of cell morphogenesis. Located in adherens junction; axon; and somatodendritic compartment. Colocalizes with excitatory synapse. Orthologous to human AFDN (afadin, adherens junction formation factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 376.1), Lung (RPKM 347.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q12

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (58041065..58170505)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (53905344..54034216)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (53713873..53861918, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study found that afadin undergoes a bi-directional trafficking to both synaptic and nuclear compartment in response to acute 17beta-estradiol (estradiol) treatment, in mixed sex neuronal cultures derived from fetal cortex. Nuclear accumulation of afadin was coincidental with an increase in the phosphorylation of histone H3 at serine 10 (H3S10p). This epigenetic modification is associated with the remodeling of chromatin.
Title: Cyto-nuclear shuttling of afadin is required for rapid estradiol-mediated modifications of histone H3.
Spatiotemporal and dynamic alternative splicing produces differential expression patterns of afadin isoforms and alternative splicing of afadin is controlled by the neuron-specific regulator(s) whose activity is triggered and dynamically altered during neuronal differentiation and maturation.
Title: Dynamic spatiotemporal patterns of alternative splicing of an F-actin scaffold protein, afadin, during murine development.
Short splicing isoform of afadin (s-Afadin) blocks the R-Ras-mediated membrane translocation of long splicing isoform of afadin (l-afadin) and axon branching by inhibiting the binding of l-afadin to R-Ras.
Title: A short splicing isoform of afadin suppresses the cortical axon branching in a dominant-negative manner.
afadin bi-directional shuttling from the cytosol to synapses and the nucleus promotes spine plasticity and histone modifications
Title: Coordinated nuclear and synaptic shuttling of afadin promotes spine plasticity and histone modifications.
afadin is required for the maintenance of dendritic structure and excitatory tone.
Title: Afadin is required for maintenance of dendritic structure and excitatory tone.
Rap1 bimodally regulates spine morphology: activated Rap1 recruits PDZ domain-containing protein AF-6 to plasma membrane and induces spine neck elongation, while inactive Rap1 dissociates AF-6 from membrane and induces spine enlargement.
Title: Activity-dependent dendritic spine structural plasticity is regulated by small GTPase Rap1 and its target AF-6.
AF6/s-afadin is a candidate for mediating control of cellular growth processes by regulated translocation to the nucleus.
Title: AF6/s-afadin is a dual residency protein and localizes to a novel subnuclear compartment.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH143971 (e-PCR)
- UniSTS:233217

RH129198 (e-PCR)
- UniSTS:212506

RH143433 (e-PCR)
- UniSTS:232680

RH129150 (e-PCR)
- UniSTS:212458

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables LIM domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables actin filament binding	ISO Inferred from Sequence Orthology more info
enables cell adhesion molecule binding	IBA Inferred from Biological aspect of Ancestor more info
enables cell adhesion molecule binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adherens junction maintenance	ISO Inferred from Sequence Orthology more info
involved_in bicellular tight junction assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within brain morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion mediated by cadherin	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebral cortex development	ISO Inferred from Sequence Orthology more info
involved_in dendrite arborization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of endothelial intestinal barrier	ISO Inferred from Sequence Orthology more info
involved_in establishment of protein localization to plasma membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within homeostasis of number of cells	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuroepithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in pore complex assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell-cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell-cell adhesion mediated by cadherin	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dendrite extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of dendrite morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of dendritic spine morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mini excitatory postsynaptic potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in postsynaptic specialization organization	IDA Inferred from Direct Assay more info	PubMed
involved_in postsynaptic specialization organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization to cell junction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within radial glial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of oligodendrocyte progenitor proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynapse assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within telencephalon development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	IDA Inferred from Direct Assay more info	PubMed
located_in adherens junction	ISO Inferred from Sequence Orthology more info
located_in apical junction complex	ISO Inferred from Sequence Orthology more info
located_in apical part of cell	ISO Inferred from Sequence Orthology more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell junction	ISO Inferred from Sequence Orthology more info
located_in cell-cell contact zone	ISO Inferred from Sequence Orthology more info
located_in cell-cell junction	IEA Inferred from Electronic Annotation more info
located_in cell-cell junction	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	TAS Traceable Author Statement more info
located_in excitatory synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of pore complex	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic density membrane	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic active zone membrane	ISO Inferred from Sequence Orthology more info
located_in somatodendritic compartment	IDA Inferred from Direct Assay more info	PubMed
located_in tight junction	ISO Inferred from Sequence Orthology more info

General protein information

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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)

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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)

NM_013217.3 → NP_037349.1 afadin

See identical proteins and their annotated locations for NP_037349.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

O35889, O35890

UniProtKB/TrEMBL

A6KS86

Related

ENSRNOP00000088861.1, ENSRNOT00000106034.1

Conserved Domains (6) summary

cd01781
Location:247 → 346

AF6_RA_repeat2; Ubiquitin domain of AT-6, second repeat

cd00060
Location:417 → 499

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:611 → 939

Myo5p-like_CBD_afadin; cargo binding domain of myosin 5-like of afadin

pfam00595
Location:1015 → 1097

PDZ; PDZ domain (Also known as DHR or GLGF)

pfam03064
Location:1599 → 1685

U79_P34; HSV U79 / HCMV P34

cl00155
Location:20 → 131

UBQ; Ubiquitin-like proteins