Psd pleckstrin and Sec7 domain containing [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Psdprovided by RGD
Official Full Name: pleckstrin and Sec7 domain containingprovided by RGD
Primary source: RGD:620297
See related: EnsemblRapid:ENSRNOG00000019435 AllianceGenome:RGD:620297
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: EFA6
Summary: Predicted to enable guanyl-nucleotide exchange factor activity. Involved in maintenance of postsynaptic density structure; neuron differentiation; and regulation of postsynapse assembly. Is active in glutamatergic synapse. Orthologous to human PSD (pleckstrin and Sec7 domain containing). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 240.5) and Uterus (RPKM 24.9) See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (255114703..255130151, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (245173279..245188681, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (266059331..266074774, 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?

EFA6A, an Exchange Factor for Arf6, Regulates NGF-Dependent TrkA Recycling From Early Endosomes and Neurite Outgrowth in PC12 Cells.
Title: EFA6A, an Exchange Factor for Arf6, Regulates NGF-Dependent TrkA Recycling From Early Endosomes and Neurite Outgrowth in PC12 Cells.
EFA6 regulates selective polarized transport and axon regeneration from the axon initial segment.
Title: EFA6 regulates selective polarised transport and axon regeneration from the axon initial segment.
EFA6A could participate in neuronal morphogenesis through the regulated expression of two functionally distinct isoforms.
Title: EFA6A encodes two isoforms with distinct biological activities in neuronal cells.
There is definitive evidence for somatodendritic localization of EFA6 mRNA in both cultured and in vivo hippocampal neurons: during postnatal development, it is dramatically increased.
Title: Somatodendritic localization of the mRNA for EFA6A, a guanine nucleotide exchange protein for ARF6, in rat hippocampus and its involvement in dendritic formation.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables guanine nucleotide transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables guanyl-nucleotide exchange factor activity	IEA Inferred from Electronic Annotation more info
enables guanyl-nucleotide exchange factor activity	ISO Inferred from Sequence Orthology more info
enables guanyl-nucleotide exchange factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables phospholipid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in guanine nucleotide transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in guanine transport	TAS Traceable Author Statement more info	PubMed
involved_in maintenance of postsynaptic density structure	IDA Inferred from Direct Assay more info	PubMed
involved_in maintenance of postsynaptic density structure	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in regulation of ARF protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cleavage furrow	IEA Inferred from Electronic Annotation more info
located_in cleavage furrow	ISO Inferred from Sequence Orthology more info
located_in cleavage furrow	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	IEA Inferred from Electronic Annotation more info
located_in dendritic spine	ISO Inferred from Sequence Orthology more info
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
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density, intracellular component	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density, intracellular component	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density, intracellular component	ISO Inferred from Sequence Orthology more info
located_in ruffle membrane	IEA Inferred from Electronic Annotation more info
located_in ruffle membrane	ISO Inferred from Sequence Orthology more info
located_in ruffle membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: PH and SEC7 domain-containing protein 1

Names: exchange factor for ADP-ribosylation factor guanine nucleotide factor 6; exchange factor for ARF6 A; pleckstrin homology and SEC7 domain-containing protein 1

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_134370.2 → NP_599197.2 PH and SEC7 domain-containing protein 1

See identical proteins and their annotated locations for NP_599197.2

Status: PROVISIONAL

Source sequence(s)

CH473986

UniProtKB/TrEMBL

A6JHM0, G3V8J5

Related

ENSRNOP00000026378.4, ENSRNOT00000026378.6

Conserved Domains (3) summary

cd00171
Location:541 → 707

Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...

cd13295
Location:752 → 876

PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

pfam00169
Location:756 → 864

PH; PH domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086019.1 Reference GRCr8

Range

255114703..255130151 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006231432.5 → XP_006231494.1 PH and SEC7 domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006231494.1

UniProtKB/TrEMBL

A6JHM0, G3V8J5

Conserved Domains (3) summary

cd00171
Location:541 → 707

Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...

cd13295
Location:752 → 876

PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

pfam00169
Location:756 → 864

PH; PH domain
XM_008760396.4 → XP_008758618.1 PH and SEC7 domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_008758618.1

UniProtKB/TrEMBL

A6JHM0, G3V8J5

Conserved Domains (3) summary

cd00171
Location:541 → 707

Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...

cd13295
Location:752 → 876

PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

pfam00169
Location:756 → 864

PH; PH domain
XM_008760394.4 → XP_008758616.1 PH and SEC7 domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_008758616.1

UniProtKB/TrEMBL

A6JHM0, G3V8J5

Conserved Domains (3) summary

cd00171
Location:541 → 707

Sec7; Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor ...

cd13295
Location:752 → 876

PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain

pfam00169
Location:756 → 864

PH; PH domain
XM_063275990.1 → XP_063132060.1 PH and SEC7 domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A6JHM0
XM_063276038.1 → XP_063132108.1 PH and SEC7 domain-containing protein 1 isoform X3
XM_039089045.2 → XP_038944973.1 PH and SEC7 domain-containing protein 1 isoform X2

Related

ENSRNOP00000094064.2, ENSRNOT00000111594.2

Conserved Domains (1) summary

cd13295
Location:279 → 403

PH_EFA6; Exchange Factor for ARF6 Pleckstrin homology (PH) domain