Dnm1 dynamin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dnm1provided by RGD
Official Full Name: dynamin 1provided by RGD
Primary source: RGD:71096
See related: Ensembl:ENSRNOG00000033835 AllianceGenome:RGD:71096
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: Dnm
Summary: Enables several functions, including D2 dopamine receptor binding activity; SH3 domain binding activity; and nitric-oxide synthase binding activity. Involved in G protein-coupled receptor internalization; positive regulation of synaptic vesicle endocytosis; and response to amyloid-beta. Located in several cellular components, including Golgi apparatus; synaptic vesicle; and varicosity. Part of protein-containing complex. Is active in presynaptic endocytic zone membrane. Biomarker of Alzheimer's disease. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 31. Orthologous to human DNM1 (dynamin 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 601.1), Adrenal (RPKM 55.1) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3p12

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (36002535..36055220, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (15604782..15648654, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (11338081..11382043, complement)

Chromosome 3 - NC_086021.1 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?

brain-derived neurotrophic factor arrests the rephosphorylation of the endocytosis enzyme dynamin I via an inhibition of glycogen synthase kinase 3.
Title: Control of synaptic vesicle endocytosis by an extracellular signalling molecule.
dynamin isoforms select appropriate vesicle reuse pathways associated with specific neuronal firing patterns
Title: Dynamin isoforms decode action potential firing for synaptic vesicle recycling.
Dynamin was identified as a septin-binding protein within neuronal membrane raft.
Title: Identification of dynamin as a septin-binding protein.
Compared to endophilinI/II, the interaction between dynamin I and endophilin III is significantly increased in clathrin-mediated endocytosis.
Title: Endophilin isoforms have distinct characteristics in interactions with N-type Ca2+ channels and dynamin I.
Phosphorylation and nitration of tyrosine residues affect functional properties of Synaptophysin and Dynamin I.
Title: Phosphorylation and nitration of tyrosine residues affect functional properties of Synaptophysin and Dynamin I, two proteins involved in exo-endocytosis of synaptic vesicles.
EHD1 inhibits dynamin-induced membrane tubulation in the presence of GTPgammaS, a phenomenon linked with dynamin helix assembly in synaptic vesicles.
Title: Regulation of synaptic vesicle budding and dynamin function by an EHD ATPase.
Ca(2+) influx regulates assembly of a fully active CaN-calmodulin complex selectively on the tail of dynIxb and the complex is recruited to sites of activity-dependent bulk endocytosis in nerve terminals
Title: Calcineurin selectively docks with the dynamin Ixb splice variant to regulate activity-dependent bulk endocytosis.
In a rat model of Alzheimer's disease, a decrease of dynamin I in hippocampal neurons is found at protein and mRNA levels.
Title: Changed clathrin regulatory proteins in the brains of Alzheimer's disease patients and animal models.
The deformation dynamics of dynamin is dominated by the draining of the membrane out of the helix, allowing quantification of helix-membrane interactions.
Title: Deformation of dynamin helices damped by membrane friction.
These results suggest that Abeta oligomers induce memory impairment via dynamin 1 degradation, which may imply that dynamin 1 degradation is one of the causes of synaptic dysfunction in Alzheimer's disease.
Title: Dynamin 1 depletion and memory deficits in rats treated with Abeta and cerebral ischemia.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Dnm1 (e-PCR), detects polymorphism
- UniSTS:531529

BF386076 (e-PCR)
- UniSTS:243567

AW533536 (e-PCR)
- UniSTS:245985

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables D2 dopamine receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables GDP binding	IEA Inferred from Electronic Annotation more info
enables GDP binding	ISO Inferred from Sequence Orthology more info
enables GDP binding	ISS Inferred from Sequence or Structural Similarity more info
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IEA Inferred from Electronic Annotation more info
enables GTPase activity	ISO Inferred from Sequence Orthology more info
enables GTPase activity	ISS Inferred from Sequence or Structural Similarity more info
enables GTPase activity	TAS Traceable Author Statement more info
enables SH3 domain binding	IDA Inferred from Direct Assay more info	PubMed
enables SH3 domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	TAS Traceable Author Statement more info	PubMed
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables nitric-oxide synthase binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphatidylinositol-3,4,5-trisphosphate binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-3,4,5-trisphosphate binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol-4,5-bisphosphate binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-4,5-bisphosphate binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol-4,5-bisphosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein kinase binding	IEA Inferred from Electronic Annotation more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein serine/threonine kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor internalization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within adult locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in clathrin coat assembly involved in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in clathrin coat assembly involved in endocytosis	ISO Inferred from Sequence Orthology more info
involved_in clathrin coat assembly involved in endocytosis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within endocytosis	ISO Inferred from Sequence Orthology more info
involved_in endocytosis	ISO Inferred from Sequence Orthology more info
involved_in endosome organization	IEA Inferred from Electronic Annotation more info
involved_in endosome organization	ISO Inferred from Sequence Orthology more info
involved_in modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in modulation of chemical synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic vesicle endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synaptic vesicle recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein homooligomerization	ISO Inferred from Sequence Orthology more info
involved_in protein homotetramerization	IEA Inferred from Electronic Annotation more info
involved_in protein homotetramerization	ISO Inferred from Sequence Orthology more info
involved_in protein homotetramerization	ISS Inferred from Sequence or Structural Similarity more info
involved_in receptor internalization	IBA Inferred from Biological aspect of Ancestor more info
involved_in receptor internalization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis	ISO Inferred from Sequence Orthology more info
involved_in receptor-mediated endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic vesicle endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of vesicle size	IEA Inferred from Electronic Annotation more info
involved_in regulation of vesicle size	ISO Inferred from Sequence Orthology more info
involved_in regulation of vesicle size	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to amyloid-beta	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within synaptic transmission, GABAergic	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle budding from presynaptic endocytic zone membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle budding from presynaptic endocytic zone membrane	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle budding from presynaptic endocytic zone membrane	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	ISO Inferred from Sequence Orthology more info
involved_in vesicle scission	IEA Inferred from Electronic Annotation more info
involved_in vesicle scission	ISO Inferred from Sequence Orthology more info
involved_in vesicle scission	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
located_in chromaffin granule	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated pit	ISS Inferred from Sequence or Structural Similarity more info
located_in clathrin-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in endocytic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
part_of membrane coat	IEA Inferred from Electronic Annotation more info
part_of membrane coat	ISO Inferred from Sequence Orthology more info
is_active_in microtubule	IBA Inferred from Biological aspect of Ancestor more info
located_in microtubule	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	ISO Inferred from Sequence Orthology more info
located_in photoreceptor ribbon synapse	IEA Inferred from Electronic Annotation more info
is_active_in photoreceptor ribbon synapse	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in presynapse	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic endocytic zone membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic endocytic zone membrane	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic endocytic zone membrane	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in varicosity	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: dynamin-1

Names: B-dynamin; D100; dynamin I; dynamin, brain

NP_542420.1

EC 3.6.5.5

XP_038960069.1

EC 3.6.5.5

XP_038960070.1

EC 3.6.5.5

XP_038960071.1

EC 3.6.5.5

XP_038960072.1

EC 3.6.5.5

XP_038960073.1

EC 3.6.5.5

XP_038960075.1

EC 3.6.5.5

XP_038960076.1

EC 3.6.5.5

XP_038960079.1

EC 3.6.5.5

XP_063139089.1

EC 3.6.5.5

XP_063139090.1

EC 3.6.5.5

XP_063139092.1

EC 3.6.5.5

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_080689.5 → NP_542420.1 dynamin-1

See identical proteins and their annotated locations for NP_542420.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A0A8L2QKR5

Related

ENSRNOP00000060845.3, ENSRNOT00000064039.5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03378
Location:752 → 844

PHA03378; EBNA-3B; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector 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_086021.1 Reference GRCr8

Range

36002535..36055220 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063283019.1 → XP_063139089.1 dynamin-1 isoform X2
XM_039104148.2 → XP_038960076.1 dynamin-1 isoform X7

UniProtKB/TrEMBL

A0A8I6ALW7, A0A8L2QKR5

Related

ENSRNOP00000095659.1

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:743 → 860

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:514 → 625

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:653 → 741

GED; Dynamin GTPase effector domain
XM_039104143.2 → XP_038960071.1 dynamin-1 isoform X4

UniProtKB/TrEMBL

A0A8L2QKR5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain

NF033913
Location:710 → 863

fibronec_FbpA; LPXTG-anchored fibronectin-binding protein FbpA
XM_039104141.2 → XP_038960069.1 dynamin-1 isoform X1

UniProtKB/TrEMBL

A0A8I6AHJ0, A0A8L2QKR5

Related

ENSRNOP00000092707.1

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:747 → 864

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
XM_039104145.2 → XP_038960073.1 dynamin-1 isoform X6

UniProtKB/TrEMBL

A0A8L2QKR5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:747 → 844

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
XM_039104147.2 → XP_038960075.1 dynamin-1 isoform X8

UniProtKB/TrEMBL

A0A8L2QKR5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:743 → 860

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:514 → 625

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:653 → 741

GED; Dynamin GTPase effector domain
XM_039104142.2 → XP_038960070.1 dynamin-1 isoform X3

UniProtKB/TrEMBL

A0A8L2QKR5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain

NF033913
Location:710 → 863

fibronec_FbpA; LPXTG-anchored fibronectin-binding protein FbpA
XM_039104144.2 → XP_038960072.1 dynamin-1 isoform X5

UniProtKB/Swiss-Prot

P21575

UniProtKB/TrEMBL

A0A8L2QKR5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:747 → 844

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
XM_039104151.2 → XP_038960079.1 dynamin-1 isoform X9

UniProtKB/TrEMBL

A0A8L2QKR5

Related

ENSRNOP00000041582.6

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03378
Location:752 → 844

PHA03378; EBNA-3B; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
XM_063283020.1 → XP_063139090.1 dynamin-1 isoform X10
XM_063283022.1 → XP_063139092.1 dynamin-1 isoform X11