Dnmbp dynamin binding protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dnmbpprovided by RGD
Official Full Name: dynamin binding proteinprovided by RGD
Primary source: RGD:1583840
See related: EnsemblRapid:ENSRNOG00000050742 AllianceGenome:RGD:1583840
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: Tuba
Summary: Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in cilium assembly and regulation of cell shape. Located in Golgi apparatus and presynapse. Is active in synaptic vesicle. Human ortholog(s) of this gene implicated in cataract 48. Orthologous to human DNMBP (dynamin binding protein). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 52.3), Liver (RPKM 45.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (252685406..252778642, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (242736189..242829431, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (263625503..263718784, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

A deficit in long term memory formation during physiological aging is associated with lower Dnmbp expression.
Title: Dynamin binding protein gene expression and memory performance in aged rats.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IBA Inferred from Biological aspect of Ancestor more info
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

Process	Evidence Code	Pubs
involved_in cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in intracellular signal transduction	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell shape	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	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 stack	IEA Inferred from Electronic Annotation more info
located_in anchoring junction	IEA Inferred from Electronic Annotation 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 cell-cell junction	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in presynapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info
is_active_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: dynamin-binding protein

Names: scaffold protein Tuba

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_001376933.1 → NP_001363862.1 dynamin-binding protein isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I5Y9I1

Conserved Domains (4) summary

cd07589
Location:263 → 454

BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein

cd11798
Location:535 → 591

SH3_DNMBP_C1; First C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd12141
Location:763 → 819

SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains

cd00160
Location:31 → 211

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
NM_001395001.1 → NP_001381930.1 dynamin-binding protein isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

M0R4F8

Related

ENSRNOP00000077401.2, ENSRNOT00000096155.2

Conserved Domains (8) summary

cd07589
Location:1017 → 1208

BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein

cd11794
Location:6 → 56

SH3_DNMBP_N1; First N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11795
Location:70 → 123

SH3_DNMBP_N2; Second N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11796
Location:149 → 199

SH3_DNMBP_N3; Third N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11798
Location:1289 → 1345

SH3_DNMBP_C1; First C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd12141
Location:1517 → 1573

SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains

cd00160
Location:785 → 965

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

cl17036
Location:247 → 296

SH3; Src Homology 3 domain superfamily

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

252685406..252778642 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063264624.1 → XP_063120694.1 dynamin-binding protein isoform X3
XM_039080062.2 → XP_038935990.1 dynamin-binding protein isoform X2

UniProtKB/Swiss-Prot

M0R4F8

Conserved Domains (8) summary

cd07589
Location:1017 → 1208

BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein

cd11794
Location:6 → 56

SH3_DNMBP_N1; First N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11795
Location:70 → 123

SH3_DNMBP_N2; Second N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11796
Location:149 → 199

SH3_DNMBP_N3; Third N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11798
Location:1289 → 1345

SH3_DNMBP_C1; First C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd12141
Location:1517 → 1573

SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains

cd00160
Location:785 → 965

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

cl17036
Location:247 → 296

SH3; Src Homology 3 domain superfamily
XM_039080066.2 → XP_038935994.1 dynamin-binding protein isoform X2

UniProtKB/Swiss-Prot

M0R4F8

Conserved Domains (8) summary

cd07589
Location:1017 → 1208

BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein

cd11794
Location:6 → 56

SH3_DNMBP_N1; First N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11795
Location:70 → 123

SH3_DNMBP_N2; Second N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11796
Location:149 → 199

SH3_DNMBP_N3; Third N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11798
Location:1289 → 1345

SH3_DNMBP_C1; First C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd12141
Location:1517 → 1573

SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains

cd00160
Location:785 → 965

RhoGEF; Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.

cl17036
Location:247 → 296

SH3; Src Homology 3 domain superfamily
XM_008760486.4 → XP_008758708.1 dynamin-binding protein isoform X1

See identical proteins and their annotated locations for XP_008758708.1

UniProtKB/TrEMBL

A0A8L2UNI9

Related

ENSRNOP00000064242.4, ENSRNOT00000074810.5

Conserved Domains (8) summary

cd07589
Location:1029 → 1220

BAR_DNMBP; The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein

cd11794
Location:18 → 68

SH3_DNMBP_N1; First N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11795
Location:82 → 135

SH3_DNMBP_N2; Second N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11796
Location:161 → 211

SH3_DNMBP_N3; Third N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd11798
Location:1301 → 1357

SH3_DNMBP_C1; First C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba

cd12141
Location:1529 → 1585

SH3_DNMBP_C2; Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains

pfam00621
Location:800 → 978

RhoGEF; RhoGEF domain

cl17036
Location:259 → 308

SH3; Src Homology 3 domain superfamily
XM_017590382.3 → XP_017445871.1 dynamin-binding protein isoform X4

UniProtKB/TrEMBL

A0A8I6A777

Related

ENSRNOP00000087128.1, ENSRNOT00000096853.2