Adarb1 adenosine deaminase, RNA-specific, B1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Adarb1provided by RGD
Official Full Name: adenosine deaminase, RNA-specific, B1provided by RGD
Primary source: RGD:2033
See related: EnsemblRapid:ENSRNOG00000001227 AllianceGenome:RGD:2033
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Red1; Adar2
Summary: This gene encodes a double-stranded-RNA-specific adenosine deaminase that is involved in editing pre-mRNAs by site-specific conversion of adenosine (A) to inosine (I). Substrates for this enzyme include ionotropic glutamate receptors (GluR2-6) and serotonin receptor (5HT2C). Studies in rodents have shown that this protein can modify its own pre-mRNA by A->I editing to create a novel acceptor splice site, alternative splicing to which results in down regulation of its protein expression. Additional splicing events result in transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression: Biased expression in Brain (RPKM 160.8), Lung (RPKM 110.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (11222171..11350416)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (11222569..11350854)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (11972352..12101022)

Chromosome 20 - NC_086038.1 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 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?

that activity-dependent regulation of ADAR2 proteostasis and GluK2 Q/R editing are key determinants of kainate receptors
Title: ADAR2-mediated Q/R editing of GluK2 regulates kainate receptor upscaling in response to suppression of synaptic activity.
lower levels of ADAR2 in the nucleus of immature neurons than in mature neurons.
Title: Accumulation of nuclear ADAR2 regulates adenosine-to-inosine RNA editing during neuronal development.
The JNK1 pathway may be functionally linked to the nutrient-sensing actions of ADAR2-mediated RNA editing in professional secretory cells.
Title: c-Jun amino-terminal kinase-1 mediates glucose-responsive upregulation of the RNA editing enzyme ADAR2 in pancreatic beta-cells.
Cleaved ADAR2 leads to a decrease or loss of GluR2 editing, which will further result in high Ca2 influx and excitotoxic neuronal death.
Title: Exposure of neurons to excitotoxic levels of glutamate induces cleavage of the RNA editing enzyme, adenosine deaminase acting on RNA 2, and loss of GLUR2 editing.
both sequence and structural elements are required to define adenosine moieties targeted for specific ADAR2-mediated deamination
Title: Structure and sequence determinants required for the RNA editing of ADAR2 substrates.
RNA structure-dependent recognition by the two double-stranded RNA binding motifs of rat ADAR2.
Title: Structure and specific RNA binding of ADAR2 double-stranded RNA binding motifs.
results implicate the carboxy-terminal domain of the large subunit of RNA polymerase II in site-selective RNA editing by ADAR2 and in coordination of editing with alternative splicing.
Title: RNA editing and alternative splicing: the importance of co-transcriptional coordination.
interaction with RNA transcripts containing selective and nonselective editing sites
Title: Biochemical analysis and scanning force microscopy reveal productive and nonproductive ADAR2 binding to RNA substrates.
the nucleolar localization of ADAR2 represents an important mechanism by which RNA editing can be modulated by the sequestration of enzymatic activity from potential RNA substrates in the nucleoplasm
Title: Modulation of RNA editing by functional nucleolar sequestration of ADAR2.
RNA editing by ADAR2 in pancreatic islets and beta-cells is metabolically regulated by nutritional and energy status
Title: RNA editing by ADAR2 is metabolically regulated in pancreatic islets and beta-cells.

Submit: New GeneRIF Correction See all GeneRIFs (11)

General gene information

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Markers

MDB0447 (e-PCR)
- UniSTS:125020

D20Got9 (e-PCR)
- UniSTS:113256

RH131354 (e-PCR)
- UniSTS:214637

BF388249 (e-PCR)
- UniSTS:244878

D10Bwg0447e (e-PCR), detects polymorphism
- UniSTS:141490

UniSTS:259034 (e-PCR)
- UniSTS:259034

Adarb1 (e-PCR), detects polymorphism
- UniSTS:259034

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables adenosine deaminase activity	IEA Inferred from Electronic Annotation more info
enables double-stranded RNA adenosine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded RNA adenosine deaminase activity	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded RNA adenosine deaminase activity	IEA Inferred from Electronic Annotation more info
enables double-stranded RNA adenosine deaminase activity	ISO Inferred from Sequence Orthology more info
enables double-stranded RNA adenosine deaminase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables double-stranded RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded RNA binding	ISS Inferred from Sequence or Structural Similarity 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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables tRNA-specific adenosine deaminase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in RNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
involved_in RNA processing	ISO Inferred from Sequence Orthology more info
involved_in RNA processing	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in adenosine to inosine editing	IBA Inferred from Biological aspect of Ancestor more info
involved_in adenosine to inosine editing	IDA Inferred from Direct Assay more info	PubMed
involved_in adenosine to inosine editing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within adenosine to inosine editing	ISO Inferred from Sequence Orthology more info
involved_in adenosine to inosine editing	ISO Inferred from Sequence Orthology more info
involved_in adenosine to inosine editing	ISS Inferred from Sequence or Structural Similarity more info
involved_in base conversion or substitution editing	IDA Inferred from Direct Assay more info	PubMed
involved_in base conversion or substitution editing	ISO Inferred from Sequence Orthology more info
involved_in facial nerve morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within facial nerve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in hypoglossal nerve morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hypoglossal nerve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in innervation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within innervation	ISO Inferred from Sequence Orthology more info
involved_in mRNA modification	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in motor behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within motor behavior	ISO Inferred from Sequence Orthology more info
involved_in motor neuron apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within motor neuron apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
involved_in muscle tissue morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within muscle tissue morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell migration	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuromuscular process controlling posture	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuromuscular process controlling posture	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular synaptic transmission	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuromuscular synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of viral genome replication	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of viral genome replication	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral genome replication	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in spinal cord ventral commissure morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within spinal cord ventral commissure morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in synapse	IEA Inferred from Electronic Annotation more info
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: double-stranded RNA-specific editase 1

Names: RNA editing deaminase of glutamate receptors; RNA-editing deaminase 1; RNA-editing enzyme 1; double stranded RNA specific deaminase RED1; dsRNA adenosine deaminase

NP_001104525.1

EC 3.5.4.37

NP_001104526.1

EC 3.5.4.37

NP_001104527.1

EC 3.5.4.37

NP_037026.2

EC 3.5.4.37

XP_006256337.1

EC 3.5.4.37

XP_006256338.1

EC 3.5.4.37

XP_038954379.1

EC 3.5.4.37

XP_038954382.1

EC 3.5.4.37

XP_063135046.1

EC 3.5.4.37

XP_063135047.1

EC 3.5.4.37

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_001111055.1 → NP_001104525.1 double-stranded RNA-specific editase 1 isoform 2

See identical proteins and their annotated locations for NP_001104525.1

Status: REVIEWED

Description

Transcript Variant: This variant (2, also referred to as 2a) uses an alternate, in-frame donor splice site at one of the internal coding exons, compared to transcript variant 1. This results in a shorter isoform (2), missing a 10 aa segment found in isoform 1.

Source sequence(s)

BF388249, CB556744, CB576423, CB720085, CB801553, CK840559, JAXUCZ010000020, U43534

UniProtKB/Swiss-Prot

P51400

UniProtKB/TrEMBL

A6JK91

Related

ENSRNOP00000099902.1, ENSRNOT00000145951.1

Conserved Domains (3) summary

cd19895
Location:75 → 146

DSRM_RED1_rpt1; first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

cd19898
Location:232 → 301

DSRM_RED1_rpt2; second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

pfam02137
Location:370 → 691

A_deamin; Adenosine-deaminase (editase) domain
NM_001111056.1 → NP_001104526.1 double-stranded RNA-specific editase 1 isoform 3

See identical proteins and their annotated locations for NP_001104526.1

Status: REVIEWED

Description

Transcript Variant: This variant (3, also referred to as 2f) results from an auto RNA editing event (AA->AI) in the intronic sequence that creates a novel acceptor splice site, splicing to which inserts 47 nt into the coding region causing a frame-shift, compared to transcript variant 1. Translation initiation from the upstream AUG will result in a very short protein of 82 aa. However, studies reported in PMID:10331393 show that leaky translation initiation from an in-frame, downstream AUG allows some protein expression, and that this isoform (3) exhibits RNA editing activity. Isoform 3 is 24 aa shorter at the N-terminus compared to isoform 1.

Source sequence(s)

BF388249, CB576423, CB801553, CK840559, JAXUCZ010000020, U43534

UniProtKB/Swiss-Prot

P51400

UniProtKB/TrEMBL

A6JK94

Related

ENSRNOP00000001642.8, ENSRNOT00000001642.8

Conserved Domains (3) summary

smart00552
Location:298 → 684

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd19895
Location:51 → 122

DSRM_RED1_rpt1; first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

cd19898
Location:208 → 277

DSRM_RED1_rpt2; second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins
NM_001111057.1 → NP_001104527.1 double-stranded RNA-specific editase 1 isoform 4

See identical proteins and their annotated locations for NP_001104527.1

Status: REVIEWED

Description

Transcript Variant: This variant (4, also referred to as 2e) results from an auto RNA editing event (AA->AI) in the intronic sequence that creates a novel acceptor splice site, splicing to which inserts 47 nt into the coding region causing a frame-shift, compared to transcript variant 2. Translation initiation from the upstream AUG will result in a very short protein of 82 aa. However, studies reported in PMID:10331393 show that leaky translation initiation from an in-frame, downstream AUG allows some protein expression, and that this isoform (3) exhibits RNA editing activity. Isoform 4 is 24 aa shorter at the N-terminus compared to isoform 2.

Source sequence(s)

BF388249, CB556744, CB576423, CB801553, CK840559, JAXUCZ010000020, U43534

UniProtKB/TrEMBL

A6JK93, A6JK95

Conserved Domains (2) summary

smart00552
Location:298 → 674

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd00048
Location:55 → 118

DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
NM_012894.2 → NP_037026.2 double-stranded RNA-specific editase 1 isoform 1

See identical proteins and their annotated locations for NP_037026.2

Status: REVIEWED

Description

Transcript Variant: This variant (1, also referred to as 2b) encodes the longest isoform (1).

Source sequence(s)

BF388249, CB576423, CB720085, CB801553, CK840559, JAXUCZ010000020, U43534

UniProtKB/Swiss-Prot

P51400

UniProtKB/TrEMBL

A6JK92

Conserved Domains (3) summary

smart00552
Location:322 → 708

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd19895
Location:75 → 146

DSRM_RED1_rpt1; first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

cd19898
Location:232 → 301

DSRM_RED1_rpt2; second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

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_086038.1 Reference GRCr8

Range

11222171..11350416

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006256275.5 → XP_006256337.1 double-stranded RNA-specific editase 1 isoform X1

UniProtKB/Swiss-Prot

P51400

Conserved Domains (2) summary

smart00552
Location:386 → 772

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd00048
Location:143 → 206

DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
XM_006256276.5 → XP_006256338.1 double-stranded RNA-specific editase 1 isoform X2

UniProtKB/Swiss-Prot

P51400

UniProtKB/TrEMBL

A0A0G2JUX0

Conserved Domains (2) summary

smart00552
Location:386 → 762

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd00048
Location:143 → 206

DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
XM_039098454.2 → XP_038954382.1 double-stranded RNA-specific editase 1 isoform X6

UniProtKB/Swiss-Prot

P51400

UniProtKB/TrEMBL

A6JK92

Conserved Domains (3) summary

smart00552
Location:322 → 708

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd19895
Location:75 → 146

DSRM_RED1_rpt1; first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

cd19898
Location:232 → 301

DSRM_RED1_rpt2; second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins
XM_039098451.2 → XP_038954379.1 double-stranded RNA-specific editase 1 isoform X5

UniProtKB/TrEMBL

G3V649

Related

ENSRNOP00000069261.3, ENSRNOT00000083851.3

Conserved Domains (3) summary

smart00552
Location:328 → 714

ADEAMc; tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase)

cd19895
Location:81 → 152

DSRM_RED1_rpt1; first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins

cd19898
Location:238 → 307

DSRM_RED1_rpt2; second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins
XM_063278976.1 → XP_063135046.1 double-stranded RNA-specific editase 1 isoform X3

UniProtKB/TrEMBL

A6JK94
XM_063278977.1 → XP_063135047.1 double-stranded RNA-specific editase 1 isoform X4

UniProtKB/TrEMBL

A6JK95