FlyBase Gene Report: Dmel\tRNA:iMet-CAT-1-3

General Information

Symbol

Dmel\tRNA:iMet-CAT-1-3

Species

D. melanogaster

Name

transfer RNA:initiator Methionine-CAT 1-3

Annotation Symbol

CR32482

Feature Type

tRNA_gene

FlyBase ID

FBgn0052482

Gene Model Status

Current

Stock Availability

None publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

tRNA_i^Met, tRNA:M-i:61D , initiator methionine tRNA

Key Links

Genomic Location

Cytogenetic map

61C9-61C9

Sequence location

3L:743,723..743,794 [-]

Recombination map

3-0.5

RefSeq locus

NT_037436 REGION:743723..743794

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (4 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables AUG codon-amino acid adaptor activity

inferred from sequence model

(Chan and Lowe, 2016)

enables triplet codon-amino acid adaptor activity

inferred from electronic annotation with Rfam:RF00005

(RNAcentral, 2018-)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in translation

inferred by curator from GO:0033436

(Chan and Lowe, 2016)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in cytosol

inferred by curator from GO:0033436

(Chan and Lowe, 2016)

Gene Group (FlyBase)

CYTOSOLIC METHIONINE-CAT TRANSFER RNAS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

CYTOSOLIC METHIONINE-CAT TRANSFER RNAS -: tRNAs with the CAT anticodon recognize the AUG codon, which codes for methionine. (Adapted from GO:0033436.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\tRNA:iMet-CAT-1-3 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure

RNA 2D structure (Predicted by RNAcentral) (RNAcentral entry URS000061EA1A)

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

tRNA:iMet-CAT-1-3-RA

FBtr0072600

Additional Transcript Data and Comments

Reported size (kB)

0.039 (unknown)

(Kikuchi et al., 1990)

Comments

External Data

Crossreferences

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\tRNA:iMet-CAT-1-3 using the Feature Mapper tool.

External Data

Crossreferences

Linkouts

Expression Data

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

NA

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\tRNA:iMet-CAT-1-3 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\tRNA:iMet-CAT-1-3

View exonic expression by tissue for Dmel\tRNA:iMet-CAT-1-3

Bulk Downloads

RNA-Seq RPKM values for all genes

Reference

See Gelbart and Emmert, 2013 for analysis details and data files for all genes.

Developmental Proteome: Life Cycle

Developmental Proteome: Embryogenesis

External Data and Images

Linkouts

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3771740/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0052482

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0052482

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 0 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 2 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of tRNA:iMet-CAT-1-3

Transgenic constructs containing regulatory region of tRNA:iMet-CAT-1-3

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)Exel6085

(Ryder, 2004.4.26)

Inferred from location ( 12 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Other Phenotypes

Allele

abnormal developmental rate

tRNA:iMet-CAT-1-3^+tRa

abnormal size

tRNA:iMet-CAT-1-3^A37G

increased body size | pupal stage

tRNA:iMet-CAT-1-3^+tRa

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (0)

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (0)

Mus musculus (laboratory mouse) (0)

Xenopus tropicalis (Western clawed frog) (0)

Danio rerio (Zebrafish) (0)

Caenorhabditis elegans (Nematode, roundworm) (0)

Anopheles gambiae (African malaria mosquito) (0)

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:tRNA:iMet-CAT-1-3. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (4)

1 of 13

1 of 13

1 of 13

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 0 )

Allele

Disease

Interaction

References

Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)

Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.

Homo sapiens (Human)

Gene name

Score

OMIM

OMIM Phenotype

DO term

Complementation?

Transgene?

Functional Complementation Data

Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.

Interactions

Summary of Physical Interactions

esyN Network Diagram

Other Interaction Browsers

Summary of Genetic Interactions

esyN Network Diagram

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

esyN Network Key:

Suppression

Enhancement

Other Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

tRNA:iMet-CAT-1-3

suppressible

InR

(Rideout et al., 2012)

tRNA:iMet-CAT-1-3

suppressible

RpS3

(Rideout et al., 2012)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

tRNA charging

External Data

Linkouts

Class of Gene

nuclear_gene

(Lowe, 2002)

tRNA_gene

(Lowe, 2002)

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-0.5

Cytogenetic map

61C9-61C9

Sequence location

3L:743,723..743,794 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

61C9-61C9

Limits computationally determined from genome sequence between P{PZ}l(3)05967⁰⁵⁹⁶⁷ and P{PZ}l(3)02640⁰²⁶⁴⁰

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

61D1-61D2

(determined by in situ hybridisation)

(Sharp et al., 1981)

Experimentally Determined Recombination Data

Location

3-0.5

(FlyBase, 2016)

3-0.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (0)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Genomic Clones (5)

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (0)

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

New annotation (CR32482) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

tRNA gene: amino acid=Met, anticodon=CAT.

(FlyBase, 1996-)

RNA component of E.coli RNase P (M1RNA) cleaves a synthetic tRNA:M-i:61D precursor at several sites within the mature tRNA sequence in vitro. Hyperprocessing of tRNA at a site between nucleotides 39 and 40 produces a tRNA fragment needed for copia retrotransposition.

(Kikuchi et al., 1990)

Relationship to Other Genes

Source for database merge of

Source for merge of: tRNA:M-i:61Da tRNA:M-i:61Db tRNA:M3:61Dd tRNA:M3:61De tRNA:M3:61Df tRNA:M3:61Dg CR32482 tRNA:M:CAT:AE002584-b

(FlyBase, 1996-)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: tRNA:iMet-CAT-1-3 tRNA:M-i:61D

(Marygold and Lowe, 2016.1.20)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (32)

Reported As

Symbol Synonym

AE002584.trna21-MetCAT

(Lowe, 2002)

CR32482

(Göktaş et al., 2017, Rojas-Benitez et al., 2015)

RNA:M-i:61D

(Rojas-Benitez et al., 2015)

chr3L.trna49-MetCAT

(Lowe and Chan, 2013)

tRNA-iMet-CAT-1-3

(Lowe and Chan, 2016)

tRNA:M-i

tRNA:M-i:61D

(Zhang et al., 2007)

tRNA:M-i:61Da

tRNA:M-i:61Db

tRNA:M3:61Dd

tRNA:M3:61De

tRNA:M3:61Df

tRNA:M3:61Dg

tRNA:M:CAT:AE002584-b

tRNA:iMet-CAT-1-3

(Marygold et al., 2022, Marygold and Lowe, 2016.1.20)

tRNA:met-i

tRNA:met-i:61Da

tRNA:met-i:61Db

tRNA:met3:61Dd

tRNA:met3:61De

tRNA:met3:61Df

tRNA:met3:61Dg

tRNA_i^Met

(Rojas-Benitez et al., 2015, Rideout et al., 2012, Kikuchi and Sasaki, 1992, Kikuchi et al., 1990)

tRNA^Met-ATG

(Schaefer et al., 2010)

Name Synonyms

initiator methionine tRNA

(Rideout et al., 2012, Kikuchi and Sasaki, 1992)

tRNA:M-i:61D

transfer RNA:initiator Methionine-CAT 1-3

(Marygold and Lowe, 2016.1.20)

transfer RNA:met-i:61Da

transfer RNA:met-i:61Db

transfer RNA:met3:61Dd

transfer RNA:met3:61De

transfer RNA:met3:61Df

transfer RNA:met3:61Dg

Secondary FlyBase IDs

FBgn0003813
FBgn0004314
FBgn0011911
FBgn0011913
FBgn0011914
FBgn0011923
FBgn0011924
FBgn0011925
FBgn0011926
FBgn0060146

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 15 )

Sequence Crossreferences

NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.

3771740

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

RNAcentral - A comprehensive ncRNA sequence collection representing all ncRNA types from a broad range of organisms

URS000061EA1A_7227

Other crossreferences

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3771740/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0052482

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0052482

FlyMine - An integrated database for Drosophila genomics

FBgn0052482

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CR32482

MARRVEL_MODEL - MARRVEL (model organism gene)

3771740

Linkouts

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0052482

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

tRNA charging

GtRNAdb - Genomic tRNA Database: tRNA gene predictions from tRNAscan-SE analysis of complete genomes

tRNA-iMet-CAT-1-3

References (28)

The following external sites may use different assemblies or annotations than FlyBase.

NA

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