Gene Dmel\tRNA:N5:42Af

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General Information

Symbol

Dmel\tRNA:N5:42Af

Species

D. melanogaster

Name

transfer RNA:asn5:42Af

Annotation symbol

CR33973

Feature type

tRNA_gene

FlyBase ID

FBgn0011936

Gene Model Status

Current

Stock availability

None publicly available

Also Known As

Asn6

Genomic Location

Chromosome (arm)

Recombination map

2-[55.2]

Cytogenetic map

42A12-42A12

Sequence location

2R:2,041,011..2,041,084 [-]

Genomic Maps

Select View:

Summary Information

Automatically generated summary

See sections below for more information

The gene transfer RNA:asn5:42Af is referred to in FlyBase by the symbol Dmel\tRNA:N5:42Af (CR33973, FBgn0011936). It is a tRNA_gene from Drosophila melanogaster. Based on sequence similarity, it is predicted to have molecular function: AAC codon-amino acid adaptor activity. It is reported to be involved in the biological process: translation. No alleles are reported. It has one annotated transcript. Summary of modENCODE Temporal Expression Profile: No expression detected at any stage of development. CAVEAT: These RNA-Seq temporal profiles depend upon RNA-Seq reads that are uniquely placed in the genome. For this reason, genes such as histones, Stellates and many classes of RNA genes that are present in multiple exact or near exact copies in the genome, expression levels may be reported as much lower than their true values. Summary of FlyAtlas Anatomical Expression Data: No FlyAtlas data available because no Affy2 ProbeSet aligns to an exon of tRNA:N5:42Af. Comments on Affy2 ProbeSet: No relevant information because no Affy2 ProbeSet aligns to an exon of tRNA:N5:42Af. Gene sequence location is 2R:2041011..2041084.

User Contributed Data

Beta version, feedback welcome

Recent Updates

Description

What does this section display?

This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms).

What does this section not display?

This section does not currently display links that were removed or gene model changes.

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FB2013_03

FB2013_02

All updates

Click here to see a list of all updates to this record from FB2010_08 and on.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

42A12-42A12

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

2-[55.2]

Left of (cM)

Right of (cM)

Notes

Gene Model & Products

Please see the GBrowse view of Dmel\tRNA:N5:42Af for information on other features

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

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

tRNA:N5:42Af-RA

FBtr0100016

Additional Transcript Data & Comments

Reported size (kB)

Comments

External Data

Crossreferences

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Name

AC007121

M14848

Mapped Features

Mapped Features have been reorganized, please see this article for details.

Additional mapped features and mutations can be found on GBrowse or related reports.

Type

Symbol & Location

Additional Notes

References

External Data

Linkouts

Crossreferences

Expression Data

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

Reference

See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.

FlyAtlas Anatomy Microarray

FlyAtlas Anatomical Expression Data (Chintapalli et al., 2007)

modENCODE Anatomy RNA-Seq

modENCODE Development RNA-Seq

modENCODE Temporal Expression Data (Graveley et al., 2011)

modENCODE Cell Lines RNA-Seq

modENCODE Treatments RNA-Seq

Expression Clusters

External Data & Images

Linkouts

Alleles & Phenotypes

Summary of Allele Phenotypes

Phenotype manifest in

Allele

Classical Alleles ( 0 )

For All Classical Alleles Show

Allele of tRNA:N5:42Af	Class	Mutagen	Stocks	Known lesion

Alleles Carried on Transgenic Constructs ( 0 )

For All Alleles Carried on Transgenic Constructs Show

Allele of tRNA:N5:42Af	Class	Mutagen	Stocks	Known lesion

Aneuploid Aberrations

Transgenic Constructs & Insertions

Transgenic Constructs

Type of construct

Name

Expression data

Insertions

Type of insertions

Name

Expression data

Gene Ontology: Function, Process & Cellular Component ( 4 unique terms )

Terms Based on Experimental Evidence ( 0 terms )

Terms Based on Predictions or Assertions ( 4 terms )

Molecular Function

CV term

Evidence

References

AAC codon-amino acid adaptor activity

inferred from sequence model

(Lowe, 2002.3.8)

triplet codon-amino acid adaptor activity

non-traceable author statement

(FlyBase, 1992-)

Biological Process

CV term

Evidence

References

translation

inferred by curator from GO:0033442

(Lowe, 2002.3.8)

non-traceable author statement

(FlyBase, 1992-)

Cellular Component

CV term

Evidence

References

cytosol

inferred by curator from GO:0033442

(Lowe, 2002.3.8)

non-traceable author statement

(FlyBase, 1992-)

Sequence Ontology: Class of Gene

Interactions & Pathways

Summary of Physical Interactions

Summary of Genetic Interactions

Interacts with

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

tRNA:N5:42Af allele

Gene

References

External Data

Linkouts

Orthologs

OrthoDB Orthologs (0) - based on analysis using Dmel annotation version 5.41

OrthoDB Ortholog Groups

OrthoDB orthology group searches

(Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288)

Drosophila inclusive ortholog search

No orthologs identified

Dipteran inclusive ortholog search

No orthologs identified

Insect inclusive ortholog search

No orthologs identified

Arthropod inclusive ortholog search

No orthologs identified

Metazoa inclusive ortholog search

No orthologs identified

Orthologs in Drosophila Species (None identified)

No orthologies identified

Orthologs in non-Drosophila Dipterans (None identified)

No non-Drosophilid orthologies identified

Orthologs in non-Dipteran Insects (None identified)

No non-Dipteran orthologies identified

Orthologs in non-Insect Arthropods (None identified)

No non-Insect Arthropod orthologies identified

Orthologs in non-Arthropod Metazoa (None identified)

No non-Arthropod Metazoa orthologies identified

Human Orthologs (0)

Gene

OMIM

HGNC

AAA Orthologs (0) based on analysis using Dmel annotation version 4.3

No orthologs identified

Stocks & Reagents

Stocks Listed in FlyBase ( 0 )

Genomic Clones ( 2 )

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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA Clones, Fully Sequenced

BDGP DGC clones

Other clones

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi & Array Information

Linkouts

GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents

•

3885600

Other Information

Discoverer

Etymology

Identification

Relationship to Other Genes

Source for database identity of

Source for database merge of

Source for merge of: tRNA:N5:42Af tRNA:N:GTT:AE002769-c

(FlyBase, 1996-)

Additional comments

No equivalent annotation in release 3.2 of the genome annotation.

(FlyBase, 1996-)

Other Comments

New annotation (CR33973) in release 4.3 of the genome annotation.

(FlyBase Genome Annotators, 2005)

tRNA:N5:42Af is not annotated in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

External Crossreferences & Linkouts

Sequence Crossreferences

DDBJ / EMBL / GenBank

•

Entrez Gene - A searchable database of RefSeq genes.

•

3885600

Other Crossreferences

Linkouts

FlyMine - Integrated genomics database for Drosophila, Anopheles, and C.elegans

•

FBgn0011936

GenomeRNAi - GenomeRNAi – A database for cell-based and in vivo RNAi phenotypes and reagents

•

3885600

modMine - Data generated by the modENCODE project.

•

FBgn0011936

Synonyms & Secondary IDs ( 8 )

Reported As

Symbol Synonym

AE002769.trna7-AsnGTT

(Lowe, 2002.3.8)

Asn6

(Takada et al., 2000, Lofquist and Sharp, 1986)

Asn-tRNA-6

(Lofquist, 1986)

CR33973

(FlyBase Genome Annotators, 2005)

tRNA:asn5:42Af

tRNA:N5:42Af

tRNA:N:GTT:AE002769-c

Name Synonym

transfer RNA:asn5:42Af

Secondary FlyBase IDs

FBgn0003759
FBgn0053973
FBgn0060131

References ( 12 )

Research paper

Takada et al., 2000, Cell 101(5): 459--469: A TRF1:BRF complex directs Drosophila RNA polymerase III transcription. [FBrf0128662]
Lofquist et al., 1988, Mol. Cell. Biol. 8: 4441--4449: A discrete region centered 22 base pairs upstream of the initiation site modulates transcription of Drosophila tRNA^Asn genes. [FBrf0048670]
Lofquist and Sharp, 1986, J. Biol. Chem. 261: 14600--14606: The 5'-flanking sequences of Drosophila melanogaster tRNA^Asn₅ genes differentially arrest RNA polymerase III. [FBrf0044676]
Gergen et al., 1981, J. Mol. Biol. 147(4): 475--499: tRNA^lys² gene cluster in Drosophila. [FBrf0036943]
Elder et al., 1980, J. Mol. Biol. 142(1): 1--17: In situ hybridization of three transfer RNAs to the polytene chromosomes of Drosophila melanogaster. [FBrf0035241]
Yen and Davidson, 1980, Cell 22(1 Pt. 1): 137--148: The gross anatomy of a tRNA gene cluster at region 42A of the Drosophila melanogaster chromosomes. [FBrf0034217]

Personal communication to FlyBase

Lowe, 2002.3.8, tRNAscan-SE analysis of the Drosophila melanogaster genome.: tRNAscan-SE analysis of the Drosophila melanogaster genome. [FBrf0145624]

FlyBase analysis

FlyBase Genome Annotators, 2005, Changes affecting gene model number or type in release 4.3 of the annotated D.melanogaster genome.: Changes affecting gene model number or type in release 4.3 of the annotated D.melanogaster genome. [FBrf0188580]
FlyBase Genome Annotators, 2002-2003, Changes affecting gene model number or type in releases 3.0 and 3.1 of the annotated D.melanogaster genome.: Changes affecting gene model number or type in releases 3.0 and 3.1 of the annotated D.melanogaster genome. [FBrf0148886]
FlyBase, 1996-, FlyBase inference based on genome sequence analysis.: FlyBase inference based on genome sequence analysis. [FBrf0104946]
FlyBase, 1992-, FlyBase curation.: FlyBase curation. [FBrf0105495]

DNA/RNA sequence record

Lofquist, 1986, GenBank/EMBL/DDBJ: M14848: D. melanogaster Asn-tRNA-6 gene. [FBrf0117496]