Gene Dmel\snRNA:U1:82Ec

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General Information

Symbol

Dmel\snRNA:U1:82Ec

Species

D. melanogaster

Name

small nuclear RNA U1 at 82Ec

Annotation symbol

Feature type

pseudogene_attribute

FlyBase ID

FBgn0004184

Gene Model Status

Unannotated

Stock availability

None publicly available

Also Known As

U1, U1 snRNA

Genomic Location

Chromosome (arm)

Recombination map

3-[47.1]

Cytogenetic map

82E-82E

Sequence location

Summary Information

Automatically generated summary

See sections below for more information

The gene small nuclear RNA U1 at 82Ec is referred to in FlyBase by the symbol Dmel\snRNA:U1:82Ec (FBgn0004184). It is a pseudogene_attribute from Drosophila melanogaster. Its molecular function is unknown. The biological processes in which it is involved are not known. No alleles are reported. It has no annotated transcripts. Gene has not been localized to the genome sequence.

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

82E-82E

Left limit from molecular mapping relative to snRNA:U1:82Eb (FBrf0052749) Right limit from molecular mapping relative to snRNA:U1:82Ea (FBrf0041598)

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-[47.1]

Left of (cM)

Right of (cM)

Notes

Gene Model & Products

Comments on Gene Model

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

Additional Transcript Data & Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

Additional Polypeptide Data & Comments

Reported size (kDa)

Comments

External Data

Linkouts

Crossreferences

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

UniProtKB/Swiss-Prot

UniProtKB/TrEMBL

Mapped Features

Type

Symbol & Location

Additional Notes

References

External Data

Linkouts

Crossreferences

Expression Data

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization (GO Cellular Component)

CV term

Evidence

References

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

modENCODE Anatomy RNA-Seq

modENCODE Development RNA-Seq

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 snRNA:U1:82Ec	Class	Mutagen	Stocks	Known lesion

Alleles Carried on Transgenic Constructs ( 0 )

For All Alleles Carried on Transgenic Constructs Show

Allele of snRNA:U1:82Ec	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 ( 0 unique terms )

Terms Based on Experimental Evidence ( 0 terms )

Terms Based on Predictions or Assertions ( 0 terms )

Sequence Ontology: Class of Gene

nuclear_gene

(Lo and Mount, 1990)

pseudogene_attribute

(Lo and Mount, 1990, Mount, 2000.5)

snRNA_gene

(Lo and Mount, 1990)

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

snRNA:U1:82Ec 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 ( 0 )

cDNA Clones ( 0 )

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

•

5656999

Antibody Information

Other Information

Discoverer

Etymology

Identification

Relationship to Other Genes

Source for database identity of

Source for database merge of

Additional comments

Other Comments

snRNA:U1:82Ec does not appear to be present in the D.melanogaster strain used for sequencing the genome; only one copy of a U1 snRNA gene (CR32862) has been detected at 82E in the sequenced strain, although 3 copies have previously been reported in clones derived from Oregon R flies - snRNA:U1:82Eb, snRNA:U1:82Ec and snRNA:U1:82Ea (FBrf0052749). The copy present in the sequenced strain appears to correspond to snRNA:U1:82Eb, while snRNA:U1:82Ec and snRNA:U1:82Ea appear to be missing from the sequenced strain (see FBrf0128209).

(FlyBase Genome Annotators, 2002-2003)

Sequences corresponding to snRNA:U1:82Ec have not been found on the Celera assembly on the date of analysis.

(Mount, 2000.5)

snRNA:U1:82Ec has been cloned and sequenced.

(Lo and Mount, 1990)

snRNA:U1:82Ec has been cloned and sequenced. snRNA:U1:82Ec is a pseudogene, it is deleted at the 5' end, missing the first 50 bases.

(Kejzlarova-Lepesant et al., 1984)

External Crossreferences & Linkouts

Sequence Crossreferences

Other Crossreferences

Linkouts

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

•

5656999

Synonyms & Secondary IDs ( 11 )

Reported As

Symbol Synonym

82.2

(Mount, 2000.5)

snRNA:U1

snRNA:U1:82Ec

snRNA-U1-82.2

(Dominski et al., 2003, Yuan et al., 2003, Saluz et al., 1988, Li et al., 2004, Kroiss et al., 2008, Gonsalvez et al., 2008, Gonsalvez et al., 2010, Kim et al., 2010)

U1-82.2

(Lo and Mount, 1990)

U1 82E(pDm6Y)

(Kejzlarova-Lepesant et al., 1984)

U1a-82Ec

(Mount and Salz, 2000)

U1 snRNA

(Labourier et al., 2001, Gonsalvez et al., 2006, Deryusheva and Gall, 2009, Labourier and Rio, 2001, Rajendra et al., 2007)

U1snRNA82Ec

Name Synonym

small nuclear RNA U1 at 82Ec

Secondary FlyBase IDs

FBgn0003917

References ( 18 )

Research paper

Gonsalvez et al., 2010, Development 137(14): 2341--2351: Sm proteins specify germ cell fate by facilitating oskar mRNA localization. [FBrf0211144]
Kim et al., 2010, Mol. Cell. Biol. 30(10): 2411--2423: Identification of SNAPc subunit domains that interact with specific nucleotide positions in the U1 and U6 gene promoters. [FBrf0214992]
Deryusheva and Gall, 2009, Mol. Biol. Cell 20(24): 5250--5259: Small Cajal Body-specific RNAs of Drosophila Function in the Absence of Cajal Bodies. [FBrf0209497]
Gonsalvez et al., 2008, RNA 14(5): 878--887: Sm protein methylation is dispensable for snRNP assembly in Drosophila melanogaster. [FBrf0205403]
Kroiss et al., 2008, Proc. Natl. Acad. Sci. U.S.A. 105(29): 10045--10050: Evolution of an RNP assembly system: a minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster. [FBrf0205768]
Rajendra et al., 2007, J. Cell Biol. 176(6): 831--841: A Drosophila melanogaster model of spinal muscular atrophy reveals a function for SMN in striated muscle. [FBrf0194681]
Gonsalvez et al., 2006, Curr. Biol. 16(11): 1077--1089: The Sm-protein methyltransferase, dart5, is essential for germ-cell specification and maintenance. [FBrf0193526]
Li et al., 2004, Mol. Cell. Biol. 24(5): 1897--1906: Architectural arrangement of cloned proximal sequence element-binding protein subunits on Drosophila U1 and U6 snRNA gene promoters. [FBrf0174956]
Dominski et al., 2003, Proc. Natl. Acad. Sci. U.S.A. 100(16): 9422--9427: Cloning and characterization of the Drosophila U7 small nuclear RNA. [FBrf0161514]
Yuan et al., 2003, Nucleic Acids Res. 31(10): 2495--2507: RNomics in Drosophila melanogaster: identification of 66 candidates for novel non-messenger RNAs. [FBrf0159270]
Labourier et al., 2001, Mol. Cell 8(2): 363--373: Modulation of P-element pre-mRNA splicing by a direct interaction between PSI and U1 snRNP 70K protein. [FBrf0139754]
Labourier and Rio, 2001, RNA 7(3): 457--470: Purification of Drosophila snRNPs and characterization of two populations of functional U1 particles. [FBrf0135940]
Mount and Salz, 2000, J. Cell Biol. 150(2): F37--F43: Pre-messenger RNA processing factors in the Drosophila genome. [FBrf0129982]
Lo and Mount, 1990, Nucleic Acids Res. 18: 6971--6979: Drosophila melanogaster genes for U1 snRNA variants and their expression during development. [FBrf0052749]
Saluz et al., 1988, Nucleic Acids Res. 16(8): 3582: The localization and estimated copy number of Drosophila melanogaster U1, U4, U5 and U6 snRNA genes. [FBrf0048816]
Kejzlarova-Lepesant et al., 1984, Nucleic Acids Res. 12: 8835--8846: A complete and a truncated U1 snRNA gene of Drosophila melanogaster are found as inverted repeats at region 82E of the polytene chromosomes. [FBrf0041598]

Personal communication to FlyBase

Mount, 2000.5, FlyBase error report on April 5, April 28 and May 12 2000.: FlyBase error report on April 5, April 28 and May 12 2000. [FBrf0128209]

FlyBase analysis

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]