FlyBase Gene Report: Dmel\SLIRP1

General Information

Symbol

Dmel\SLIRP1

Species

D. melanogaster

Name

SRA stem-loop interacting RNA binding protein 1

Annotation Symbol

CG33714

Feature Type

protein_coding_gene

FlyBase ID

FBgn0064117

Gene Model Status

Current

Stock Availability

3 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Interactive Fly

Also Known As

DmSLIRP1

Key Links

Genomic Location

Cytogenetic map

19F4-19F4

Sequence location

X:21,317,936..21,319,296 [-]

Recombination map

1-65

RefSeq locus

NC_004354 REGION:21317936..21319296

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 mRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN008729238

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity

(Lasko, 2000)

enables RNA binding

inferred from electronic annotation with InterPro:IPR000504

(InterPro Project Members, 2004-)

Biological Process (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in mitochondrial matrix

traceable author statement

(Matsushima et al., 2017)

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN002690849

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\SLIRP1 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q0KHQ1)

If you don't see a structure in the viewer, refresh your browser.

Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.52

Gene model reviewed during 5.55

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

FBtr0091703

1278

FBtr0091704

1279

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

SLIRP1-PA

FBpp0076925

10.0

10.19

FBpp0076923

10.0

10.19

Q0KHQ1

NP_001027083

AAN09672

Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

90 aa isoforms: SLIRP1-PA, SLIRP1-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q0KHQ1

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\SLIRP1 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

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 11 -- 12

anal pad primordium

Comment: reported as anal pad specific anlage

(Fisher et al., 2012)

anterior midgut primordium

(Fisher et al., 2012)

head mesoderm

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

salivary gland body primordium

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 13 -- 16

dorsal pharyngeal muscle cell

(Fisher et al., 2012)

embryonic anal pad

(Fisher et al., 2012)

embryonic hindgut

(Fisher et al., 2012)

embryonic midgut chamber

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

larval muscle system

(Fisher et al., 2012)

larval somatic muscle cell

(Fisher et al., 2012)

gastric caecum

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

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\SLIRP1 in JBrowse

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

View exonic expression by developmental stage for Dmel\SLIRP1

View exonic expression by tissue for Dmel\SLIRP1

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

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0064116

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

3772560/tissue=All

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

FBgn0064117

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

FBgn0064117

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 2 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 1 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of SLIRP1

Transgenic constructs containing regulatory region of SLIRP1

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 24 )

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 feeding behavior

SLIRP1^GS1189

abnormal smell perception

SLIRP1^GS1189

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) (31)

Hsap\SLIRP

5 of 14

Yes

Hsap\RBM24

2 of 14

Yes

Hsap\RBM38

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

143

Hsap\U2AF2

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (18)

Rnor\Slirp

7 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Rnor\Rbm28

1 of 14

Rnor\Rbm38

1 of 14

Yes

Rnor\Tardbp

1 of 14

Mus musculus (laboratory mouse) (19)

Mmus\Slirp

7 of 14

Yes

Mmus\Rbm24

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mmus\Tardbp

1 of 14

Xenopus tropicalis (Western clawed frog) (22)

Xtro\slirp

7 of 13

Yes

Xtro\rbm24

2 of 13

Yes

Xtro\rbm38

2 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (26)

Drer\slirp

6 of 14

Yes

Drer\rbm24a

2 of 14

Yes

Drer\rbm24b

2 of 14

Yes

Drer\rbm38

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (13)

Cele\slrp-1

5 of 14

Yes

Cele\sup-12

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (12)

Agam\AgaP_AGAP013440

8 of 12

Yes

Agam\AgaP_AGAP013048

3 of 12

Agam\AgaP_AGAP011956

2 of 12

Yes

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (54)

Atha\AT1G20880

2 of 13

Yes

Atha\AT1G22330

2 of 13

Yes

Atha\AT1G22910

2 of 13

Yes

Atha\AT1G33470

2 of 13

Yes

Atha\AT1G76460

2 of 13

Yes

Atha\AT1G78260

2 of 13

Yes

Atha\AT2G46780

2 of 13

Yes

Atha\AT3G06970

2 of 13

Yes

Atha\AT5G11412

2 of 13

Yes

Atha\AT5G53680

2 of 13

Yes

Atha\AT5G53720

2 of 13

Yes

Atha\ATRZ-1A

2 of 13

Yes

Atha\ARP1

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\GR-RBP5

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\HRP1

1 of 13

Yes

Scer\SGN1

1 of 13

Yes

Scer\SNP1

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPBC660.15

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:SLIRP1. 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) (21)

6 of 13

2 of 13

2 of 13

2 of 13

2 of 13

msi

2 of 13

Rb97D

2 of 13

Rbp6

2 of 13

sqd

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Syp

1 of 13

U2af50

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?

SLIRP; SRA stem-loop interacting RNA binding protein

5 of 14

610211

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

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

534157

DroID - A comprehensive database of gene and protein interactions.

FBgn0064117

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_dicistronic_mRNA

(FlyBase Genome Annotators, 2002-2003)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-65

Cytogenetic map

19F4-19F4

Sequence location

X:21,317,936..21,319,296 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

19F4-19F4

Limits computationally determined from genome sequence between P{EP}CG1702^EP1525 and P{EP}EP1465&P{EP}CG1486^EP1192

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-65

(FlyBase, 2016)

1-65.9

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (3)

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

Bloomington

14147

y¹ P{SUPor-P}Acbp-Ank^KG06423 SLIRP1^KG06423

55374

y¹ sc^* v¹ sev²¹; P{TRiP.HMC04062}attP40/CyO

Kyoto

200175

y¹ w^67c23 P{GSV1}SLIRP1^GS1189/C(1)DX, y¹ w¹ f¹

Genomic Clones (6)

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

cDNA Clones (109)

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

DPiM_GM05135

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.

FBgn0064117

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0064117

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Matsushima et al., 2017, Ryuda et al., 2011)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Sequence comparison across multiple species (MSA) available in Supplementary Information.

(Takahashi et al., 2020)

Relationship to Other Genes

Source for database merge of

Additional comments

Dicistronic annotation CG33071 split out into separate annotations for each open reading frame, CG33714 and CG33713, in release 4.2 of the genome annotation.

(FlyBase Genome Annotators, 2005)

One or more of the processed transcripts for this gene contain(s) two non-overlapping open reading frames (ORFs). The non-overlapping ORFs are represented by CG33714 and CG33713.

(FlyBase Genome Annotators, 2002-2003)

Nomenclature History

Source for database identify of

Source for identity of: SLIRP1 CG33714

(Baggio et al., 2014)

Nomenclature comments

Etymology

Named 'SLIRP1 / SRA stem-loop interacting RNA binding protein 1' after the human ortholog.

(Baggio et al., 2014)

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

CG1704

(Liu et al., 2011, Orian et al., 2003)

CG33071

(Ryuda et al., 2011, Ryuda et al., 2008, Peng et al., 2007, Giot et al., 2003)

CG33071-ORFA

CG33071ORFA

(Hayden and Bosco, 2008)

CG33714

(Zhang et al., 2016, Baggio et al., 2014, Lu et al., 2014, Kwon et al., 2013, Ryuda et al., 2011, Hayden and Bosco, 2008, Ryuda et al., 2008)

DmSLIRP1

(Matsushima et al., 2017, Baggio et al., 2014)

Dromel_CG33713_FBtr0091704_uORF

(Hayden and Bosco, 2008)

RRM

(Ryuda et al., 2011)

SLIRP1

(Pham et al., 2024, Hou et al., 2020)

cg1704

(Lasko, 2000)

Name Synonyms

CPuORF of FBgn0064116

(Takahashi et al., 2020)

SRA stem-loop interacting RNA binding protein 1

Secondary FlyBase IDs

FBgn0031172
FBgn0053071
FBgn0053714
FBtr0077228
FBtr0077229
FBtr0077230

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 36 )

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.

3772560

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

GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.

Q0KHQ1

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

Q0KHQ1

Other crossreferences

AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.

Q0KHQ1

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0064116

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

3772560/tissue=All

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

FBgn0064117

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

FBgn0064117

FlyMine - An integrated database for Drosophila genomics

FBgn0064117

InterPro - A database of protein families, domains and functional sites

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

dme:Dmel_CG33714

MARRVEL_MODEL - MARRVEL (model organism gene)

3772560

Linkouts

BioGRID - A database of protein and genetic interactions.

534157

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0064117

DroID - A comprehensive database of gene and protein interactions.

FBgn0064117

DRSC - Results frm RNAi screens

FBgn0064117

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0064117

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

References (29)

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

NA

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