FlyBase Gene Report: Dmel\Ref1

General Information

Symbol

Dmel\Ref1

Species

D. melanogaster

Name

RNA and export factor binding protein 1

Annotation Symbol

CG1101

Feature Type

protein_coding_gene

FlyBase ID

FBgn0010774

Gene Model Status

Current

Stock Availability

7 publicly available

Gene Summary

Contribute a Gene Snapshot for this gene.

All Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

Aly, l(3)02267

Key Links

Genomic Location

Cytogenetic map

84B2-84B2

Sequence location

3R:7,077,904..7,080,387 [-]

Recombination map

3-48

RefSeq locus

NT_033777 REGION:7077904..7080387

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 (11 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables mRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN000462807

(GO Reference Genome Project, 2011-)

inferred from sequence or structural similarity

(Lasko, 2000)

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR035979

(InterPro Project Members, 2004-)

enables RNA binding

inferred from electronic annotation with InterPro:IPR000504

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in mRNA export from nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000462807

(GO Reference Genome Project, 2011-)

involved_in mRNA splicing, via spliceosome

inferred by curator from GO:0071011,GO:0071013

(Herold et al., 2009)

Cellular Component (6 terms)

Terms Based on Experimental Evidence (5 terms)

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in nuclear membrane

inferred from direct assay

(Buszczak and Spradling, 2006)

located_in nucleoplasm

inferred from direct assay

(Buszczak and Spradling, 2006)

located_in nucleus

inferred from direct assay

(Swenson et al., 2016)

part_of precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000462807

(GO Reference Genome Project, 2011-)

part_of transcription export complex

inferred from sequence or structural similarity with UniProtKB:Q86V81

(Gene Ontology Curators, 2002-)

Gene Group (FlyBase)

TRANSCRIPTION EXPORT COMPLEX

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

TRANSCRIPTION EXPORT COMPLEX -: The Transcription and export (TREX) complex is a multisubunit complex, which acts throughout RNA biogenesis to couple transcription with nuclear export. (Adapted from FBrf0233979 and PMID:27679854).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Ref1 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 Q9V3E7)

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

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.47

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Ref1-RA

FBtr0081642

NM_143711

1328

266

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

Ref1-PA

FBpp0081156

27.9

266

11.23

Q9V3E7

NP_651968

AAF54070

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

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

Q9V3E7

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Ref1 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).

1.05

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 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 11 -- 12

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

Comment: expression assayed in cultured cells

(Gatfield and Izaurralde, 2002)

Additional Descriptive Data

Aly transcripts are expressed in S2 cells.

(Gatfield and Izaurralde, 2002)

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)

western blot

Stage

Tissue/Position (including subcellular localization)

Reference

Comment: expression assayed in cultured cells

(Gatfield and Izaurralde, 2002)

Additional Descriptive Data

Aly protein is detected in S2 cells.

(Gatfield and Izaurralde, 2002)

Marker for

Subcellular Localization

CV Term

Evidence

References

part_of catalytic step 2 spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

located_in nuclear membrane

inferred from direct assay

(Buszczak and Spradling, 2006)

located_in nucleoplasm

inferred from direct assay

(Buszczak and Spradling, 2006)

located_in nucleus

inferred from direct assay

(Swenson et al., 2016)

part_of precatalytic spliceosome

inferred from high throughput direct assay

(Herold et al., 2009)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ref1 in JBrowse

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

View exonic expression by developmental stage for Dmel\Ref1

View exonic expression by tissue for Dmel\Ref1

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

FBgn0010774

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

44029/tissue=All

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

FBgn0010774

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0010774

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

FBgn0010774

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG1101

Flygut - An atlas of the Drosophila adult midgut

FBgn0010774

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 4 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Ref1

Transgenic constructs containing regulatory region of Ref1

Aberrations (Deficiencies and Duplications) ( 2 )

Inferred from experimentation ( 2 )

Gene disrupted in

Df(3R)Antp17

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

Gene not disrupted in

Df(3R)awd-KRB

(Spradling et al., 1999, BDGP Project Members, 1994-1999)

Inferred from location ( 4 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

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

Lethality

Allele

lethal | female limited, with Scer\GAL4^dome-PG14

Ref1^HMS01301

lethal | recessive

Ref1⁰²²⁶⁷

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Ref1^GD4683

viable, with Scer\GAL4^pnr-MD237

Ref1^GD4683

viable, with Scer\GAL4^tin.CΔ4

Ref1^GD4683

Sterility

Allele

female fertile, with Scer\GAL4^nanos.PG

Ref1^KK109076

female semi-fertile, with Scer\GAL4^VP16.otu

Ref1^HMS01301

female semi-sterile, with Scer\GAL4^nanos.PG

Ref1^GD4683

Other Phenotypes

Allele

abnormal pain response | adult stage, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

Ref1^GD4683

abnormal planar polarity, with Scer\GAL4^pnr-MD237

Ref1^GD4683

abnormal size | third instar larval stage, with Scer\GAL4^Cg.PA

Ref1^HMS01301

visible, with Scer\GAL4^pnr-MD237

Ref1^GD4683

Phenotype manifest in

Allele

embryonic/larval fat body | third instar larval stage, with Scer\GAL4^Cg.PA

Ref1^HMS01301

mitochondrion | third instar larval stage, with Scer\GAL4^Cg.PA

Ref1^HMS01301

trichogen cell | increased number, with Scer\GAL4^pnr-MD237

Ref1^GD4683

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) (73)

Hsap\ALYREF

12 of 14

Yes

3 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

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

Yes

Hsap\RBMY1A1

1 of 14

Hsap\RBMY1B

1 of 14

Hsap\RBMY1C

1 of 14

Yes

Hsap\RBMY1D

1 of 14

Hsap\RBMY1E

1 of 14

Yes

Hsap\RBMY1F

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

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

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (49)

Rnor\Alyref

11 of 14

Yes

3 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

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

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

Mus musculus (laboratory mouse) (77)

Mmus\Alyref

13 of 14

Yes

Mmus\Alyref2

11 of 14

Yes

Mmus\Gm4301

10 of 14

Yes

Mmus\Gm4302

10 of 14

Yes

Mmus\Gm4307

10 of 14

Yes

Mmus\Gm4312

10 of 14

Yes

Mmus\Gm4340

10 of 14

Yes

Mmus\Gm21293

10 of 14

Yes

Mmus\4931428L18Rik

9 of 14

Yes

Mmus\Gm4303

9 of 14

Yes

Mmus\Gm4305

9 of 14

Yes

Mmus\Gm5698

9 of 14

Yes

Mmus\Poldip3

3 of 14

Mmus\Gm6763

2 of 14

Yes

Mmus\Gm8764

2 of 14

Yes

Mmus\Gm21304

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

Yes

Mmus\Gm10352

1 of 14

Mmus\Gm20765

1 of 14

Yes

Mmus\Gm21312

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

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

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

Yes

Xenopus tropicalis (Western clawed frog) (30)

Xtro\alyref

11 of 13

Yes

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

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

Yes

Danio rerio (Zebrafish) (61)

Drer\alyref

14 of 14

Yes

2 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

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

Yes

Drer\safb

1 of 14

Drer\sart3

1 of 14

Drer\sf3b4

1 of 14

Drer\si:ch1073-335m2.2

1 of 14

Drer\snrnp35

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

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (33)

Cele\aly-2

10 of 14

Yes

Cele\aly-3

9 of 14

Yes

Cele\aly-1

8 of 14

Yes

Cele\C02B10.4

3 of 14

Yes

Cele\Y37E11AL.9

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

1 of 14

Anopheles gambiae (African malaria mosquito) (41)

Agam\AgaP_AGAP006733

12 of 12

Yes

2 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

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

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

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

1 of 12

1 of 12

1 of 12

Yes

Agam\NCBP2_ANOGA

1 of 12

Arabidopsis thaliana (thale-cress) (94)

Atha\AT5G02530

12 of 13

Yes

Atha\AT5G59950

12 of 13

Yes

Atha\ALY4

9 of 13

Yes

Atha\AT1G66260

9 of 13

Yes

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

Yes

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

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

Atha\GR-RBP6

1 of 13

Atha\LIF2

1 of 13

Atha\ML1

1 of 13

Yes

Atha\ML2

1 of 13

Atha\ML3

1 of 13

Yes

Atha\ML4

1 of 13

Yes

Atha\ML5

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

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

Yes

Atha\UBP1A

1 of 13

Atha\UBP1B

1 of 13

Atha\Y14

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (12)

Scer\YRA1

4 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Scer\NPL3

1 of 13

Scer\NSR1

1 of 13

Yes

Scer\PAB1

1 of 13

Scer\PUB1

1 of 13

Scer\YRA2

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (15)

Spom\mlo3

8 of 12

Yes

Spom\SPBC106.12c

5 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

1 of 12

1 of 12

1 of 12

Yes

Spom\usp102

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Ref1. 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) (31)

8 of 13

4 of 13

4 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

hfp

1 of 13

Hrb27C

1 of 13

lark

1 of 13

LS2

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

snf

1 of 13

Spx

1 of 13

sqd

1 of 13

ssx

1 of 13

Sxl

1 of 13

TBPH

1 of 13

tra2

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 1 )

Allele

Disease

Evidence

References

Ref1^HMS01301

model of alcohol use disorder

CEA

(Petruccelli et al., 2020)

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 4 )

Allele

Disease

Interaction

References

Ref1^HMS01301

ameliorates amyotrophic lateral sclerosis type 10

modeled by Hsap\TARDBP^UAS.cEa

(Berson et al., 2019)

modeled by Hsap\ATXN2^32Q.UAS, Hsap\TARDBP^UAS.cEa

(Berson et al., 2019)

ameliorates C9orf72 frontotemporal dementia and/or amyotrophic lateral sclerosis

modeled by Zzzz\GGGGCC^49.UAS

(Berson et al., 2019)

modeled by Zzzz\GGGGCC^{44.UAS.LDS.GFP}

(Berson et al., 2019)

Ref1^GD4683

DOES NOT ameliorate amyotrophic lateral sclerosis

modeled by Zzzz\GGGGCC^36.UAS

(Hautbergue et al., 2017)

Ref1⁰²²⁶⁷

ameliorates amyotrophic lateral sclerosis

modeled by Zzzz\GGGGCC^58.UAS.EGFP

(Freibaum et al., 2015)

ameliorates frontotemporal dementia

modeled by Zzzz\GGGGCC^58.UAS.EGFP

(Freibaum et al., 2015)

Ref1^KK109076

DOES NOT ameliorate amyotrophic lateral sclerosis

modeled by Zzzz\GGGGCC^36.UAS

(Hautbergue et al., 2017)

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?

ALYREF; Aly/REF export factor

12 of 14

604171

POLDIP3; DNA polymerase delta interacting protein 3

3 of 14

611520

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

Interaction Browsers

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

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

Ref1 - CG7824

two hybrid

(Hu et al., 2017.6.13)

Ref1 - Lkb1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - Odj

two hybrid

(Hu et al., 2017.6.13)

Ref1 - PQBP1

pull down, peptide massfingerprinting

(Wan et al., 2015)

Ref1 - Rheb

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - S6kII

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - Thor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - dachs

anti tag coimmunoprecipitation, peptide massfingerprinting

(Kwon et al., 2013)

Ref1 - fj

anti tag coimmunoprecipitation, peptide massfingerprinting

(Kwon et al., 2013)

Ref1 - foxo

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - gig

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - mip40

anti bait coimmunoprecipitation, Identification by mass spectrometry

(Beall et al., 2007)

Ref1 - rictor

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Ref1 - sima

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Vinayagam et al., 2016)

Summary of Genetic Interactions

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

mbl

suppressible

Ref1

(Vicente-Crespo et al., 2008)

suppressible

Ref1

(McClure and Schubiger, 2008)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

68788

DroID - A comprehensive database of gene and protein interactions.

FBgn0010774

MIST (protein-protein) - An integrated Molecular Interaction Database

44029

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-48

Cytogenetic map

84B2-84B2

Sequence location

3R:7,077,904..7,080,387 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

84B2-84B2

Limits computationally determined from genome sequence between P{lacW}l(3)L2100^L2100 and P{EP}EP3060^EP3060

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

84C1-84C2

(determined by in situ hybridisation)

(Spradling et al., 1999)

84C1-84C2

(BDGP Project Members, 1994-1999)

Experimentally Determined Recombination Data

Location

3-48

(FlyBase, 2016)

3-44.2

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (7)

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

Bloomington

63373

w¹¹¹⁸; PBac{IT.GAL4}Ref1^0516-G4

11562

P{PZ}Ref1⁰²²⁶⁷ ry⁵⁰⁶/TM3, ry^RK Sb¹ Ser¹

34626

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01301}attP2/TM3, Sb¹

NIG-Fly

HMS01301

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01301}attP2/TM3, Sb¹

VDRC

v104471

P{KK109076}VIE-260B

v12031

w¹¹¹⁸ P{GD4683}v12031

v318689

PBac{fTRG00846.sfGFP-TVPTBF}VK00002

Genomic Clones (14)

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

cDNA Clones (172)

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

LD24793

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.

FBgn0010774

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0010774

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Ref2 is an RNA-based duplicate gene of Ref1.

(Chen et al., 2010)

Identified as a potential component of the hh signalling pathway in a genome-wide RNAi screen. dsRNA made from templates generated with primers directed affects the extent of expression of a hh signaling reporter construct in Clone 8 cells.

(Nybakken et al., 2005)

Relationship to Other Genes

Source for database merge of

Source for merge of: Aly BcDNA:LD24793

(Misra, 2000.8.9)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: BcDNA:LD24793 CG1101

(Zhao, 1999.11)

Source for identity of: Ref1 Aly

(Gatfield and Izaurralde, 2002)

Nomenclature comments

FlyBase Curator comment: This gene (FBgn0010774) was originally named 'Aly' in FBrf0111489 based on its orthology to a mouse gene. It has since been renamed to 'Ref1' in FlyBase because: i) the first paper to characterize the gene (FBrf0152118) refers to it as such; ii) the mouse ortholog is not known as 'Aly' in MGI nowadays; iii) all published papers that focus on the gene refer to it as 'Ref1' (or a variant thereof); iv) it reduces confusion with the 'aly' gene (FBgn0004372).

(Gatfield and Izaurralde, 2002)

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

ALY

(Sofola et al., 2007)

ALYREF

(Hautbergue et al., 2017)

Aly

(Wan et al., 2015, Czech et al., 2013, Kwon et al., 2013, Katahira, 2012, Friedman et al., 2011, Herold et al., 2009, Garcia-Lopez et al., 2008, McClure and Schubiger, 2008, Vicente-Crespo et al., 2008, Kaplow et al., 2007, Sofola et al., 2007, Buszczak and Spradling, 2006, Morozova et al., 2006, Provost et al., 2006, Nybakken et al., 2005, Rehwinkel et al., 2004)

BcDNA:LD24793

CG1101

(Kolkhof et al., 2017, Çiçek et al., 2016, Brooks et al., 2015, Rosa-Ferreira et al., 2015, Chen et al., 2012, Chen et al., 2010, Ni et al., 2010.12.1, Zhang et al., 2010, Herold et al., 2009, Keleman et al., 2009.8.5, Pan and Zhang, 2009, Provost et al., 2006, Nybakken et al., 2005, Rehwinkel et al., 2004, Gatfield and Izaurralde, 2002)

DmREF1

(Herold et al., 2001)

REF1

(Kozlova et al., 2006, Rehwinkel et al., 2004, Gatfield et al., 2003, Herold et al., 2003, Gatfield and Izaurralde, 2002)

Ref1

(Evans et al., 2021, Liguori et al., 2021, van der Graaf et al., 2021, Watanabe and Riddle, 2021, Berson et al., 2019, Zhou et al., 2019, Wang et al., 2018, Wang et al., 2018, Hu et al., 2017.6.13, Clandinin and Owens, 2016-, Lee et al., 2016, Sarov et al., 2016, Brooks et al., 2015, Freibaum et al., 2015, Wan et al., 2015, Hayashi et al., 2014, Hughes et al., 2014, Kwon et al., 2013, Le Thomas et al., 2013)

aly

(Czech et al., 2013)

alyref

(Ramesh et al., 2020)

cg1101

(Lasko, 2000)

dmREF1

(Stutz et al., 2000)

l(3)02267

(Provost et al., 2006, Beaton, 2000.1.31, Meister and Braun, 1995.10, BDGP Project Members, 1994-1999)

ref1

(Hughes et al., 2024, Rehwinkel et al., 2004, Herold et al., 2003)

Name Synonyms

Aly

(Vicente-Crespo et al., 2008)

RNA and export factor binding protein 1

Secondary FlyBase IDs

FBgn0027857

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 50 )

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.

44029

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.

Q9V3E7

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

Q9V3E7

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.

Q9V3E7

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0010774

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

44029/tissue=All

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

FBgn0010774

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

FBgn0010774

FlyMine - An integrated database for Drosophila genomics

FBgn0010774

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

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

dme:Dmel_CG1101

MARRVEL_MODEL - MARRVEL (model organism gene)

44029

Linkouts

BioGRID - A database of protein and genetic interactions.

68788

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

FBgn0010774

DroID - A comprehensive database of gene and protein interactions.

FBgn0010774

DRSC - Results frm RNAi screens

FBgn0010774

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0010774

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0010774

Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns

CG1101

Flygut - An atlas of the Drosophila adult midgut

FBgn0010774

FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.

FBgn0010774

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

TC011974

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

MIST (protein-protein) - An integrated Molecular Interaction Database

44029

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

References (104)

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

1.05

Report Sections