FlyBase Gene Report: Dmel\Rnp4F

General Information

Symbol

Dmel\Rnp4F

Species

D. melanogaster

Name

RNA-binding protein 4F

Annotation Symbol

CG3312

Feature Type

protein_coding_gene

FlyBase ID

FBgn0014024

Gene Model Status

Current

Stock Availability

9 publicly available

Gene Summary

RNA-binding protein 4F (Rnp4F) encodes an essential evolutionarily-conserved RNA-binding protein. Rnp4F gene expression is post-transcriptionally regulated by interaction with a stable stem-loop structure in the 5'-UTR of the mRNA with trans-acting factors. [Date last reviewed: 2018-09-13] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
UniProtKB
Interactive Fly

Also Known As

4f-rnp, rnp-4f

Key Links

Genomic Location

Cytogenetic map

4F5-4F5

Sequence location

X:5,318,928..5,322,696 [-]

Recombination map

1-11

RefSeq locus

NC_004354 REGION:5318928..5322696

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 (9 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 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 (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

involved_in central nervous system development

inferred from mutant phenotype

(Chen et al., 2007)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in mRNA splicing, via spliceosome

inferred from biological aspect of ancestor with PANTHER:PTN000397856

(GO Reference Genome Project, 2011-)

involved_in RNA processing

inferred from electronic annotation with InterPro:IPR003107

(InterPro Project Members, 2004-)

Cellular Component (3 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

part_of ASAP complex

inferred from biological aspect of ancestor with PANTHER:PTN000397856

(GO Reference Genome Project, 2011-)

is_active_in cytoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000397856

(GO Reference Genome Project, 2011-)

is_active_in nucleoplasm

inferred from biological aspect of ancestor with PANTHER:PTN000397856

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Protein Function (UniProtKB)

May be involved in gene regulation during development. Binds RNA.

(UniProt, Q9W4D2)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Rnp4F 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 Q9W4D2)

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 5.50

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

Gene model reviewed during 5.55

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Rnp4F-RA

FBtr0070752

NM_078492

3323

941

Rnp4F-RB

FBtr0070753

NM_206630

3242

941

Rnp4F-RD

FBtr0112876

NM_001103414

3146

941

Rnp4F-RF

FBtr0340477

NM_001103413

3116

941

Additional Transcript Data and Comments

Reported size (kB)

3.127 (longest cDNA)

(Petschek et al., 1997)

3.5, 3.2 (northern blot)

(Hess et al., 1996)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Rnp4F-PA

FBpp0070720

106.7

941

4.75

FBpp0089396

106.7

941

4.75

FBpp0111789

106.7

941

4.75

FBpp0309418

106.7

941

4.75

Q9W4D2

NP_001096883

ABW09339

Polypeptides with Identical Sequences

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

941 aa isoforms: Rnp4F-PA, Rnp4F-PB, Rnp4F-PD, Rnp4F-PF

Additional Polypeptide Data and Comments

Reported size (kDa)

943, 639, 555 (aa); 124, 84, 70 (kD predicted)

(Petschek et al., 1997)

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

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Rnp4F using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

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).

-0.70

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 1 -- 4

organism | ubiquitous

(Chen et al., 2007)

embryonic stage 4

primordial germ cell

(Hess et al., 1996)

embryonic stage 4 -- 16

(Hess et al., 1996)

embryonic stage 6

cephalic furrow

(Chen et al., 2007)

mesoderm

(Chen et al., 2007)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

anterior endoderm

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

posterior endoderm

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

germ band

(Chen et al., 2007)

amnioproctodeal invagination

(Chen et al., 2007)

embryonic stage 10

stomodeum

(Hess et al., 1996)

proctodeum

(Hess et al., 1996)

embryonic stage 11 -- 12

anterior midgut primordium

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

posterior midgut primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13

presumptive embryonic/larval central nervous system

(Hess et al., 1996)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic/larval midgut

(Fisher et al., 2012)

larval nervous system

(Fisher et al., 2012)

germline cell

(Fisher et al., 2012)

gonad

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

embryonic stage 14

larval ventral nerve cord | dorsal | segmentally repeated

(Hess et al., 1996)

larval brain

(Chen et al., 2007)

larval ventral nerve cord | dorsal

(Chen et al., 2007)

embryonic/larval gut

(Chen et al., 2007)

embryonic stage 14 -- 16

embryonic/larval foregut

(Hess et al., 1996)

larval ventral nerve cord commissure

(Hess et al., 1996)

embryonic/larval hindgut

(Hess et al., 1996)

epidermis

(Hess et al., 1996)

larval longitudinal connective

(Hess et al., 1996)

muscle system | restricted

(Hess et al., 1996)

oogenesis stage S6 -- S14

(Hess et al., 1996)

nurse cell

(Hess et al., 1996)

oogenesis stage S10A -- S14

oocyte

(Hess et al., 1996)

microinjection

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Petschek et al., 1997)

pupal stage

(Petschek et al., 1997)

adult stage

adult head

(Petschek et al., 1997)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage & larval stage & adult stage

(Hess et al., 1996)

Additional Descriptive Data

The relative proportions of the long and short Rnp4F, which differ with respect to splicing of an untranslated upstream exon, change significiantly over the course of embryogenesis.

(Chen et al., 2007)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 5

organism | ubiquitous

(Chen et al., 2007)

embryonic stage 6

mesoderm anlage

(Chen et al., 2007)

embryonic stage 6 -- 7

cephalic furrow

(Chen et al., 2007)

embryonic stage 7 -- 10

amnioproctodeal invagination

(Chen et al., 2007)

germ band

(Chen et al., 2007)

embryonic stage 14

larval ventral nerve cord

(Chen et al., 2007)

embryonic brain

(Chen et al., 2007)

embryonic somatic muscle cell

(Chen et al., 2007)

embryonic/larval gut

(Chen et al., 2007)

adult stage

adult fat body

(Chen et al., 2007)

oogenesis

nurse cell

(Chen et al., 2007)

oocyte

(Chen et al., 2007)

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\Rnp4F in JBrowse

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

View exonic expression by developmental stage for Dmel\Rnp4F

View exonic expression by tissue for Dmel\Rnp4F

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

FBgn0014024

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

31448/tissue=All

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

FBgn0014024

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0014024

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

FBgn0014024

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

CG3312

Flygut - An atlas of the Drosophila adult midgut

FBgn0014024

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\Rnp4F

Stages(s) 1-3
Stages(s) 7-8
Stages(s) 9-10
Stages(s) 11-12
Stages(s) 13-16

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 ( 9 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Rnp4F

Transgenic constructs containing regulatory region of Rnp4F

Aberrations (Deficiencies and Duplications) ( 3 )

Inferred from experimentation ( 3 )

Gene duplicated in

Dp(1;3)CH322-188C18

(Blumröder et al., 2016)

Gene partially duplicated in

Dp(1;3)CH322-15H1

(Blumröder et al., 2016)

Gene not duplicated in

Dp(1;3)CH322-89M16

(Blumröder et al., 2016)

Inferred from location ( 13 )

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 | recessive

Rnp4F⁵³²

lethal - all die during embryonic stage, with Scer\GAL4^elav.PU

partially lethal - majority die, with Scer\GAL4^Tub.PU

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

Rnp4F^GD10932

viable, with Scer\GAL4^Mef2.PR

Rnp4F^GD10932

viable, with Scer\GAL4^pnr-MD237

Rnp4F^GD10932

viable, with Scer\GAL4^tin.CΔ4

Rnp4F^GD10932

Sterility

Allele

male sterile, with Scer\GAL4^Tub.PU

Other Phenotypes

Allele

abnormal cell number | spermatogenesis, with Scer\GAL4^tj.PU

Rnp4F^KK102446

abnormal cell number | spermatogenesis, with Scer\GAL4^Tub.PU

Rnp4F^HMJ22145

abnormal neuroanatomy | embryonic stage, with Scer\GAL4^elav.PU

abnormal neuroanatomy | embryonic stage, with Scer\GAL4^Tub.PU

atrophy | adult stage, with Scer\GAL4^Tub.PU

short lived, with Scer\GAL4^Tub.PU

Rnp4F^KK102446

some die during embryonic stage, with Scer\GAL4^Tub.PU

Rnp4F^HMJ22145

some die during P-stage, with Scer\GAL4^Tub.PU

wild-type

Rnp4F^hs.PP

Phenotype manifest in

Allele

larval central nervous system | embryonic stage, with Scer\GAL4^Tub.PU

Rnp4F^HMJ22145

male germline cell | adult stage | increased number, with Scer\GAL4^tj.PU

Rnp4F^KK102446

midline primordium, with Scer\GAL4^elav.PU

Rnp4F^HMJ22145

midline primordium, with Scer\GAL4^Tub.PU

Rnp4F^KK102446

proboscis, with Scer\GAL4^Tub.PU

Rnp4F^KK102446

spermatid | adult stage | decreased number, with Scer\GAL4^Tub.PU

Rnp4F^HMJ22145

spermatid | decreased number, with Scer\GAL4^tj.PU

Rnp4F^KK102446

spermatocyte | decreased number, with Scer\GAL4^Tub.PU

Rnp4F^HMJ22145

spermatozoon | decreased number, with Scer\GAL4^tj.PU

Rnp4F^KK102446

testis, with Scer\GAL4^tj.PU

Rnp4F^KK102446

testis, with Scer\GAL4^Tub.PU

Rnp4F^HMJ22145

wing, with Scer\GAL4^Tub.PU

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) (65)

Hsap\SART3

11 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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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

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) (40)

Rnor\Sart3

11 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

Yes

Mus musculus (laboratory mouse) (55)

Mmus\Sart3

10 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

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

Xenopus tropicalis (Western clawed frog) (36)

Xtro\sart3

7 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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Danio rerio (Zebrafish) (53)

Drer\sart3

11 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

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

Caenorhabditis elegans (Nematode, roundworm) (26)

Cele\sart-3

9 of 14

Yes

Cele\aly-3

1 of 14

Cele\C02B10.4

1 of 14

Cele\C53C11.4

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

Yes

Cele\ztf-4

1 of 14

Anopheles gambiae (African malaria mosquito) (27)

Agam\AgaP_AGAP002959

10 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

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

Arabidopsis thaliana (thale-cress) (52)

Atha\EMB140

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

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Atha\AT5G03580

1 of 13

Atha\AT5G04600

1 of 13

Atha\AT5G06210

1 of 13

Yes

Atha\AT5G12190

1 of 13

Atha\AT5G19960

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

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

Saccharomyces cerevisiae (Brewer's yeast) (12)

Scer\PRP24

3 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

Schizosaccharomyces pombe (Fission yeast) (14)

Spom\SPBC1861.04c

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

1 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Rnp4F. 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) (29)

B52

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

crn

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

LS2

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

SF2

1 of 13

Sf3b6

1 of 13

sqd

1 of 13

Sxl

1 of 13

TBPH

1 of 13

tra2

1 of 13

tsu

1 of 13

x16

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

Rnp4F^KK102446

model of spermatogenic failure

CEA

(Ayers et al., 2023)

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?

SART3; spliceosome associated factor 3, U4/U6 recycling protein

11 of 14

611684

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

Rnp4F - CG17768

experimental knowledge based

(Guruharsha et al., 2011)

Rnp4F - CG9344

experimental knowledge based

(Guruharsha et al., 2011)

Rnp4F - LSm3

experimental knowledge based

(Guruharsha et al., 2011)

Summary of Genetic Interactions

Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0014024

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

31448

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

gene_with_edited_transcript

(Graveley et al., 2011)

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-11

Cytogenetic map

4F5-4F5

Sequence location

X:5,318,928..5,322,696 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

4F5-4F5

Limits computationally determined from genome sequence between P{EP}EP425 and P{EP}CG3249^EP1400

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

4F1-4F2

(determined by in situ hybridisation)

(Hess et al., 1996, Petschek et al., 1996, Petscheck, 1995)

Experimentally Determined Recombination Data

Location

1-11

(FlyBase, 2016)

1-13.4

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

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

Bloomington

58168

y¹ v¹; P{TRiP.HMJ22145}attP40

35457

y¹ sc^* v¹ sev²¹; P{TRiP.GL00383}attP2

56854

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02384}attP40

Korea

10732

P{EP}Rnp4F^G977

NIG-Fly

HMJ22562

y¹ v¹; P{TRiP.HMJ22562}attP40/CyO

GL00383

y¹ sc^* v¹ sev²¹; P{TRiP.GL00383}attP2

HMS02384

y¹ sc^* v¹ sev²¹; P{TRiP.HMS02384}attP40/CyO

VDRC

v107063

P{KK102446}VIE-260B

v24743

w¹¹¹⁸; P{GD10932}v24743

Genomic Clones (15)

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

cDNA Clones (45)

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

LD32008

Other clones

DPiM_LD32008

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.

FBgn0014024

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0014024

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Chen et al., 2007)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

RNAi knockdown shows that the long Rnp4F isoform is required for normal central nervous system (CNS) development and acts upstream of other genes that are important for CNS development.

(Chen et al., 2007)

Isolated Rnp4F cDNAs represent three structurally different transcripts arising from alternative splicing and editing of Rnp4F via A-to-G conversions.

(Petschek et al., 1997)

RNA editing occurs in an alternatively spliced adult head transcript arising from the single-copy nuclear Rnp4F gene via numerous A to G conversions (as shown by comparison of genomic and cDNA nucleotide sequences).

(Petschek et al., 1996)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Rnp4F CG3312

(Zhong, 1999.11)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (10)

Reported As

Symbol Synonym

4F-rnp

(Feiber et al., 2000, Hess et al., 1996)

CG3312

(National Institute of Genetics Fly Stocks, 2023-, Çiçek et al., 2016, Brooks et al., 2015, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Keleman et al., 2009.8.5)

RNP-4F

(Chen et al., 2007, Petschek and Concel, 2003)

Rnp-4F

(Keegan et al., 2011)

Rnp4F

(Lee et al., 2024, Mohr et al., 2017, Blumröder et al., 2016, Brooks et al., 2015, Kwon et al., 2013)

Rnp4f

(Ayers et al., 2023)

rnp-4f

(Chen et al., 2013, Ghosh et al., 2013, Vaughn et al., 2013, Lakshmi et al., 2012, Chen et al., 2009, Chen et al., 2007, Chen et al., 2007, Fetherson et al., 2006, Fetherson et al., 2006, Rajeshwaran et al., 2006, Fetherson and Vaughn, 2004, Rangarajan et al., 2004, Petschek and Concel, 2003, Petschek and Concel, 2002)

Name Synonyms

RNA-binding protein 4F

(Petschek et al., 1995)

splicing assembly factor rnp-4f

(Chen et al., 2007)

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 63 )

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.

31448

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.

Q9W4D2

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q9W4D2

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

A8JUY0

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.

Q9W4D2

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0014024

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

31448/tissue=All

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

FBgn0014024

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

FBgn0014024

FlyMine - An integrated database for Drosophila genomics

FBgn0014024

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

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

dme:Dmel_CG3312

MARRVEL_MODEL - MARRVEL (model organism gene)

31448

Linkouts

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

FBgn0014024

DroID - A comprehensive database of gene and protein interactions.

FBgn0014024

DRSC - Results frm RNAi screens

FBgn0014024

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0014024

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0014024

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

CG3312

Flygut - An atlas of the Drosophila adult midgut

FBgn0014024

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

31448

References (81)

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

-0.70

Report Sections