FlyBase Gene Report: Dmel\HLH54F

General Information

Symbol

Dmel\HLH54F

Species

D. melanogaster

Name

HLH54F

Annotation Symbol

CG5005

Feature Type

protein_coding_gene

FlyBase ID

FBgn0022740

Gene Model Status

Current

Stock Availability

11 publicly available

Gene Snapshot

HLH54F (HLH54F) encodes a bHLH transcription factor that regulates caudal visceral mesoderm development. [Date last reviewed: 2019-03-07]

Other Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

bHLH54F

Key Links

Genomic Location

Cytogenetic map

54E8-54E8

Sequence location

2R:17,757,405..17,760,517 [+]

Recombination map

2-84

RefSeq locus

NT_033778 REGION:17757405..17760517

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

Help me choose

Other Genome Views

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

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (8 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables protein heterodimerization activity

inferred from physical interaction with FLYBASE:da; FB:FBgn0267821

(Georgias et al., 1997)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from biological aspect of ancestor with PANTHER:PTN002360678

(assigned by GO_Central )

(Gaudet et al., 2011)

inferred from sequence or structural similarity with MGI:MGI:1202715

(Ismat et al., 2010)

enables RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN002360678

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in positive regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Ismat et al., 2010)

involved_in visceral muscle development

inferred from mutant phenotype

(Ismat et al., 2010)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in developmental process

inferred from biological aspect of ancestor with PANTHER:PTN002360678

(assigned by GO_Central )

(Gaudet et al., 2011)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN002360678

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from sequence or structural similarity with MGI:MGI:1202715

(Ismat et al., 2010)

inferred from sequence or structural similarity with MGI:MGI:1333884

(Ismat et al., 2010)

Gene Group (FlyBase)

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Group (FlyBase)

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS -: Basic helix-loop-helix (bHLH) transcription factors are sequence-specific DNA-binding proteins that regulate transcription. They are characterized by a 60 amino acid region comprising a basic DNA binding domain followed by a HLH motif formed from two amphipathic α-helices connected by a loop. bHLH transcription factors form homo- and hetero-dimeric complexes, which bind to a E box consensus sequence. (Adapted from PMID:15186484).

Summary (Interactive Fly)

bHLH transcription factor - earliest specific regulator of caudal visceral mesoderm development

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\HLH54F 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

Comments on Gene Model

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

HLH54F-RA

FBtr0089547

NM_057954

1078

242

Additional Transcript Data and Comments

Reported size (kB)

1.3 (northern blot)

(Georgias et al., 1997)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

HLH54F-PA

FBpp0088516

26.9

242

7.69

NP_477302

AAF57795

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)

242 (aa)

(Georgias et al., 1997)

Comments

External Data

Crossreferences

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

Linkouts

Sequences Consistent with the Gene Model

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\HLH54F using the Feature Mapper tool.

External Data

Crossreferences

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

HLH54F_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

visceral mesoderm | precursor

(Georgias et al., 1997)

embryonic stage 13

longitudinal visceral muscle primordium

(Zaffran et al., 2001)

embryonic stage 1 -- 3

organism | faint | ubiquitous

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

mesoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

organism | anterior

(Fisher et al., 2012)

organism | posterior

(Fisher et al., 2012)

organism | segmentally repeated

(Fisher et al., 2012)

trunk mesoderm anlage

Comment: anlage in statu nascendi

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | posterior

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 11 -- 12

dorsal pharyngeal muscle primordium

(Fisher et al., 2012)

longitudinal visceral muscle primordium

(Fisher et al., 2012)

organism | segmentally repeated

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 13 -- 16

dorsal pharyngeal muscle

(Fisher et al., 2012)

longitudinal visceral muscle fiber

(Fisher et al., 2012)

embryonic stage 16

prothoracic gland

(Namiki et al., 2009)

embryonic stage 15 -- 16

ring gland

(Namiki et al., 2009)

embryonic stage 5

organism | posterior

(Namiki et al., 2009)

embryonic stage 8 -- 10

thoracic segment | restricted

(Namiki et al., 2009)

abdominal segment | restricted

(Namiki et al., 2009)

embryonic stage 14 -- 16

embryonic/larval midgut

(Namiki et al., 2009)

embryonic stage 11 -- 13

visceral muscle primordium

(Reim et al., 2012)

longitudinal visceral muscle primordium

(Reim et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Georgias et al., 1997)

somatic mesoderm | restricted

(Georgias et al., 1997)

visceral mesoderm

(Georgias et al., 1997)

Additional Descriptive Data

HLH54F transcripts are detected only in embryos on northern blots. They are first detected by in situ hybridization at the cellular blastoderm stage at the posterior end of the mesoderm anlage. After gastrulation, these cells move out of the mesoderm layer and enter the space between the germ band and the posterior midgut anlage. They then separate in to two lateral populations. By the end of germ band retraction, they are distributed throughout the trunk region of the embryo. They begin to ensheath the midgut after it fuses. These cells are thought to be visceral mesoderm. 11 groups of cells within the somatic mesoderm also express HLH54F transcripts. They may correspond to clusters from which muscle progenitors segregate.

(Georgias et al., 1997)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{HLH54Fb-lacZ.H-Pelican}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 11 -- 13

visceral muscle primordium

(Reim et al., 2012)

longitudinal visceral muscle primordium

(Reim et al., 2012)

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\HLH54F in GBrowse 2

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

View exonic expression by developmental stage for Dmel\HLH54F

View exonic expression by tissue for Dmel\HLH54F

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

FBgn0022740

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0022740

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG5005-RA

Flygut - An atlas of the Drosophila adult midgut

FBgn0022740

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 14 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of HLH54F

Transgenic constructs containing regulatory region of HLH54F

Aberrations (Deficiencies and Duplications) ( 3 )

Inferred from experimentation

Gene disrupted in

Df(2R)Exel7150

(Ryder, 2004.4.26)

Df(2R)HLH54F^Δ598

(Ismat et al., 2010)

Gene partially disrupted in

Df(2R)HLH54F^Δ219

(Ismat et al., 2010)

Inferred from location

Phenotypes

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

Lethality

Allele

lethal

HLH54F^S0323

partially lethal - majority die (with Df(2R)02B10Y-12)

partially lethal - majority die (with Df(2R)14H10W-21)

partially lethal - majority die (with HLH54F^S0323)

HLH54F^Δ598

partially lethal - majority die (with HLH54F^S1750)

HLH54F^Δ598

partially lethal - majority die (with HLH54F^Δ598)

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

HLH54F^GD4358

viable, with Scer\GAL4^Mef2.PR

HLH54F^GD4358

viable, with Scer\GAL4^pnr-MD237

HLH54F^GD4358

viable, with Scer\GAL4^tin.CΔ4

HLH54F^GD4358

Other Phenotypes

Allele

increased cell death

HLH54F^Δ598

visible, with Scer\GAL4^Bx-MS1096

HLH54F^{UAS.ORF.GW.Tag:HA}

visible, with Scer\GAL4^pnr-MD237

HLH54F^GD4358

visible | cold sensitive, with Scer\GAL4^Bx-MS1096

HLH54F^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

cardioblast, with Scer\GAL4^how-24B, Scer\GAL4^twi.2PE

HLH54F^UAS.cIa

embryonic/larval midgut muscle

embryonic/larval midgut muscle, with Scer\GAL4^how-24B, Scer\GAL4^twi.2PE

HLH54F^UAS.cIa

embryonic/larval midgut muscle (with HLH54F^S1750)

HLH54F^Δ598

embryonic/larval midgut muscle (with HLH54F^Δ598)

HLH54F^S1750

embryonic somatic muscle, with Scer\GAL4^how-24B, Scer\GAL4^twi.2PE

HLH54F^UAS.cIa

longitudinal muscle

longitudinal muscle, with Scer\GAL4^d.HLH54F

HLH54F^KK103428

longitudinal muscle (with HLH54F^S1750)

HLH54F^Δ598

longitudinal muscle (with HLH54F^Δ598)

HLH54F^S1750

longitudinal visceral muscle fiber

longitudinal visceral muscle fiber, with Scer\GAL4^d.HLH54F

HLH54F^KK103428

longitudinal visceral muscle fiber (with HLH54F^S1750)

HLH54F^Δ598

longitudinal visceral muscle fiber (with HLH54F^Δ598)

HLH54F^S1750

longitudinal visceral muscle primordium

longitudinal visceral muscle primordium, with Scer\GAL4^d.HLH54F

HLH54F^KK103428

longitudinal visceral muscle primordium (with HLH54F^S1750)

HLH54F^Δ598

longitudinal visceral muscle primordium (with HLH54F^Δ598)

HLH54F^S1750

mesothoracic tergum, with Scer\GAL4^pnr-MD237

HLH54F^GD4358

wing, with Scer\GAL4^Bx-MS1096

HLH54F^{UAS.ORF.GW.Tag:HA}

wing | cold sensitive, with Scer\GAL4^Bx-MS1096

HLH54F^{UAS.ORF.GW.Tag:HA}

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (27)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\TCF21

7 of 15

Yes

Hsap\MSC

6 of 15

Yes

Hsap\FERD3L

2 of 15

Hsap\FIGLA

2 of 15

Yes

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

Yes

Hsap\TCF24

2 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (28)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Tcf21

7 of 15

Yes

Mmus\Msc

6 of 15

Yes

Mmus\Ferd3l

2 of 15

Mmus\Figla

2 of 15

Yes

2 of 15

2 of 15

2 of 15

2 of 15

2 of 15

Yes

Mmus\Tcf24

2 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Rattus norvegicus (Norway rat) (26)

Rnor\Tcf21

6 of 13

Yes

Rnor\Msc

5 of 13

Yes

Rnor\Ferd3l

2 of 13

Rnor\Figla

2 of 13

Yes

2 of 13

2 of 13

2 of 13

2 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

Yes

Rnor\Tmem9b

1 of 13

Rnor\Twist1

1 of 13

Rnor\Twist2

1 of 13

Xenopus tropicalis (Western clawed frog) (19)

Xtro\msc

6 of 12

Yes

Xtro\tcf21

6 of 12

Yes

Xtro\figla

2 of 12

Yes

2 of 12

2 of 12

2 of 12

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

Danio rerio (Zebrafish) (27)

Drer\msc

7 of 15

Yes

Drer\tcf21

7 of 15

Yes

Drer\figla

2 of 15

Yes

Drer\hand2

2 of 15

Drer\scxa

2 of 15

Drer\scxb

2 of 15

Drer\si:ch211-246m6.4

2 of 15

Drer\tcf15

2 of 15

Drer\tcf23

2 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (10)

Cele\hlh-10

4 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Yes

1 of 15

1 of 15

1 of 15

1 of 15

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (0)

No records found.

Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190H9L )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila suzukii

Spotted wing Drosophila

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA18588

Drosophila persimilis

Dper\GL17221

Drosophila willistoni

Dwil\GK22890

Drosophila virilis

Dvir\GJ22243

Drosophila mojavensis

Dmoj\GI19113

Drosophila grimshawi

Dgri\GH22024

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150C9B )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17021754

Glossina morsitans

Tsetse fly

Gmor\GMOY010775

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_11550

Mayetiola destructor

Hessian fly

Mdes\Mdes008148

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0SKI )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA012033

Danaus plexippus

Monarch butterfly

Dple\DPOGS207303-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL007364

Apis florea

Little honeybee

Aflo\3692063284

Apis mellifera

Western honey bee

Amel\GB42177

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP14678

Bombus terrestris

Buff-tailed bumblebee

Bter\15209781

Linepithema humile

Argentine ant

Lhum\LH22462

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:00195e

Tribolium castaneum

Red flour beetle

Tcas\TC002349

Pediculus humanus

Human body louse

Phum\PHUM294350

Cimex lectularius

Bed bug

Clec\CLEC012607

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI002601

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_12128

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0QTP )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR006929

Ixodes scapularis

Black-legged tick

Isca\ISCW019706

Stegodyphus mimosarum

African social velvet spider

Smim\KFM56721.1

Tetranychus urticae

Two-spotted spider mite

Turt\tetur13g02170

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_37461

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0N6P )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Myor2

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000029024

Gallus gallus

Domestic chicken

Ggal\MSC

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (12)

Gene Symbol

Score

Source

Alignment

3 of 10

3 of 10

3 of 10

3 of 10

3 of 10

twi

2 of 10

1 of 10

ase

1 of 10

HLH3B

1 of 10

HLH4C

1 of 10

l(1)sc

1 of 10

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Model Summary Ribbon

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 v8.0 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?

TCF21; transcription factor 21

7 of 15

603306

MSC; musculin

6 of 15

603628

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

Interactions Browser

View in Interactions Browser

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

HLH54F - CG12744

two hybrid array

(Shokri et al., 2019)

HLH54F - CG15269

two hybrid array

(Shokri et al., 2019)

HLH54F - CG17195

two hybrid array

(Shokri et al., 2019)

HLH54F - Hr78

two hybrid array

(Shokri et al., 2019)

HLH54F - Ubx

bimolecular fluorescence complementation, fluorescence microscopy

(Bischof et al., 2018)

HLH54F - Uev1A

anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based

(Rhee et al., 2014)

HLH54F - abd-A

bimolecular fluorescence complementation, fluorescence microscopy

(Bischof et al., 2018)

HLH54F - bsh

two hybrid array

(Shokri et al., 2019)

HLH54F - da

two hybrid

(Georgias et al., 1997)

HLH54F - svp

two hybrid array

(Shokri et al., 2019)

Summary of Genetic Interactions

esyN Network Diagram

esyN Network Key:

Suppression

Enhancement

View in Interactions Browser

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

HLH54F

enhanceable

(Ismat et al., 2010)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

enhanceable

HLH54F

(Ismat et al., 2010)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

62712

DroID - A comprehensive database of gene and protein interactions.

FBgn0022740

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

37027

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

HLH54F

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

2-84

Cytogenetic map

54E8-54E8

Sequence location

2R:17,757,405..17,760,517 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

54E8-54E8

Limits computationally determined from genome sequence between P{EP}sub^EP616 and P{PZ}grh⁰⁶⁸⁵⁰&P{lacW}olf186-F^k11505

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

54F-54F

(Hinz, 1997.9.9)

54F-55A

(determined by in situ hybridisation)

(Georgias et al., 1997)

Experimentally Determined Recombination Data

Location

2-84

(FlyBase, 2016)

2-86.8

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (11)

Bloomington

55841

w¹¹¹⁸; PBac{HLH54F-GFP.FPTB}VK00033

28698

y¹ v¹; P{TRiP.JF03114}attP2

78726

y¹ sc^* v¹ sev²¹; P{TOE.GS02196}attP40

65244

y¹ sc^* v¹ sev²¹; P{TRiP.HMC06030}attP2

83187

y¹ w^*; TI{CRIMIC.TG4.0}HLH54F^{CR00737-TG4.0}/SM6a

FlyORF

F003322

M{UAS-HLH54F.ORF-CC}ZH-21F

F000024

M{UAS-HLH54F.ORF.3xHA.GW}ZH-86Fb

VDRC

v103965

P{KK103428}VIE-260B

v13725

w¹¹¹⁸; P{GD4358}v13725

v318060

PBac{fTRG00153.sfGFP-TVPTBF}VK00033

v341442

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD00509}attP40/CyO-GFP

Genomic Clones (15)

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

cDNA Clones (34)

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

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.

FBgn0022740

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0022740

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

37027

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Additional comments

Other Comments

HLH54F is required for the specification of the caudal viscerl mesoderm. The development of the longitudinal visceral muscles is critically dependent on HLH54F function.

(Ismat et al., 2010)

HLH54F is required not only for the survival of the caudal visceral mesoderm, but also for the initia specification and, in this context, for the correct migratory properties of these cells.

(Ismat et al., 2010)

HLH54F is required for the specification and migration of longitudinal gut muscle founders from the caudal mesoderm.

(Ismat et al., 2010)

HLH54F has been cloned and characterised. Isolated using the yeast two-hybrid system in a screen for proteins that interact with da protein.

(Georgias et al., 1997)

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 30 )

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.

37027

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

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0022740

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

FBgn0022740

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

HLH54F_1

Flygut - An atlas of the Drosophila adult midgut

FBgn0022740

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

37027

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

TC002349

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

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

Dmel_CG5005

modMine - A data warehouse for the modENCODE project

FBgn0022740

Linkouts

BioGRID - A database of protein and genetic interactions.

62712

DPiM - Drosophila Protein interaction map

FBgn0022740

DroID - A comprehensive database of gene and protein interactions.

FBgn0022740

DRSC - Results frm RNAi screens

FBgn0022740

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

FBgn0022740

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG5005-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0022740

FlyMine - An integrated database for Drosophila genomics

FBgn0022740

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.

37027

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

HLH54F

Synonyms and Secondary IDs (7)

Reported As

Symbol Synonym

CG5005

(Hosono et al., 2015, Keleman et al., 2009.8.5, Perkins et al., 2009, Stevens et al., 2008, Stevens et al., 2008)

HLH102C

HLH54

(Stepanik et al., 2016)

HLH54F-Dm

(Namiki et al., 2009)

bHLH54F

(Frasch et al., 2007, Ismat et al., 2006, Kalscheuer et al., 2001, San Martin et al., 2001, Zaffran et al., 2001, Hinz, 1997.9.9)

bHLHa9

(Stevens et al., 2008)

Name Synonyms

HLH54F

Secondary FlyBase IDs

FBgn0020923

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (68)

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

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