FlyBase Gene Report: Dmel\HLH4C

General Information

Symbol

Dmel\HLH4C

Species

D. melanogaster

Name

Helix loop helix protein 4C

Annotation Symbol

CG3052

Feature Type

protein_coding_gene

FlyBase ID

FBgn0011277

Gene Model Status

Current

Stock Availability

9 publicly available

Gene Snapshot

Contributions welcome

Other Summaries

Alliance
Auto summary
Gene Group
Interactive Fly

Key Links

Genomic Location

Cytogenetic map

4C10-4C11

Sequence location

X:4,645,127..4,647,414 [-]

Recombination map

1-8

RefSeq locus

NC_004354 REGION:4645127..4647414

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 (4 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 DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from biological aspect of ancestor with PANTHER:PTN001015390

(assigned by GO_Central )

(Gaudet et al., 2011)

enables protein dimerization activity

inferred from electronic annotation with InterPro:IPR011598

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

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

inferred from biological aspect of ancestor with PANTHER:PTN001015390

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN001015390

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

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).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\HLH4C 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

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.44

Gene model reviewed during 5.52

Sequence Ontology: Class of Gene

gene_with_stop_codon_read_through

(Jungreis et al., 2011)

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

HLH4C-RA

FBtr0070691

NM_057641

1424

167

HLH4C-RB

FBtr0331163

NM_001272314

1424

191

Additional Transcript Data and Comments

Reported size (kB)

1.5 (northern blot)

(Varterasian et al., 1993)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

HLH4C-PA

FBpp0070659

19.0

167

9.63

NP_476989

AAF45967

HLH4C-PB

FBpp0303590

21.4

191

8.80

NP_001259243

AGB95089

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

162 (aa); 18 (kD predicted)

(Varterasian et al., 1993)

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\HLH4C using the Feature Mapper tool.

External Data

Crossreferences

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

HLH4C_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 11 -- 12

ventral nerve cord primordium

(Fisher et al., 2012)

central brain primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic pars intercerebralis

(Fisher et al., 2012)

ventral nerve cord

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Varterasian et al., 1993)

embryonic stage 12 -- 17

neuron

(Varterasian et al., 1993)

presumptive embryonic/larval central nervous system | restricted

(Varterasian et al., 1993)

Additional Descriptive Data

HLH4C transcripts are detected in embryos on northern blots. They are detected by in situ hybridization from stage 12 on in mature neurons of the CNS.

(Varterasian et al., 1993)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\HLH4C 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\HLH4C

View exonic expression by tissue for Dmel\HLH4C

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

FBgn0011277

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

FBgn0011277

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG3052-RA

Flygut - An atlas of the Drosophila adult midgut

FBgn0011277

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 1 )

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 HLH4C

Transgenic constructs containing regulatory region of HLH4C

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation

Inferred from location

Phenotypes

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

Lethality

Allele

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

HLH4C^GD4357

viable, with Scer\GAL4^Mef2.PR

HLH4C^GD4357

viable, with Scer\GAL4^pnr-MD237

HLH4C^GD4357

viable, with Scer\GAL4^tin.CΔ4

HLH4C^GD4357

Other Phenotypes

Allele

visible, with Scer\GAL4^Bx-MS1096

HLH4C^{UAS.ORF.GW.Tag:HA}

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

HLH4C^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

wing, with Scer\GAL4^Bx-MS1096

HLH4C^{UAS.ORF.GW.Tag:HA}

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

HLH4C^{UAS.ORF.GW.Tag:HA}

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v8.0)

Homo sapiens (Human) (23)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\NHLH1

7 of 15

Yes

Hsap\NHLH2

5 of 15

Yes

2 of 15

2 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

1 of 15

1 of 15

Model Organism Orthologs (via DIOPT v8.0)

Mus musculus (laboratory mouse) (24)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Nhlh1

8 of 15

Yes

Mmus\Nhlh2

6 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

1 of 15

1 of 15

1 of 15

1 of 15

Rattus norvegicus (Norway rat) (22)

Rnor\Nhlh1

7 of 13

Yes

Rnor\Nhlh2

3 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

Xenopus tropicalis (Western clawed frog) (17)

Xtro\nhlh1

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

1 of 12

1 of 12

1 of 12

Danio rerio (Zebrafish) (20)

Drer\nhlh2

7 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

Drer\si:ch211-246m6.4

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (7)

Cele\hlh-15

8 of 15

Yes

1 of 15

1 of 15

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) ( EOG09190I4T )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA15893

Drosophila persimilis

Dper\GL14555

Drosophila willistoni

Dwil\GK16457

Drosophila virilis

Dvir\GJ15714

Drosophila mojavensis

Dmoj\GI16068

Drosophila grimshawi

Dgri\GH17630

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150H1S )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17027348

Musca domestica

House fly

Mdoa\17006630

Glossina morsitans

Tsetse fly

Gmor\GMOY003780

Mayetiola destructor

Hessian fly

Mdes\Mdes003895

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL004428

Anopheles darlingi

American malaria mosquito

Adar\ADAC006978

Anopheles gambiae

Malaria mosquito

Agam\AGAP004907

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0LVF )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA008476

Danaus plexippus

Monarch butterfly

Dple\DPOGS207889-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL010237

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG001563

Tribolium castaneum

Red flour beetle

Tcas\GLEAN_07725

Cimex lectularius

Bed bug

Clec\CLEC002464

Acyrthosiphon pisum

Pea aphid

Apim\ACYPI007008

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0M37 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR007908

Ixodes scapularis

Black-legged tick

Isca\ISCW014797

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0RR2 )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_011082gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Ptf1a

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Ncsl

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Par1

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000000045

Ciona intestinalis

Vase tunicate

Cint\LOC778542

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000025817

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000026276

Gallus gallus

Domestic chicken

Ggal\ENSGALG00000027144

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v8.0)

Drosophila melanogaster (Fruit fly) (11)

Gene Symbol

Score

Source

Alignment

2 of 10

1 of 10

ase

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

1 of 10

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?

NHLH1; nescient helix-loop-helix 1

7 of 15

162360

NHLH2; nescient helix-loop-helix 2

5 of 15

162361

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

HLH4C - CG14965

two hybrid array

(Shokri et al., 2019)

HLH4C - l(2)05714

two hybrid

(Hu et al., 2017.6.13)

Summary of Genetic Interactions

esyN Network Diagram

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.

57914

DroID - A comprehensive database of gene and protein interactions.

FBgn0011277

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

31397

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

HLH4C

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

External Data

Linkouts

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-8

Cytogenetic map

4C10-4C11

Sequence location

X:4,645,127..4,647,414 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

4C10-4C11

Limits computationally determined from genome sequence between P{EP}CG2930^EP1352 and P{EP}EP425

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

4C3-4C4

(Varterasian, 1993)

4C3-4C4

(determined by in situ hybridisation)

(Varterasian et al., 1993)

Experimentally Determined Recombination Data

Location

1-8

(FlyBase, 2016)

1-7.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (9)

Bloomington

26589

w^* P{EP}HLH4C^G351

25976

y¹ v¹; P{TRiP.JF01998}attP2

61837

y¹ v¹; P{TRiP.HMJ23320}attP40

83666

y¹ w^*; PBac{HLH4C-GFP.FPTB}VK00037

65128

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05984}attP40

FlyORF

F003315

M{UAS-HLH4C.ORF-CC}ZH-21F

F000905

M{UAS-HLH4C.ORF.3xHA.GW}ZH-86Fb

VDRC

v100779

P{KK108583}VIE-260B

v13724

w¹¹¹⁸; P{GD4357}v13724

Genomic Clones (13)

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

cDNA Clones (1)

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

IP01307

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.

FBgn0011277

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0011277

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

31397

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for identity of: HLH4C CG3052

(Zhao, 1999.11)

Source for database merge of

Additional comments

Other Comments

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 32 )

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.

31397

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

FBgn0011277

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

FBgn0011277

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

HLH4C_1

Flygut - An atlas of the Drosophila adult midgut

FBgn0011277

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

31397

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

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

Dmel_CG3052

modMine - A data warehouse for the modENCODE project

FBgn0011277

Linkouts

BioGRID - A database of protein and genetic interactions.

57914

DroID - A comprehensive database of gene and protein interactions.

FBgn0011277

DRSC - Results frm RNAi screens

FBgn0011277

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

FBgn0011277

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG3052-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0011277

FlyMine - An integrated database for Drosophila genomics

FBgn0011277

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

31397

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

HLH4C

Synonyms and Secondary IDs (6)

Reported As

Symbol Synonym

CG3052

(Keleman et al., 2009.8.5, Perkins et al., 2009, Perkins et al., 2009.1.15, Stevens et al., 2008, Stevens et al., 2008)

DroNHLH

(Varterasian et al., 1993)

EG:84H4.2

HLH4C

(Shokri et al., 2019, Bischof et al., 2018, Hu et al., 2017.6.13, model organism Encyclopedia of Regulatory Network (modERN) Project, 2015-, Schertel et al., 2015, Japanese National Institute of Genetics, 2012.5.21, Guest et al., 2011, Jungreis et al., 2011, Park et al., 2008, Hoskins et al., 2005, Wang et al., 2004)

bHLH36

(Stevens et al., 2008)

Name Synonyms

Helix loop helix protein 4C

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (44)

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

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