FlyBase Gene Report: Dmel\Six4

General Information

Symbol

Dmel\Six4

Species

D. melanogaster

Name

Six4

Annotation Symbol

CG3871

Feature Type

protein_coding_gene

FlyBase ID

FBgn0027364

Gene Model Status

Current

Stock Availability

10 publicly available

Gene Summary

Six4 (Six4) encodes a homeodomain-containing transcription factor required for mesodermal patterning to form the embryonic gonad. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

DSix4, D-Six4

Key Links

Genomic Location

Cytogenetic map

77E6-77E6

Sequence location

3L:20,788,886..20,792,777 [-]

Recombination map

3-47

RefSeq locus

NT_037436 REGION:20788886..20792777

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 DNA binding

inferred from electronic annotation with InterPro:IPR001356

(InterPro Project Members, 2004-)

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

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000044272

(GO Reference Genome Project, 2011-)

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

inferred from biological aspect of ancestor with PANTHER:PTN000044272

(GO Reference Genome Project, 2011-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

involved_in fat body development

inferred from mutant phenotype

(Clark et al., 2006)

involved_in gonad development

inferred from mutant phenotype

(Kirby et al., 2001)

involved_in mesoderm development

inferred from mutant phenotype

(Clark et al., 2006)

involved_in myoblast fusion

inferred from mutant phenotype

(Kirby et al., 2001)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in regulation of DNA-templated transcription

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN000044272

(GO Reference Genome Project, 2011-)

Cellular Component (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000044272

(GO Reference Genome Project, 2011-)

part_of transcription regulator complex

inferred from biological aspect of ancestor with PANTHER:PTN000044272

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

SINE OCULIS HOMEOBOX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Six4 (Six4) encodes a homeodomain-containing transcription factor required for mesodermal patterning to form the embryonic gonad. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

SINE OCULIS HOMEOBOX TRANSCRIPTION FACTORS -: Sine oculis homeobox (SIX) transcription factors are sequence-specific DNA binding proteins that regulate transcription and play important role in development. They are characterized by 120 amino acid SIX-type DNA-binding domain N-terminal to a homeodomain. (Adapted from FBrf0232555, FBrf0128773 and PMID:18797923).

Summary (Interactive Fly)

homeodomain transcription factor - confers ventral mesodermal cell fate - regulates somatic cell function during gonadogenesis

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Six4 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 Q9Y1P6)

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 5.45

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Six4-RA

FBtr0078274

NM_140999

1849

392

Six4-RB

FBtr0078275

NM_168872

1426

392

Additional Transcript Data and Comments

Reported size (kB)

1.845 (compiled cDNA)

(Seo et al., 1999)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

Six4-PA

FBpp0077932

43.7

392

8.20

FBpp0077933

43.7

392

8.20

Q9Y1P6

NP_730566

AAN12144

Polypeptides with Identical Sequences

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

392 aa isoforms: Six4-PA, Six4-PB

Additional Polypeptide Data and Comments

Reported size (kDa)

392 (aa)

(Seo et al., 1999)

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

Q9Y1P6

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Six4 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).

3.04

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

procephalic segment

(Seo et al., 1999)

embryonic brain

(Seo et al., 1999)

organism | 80-90% egg length

Comment: 85-90% egg length

(Seo et al., 1999)

embryonic stage 4 -- 6

central brain anlage in statu nascendi

(Fisher et al., 2012)

antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)

dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)

visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

(Fisher et al., 2012)

embryonic stage 7 -- 8

antennal anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

central brain anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

visual anlage

Comment: reported as procephalic ectoderm anlage

(Fisher et al., 2012)

ventral ectoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

mesoderm

(Seo et al., 1999)

central brain primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 9 -- 11

trunk mesoderm

(Clark et al., 2006)

embryonic stage 10

trunk mesoderm | lateral | ventral

(Clark et al., 2006)

embryonic stage 11

gonadal sheath proper primordium

(Clark et al., 2006)

embryonic stage 11 -- 12

central brain primordium

(Fisher et al., 2012)

pars intercerebralis primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic stage 15

larval ventral nerve cord

(Seo et al., 1999)

gonad

(Seo et al., 1999)

oogenesis stage S9 -- S10

border follicle cell

(Borghese et al., 2006)

Additional Descriptive Data

Six4 is highly expressed in migrating border follicle cells.

(Borghese et al., 2006)

Six4 transcript is expressed in the trunk mesoderm, and is excluded from the cephalic mesoderm of the developing embryo. Expression begins at embryonic stage 9, and is initially broadly distributed in a pattern coinciding with that of Mef2. By stage 10, Six4 transcript is restricted to ventral and lateral mesoderm. After embryonic stage 11, Six4 transcript expression is rapidly lost from all mesodermal cells except the gonadal sheath proper primordium (somatic gonadal precursor cells).

(Clark et al., 2006)

Six4 transcripts are first expressed in cellular blastoderm embryos in a dorsal patch at 85-90% egg length. The patch is wider at the center than at the lateral edges. The pattern splits into two bilateral domains and persists in the dorsal part of the procephalic lobe during gastrulation and germ band extension. By stage 9-10, transcripts are detected in the mesoderm along the length of the entire germ band. Mesodermal staining occurs in a bilateral pair of longitudinal bands connected by transverse stripes. The mesodermal staining disappears by stage 11. As the germ band retracts, the two domains of Six4 expression narrow and lengthen and become associated with the dorsal and medial parts of the two brain hemispheres. By stage 15, some expression is observed in the ventral cord and the gonads.

(Seo et al., 1999)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage | female & oogenesis

prefollicle cell

(Johnston et al., 2016)

oogenesis & adult stage | female

main body follicle cell

(Johnston et al., 2016)

Additional Descriptive Data

Six4 protein is detected throughout the follicle cells in the germarium, and in nuclei of later stage oocyte associated (main body) follicle cells, but not in interfollicle (stalk) cells.

(Johnston et al., 2016)

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{Six4-III-H-Stinger}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 10

trunk mesoderm

(Clark et al., 2006)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Six4 in JBrowse

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

View exonic expression by developmental stage for Dmel\Six4

View exonic expression by tissue for Dmel\Six4

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

FBgn0027364

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

40297/tissue=All

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

FBgn0027364

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0027364

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

FBgn0027364

Flygut - An atlas of the Drosophila adult midgut

FBgn0027364

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 ( 14 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Six4

Transgenic constructs containing regulatory region of Six4

Aberrations (Deficiencies and Duplications) ( 1 )

Inferred from experimentation ( 1 )

Gene disrupted in

Df(3L)ri^XT106

(Kirby et al., 2001)

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

Six4¹⁰⁸

lethal (with Six4¹⁰⁸)

Six4²⁸⁹

lethal (with Six4²⁸⁹)

Six4¹⁰⁸

lethal | larval stage | partially | recessive

Six4¹³¹

lethal | partially | pupal stage | recessive

Six4¹³¹

lethal - all die during embryonic stage | recessive

Six4²⁸⁹

viable

Six4^EY09833

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

Six4^GD4133

viable, with Scer\GAL4^pnr-MD237

Six4^GD4133

viable, with Scer\GAL4^tin.CΔ4

Sterility

Allele

fertile

Six4^EY09833

Other Phenotypes

Allele

abnormal cell number | larval stage, with Scer\GAL4^pnt-14-94

Six4^HM05254

abnormal neuroanatomy | larval stage, with Scer\GAL4^GMR9D11

Six4^HM05254

abnormal neuroanatomy | larval stage, with Scer\GAL4^pnt-14-94

decreased cell number | larval stage, with Scer\GAL4^pnt-14-94

Six4^{UAS.ORF.GW.Tag:HA}

increased cell death

Six4²⁸⁹

increased cell number | larval stage, with Scer\GAL4^GMR9D11

Six4^HM05254

increased cell number | larval stage, with Scer\GAL4^pnt-14-94

increased cell number | oogenesis, with Scer\GAL4^109-30

Six4^{UAS.ORF.GW.Tag:HA}

increased cell number | oogenesis | somatic clone, with Scer\GAL4^109-30

Six4¹⁰⁸

some die during embryonic stage | recessive

Six4²⁸⁹

visible, with Scer\GAL4^Bx-MS1096

Six4^{UAS.ORF.GW.Tag:HA}

Phenotype manifest in

Allele

adult abdomen

Six4¹³¹

basal stalk, with Scer\GAL4^109-30

basal stalk | somatic clone

Six4¹⁰⁸

border follicle cell | ectopic | somatic clone

Six4²⁸⁹

crop

Six4¹³¹

egg chamber, with Scer\GAL4^109-30

Six4^HM05254

egg chamber | somatic clone

Six4¹⁰⁸

embryonic somatic muscle cell

Six4²⁸⁹

eye, with Scer\GAL4^GMR.PU

Six4^UAS.cCa

fat body/gonad primordium

Six4²⁸⁹

follicle cell, with Scer\GAL4^109-30

follicle stem cell | somatic clone

Six4¹⁰⁸

follicle stem cell | somatic clone, with Scer\GAL4^Tub.PU

Six4^HM05254

germarium | somatic clone

Six4¹⁰⁸

germarium | somatic clone, with Scer\GAL4^Tub.PU

Six4^HM05254

germline cell | embryonic stage

Six4¹³¹

gonad | embryonic stage

intermediate neuronal progenitor | decreased number | larval stage, with Scer\GAL4^GMR9D11

Six4^HM05254

intermediate neuronal progenitor | decreased number | larval stage, with Scer\GAL4^pnt-14-94

Six4^{UAS.ORF.GW.Tag:HA}

larval brain | larval stage, with Scer\GAL4^GMR9D11

Six4^HM05254

larval brain | larval stage, with Scer\GAL4^pnt-14-94

larval muscle system

ovary

Six4¹³¹

segment border muscle cell

Six4²⁸⁹

stalk follicle cell, with Scer\GAL4^109-30

Six4^{UAS.ORF.GW.Tag:HA}

testis

Six4¹³¹

type II neuroblast | increased number | larval stage, with Scer\GAL4^GMR9D11

Six4^HM05254

type II neuroblast | increased number | larval stage, with Scer\GAL4^pnt-14-94

ventral longitudinal muscle cell

Six4²⁸⁹

ventral oblique muscle cell

Six4²⁸⁹

wing, with Scer\GAL4^Bx-MS1096

Six4^{UAS.ORF.GW.Tag:HA}

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) (54)

Hsap\SIX4

8 of 14

Yes

Hsap\SIX5

4 of 14

Yes

3 of 14

3 of 14

2 of 14

2 of 14

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

Yes

Hsap\DRGX

1 of 14

Hsap\DUX4

1 of 14

Hsap\DUX4L4

1 of 14

Yes

Hsap\DUX4L7

1 of 14

Yes

Hsap\DUXA

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

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (64)

Rnor\Six4

8 of 14

Yes

Rnor\Six1

3 of 14

Rnor\Six5

3 of 14

Yes

2 of 14

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

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

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

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

Yes

Rnor\Rhox3

1 of 14

Yes

Rnor\Rhox4g

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

Yes

Mus musculus (laboratory mouse) (80)

Mmus\Six4

8 of 14

Yes

Mmus\Six5

4 of 14

Yes

3 of 14

3 of 14

2 of 14

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

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

Yes

Mmus\Rhox2a

1 of 14

Yes

Mmus\Rhox2b

1 of 14

Yes

Mmus\Rhox2c

1 of 14

Yes

Mmus\Rhox2d

1 of 14

Yes

Mmus\Rhox2e

1 of 14

Yes

Mmus\Rhox2f

1 of 14

Yes

Mmus\Rhox2g

1 of 14

Yes

Mmus\Rhox2h

1 of 14

Yes

Mmus\Rhox3a2

1 of 14

Yes

Mmus\Rhox3a

1 of 14

Yes

Mmus\Rhox3c

1 of 14

Yes

Mmus\Rhox3e

1 of 14

Yes

Mmus\Rhox3f

1 of 14

Yes

Mmus\Rhox3g

1 of 14

Yes

Mmus\Rhox3h

1 of 14

Yes

Mmus\Rhox4a2

1 of 14

Yes

Mmus\Rhox4a

1 of 14

Yes

Mmus\Rhox4b

1 of 14

Yes

Mmus\Rhox4c

1 of 14

Yes

Mmus\Rhox4d

1 of 14

Yes

Mmus\Rhox4e

1 of 14

Yes

Mmus\Rhox4f

1 of 14

Yes

Mmus\Rhox4g

1 of 14

Yes

Mmus\Rhox6

1 of 14

Yes

Mmus\Rhox7a

1 of 14

Yes

Mmus\Rhox7b

1 of 14

Yes

Mmus\Rhox9

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

Xenopus tropicalis (Western clawed frog) (43)

Xtro\six4

4 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

Xtro\homeobox100496651-provisional

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

Xtro\sia3

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

Danio rerio (Zebrafish) (67)

Drer\six4a

6 of 14

Yes

Drer\six4b

6 of 14

Yes

Drer\six5

5 of 14

Yes

3 of 14

3 of 14

3 of 14

3 of 14

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

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

1 of 14

1 of 14

Yes

Drer\zhx2a

1 of 14

Yes

Caenorhabditis elegans (Nematode, roundworm) (21)

Cele\ceh-33

4 of 14

Yes

Cele\ceh-34

4 of 14

Yes

Cele\unc-39

4 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

Anopheles gambiae (African malaria mosquito) (18)

Agam\AgaP_AGAP011067

11 of 12

Yes

Agam\AgaP_AGAP011065

10 of 12

Yes

4 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) (17)

Atha\AT4G12750

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

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\TOS8

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Six4. 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) (15)

8 of 13

Optix

7 of 13

1 of 13

B-H1

1 of 13

B-H2

1 of 13

CG34367

1 of 13

Dbx

1 of 13

Dll

1 of 13

exd

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

tup

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 1 )

Human Ortholog

Disease

Evidence

References

SIX5; SIX homeobox 5

model of branchiootorenal syndrome 2

IEA

(FlyBase, 2019-)

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?

8 of 14

4 of 14

BRANCHIOOTORENAL SYNDROME 2; BOR2

branchiootorenal syndrome 2

ANHX; anomalous homeobox

3 of 14

SIX2; SIX homeobox 2

3 of 14

604994

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

Six4 - CG18599

two hybrid array

(Shokri et al., 2019)

Six4 - Ubx

bimolecular fluorescence complementation, fluorescence microscopy

(Bischof et al., 2018)

Six4 - abd-A

bimolecular fluorescence complementation, fluorescence microscopy

(Bischof et al., 2018)

Six4 - erm

anti tag coimmunoprecipitation, anti tag western blot

(Chen et al., 2021)

Six4 - pnt

anti tag coimmunoprecipitation, anti tag western blot

(Chen et al., 2021)

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

Six4

suppressible

pros

(Chen et al., 2021)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

erm

suppressible

Six4

(Chen et al., 2021)

erm

enhanceable

Six4

(Chen et al., 2021)

pnt

suppressible

Six4

(Chen et al., 2021)

suppressible

Six4

(Weasner and Kumar, 2009)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0027364

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

40297

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-47

Cytogenetic map

77E6-77E6

Sequence location

3L:20,788,886..20,792,777 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

77E6-77E6

Limits computationally determined from genome sequence between P{EP}trbl^EP3519 and P{EP}fng^EP3082&P{lacW}skd^L7062

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-47

(FlyBase, 2016)

3-43.7

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (10)

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

Bloomington

67733

y¹ w^*; P{Six4-GFP.FPTB}attP40/CyO

68232

w^*; Six4¹⁰⁸ P{FRT(w^hs)}2A/TM2

16956

y¹ w^67c23; P{EPgy2}Six4^EY09833

30510

y¹ sc^* v¹ sev²¹; P{TRiP.HM05254}attP2

79880

y¹ sc^* v¹ sev²¹; P{TOE.GS02111}attP40

FlyORF

F003236

M{UAS-Six4.ORF-CC}ZH-21F

F000049

M{UAS-Six4.ORF.3xHA.GW}ZH-86Fb

VDRC

v104958

P{KK112512}VIE-260B

v48598

w¹¹¹⁸; P{GD16294}v48598

v341914

P{hsFLP}1, y¹ w¹¹¹⁸; P{HD_CFD01174}attP40/CyO-GFP

Genomic Clones (24)

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

cDNA Clones (7)

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

GM13131

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.

FBgn0027364

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0027364

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Hwang and Rulifson, 2011)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Six4 has a role in the regulation of cell recognition events required for myoblast fusion.

(Kirby et al., 2001)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (9)

Reported As

Symbol Synonym

CG3871

(Datta et al., 2011, Hazelett et al., 2009, Keleman et al., 2009.8.5, Perkins et al., 2009, Sepp et al., 2008)

D-Six4

(Clark et al., 2005, Kiosses et al., 2005, Kirby et al., 2001, Kawakami et al., 2000, Seo et al., 1999)

D-six4

(Maire et al., 2020, Sano et al., 2012, Clark et al., 2006)

DSix4

(Mbodj et al., 2016, Anderson et al., 2012, Datta et al., 2011, Weasner and Kumar, 2009, Henderson and Kumar, 2008, Weasner and Kumar, 2008, Kumar and Henderson, 2007, Kumar and Weasner, 2007)

Dsix4

(Gehring, 2011, Seimiya and Gehring, 2000)

six4

(Sutton et al., 2024, Saha et al., 2022, Anllo et al., 2019, Gehring, 2011, Borghese et al., 2006, Borghese et al., 2005)

six4/5

(Santos and Lehmann, 2004)

Name Synonyms

Six4

(Saadin and Starz-Gaiano, 2016, Clark et al., 2007)

myotonix

(Hamilton, 2000.3.22)

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 ( 37 )

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.

40297

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.

Q9Y1P6

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

Q9Y1P6

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.

Q9Y1P6

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0027364

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

40297/tissue=All

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

FBgn0027364

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

FBgn0027364

FlyMine - An integrated database for Drosophila genomics

FBgn0027364

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

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

dme:Dmel_CG3871

MARRVEL_MODEL - MARRVEL (model organism gene)

40297

Linkouts

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

FBgn0027364

DroID - A comprehensive database of gene and protein interactions.

FBgn0027364

DRSC - Results frm RNAi screens

FBgn0027364

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

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0027364

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0027364

Flygut - An atlas of the Drosophila adult midgut

FBgn0027364

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

TC003852

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

Interactive Fly

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

40297

References (90)

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

3.04

Report Sections