FlyBase Gene Report: Dmel\bap

General Information

Symbol

Dmel\bap

Species

D. melanogaster

Name

bagpipe

Annotation Symbol

CG7902

Feature Type

protein_coding_gene

FlyBase ID

FBgn0004862

Gene Model Status

Current

Stock Availability

19 publicly available

Gene Summary

bagpipe (bap) encodes an important homeodomain transcription factor for visceral mesoderm formation, which differentiates into gut musculature. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Red Book
Interactive Fly

Also Known As

NK3, NK-3, bgp

Key Links

Genomic Location

Cytogenetic map

93D10-93D10

Sequence location

3R:21,388,880..21,390,449 [+]

Recombination map

3-71

RefSeq locus

NT_033777 REGION:21388880..21390449

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 (12 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables DNA binding

inferred from direct assay

(Zaffran and Frasch, 2002)

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

inferred from genetic interaction with FLYBASE:βTub60D; FB:FBgn0288686

(Zaffran and Frasch, 2002)

enables sequence-specific DNA binding

inferred from direct assay

(Zaffran and Frasch, 2002)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables DNA binding

inferred from electronic annotation with InterPro:IPR001356, InterPro:IPR020479

(InterPro Project Members, 2004-)

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

inferred from biological aspect of ancestor with PANTHER:PTN000678271

(GO Reference Genome Project, 2011-)

inferred from electronic annotation with InterPro:IPR017970

(InterPro Project Members, 2004-)

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

inferred from biological aspect of ancestor with PANTHER:PTN000678271

(GO Reference Genome Project, 2011-)

Biological Process (7 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in mesoderm development

inferred from expression pattern

(Furlong et al., 2001)

involved_in positive regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Zaffran and Frasch, 2002)

inferred from mutant phenotype

(Mendoza-García et al., 2017)

involved_in regulation of transcription by RNA polymerase II

inferred from mutant phenotype

(Zaffran and Frasch, 2002)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

involved_in cell differentiation

inferred from biological aspect of ancestor with PANTHER:PTN000678271

(GO Reference Genome Project, 2011-)

involved_in mesodermal cell fate commitment

traceable author statement

(Cripps and Olson, 2002)

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:PTN000678271

(GO Reference Genome Project, 2011-)

involved_in visceral muscle development

non-traceable author statement

(Furlong et al., 2001)

Cellular Component (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Reim and Frasch, 2005, Lee et al., 2003)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN000678271

(GO Reference Genome Project, 2011-)

located_in nucleus

inferred by curator from GO:0003677

(Zaffran and Frasch, 2002)

Gene Group (FlyBase)

NK-LIKE HOMEOBOX TRANSCRIPTION FACTORS

Protein Family (UniProt)

Belongs to the NK-3 homeobox family. (P22809)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

bagpipe (bap) encodes an important homeodomain transcription factor for visceral mesoderm formation, which differentiates into gut musculature. [Date last reviewed: 2019-03-07]

Gene Group (FlyBase)

NK-LIKE HOMEOBOX TRANSCRIPTION FACTORS -: NK-like (NKL) homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. NKL transcription factors are homeobox genes closely related to Hox-like genes, a number of which are found in the NK cluster. Many of the NKL members contain an Engrailed Homology 1 (EH1) motif. (Adapted from FBrf0232555 and PMID:22094586).

Protein Function (UniProtKB)

Involved in the determination of cell fates in the dorsal mesoderm.

(UniProt, P22809)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

NK3 (M. Nirenberg)

Homeobox gene expressed transiently during embryonic development in some mesodermal cells (foregut and hindgut visceral muscle cells). NK3 poly A+ RNA was not detected in 0-3-hour embryos, but was found in low abundance in RNA from 3-6-hour embryos. The abundance was maximum in RNA from 6-12-hour embryos and then declined during further embryonic development.

Summary (Interactive Fly)

transcription factor - homeodomain - NK-2 class - forms visceral mesoderm that differentiates into gut musculature - essential for differentiated heart function.

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\bap 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 P22809)

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 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

bap-RA

FBtr0084087

NM_169958

1449

382

Additional Transcript Data and Comments

Reported size (kB)

1.55 (northern blot)

(Azpiazu and Frasch, 1993)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

bap-PA

FBpp0083486

42.0

382

9.06

P22809

NP_732637

AAF55891

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)

382 (aa)

(Azpiazu and Frasch, 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\bap using the Feature Mapper tool.

External Data

Crossreferences

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

bap_1

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).

-0.56

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | ubiquitous

(Fisher et al., 2012)

embryonic stage 7 -- 8

organism | ubiquitous

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 9 -- 10

head mesoderm

(Fisher et al., 2012)

organism | ubiquitous

(Fisher et al., 2012)

trunk mesoderm

(Fisher et al., 2012)

embryonic stage 10

hindgut visceral muscle primordium

(Lee and Frasch, 2005, San Martin and Bate, 2001)

foregut visceral muscle primordium

(Lee and Frasch, 2005)

visceral trunk mesoderm

Comment: reference states trunk visceral mesoderm

(Lee and Frasch, 2005)

embryonic stage 11

visceral trunk mesoderm | segmentally repeated

(Zhai et al., 2010)

inclusive hindgut primordium

(Zhai et al., 2010)

embryonic stage 11 -- 12

cephalic vascular primordium

(Fisher et al., 2012)

procrystal cell

(Fisher et al., 2012)

somatic muscle primordium

Comment: reported as muscle system primordium

(Fisher et al., 2012)

trunk visceral muscle primordium

Comment: reported as muscle system primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

larval muscle system

(Fisher et al., 2012)

larval somatic muscle cell

(Fisher et al., 2012)

northern blot

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

(Azpiazu and Frasch, 1993)

mesoderm | dorsal

(Azpiazu and Frasch, 1993)

embryonic stage 10 -- 11

visceral trunk mesoderm of embryonic/larval midgut

(Azpiazu and Frasch, 1993)

embryonic stage 11 -- 15

visceral trunk mesoderm of embryonic/larval hindgut

(Azpiazu and Frasch, 1993)

visceral trunk mesoderm of embryonic/larval foregut

(Azpiazu and Frasch, 1993)

embryonic stage 13 -- 17

dorsal vessel wall cell

(Azpiazu and Frasch, 1993)

Additional Descriptive Data

bap is first expressed in 4-8hr embryos, peaks between 4 and 12 hours of embryogenesis and drops off dramatically subsequently. bap is expressed from embryonic stage 10 in the dorsal-most cells of the mesoderm. The bap expression occurs in patches along the anterior-posterior axis in the region corresponding to parasegments 2-12 of the epidermis which will give rise to the visceral mesoderm. Double staining for bap and en shows that the anterior border of each patch aligns with the anterior parasegmental borders. This expression is transient and disappears during stage 11. bap is also expressed in mesodermal cells at the proctodeum and stomodeum. These will develop into the visceral mesoderm of the hindgut and foregut and they continue bap expression until late embryogenesis. After stage 12, bap is also expressed in a subset of heart progenitors.

(Azpiazu and Frasch, 1993)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 10

mesoderm | striped

(Lee and Frasch, 2000)

embryonic stage 10 -- 11

visceral trunk mesoderm | striped

(Weiss et al., 2001)

embryonic stage 11

foregut primordium

(Zaffran et al., 2001)

foregut visceral muscle primordium

(Zaffran et al., 2001)

hindgut proper primordium

(Zaffran et al., 2001)

Additional Descriptive Data

At embryonic stage 10 bap expressing cell clusters are interdigitated with jeb-expressing cell clusters. At embryonic stage 11, bap-expressing cells form stripes that are adjacent and dorsal to jeb-expressing cells.

(Weiss et al., 2001)

Stripes alternate with slp.

(Lee and Frasch, 2000)

Marker for

visceral trunk mesoderm

(Weiss et al., 2001)

Subcellular Localization

CV Term

Evidence

References

located_in nucleus

inferred from direct assay

(Reim and Frasch, 2005, Lee et al., 2003)

Expression Deduced from Reporters

Reporter: P{bap-GAL4.3}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

visceral trunk mesoderm

(Hosono et al., 2003, Lee et al., 2003, Weiss et al., 2001)

embryonic stage 10 -- 17

visceral trunk mesoderm

(Stute et al., 2004)

embryonic stage 11 -- 13

visceral trunk mesoderm

(Zaffran et al., 2001)

Reporter: P{bap-lacZ.3}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 10

visceral trunk mesoderm | dorsal

Comment: reference states trunk visceral mesoderm

(Lee and Frasch, 2005)

embryonic stage 10 -- 15

circular trunk visceral muscle primordium | segmentally repeated

(Zaffran et al., 2001)

embryonic stage 10 -- 17

visceral trunk mesoderm | segmentally repeated

(Zaffran et al., 2001)

circular trunk visceral muscle primordium of midgut

(Zaffran et al., 2001)

circular trunk visceral muscle primordium | restricted

(Zaffran et al., 2001)

midgut | restricted

(Zaffran et al., 2001)

embryonic stage 11

myoblast

(Stute et al., 2004)

visceral trunk mesoderm

(Stute et al., 2004)

embryonic stage 11 -- 13

visceral trunk mesoderm

(Reim et al., 2012)

embryonic stage 12

visceral trunk mesoderm

(Zaffran and Frasch, 2002)

embryonic stage 12 -- 13

visceral trunk mesoderm

(Lee et al., 2003)

embryonic stage 12 -- 15

trunk mesoderm

(Zaffran et al., 2001)

embryonic stage 12 -- 16

visceral trunk mesoderm | segmentally repeated

(Kolsch and Paululat, 2002)

Reporter: P{bap-lacZ.4.5}

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

visceral trunk mesoderm

(Azpiazu and Frasch, 1993)

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\bap in JBrowse

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

View exonic expression by developmental stage for Dmel\bap

View exonic expression by tissue for Dmel\bap

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

FBgn0004862

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

42537/tissue=All

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

FBgn0004862

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004862

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

FBgn0004862

Flygut - An atlas of the Drosophila adult midgut

FBgn0004862

Images

FlyExpress - Embryonic expression images (BDGP data)

Show all FlyExpress processed images for Dmel\bap

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

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 17 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 17 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of bap

Transgenic constructs containing regulatory region of bap

Aberrations (Deficiencies and Duplications) ( 7 )

Inferred from experimentation ( 7 )

Gene disrupted in

Df(3R)e-BS2

(Jagla et al., 1997)

Df(3R)e-D7

(Lo and Frasch, 1998, Azpiazu and Frasch, 1993)

Df(3R)e-F1

(Jagla et al., 1997)

Gene partially disrupted in

Df(3R)e-F1

(De Graeve et al., 2004)

Df(3R)lb

(De Graeve et al., 2004)

Gene not disrupted in

Df(2R)gsb

(Azpiazu et al., 1996)

Df(3R)e-Gp4

(Jagla et al., 1997)

Df(3R)GC14

(Jagla et al., 1997, Azpiazu and Frasch, 1993, Bodmer, 1993)

Inferred from location ( 2 )

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

bap²⁰⁸

Other Phenotypes

Allele

visible | male limited, with Scer\GAL4^Bx-MS1096

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

wild-type

bap^+t11

Phenotype manifest in

Allele

embryonic/larval midgut | embryonic stage

bap²⁰⁸

embryonic/larval midgut muscle cell

bap²⁰⁸

wing | male limited, with Scer\GAL4^Bx-MS1096

bap^{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) (140)

Hsap\NKX3-2

8 of 14

Yes

Hsap\NKX3-1

4 of 14

Yes

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

Yes

Hsap\DRGX

1 of 14

Hsap\DUX1

1 of 14

Yes

Hsap\DUX3

1 of 14

Yes

Hsap\DUX4

1 of 14

Hsap\DUX4L4

1 of 14

Yes

Hsap\DUX4L7

1 of 14

Yes

Hsap\DUX4L9

1 of 14

Yes

Hsap\DUX5

1 of 14

Yes

Hsap\DUXA

1 of 14

Yes

Hsap\DUXB

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

Hsap\HHEX

1 of 14

Hsap\HLX

1 of 14

Hsap\HMBOX1

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

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

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

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

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (86)

Rnor\Nkx3-2

7 of 14

Yes

Rnor\Nkx3-1

4 of 14

Yes

3 of 14

3 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

Yes

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

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

Mus musculus (laboratory mouse) (100)

Mmus\Nkx3-2

9 of 14

Yes

Mmus\Nkx3-1

4 of 14

Yes

3 of 14

2 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

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

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

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\Rhox7b

1 of 14

Yes

Mmus\Rhox11

1 of 14

Mmus\Sebox

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (110)

Xtro\nkx3-2

6 of 13

Yes

Xtro\nkx3-3

6 of 13

Yes

Xtro\nkx3-1

2 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

Yes

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

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

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

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

Danio rerio (Zebrafish) (145)

Drer\nkx3.3

10 of 14

Yes

Drer\nkx3-2

9 of 14

Yes

Drer\nkx3-1

4 of 14

Yes

3 of 14

2 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

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

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

Caenorhabditis elegans (Nematode, roundworm) (47)

Cele\ceh-24

2 of 14

Yes

Cele\ceh-28

2 of 14

Yes

Cele\unc-30

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (50)

Agam\AgaP_AGAP003671

10 of 12

Yes

3 of 12

3 of 12

3 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

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

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) (32)

Atha\ATHB13

2 of 13

Yes

Atha\AtHB23

2 of 13

Yes

Atha\ATHB54

2 of 13

Yes

Atha\HAT3

2 of 13

Yes

Atha\HB-3

2 of 13

Yes

Atha\HB5

2 of 13

Yes

Atha\HB20

2 of 13

Yes

Atha\HB51

2 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

Yes

Atha\WOX8

1 of 13

Yes

Atha\WOX10

1 of 13

Yes

Atha\WOX13

1 of 13

Yes

Atha\WOX14

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (2)

Scer\HMRA1

1 of 13

Yes

Scer\PHO2

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\phx1

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:bap. 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) (82)

scro

6 of 13

vnd

6 of 13

HGTX

5 of 13

NK7.1

5 of 13

slou

5 of 13

tin

5 of 13

ems

4 of 13

B-H2

3 of 13

bsh

3 of 13

btn

3 of 13

cad

3 of 13

CG18599

3 of 13

exex

3 of 13

ftz

3 of 13

HHEX

3 of 13

Hmx

3 of 13

inv

3 of 13

lms

3 of 13

unpg

3 of 13

zen2

3 of 13

zen

3 of 13

2 of 13

Antp

2 of 13

Awh

2 of 13

bcd

2 of 13

B-H1

2 of 13

C15

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Dbx

2 of 13

Dfd

2 of 13

Dll

2 of 13

Drgx

2 of 13

eve

2 of 13

H2.0

2 of 13

hbn

2 of 13

ind

2 of 13

lab

2 of 13

lbe

2 of 13

lbl

2 of 13

Lim1

2 of 13

Lim3

2 of 13

Pph13

2 of 13

Scr

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

exd

1 of 13

eyg

1 of 13

gsb

1 of 13

gsb-n

1 of 13

Gsc

1 of 13

Lmx1a

1 of 13

mirr

1 of 13

OdsH

1 of 13

otp

1 of 13

PHDP

1 of 13

prd

1 of 13

Ptx1

1 of 13

repo

1 of 13

toy

1 of 13

tup

1 of 13

Ubx

1 of 13

1 of 13

1 of 13

1 of 13

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 ( 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?

NKX3-2; NK3 homeobox 2

8 of 14

602183

SPONDYLO-MEGAEPIPHYSEAL-METAPHYSEAL DYSPLASIA; SMMD

NKX3-1; NK3 homeobox 1

4 of 14

602041

NKX2-2; NK2 homeobox 2

3 of 14

604612

NKX2-8; NK2 homeobox 8

3 of 14

603245

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

RNA-RNA

Physical Interaction

Assay

References

bap - mir-4

fluorescence technology

(Brennecke et al., 2005)

bap - mir-79

fluorescence technology

(Brennecke et al., 2005)

protein-protein

Physical Interaction

Assay

References

bap - Abd-B

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

bap - Antp

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

bap - BEAF-32

two hybrid array

(Shokri et al., 2019)

bap - CG8319

two hybrid array

(Shokri et al., 2019)

bap - D

two hybrid array

(Shokri et al., 2019)

bap - Deaf1

two hybrid array

(Shokri et al., 2019)

bap - Ets65A

two hybrid array

(Shokri et al., 2019)

bap - Hr78

two hybrid array

(Shokri et al., 2019)

bap - Paris

two hybrid array

(Shokri et al., 2019)

bap - Rel

two hybrid array

(Shokri et al., 2019)

bap - Scr

bimolecular fluorescence complementation, fluorescence microscopy

(Baëza et al., 2015)

bap - Ubx

bimolecular fluorescence complementation, fluorescence microscopy

(Bischof et al., 2018, Baëza et al., 2015)

bap - abd-A

bimolecular fluorescence complementation, fluorescence microscopy, anti tag coimmunoprecipitation, anti tag western blot

(Bischof et al., 2018, Baëza et al., 2015)

bap - brk

two hybrid array

(Shokri et al., 2019)

bap - dimm

two hybrid array

(Shokri et al., 2019)

bap - exd

bimolecular fluorescence complementation, fluorescence microscopy

(Bischof et al., 2018)

bap - gro

pull down, autoradiography

(Goldstein et al., 2005)

bap - kn

two hybrid array

(Shokri et al., 2019)

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.

FBgn0004862

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

42537

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P22809

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-71

Cytogenetic map

93D10-93D10

Sequence location

3R:21,388,880..21,390,449 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

93D10-93D10

Limits computationally determined from genome sequence between P{PZ}mod(mdg4)⁰⁷⁰³⁸&P{lacW}mod(mdg4)^L3101 and P{PZ}InR⁰⁵⁵⁴⁵

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

93E1-93E1

(Kim, 1993)

93E1-93E3

(determined by in situ hybridisation)

(Kim and Nirenberg, 1989)

Experimentally Determined Recombination Data

Location

3-71

(FlyBase, 2016)

3-74.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (19)

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

Bloomington

91541

w^*; P{UAS-bap.Z}1

41242

w¹¹¹⁸; P{GMR41F12-GAL4}attP2

74501

w¹¹¹⁸; P{VT045194-p65.AD}attP40

75501

w¹¹¹⁸; P{VT045194-GAL4.DBD}attP2

91540

y¹ w^*; P{bap-GAL4.3}1.1

27061

y¹ v¹; P{TRiP.JF02404}attP2

96796

y¹ w^*; P{bap-GFP.FPTB}attP40

FlyORF

F003275

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

F000006

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

Korea

12764

P{VT045194-GAL4}attP2

VDRC

v101354

P{KK108567}VIE-260B

v318064

PBac{fTRG00160.sfGFP-TVPTBF}VK00033

More stocks available...

Genomic Clones (14)

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

cDNA Clones (3)

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

RE13967

Other clones

DPiM_RE13967

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.

FBgn0004862

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

EC25665

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004862

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Jakobsen et al., 2007, Lee and Frasch, 2000)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

bap and bin are required for activation of βTub60D in the visceral mesoderm.

(Zaffran and Frasch, 2002)

vimar is one of the bap target genes that are required for normal development and differentiation of the midgut visceral mesoderm.

(Lo and Frasch, 1998)

hh is required for the normal activation of bap and srp in anterior portions of each parasegment, whereas wg is required to suppress bap and srp expression in posterior portions. hh and wg play opposing roles in mesoderm segmentation.

(Azpiazu et al., 1996)

hh and wg activities in the gut epithelial cells are required for the expression of the homeobox gene bap in the ensheathing visceral mesoderm.

(Hoch and Pankratz, 1996)

The bap gene product is required for the specification of the visceral mesoderm.

(Azpiazu and Frasch, 1993)

Homeobox gene expressed transiently during embryonic development in some mesodermal cells (foregut and hindgut visceral muscle cells). bap poly(A)⁺ RNA was not detected in 0-3-hour embryos, but was found in low abundance in RNA from 3-6-hour embryos. The abundance was maximum in RNA from 6-12-hour embryos and then declined during further embryonic development.

Relationship to Other Genes

Source for database merge of

Additional comments

The suggestion that bap and prd9 are the same is incorrect (Frasch, pers. comm. to FlyBase 24th March 1995)

(Kim and Nirenberg, 1989)

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (15)

Reported As

Symbol Synonym

BAP

(Titsias et al., 2012)

Bag

(Bischof et al., 2018)

Bap

(Bhogale and Sinha, 2022, Kögler et al., 2021, Khoueiry et al., 2017, Mbodj et al., 2016, Seyres et al., 2016, Baëza et al., 2015, Van Bortle et al., 2015, Borner et al., 2014, Erceg et al., 2014, Mukherjee et al., 2014, Gisselbrecht et al., 2013, Stojnic et al., 2012, Hazelett et al., 2009, Zinzen et al., 2009, Jakobsen et al., 2007, Goldstein et al., 2005)

Bap1

(Navarro-Costa et al., 2016)

CG7902

(Hazelett et al., 2009, Keleman et al., 2009.8.5, Perkins et al., 2009.3.31)

NK-3

(Kim et al., 1998, Walldorf and Gehring, 1992, Webber et al., 1990)

NK3

(Fyrberg et al., 1994, Bodmer, 1993, Lints et al., 1993)

Nkx3.2

(Seyres et al., 2016)

bag

(Wang et al., 2015)

bap

(Nelson et al., 2025, Pollex et al., 2024, Deshpande et al., 2022, Saha et al., 2022, Waters et al., 2021, Chetverina et al., 2020, Lau et al., 2020, Peng et al., 2019, Shokri et al., 2019, Wu et al., 2019, Bischof et al., 2018, Transgenic RNAi Project members, 2017-, Bürglin and Affolter, 2016, Sarov et al., 2016, model organism Encyclopedia of Regulatory Network (modERN) Project, 2015-, Monfort and Furlong, 2015.1.15, Schertel et al., 2015, Wang et al., 2015, Jiang and Singh, 2014, Schäfer et al., 2014, Spahn et al., 2014, Aleksic et al., 2013, Reim et al., 2012, Steiner et al., 2012, Bantignies et al., 2011, Nègre et al., 2011, Biehs et al., 2010, Itasaki and Hoppler, 2010, Williams et al., 2010, Yan et al., 2010, Zhai et al., 2010, Liu et al., 2009, Wolfstetter et al., 2009, McDermott and Kliman, 2008, Jakobsen et al., 2007, Nekrasov et al., 2007, Popichenko et al., 2007, Zeitlinger et al., 2007, Sandmann et al., 2006, Brennecke et al., 2005, Copley, 2005, Zaffran and Frasch, 2005, Lee et al., 2003, Zaffran and Frasch, 2002)

bgp

(Xu et al., 1996)

dNK-3

(Nakagoshi et al., 1998)

nk-3

(Bodmer et al., 1990)

Name Synonyms

Secondary FlyBase IDs

FBgn0002943

Datasets (1)

Study focus (1)

Experimental Role

Project

Project Type

Title

bait_protein

Furlong_ChIP-chip

genome binding

ChIP-chip identification of binding sites for transcription factors that regulate mesodermal development.

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 94 )

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.

42537

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.

P22809

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

P22809

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

Q53YH4

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.

P22809

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004862

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

42537/tissue=All

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

FBgn0004862

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

FBgn0004862

FlyMine - An integrated database for Drosophila genomics

FBgn0004862

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

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

dme:Dmel_CG7902

MARRVEL_MODEL - MARRVEL (model organism gene)

42537

Linkouts

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

FBgn0004862

DroID - A comprehensive database of gene and protein interactions.

FBgn0004862

DRSC - Results frm RNAi screens

FBgn0004862

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

bap_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004862

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004862

Flygut - An atlas of the Drosophila adult midgut

FBgn0004862

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

TC012743

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

Interactive Fly

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

42537

SignaLink - A signaling pathway resource with multi-layered regulatory networks.

P22809

References (210)

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

-0.56

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