FlyBase Gene Report: Dmel\Dip-B

Structural gene for dipeptidase B [DIP-B(EC 3.4.14.?.)], which is virtually monomorphic in natural populations but which differs in electrophoretic mobility from dipeptidase-B variants in D. simulans. Substrate specificities determined by Laurie-Ahlberg (1982, Biochem. Genet. 20: 407-24).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the GBrowse view of Dmel\Dip-B or the JBrowse view of Dmel\Dip-B 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 5.55

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

Gene model reviewed during 5.54

Gene model reviewed during 5.56

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Dip-B-RA

FBtr0082831

NM_142061

2034

508

Dip-B-RB

FBtr0082833

NM_169557

1938

508

Dip-B-RC

FBtr0082832

NM_169558

2047

508

Dip-B-RD

FBtr0345229

NM_001300387

1813

508

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

RefSeq ID

GenBank

Dip-B-PA

FBpp0082299

55.5

508

6.74

NP_650318

AAF54991

Dip-B-PB

FBpp0082301

55.5

508

6.74

NP_731863

AAN13593

Dip-B-PC

FBpp0082300

55.5

508

6.74

NP_731864

AAN13594

Dip-B-PD

FBpp0311421

55.5

508

6.74

NP_001287316

AHN57315

Polypeptides with Identical Sequences

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

508 aa isoforms: Dip-B-PA, Dip-B-PB, Dip-B-PC, Dip-B-PD

Additional Polypeptide Data and Comments

Reported size (kDa)

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

Q9VFQ9

Mapped Features

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

External Data

Crossreferences

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

Linkouts

Gene Ontology (6 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

dipeptidyl-peptidase activity

inferred from direct assay

(Laurie-Ahlberg, 1982)

tripeptidyl-peptidase activity

inferred from direct assay

(Laurie-Ahlberg, 1982)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

manganese ion binding

inferred from electronic annotation with InterPro:IPR011356

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

metalloexopeptidase activity

inferred from electronic annotation with InterPro:IPR011356

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

Biological Process (1 term)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

proteolysis

inferred from direct assay

(Laurie-Ahlberg, 1982)

Terms Based on Predictions or Assertions (0 terms)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

cytoplasm

inferred from electronic annotation with InterPro:IPR011356

(assigned by InterPro )

(FlyBase Curators et al., 2004-)

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 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic hindgut

(Fisher et al., 2012)

embryonic Malpighian tubule

(Fisher et al., 2012)

embryonic/larval garland cell

(Fisher et al., 2012)

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

adult stage

adult head

• membrane

(Aradska et al., 2015)

day 5 of adulthood & male -- day 7 of adulthood & male

spermatozoon

(Wasbrough et al., 2010)

day 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

Additional Descriptive Data

Dip-B is present atfairly uniform specific activities throughout development. Specificactivity is highest in pupae and lowest in feeding stages. Dip-Bspecific activity was also found to be fairly uniform in all tissuesstudied except in gut and Malphigian tubules where it is higher thanaverage and adult thorax where it is low.

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\Dip-B 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\Dip-B

View exonic expression by tissue for Dmel\Dip-B

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

FBgn0000454

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

FBgn0000454

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG9285-RA

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

CG9285

Flygut - An atlas of the Drosophila adult midgut

FBgn0000454

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, and Transgenic Constructs

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 3 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Dip-B

Transgenic constructs containing regulatory region of Dip-B

Deletions and Duplications ( 11 )

Disrupted in

Df(3R)293γ5

(Jarman and Collett, 1998)

Df(3R)Exel6170

(Ryder, 2004.4.26)

Df(3R)red3l

(Jarman and Collett, 1998)

Df(3R)urd

(Jarman and Collett, 1998)

Not disrupted in

Df(3R)293γ7

(Jarman and Collett, 1998)

Df(3R)l26c

(Jarman and Collett, 1998)

Df(3R)M36

(Jarman and Collett, 1998)

Df(3R)M49

(Jarman and Collett, 1998)

Df(3R)red-P1

(Jarman and Collett, 1998)

Df(3R)red-P52

(Jarman and Collett, 1998)

Df(3R)su(Hw)7

(Jarman and Collett, 1998)

Phenotypes

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

Lethality

Allele

viable

Dip-B^EY00740

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

Dip-B^GD1317

viable, with Scer\GAL4^Mef2.PR

Dip-B^GD1317

viable, with Scer\GAL4^pnr-MD237

Dip-B^GD1317

Sterility

Allele

fertile

Dip-B^EY00740

Other Phenotypes

Allele

electrophoretic variant

Phenotype manifest in

Allele

Orthologs

Downloads

Download All DIOPT Orthologs

Download All OrthoDB Orthologs

Human Orthologs (via DIOPT v7.1)

Homo sapiens (Human) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Hsap\NPEPL1

2 of 15

Yes

Hsap\LAP3

1 of 15

Model Organism Orthologs (via DIOPT v7.1)

Mus musculus (laboratory mouse) (2)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Mmus\Npepl1

3 of 15

Yes

Mmus\Lap3

2 of 15

Rattus norvegicus (Norway rat) (2)

Rnor\Lap3

1 of 13

Yes

Rnor\Npepl1

1 of 13

Yes

Xenopus tropicalis (Western clawed frog) (1)

Xtro\lap3

2 of 12

Yes

Danio rerio (Zebrafish) (3)

Drer\zgc:152830

10 of 15

Yes

Drer\lap3

2 of 15

Drer\npepl1

1 of 15

Caenorhabditis elegans (Nematode, roundworm) (2)

Cele\lap-2

12 of 15

Yes

Cele\lap-1

2 of 15

Arabidopsis thaliana (thale-cress) (0)

No records found.

Saccharomyces cerevisiae (Brewer's yeast) (0)

No records found.

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\SPAC13A11.05

1 of 12

Yes

Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190745 )

Organism

Common Name

Gene

AAA Syntenic Ortholog

Multiple Dmel Genes in this Orthologous Group

Drosophila melanogaster

fruit fly

Drosophila simulans

Drosophila sechellia

Drosophila erecta

Drosophila yakuba

Drosophila ananassae

Drosophila pseudoobscura pseudoobscura

Dpse\GA21669

Drosophila persimilis

Dper\GL23475

Drosophila willistoni

Dwil\GK14202

Drosophila virilis

Dvir\GJ14485

Drosophila mojavensis

Dmoj\GI23169

Drosophila grimshawi

Dgri\GH14277

Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504JL )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Musca domestica

House fly

Mdoa\17020304

Glossina morsitans

Tsetse fly

Gmor\GMOY001946

Lucilia cuprina

Australian sheep blowfly

Lcup\FF38_12554

Aedes aegypti

Yellow fever mosquito

Aaeg\AAEL002978

Anopheles darlingi

American malaria mosquito

Adar\ADAC010600

Anopheles gambiae

Malaria mosquito

Agam\AGAP003475

Culex quinquefasciatus

Southern house mosquito

Cqui\CPIJ009825

Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W07DG )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Bombyx mori

Silkmoth

Bmor\BGIBMGA001803

Danaus plexippus

Monarch butterfly

Dple\DPOGS210662-PA

Heliconius melpomene

Postman butterfly

Hmel\HMEL010784

Apis florea

Little honeybee

Aflo\3151042308

Apis mellifera

Western honey bee

Amel\GB50527

Bombus impatiens

Common eastern bumble bee

Bimp\BIMP19515

Bombus terrestris

Buff-tailed bumblebee

Bter\15210975

Linepithema humile

Argentine ant

Lhum\LH21189

Megachile rotundata

Alfalfa leafcutting bee

Mrot\MROTU:001e16

Nasonia vitripennis

Parasitic wasp

Nvit\Nasvi2EG005714

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_04424

Dendroctonus ponderosae

Mountain pine beetle

Dpod\YQE_04425

Tribolium castaneum

Red flour beetle

Tcas\TC012824

Pediculus humanus

Human body louse

Phum\PHUM432710

Rhodnius prolixus

Kissing bug

Rpro\RPRC009154

Cimex lectularius

Bed bug

Clec\CLEC003014

Cimex lectularius

Bed bug

Clec\CLEC003015

Cimex lectularius

Bed bug

Clec\CLEC002053

Cimex lectularius

Bed bug

Clec\CLEC003016

Zootermopsis nevadensis

Nevada dampwood termite

Znev\Znev_13541

Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X078N )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strigamia maritima

European centipede

Smar\SMAR014261

Ixodes scapularis

Black-legged tick

Isca\ISCW003100

Stegodyphus mimosarum

African social velvet spider

Smim\KFM82894.1

Daphnia pulex

Water flea

Dpux\DAPPUDRAFT_301437

Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0B5P )

Organism

Common Name

Gene

Multiple Dmel Genes in this Orthologous Group

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_022944gn

Strongylocentrotus purpuratus

Purple sea urchin

Spur\Sp-Ap

Strongylocentrotus purpuratus

Purple sea urchin

Spur\SPU_002690gn

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000004383

Ciona intestinalis

Vase tunicate

Cint\ENSCING00000008044

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v7.1)

Drosophila melanogaster (Fruit fly) (10)

Gene Symbol

Score

Source

Alignment

5 of 10

4 of 10

4 of 10

4 of 10

4 of 10

4 of 10

4 of 10

3 of 10

3 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

Comments on Models/Modifiers Based on Experimental Evidence ( 0 )

Disease Associations of Human Orthologs (via DIOPT v7.1 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?

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

Dip-B

two hybrid

(Hu et al., 2017.6.13)

Dip-B - CG18518

experimental knowledge based

(Guruharsha et al., 2011)

Dip-B - CG5445

experimental knowledge based

(Guruharsha et al., 2011)

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.

71397

DroID - A comprehensive database of gene and protein interactions.

FBgn0000454

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

48450

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

Dip-B

Pathways

Gene Group - Pathway Membership (FlyBase)

External Data

Linkouts

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

wound-induced proteolysis I

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-54

Cytogenetic map

87F13-87F13

Sequence location

3R:13,782,288..13,785,676 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

87F13-87F13

Limits computationally determined from genome sequence between P{PZ}flfl⁰¹⁹⁴⁹ and P{lacW}trx^j14A6&P{PZ}trx⁰⁰³⁴⁷

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

3-54

(FlyBase, 2016)

3-51.3

(Comeron et al., 2012)

3-53.6

(Laurie-Ahlberg, 1982)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

Bloomington

54045

y¹ v¹; P{TRiP.HMJ21488}attP40

20098

y¹ w^67c23; P{EPgy2}Dip-B^EY00740

Harvard

d06483

P{XP}Dip-B^d06483

VDRC

v6296

w¹¹¹⁸; P{GD1317}v6296

v6297

w¹¹¹⁸; P{GD1317}v6297/TM3

Genomic Clones (18)

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

cDNA Clones (175)

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 sequences

BDGP DGC clones

LD41062

Other clones

DPiM_LD41062

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.

FBgn0000454

cDNA Clones, End Sequenced (ESTs)

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0000454

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

48450

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Other Information

Relationship to Other Genes

Source for database identify of

Source for database merge of

Source for merge of: Dip-B CG9285

(Collett, 2002.4.9)

Additional comments

Other Comments

Shows particularly robust cycling of transcription in adult heads, as assessed by expression analysis using high density oligonucleotide arrays with probe generated during three 12-point time course experiments over the course of 6 days. Shows significant change of expression pattern in circadian mutant background; decreased expression in per⁰¹, tim⁰¹ and increased expression in Clk^Jrk background.

(Claridge-Chang et al., 2001)

A screen to identify modifiers for the dipeptidase locates them on the X, second and third chromosomes.

(Hiraizumi et al., 1993)

Larvae of genetically different lines were reared under varying levels of osmotic stress to study the genetic basis of the correlation of peptidase activities in response to environmental challenge.

(Hiraizumi et al., 1992)

The developmental variation and tissue locations of Dip-A and Dip-B are determined.

(Hall, 1988)

Examination of D.melanogaster lines revealed genetic variation of Dip-A and Dip-B within sets of lines that only differed in the second or third chromosome. Experiments were undertaken to identify the types of activity modifiers that may be polymorphic in natural populations and to characterize the genetic organization of the modifiers.

(Hiraizumi and Laurie, 1988)

Dip-B activity is high in postembryonic stages, the activity in the adult is proportional to gene dosage.

(Hall, 1986)

Structural gene for dipeptidase B (DIP-B), which is virtually monomorphic in natural populations but which differs in electrophoretic mobility from dipeptidase-B variants in D.simulans. Substrate specificities determined (Laurie-Ahlberg, 1982).

Origin and Etymology

Discoverer

Etymology

Identification

External Crossreferences and Linkouts ( 45 )

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.

48450

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

Q9VFQ9

Other crossreferences

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0000454

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

FBgn0000454

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

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

CG9285

Flygut - An atlas of the Drosophila adult midgut

FBgn0000454

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

48450

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

TC012824

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

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

Dmel_CG9285

modMine - A data warehouse for the modENCODE project

FBgn0000454

Linkouts

BioGRID - A database of protein and genetic interactions.

71397

DPiM - Drosophila Protein interaction map

FBgn0000454

DroID - A comprehensive database of gene and protein interactions.

FBgn0000454

DRSC - Results frm RNAi screens

FBgn0000454

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

FBgn0000454

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

CG9285-RA

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0000454

FlyCyc Pathways - Pathways from a BioCyc PGDB for Dmel

wound-induced proteolysis I

FlyMine - An integrated database for Drosophila genomics

FBgn0000454

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

48450

KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.

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

Dip-B

Synonyms and Secondary IDs (4)

Reported As

Symbol Synonym

Name Synonyms

Dipeptidase B

(McEachern et al., 2014, Cammarato et al., 2011)

Secondary FlyBase IDs

FBgn0038184

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

References (62)

Report Sections

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