FlyBase Gene Report: Dmel\βggt-I

General Information

Symbol

Dmel\βggt-I

Species

D. melanogaster

Name

β subunit of type I geranylgeranyl transferase

Annotation Symbol

CG3469

Feature Type

protein_coding_gene

FlyBase ID

FBgn0015000

Gene Model Status

Current

Stock Availability

8 publicly available

Enzyme Name (EC)

protein geranylgeranyltransferase type I (2.5.1.59)

Gene Summary

β subunit of type I geranylgeranyl transferase (βggt-I) encodes a protein involved in embryonic heart tube development. [Date last reviewed: 2019-09-19] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Interactive Fly

Also Known As

βGGTI, beta GGT-I, SR2-2

Key Links

Genomic Location

Cytogenetic map

25B4-25B4

Sequence location

2L:4,945,579..4,948,324 [+]

Recombination map

2-14

RefSeq locus

NT_033779 REGION:4945579..4948324

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 (7 terms)

Molecular Function (4 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

contributes_to CAAX-protein geranylgeranyltransferase activity

inferred from biological aspect of ancestor with PANTHER:PTN000206684

(GO Reference Genome Project, 2011-)

enables catalytic activity

inferred from electronic annotation with InterPro:IPR001330

(InterPro Project Members, 2004-)

enables protein geranylgeranyltransferase activity

inferred from electronic annotation with InterPro:IPR041960

(InterPro Project Members, 2004-)

enables protein prenyltransferase activity

inferred from electronic annotation with InterPro:IPR045089

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (2 terms)

CV Term

Evidence

References

involved_in embryonic heart tube development

inferred from mutant phenotype

(Yi et al., 2006)

involved_in positive regulation of Ras protein signal transduction

inferred from high throughput genetic interaction with FLYBASE:Ras85D; FB:FBgn0003205

(Ashton-Beaucage et al., 2014)

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

part_of CAAX-protein geranylgeranyltransferase complex

inferred from electronic annotation with InterPro:IPR041960

(InterPro Project Members, 2004-)

inferred from biological aspect of ancestor with PANTHER:PTN000206684

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

PROTEIN PRENYLTRANSFERASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

protein geranylgeranyltransferase activity
RHEA 21240: CAAX-protein geranylgeranyltransferase activity

geranylgeranyl diphosphate + L-cysteinyl-[protein] = S-geranylgeranyl-L- cysteinyl-[protein] + diphosphate (2.5.1.59)

Summaries

Gene Snapshot

β subunit of type I geranylgeranyl transferase (βggt-I) encodes a protein involved in embryonic heart tube development. [Date last reviewed: 2019-09-19]

Gene Group (FlyBase)

PROTEIN PRENYLTRANSFERASES -: Protein prenyltransferases are heterodimeric enzymes that catalyze the transfer of the carbon moiety of C[[15]] farnesyl pyrophosphate (FPP) or C[[20]] geranylgeranyl pyrophosphate (GGPP) to a conserved cysteine residue in a CaaX motif of protein and peptide substrates. This postranslational modification is essential for a number of proteins including Ras, Rab, nuclear lamins, trimeric G-protein gamma subunits, protein kinases, and small Ras-related GTP-binding proteins. The addition of a farnesyl group to these proteins, for example, is required to anchor them to the cell membrane, a step required for them to function. (Adapted from PMID:12135472, PMID:12702202 and PMID:26216239.)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\βggt-I 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 Q24173)

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

Alternative translation stop created by use of multiphasic reading frames within coding region.

Gene model reviewed during 5.44

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

Gene model reviewed during 5.48

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

βggt-I-RA

FBtr0078991

NM_080361

1784

395

βggt-I-RB

FBtr0330714

NM_001273132

1693

376

Additional Transcript Data and Comments

Reported size (kB)

1.770 (longest cDNA)

(Therrien et al., 1995)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

βggt-I-PA

FBpp0078630

44.1

395

5.56

FBpp0303558

42.2

376

5.72

M9PEL6

NP_001260061

AGB92597

Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments

Reported size (kDa)

395 (aa)

(Therrien et al., 1995)

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\βggt-I using the Feature Mapper tool.

External Data

Crossreferences

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

betaggt-I_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).

-0.31

Transcript Expression

Additional Descriptive Data

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

JBrowse - Visual display of RNA-Seq signals

View Dmel\βggt-I in JBrowse

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

View exonic expression by developmental stage for Dmel\βggt-I

View exonic expression by tissue for Dmel\βggt-I

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

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

33704/tissue=All

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

FBgn0015000

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0015000

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

FBgn0015000

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

CG3469

Flygut - An atlas of the Drosophila adult midgut

FBgn0015000

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 8 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 5 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of βggt-I

Transgenic constructs containing regulatory region of βggt-I

Aberrations (Deficiencies and Duplications) ( 6 )

Inferred from experimentation ( 6 )

Gene disrupted in

Df(2L)BSC51

(Deal and Cook, 2004.5.27)

Df(2L)BSC52

(Deal and Cook, 2004.5.27)

Df(2L)BSC811

(Christensen et al., 2009.5.6)

Df(2L)Exel7021

(Ryder, 2004.4.26)

Df(2L)Exel8012

(Ryder, 2004.4.26)

In(2)βggt-I^S-2126

(Therrien et al., 1995)

Inferred from location ( 8 )

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, with Scer\GAL4^insc-Mz1407

βggt-I^GD10976

lethal | recessive

lethal - all die before end of pupal stage, with Scer\GAL4^pnr-MD237

βggt-I^GD10976

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

βggt-I^GD10976

viable, with Scer\GAL4^tin.CΔ4

βggt-I^GD10976

Other Phenotypes

Allele

abnormal neuroanatomy | larval stage, with Scer\GAL4^insc-Mz1407

βggt-I^GD10976

flightless, with Scer\GAL4^Mef2.PR

βggt-I^GD10976

some die during pupal stage, with Scer\GAL4^pnr-MD237

βggt-I^GD10976

Phenotype manifest in

Allele

dorsal vessel wall cell

βggt-I^S-2554

embryonic pericardial cell

βggt-I^S-2554

ganglion mother cell | larval stage, with Scer\GAL4^insc-Mz1407

βggt-I^GD10976

larval neuroblast | larval stage, with Scer\GAL4^insc-Mz1407

βggt-I^GD10976

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) (5)

Hsap\PGGT1B

14 of 14

Yes

3 of 14

3 of 14

3 of 14

1 of 14

Yes

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (4)

Rnor\Pggt1b

14 of 14

Yes

Rnor\Fntb

3 of 14

Rnor\Rabggtb

3 of 14

Rnor\Ccdc112

1 of 14

Yes

Mus musculus (laboratory mouse) (4)

Mmus\Pggt1b

13 of 14

Yes

Mmus\Fntb

3 of 14

Mmus\Rabggtb

2 of 14

Mmus\Ccdc112

1 of 14

Yes

Xenopus tropicalis (Western clawed frog) (5)

Xtro\pggt1b

8 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (3)

Drer\pggt1b

13 of 14

Yes

Drer\fntb

3 of 14

Drer\rabggtb

3 of 14

Caenorhabditis elegans (Nematode, roundworm) (3)

Cele\fntb-1

3 of 14

Yes

Cele\ggtb-1

2 of 14

Cele\Y48E1B.3

2 of 14

Yes

Anopheles gambiae (African malaria mosquito) (3)

Agam\AgaP_AGAP008406

12 of 12

Yes

Agam\AgaP_AGAP001729

3 of 12

Agam\AgaP_AGAP013277

3 of 12

Arabidopsis thaliana (thale-cress) (5)

Atha\PGGT-I

12 of 13

Yes

3 of 13

3 of 13

3 of 13

1 of 13

Yes

Saccharomyces cerevisiae (Brewer's yeast) (3)

Scer\CDC43

8 of 13

Yes

Scer\BET2

2 of 13

Scer\RAM1

2 of 13

Schizosaccharomyces pombe (Fission yeast) (3)

Spom\cwg2

11 of 12

Yes

Spom\cpp1

2 of 12

Spom\ptb1

2 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:βggt-I. 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) (2)

Fntb

5 of 13

RabGGTb

5 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?

PGGT1B; protein geranylgeranyltransferase type I subunit beta

14 of 14

602031

CHURC1-FNTB; CHURC1-FNTB readthrough

3 of 14

FNTB; farnesyltransferase, CAAX box, subunit beta

3 of 14

134636

RABGGTB; Rab geranylgeranyltransferase subunit beta

3 of 14

179080

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

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

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Ras85D

suppressible

βggt-I

(Karim et al., 1996, Therrien et al., 1995)

sev|Ras85D

suppressible

βggt-I

(Maixner et al., 1998)

yki

suppressible

βggt-I

(Sorrentino et al., 2014)

External Data

Linkouts

BioGRID - A database of protein and genetic interactions.

59889

DroID - A comprehensive database of gene and protein interactions.

FBgn0015000

MIST (genetic) - An integrated Molecular Interaction Database

33704

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

2-14

Cytogenetic map

25B4-25B4

Sequence location

2L:4,945,579..4,948,324 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

25B4-25B4

Limits computationally determined from genome sequence between P{lacW}l(2)k10004^k10004&P{EP}CG3036^EP963 and P{PZ}l(2)05714⁰⁵⁷¹⁴

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

25B4-25B6

(Therrien, 1995.12.19)

Experimentally Determined Recombination Data

Location

2-14

(FlyBase, 2016)

2-16.0

(Comeron et al., 2012)

(Therrien, 1995.12.19)

2-15

(Therrien et al., 1995)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (8)

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

Bloomington

5681

βggt-I^S-2554/CyO

65487

w¹¹¹⁸; PBac{IT.GAL4}βggt-I^1165-G4/CyO

34687

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01165}attP2

80631

y¹ w^*; TI{CRIMIC.TG4.0}βggt-I^{CR00733-TG4.0}/SM6a

NIG-Fly

HMJ22061

y¹ v¹; P{TRiP.HMJ22061}attP40/CyO

HMS01165

y¹ sc^* v¹ sev²¹; P{TRiP.HMS01165}attP2

2LG-1467

y² VhaAC39-1^cho-1 v¹; P{U6-βggt-I.NIG.sgRNA}attP40/CyO

VDRC

v110288

P{KK105673}VIE-260B

Genomic Clones (9)

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

SD20823

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.

FBgn0015000

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

SD26063

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0015000

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R⁺ cell morphology.

(Kiger et al., 2003)

A screen to identify mutations affecting the Ras85D signalling pathway identified alleles of phl, Dsor1, rl, aop, βggt-I, mts, ksr and phyl.

(Therrien et al., 1995)

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 (18)

Reported As

Symbol Synonym

CG3469

(National Institute of Genetics Fly Stocks, 2023-, National Institute of Genetics Fly Stocks, 2022-, Hosono et al., 2015, Ni et al., 2010.12.1, Keleman et al., 2009.8.5)

GGT1

(Santos and Lehmann, 2004)

SR2-2

(Chang et al., 1994)

beta GGT-I

(Therrien, 1995.12.19, Therrien, 1995.12.19)

betaggt-I

(Sawyer et al., 2020, Levis, 2018.8.30, Clandinin and Owens, 2016-, Kuleesha et al., 2016, Christensen et al., 2009.5.6, Giot et al., 2003)

bro3

(Yi et al., 2006)

ggt-1

ggt-I

(Sorrentino et al., 2014)

ggt1

(Chang et al., 1994)

β-GGT

(Maixner et al., 1998)

βGGT

(Jones and Macdonald, 2015)

βGGT-I

(Yi, 2006, Yi et al., 2006, Karim et al., 1996, Therrien et al., 1995)

βGGTI

(Ricardo and Lehmann, 2009, Ricardo and Lehmann, 2009)

βggt

(Jones and Macdonald, 2015)

βggt-I

(Majane et al., 2022, Liang et al., 2021, Ashton-Beaucage et al., 2014, Sorrentino et al., 2014)

Name Synonyms

Suppressor of Ras1 2-2

type I Geranylgeranyl Transferase

(Karim et al., 1997)

β subunit of type I geranylgeranyl transferase

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 ( 41 )

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.

33704

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.

Q24173

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

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.

Q24173

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

33704/tissue=All

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

FBgn0015000

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

FBgn0015000

FlyMine - An integrated database for Drosophila genomics

FBgn0015000

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

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

dme:Dmel_CG3469

MARRVEL_MODEL - MARRVEL (model organism gene)

33704

Linkouts

BioGRID - A database of protein and genetic interactions.

59889

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

FBgn0015000

DroID - A comprehensive database of gene and protein interactions.

FBgn0015000

DRSC - Results frm RNAi screens

FBgn0015000

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

betaggt-I_1

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0015000

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0015000

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

CG3469

Flygut - An atlas of the Drosophila adult midgut

FBgn0015000

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

TC004960

MIST (genetic) - An integrated Molecular Interaction Database

33704

References (56)

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

-0.31

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