FlyBase Gene Report: Dmel\Had1

General Information

Symbol

Dmel\Had1

Species

D. melanogaster

Name

β Hydroxy acid dehydrogenase 1

Annotation Symbol

CG9914

Feature Type

protein_coding_gene

FlyBase ID

FBgn0286508

Gene Model Status

Current

Stock Availability

7 publicly available

Enzyme Name (EC)

L-gulonate 3-dehydrogenase (1.1.1.45)

Gene Summary

β Hydroxy acid dehydrogenase 1 (Had1) encodes an enzyme that catalyzes the dehydrogenation of L-gulonate into dehydro-L-gulonate and is predicted to be involved in the catabolism of D-glucuronate into D-xylulose 5-phosphate. [Date last reviewed: 2024-09-19] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
Red Book
Interactive Fly

Also Known As

Had

Key Links

Genomic Location

Cytogenetic map

14B9-14B9

Sequence location

X:16,306,912..16,308,667 [-]

Recombination map

1-53

RefSeq locus

NC_004354 REGION:16306912..16308667

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 (6 terms)

Molecular Function (3 terms)

Terms Based on Experimental Evidence (1 term)

CV Term

Evidence

References

enables L-gulonate 3-dehydrogenase activity

inferred from mutant phenotype

(Tobler and Grell, 1978)

inferred from direct assay

(Borack and Sofer, 1971)

Terms Based on Predictions or Assertions (3 terms)

CV Term

Evidence

References

enables L-gulonate 3-dehydrogenase activity

inferred from biological aspect of ancestor with PANTHER:PTN000592731

(GO Reference Genome Project, 2011-)

enables NAD+ binding

inferred from electronic annotation with InterPro:IPR006176, InterPro:IPR022694

(InterPro Project Members, 2004-)

enables oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

inferred from electronic annotation with InterPro:IPR006108, InterPro:IPR006180, InterPro:IPR022694

(InterPro Project Members, 2004-)

Biological Process (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

involved_in D-glucuronate catabolic process to D-xylulose 5-phosphate

inferred from sequence or structural similarity with UniProtKB:Q99KP3

(Gene Ontology Curators, 2002-)

involved_in fatty acid metabolic process

inferred from electronic annotation with InterPro:IPR006108, InterPro:IPR006176, InterPro:IPR006180, InterPro:IPR022694

(InterPro Project Members, 2004-)

Cellular Component (1 term)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

is_active_in cytosol

inferred from sequence or structural similarity with UniProtKB:Q99KP3

(Gene Ontology Curators, 2002-)

Gene Group (FlyBase)

BETA HYDROXY ACID DEHYDROGENASES

Protein Family (UniProt)

Protein Signatures (InterPro)

Catalytic Activity (EC/Rhea)

L-gulonate 3-dehydrogenase activity

L-gulonate + NAD(+) = 3-dehydro-L-gulonate + NADH + H(+) (1.1.1.45)

RHEA 12889:

Summaries

Gene Snapshot

Gene Group (FlyBase)

BETA HYDROXY ACID DEHYDROGENASES -: Beta hydroxy acid dehydrogenases catalyze the NAD(+)-linked dehydrogenation of L-gulonate into dehydro-L-gulonate in the uronate cycle. The uronate cycle, an alternative glucose metabolic pathway that is linked to the pentose phosphate cycle via nonphosphorylated sugar metabolites, plays essential roles in glucuronide formation and the synthesis of glycosaminoglycan and ascorbic acid. (Adapted from PMID: 15809331.)

Phenotypic Description (Red Book; Lindsley and Zimm 1992)

Had: β-Hydroxy-acid-dehydrogenase

Thought to be the structural gene for β Hydroxy acid dehydrogenase (L-β-hydroxyacid: NAD oxidoreductase, E.C 1.1.1.45). The enzyme is a dimer, based on the formation of hybrid enzyme in D.simulans X D. melanogaster hybrids, of molecular weight 6.3 X 104 daltons. Purification and biochemistry by Borak and Sofer. Activity high in Malpighian tubules, less in muscles, intestine, and fat body; absent from brain, salivary gland, and imaginal disks. (Borak, 1972, DIS 48: 73). Activity peaks at 72 hr after hatching, then declines through larval and pupal stages, and increases to stable maximum level at 6 days of adult life (Tobler and Grell). Enzyme expendible; hemizygotes and homozygotes for null allele survive normally (Tobler and Grell).

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\Had1 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 Q9VXI1)

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 5.48

Gene model reviewed during 5.56

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

Had1-RA

FBtr0074240

NM_132886

1171

315

Had1-RB

FBtr0346059

NM_001298391

1445

315

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

UniProt

RefSeq ID

GenBank

Had1-PA

FBpp0074019

34.8

315

8.01

FBpp0311907

34.8

315

8.01

Q9VXI1

NP_001285320

AHN59790

Polypeptides with Identical Sequences

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

315 aa isoforms: Had1-PA, Had1-PB

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

Q9VXI1

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Had1 using the Feature Mapper tool.

External Data

Crossreferences

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).

-0.41

Transcript Expression

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 7 of adulthood -- day 49 of adulthood

adult heart

(Cammarato et al., 2011)

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\Had1 in JBrowse

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

View exonic expression by developmental stage for Dmel\Had1

View exonic expression by tissue for Dmel\Had1

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

32592/tissue=All

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

FBgn0286508

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030737

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

FBgn0286508

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 5 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 4 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of Had1

Transgenic constructs containing regulatory region of Had1

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 13 )

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

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

Had1^GD14720

viable, with Scer\GAL4^Mef2.PR

Had1^GD14720

viable, with Scer\GAL4^pnr-MD237

Had1^GD14720

viable, with Scer\GAL4^tin.CΔ4

Had1^GD14720

Other Phenotypes

Allele

electrophoretic variant

Phenotype manifest in

Allele

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) (4)

Hsap\CRYL1

14 of 14

Yes

Hsap\HADH

2 of 14

Yes

Hsap\EHHADH

1 of 14

Hsap\HADHA

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) (4)

Rnor\Cryl1

14 of 14

Yes

Rnor\Hadh

2 of 14

Yes

Rnor\Ehhadh

1 of 14

Rnor\Hadha

1 of 14

Mus musculus (laboratory mouse) (4)

Mmus\Cryl1

13 of 14

Yes

Mmus\Hadh

2 of 14

Yes

Mmus\Ehhadh

1 of 14

Mmus\Hadha

1 of 14

Xenopus tropicalis (Western clawed frog) (4)

Xtro\cryl1

7 of 13

Yes

Xtro\acsl6

1 of 13

Xtro\ehhadh

1 of 13

Xtro\klhl41

1 of 13

Yes

Danio rerio (Zebrafish) (5)

Drer\cryl1

13 of 14

Yes

Drer\hadh

2 of 14

Yes

Drer\ehhadh

1 of 14

Drer\hadhaa

1 of 14

Drer\hadhab

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (8)

Cele\Y71F9B.9

12 of 14

Yes

Cele\B0272.3

2 of 14

Yes

Cele\F54C8.1

2 of 14

Yes

Cele\hacd-1

2 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (4)

Agam\AgaP_AGAP013544

12 of 12

Yes

Agam\AgaP_AGAP012935

2 of 12

Yes

Agam\AgaP_AGAP007784

1 of 12

Agam\AgaP_AGAP008236

1 of 12

Arabidopsis thaliana (thale-cress) (4)

Atha\AT3G15290

3 of 13

Yes

Atha\AIM1

1 of 13

Atha\AT2G30650

1 of 13

Atha\MFP2

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (1)

Scer\BNA4

1 of 13

Yes

Schizosaccharomyces pombe (Fission yeast) (0)

Escherichia coli (enterobacterium) (3)

Ecol\paaH

3 of 11

Yes

Ecol\fadB

2 of 11

Ecol\fadJ

2 of 11

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:Had1. 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)

Had2

11 of 13

Mtpα

2 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 ( 1 )

Allele

Disease

Interaction

References

Had1^KK108568

ameliorates amyotrophic lateral sclerosis type 10

modeled by Hsap\TARDBP^{M337V.UAS.Tag:MYC}

(Huber et al., 2023)

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?

CRYL1; crystallin lambda 1

14 of 14

609877

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

Show neighbor-neighbor interactions:

Off

Show/hide secondary interactors
(data from AllianceMine provided by esyN)

Select Layout:

Force Directed

Circle

Concentric

Legend:

Protein

RNA

Selected Interactor(s)

Other 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

Had1 - Nrd1

anti tag coimmunoprecipitation, Identification by mass spectrometry

(Yoon et al., 2017)

Summary of Genetic Interactions

esyN Network Diagram

Other Interaction Browsers

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

External Data

Linkouts

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.

Formation of xylulose-5-phosphate

External Data

Linkouts

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Formation of xylulose-5-phosphate

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

1-53

Cytogenetic map

14B9-14B9

Sequence location

X:16,306,912..16,308,667 [-]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

14B9-14B9

Limits computationally determined from genome sequence between P{EP}kat80^EP620&P{EP}caz^EP1564 and P{EP}Cyp1^EP1073&P{EP}Dsp1^EP355

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

Experimentally Determined Recombination Data

Location

1-53

(FlyBase, 2016)

1-54.5

(Comeron et al., 2012)

(Choudhary et al., 1992)

1-54.4

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (7)

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

Bloomington

26582

w^* P{EP}asRNA:CR45485^G74

1037

y² cv¹ v¹ Had1^nl; bw¹

62273

y¹ sc^* v¹ sev²¹; P{TRiP.HMC05280}attP40

Korea

10604

P{EP}asRNA:CR45485^G74

NIG-Fly

HMJ22681

y¹ v¹; P{TRiP.HMJ22681}attP40/CyO

VDRC

v106649

P{KK108568}VIE-260B

v29322

w¹¹¹⁸; P{GD14720}v29322

Genomic Clones (15)

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

cDNA Clones (21)

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

RH68464

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.

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Thought to be the structural gene for β Hydroxy acid dehydrogenase (L-β-hydroxyacid: NAD oxidoreductase). The enzyme is a dimer, based on the formation of hybrid enzyme in D.simulans X D.melanogaster hybrids, of molecular weight 6.3 x 10⁴ daltons. Purification and biochemistry by Borak and Sofer (1971. Activity high in Malpighian tubules, less in muscles, intestine and fat body; absent from brain, salivary gland and imaginal discs. (Borak, 1972). Activity peaks at 72 hr after hatching, then declines through larval and pupal stages and increases to stable maximum level at 6 days of adult life (Tobler and Grell, 1978). Enzyme expendable; hemizygotes and homozygotes for null allele survive normally (Tobler and Grell, 1978).

Relationship to Other Genes

Source for database merge of

Source for merge of: Had CG9914

(Marygold, 2018.6.26)

Additional comments

Nomenclature History

Source for database identify of

Source for identity of: Had1 Had

(Marygold, 2018.6.26)

Nomenclature comments

Etymology

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

Name Synonyms

3-hydroxyacyl-CoA dehydrogenase

(Paiardi et al., 2017)

B-L-hydroxy acid dehydrogenase

(Borack, 1972)

Enoyl-CoA hydratase mitochondrial

(de Morais Guedes et al., 2003)

β Hydroxy acid dehydrogenase

β Hydroxy acid dehydrogenase 1

β-L-hydroxy acid dehydrogenase

(Borack and Sofer, 1971)

β-hydroxy acid dehydrogenase

(Tobler and Grell, 1978)

Secondary FlyBase IDs

FBgn0001172
FBgn0030737

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 34 )

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.

32592

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.

Q9VXI1

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

Q9VXI1

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.

Q9VXI1

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

32592/tissue=All

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

FBgn0286508

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

FBgn0286508

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

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

dme:Dmel_CG9914

MARRVEL_MODEL - MARRVEL (model organism gene)

32592

Linkouts

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0030737

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0286508

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

TC015170

KEGG Metabolic Pathways - A collection of manually drawn metabolic pathway maps representing knowledge of molecular interaction, reaction and relation networks.

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.

Formation of xylulose-5-phosphate

Reactome Metabolic Pathways - An open-source, open access, manually curated and peer-reviewed metabolic pathway database.

Formation of xylulose-5-phosphate

References (55)

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

-0.41

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