FB2022_02, released March 29, 2022

Gene: Dmel\her

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General Information
Symbol
Dmel\her
Species
D. melanogaster
Name
hermaphrodite
Annotation Symbol
CG4694
Feature Type
protein_coding_gene
FlyBase ID
FBgn0001185
Gene Model Status
Current
Stock Availability
14 publicly available
Gene Summary
hermaphrodite (her) encodes a zinc finger C2H2 transcription factor involved in sex determination and differentiation. [Date last reviewed: 2019-06-13] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(2)mat

Key Links
Genomic Location
Cytogenetic map
36A10-36A10
Sequence location
Recombination map
2-52
RefSeq locus
NT_033779 REGION:16677185..16679691
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
enables DNA binding
traceable author statement
(Christiansen et al., 2002)
enables DNA-binding transcription factor activity, RNA polymerase II-specific
inferred from biological aspect of ancestor with PANTHER:PTN002810938
(assigned by GO_Central )
(Gaudet et al., 2011)
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN002810938
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (7 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in sex determination
inferred from mutant phenotype
(Pultz et al., 1994)
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
involved_in female somatic sex determination
non-traceable author statement
(Zarkower, 2001)
involved_in positive regulation of transcription by RNA polymerase II
traceable author statement
(Christiansen et al., 2002)
involved_in regulation of transcription by RNA polymerase II
traceable author statement
(Schutt and Nothiger, 2000)
involved_in regulation of transcription, DNA-templated
inferred from biological aspect of ancestor with PANTHER:PTN001227002
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in sex determination, primary response to X:A ratio
traceable author statement
(Schutt and Nothiger, 2000)
involved_in sex differentiation
traceable author statement
(Christiansen et al., 2002)
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
hermaphrodite (her) encodes a zinc finger C2H2 transcription factor involved in sex determination and differentiation. [Date last reviewed: 2019-06-13]
Gene Group (FlyBase)
C2H2 ZINC FINGER TRANSCRIPTION FACTORS -
Zinc finger C2H2 transcription factors are sequence-specific DNA binding proteins that regulate transcription. They possess DNA-binding domains that are formed from repeated Cys2His2 zinc finger motifs. (Adapted from PMID:1835093, FBrf0220103 and FBrf0155739).
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
her: hermaphrodite (G.S. Carson)
Original allele was recovered as a recessive temperature-sensitive lethal with low homozygous viability (3-7% of the viability her/+) at 29 C and near-normal viability at 18 C in both sexes. Surviving 29 C homozygotes have small bodies, rough eyes, incised wings, and etched abdominal tergites. XX homozygotes surviving at 29 C are intersexual, with partially formed sexcombs, male-colored abdominal patches, and rudimentary male and female external genitalia. XY escapers have female-like sixth abdominal sternite bristles, but otherwise appear sexually normal. her/her flies of both sexes raised at 18 C are morphologically normal and fertile; however, XX homozygotes exhibit reversible temperature-dependent sterility when mated at 29 C. Homozygous females exert a mild maternal effect upon the sexual phenotype of her/+ offspring which develop at 29 C; females show abnormal basitarsal bristle arrangement and patches of male abdominal pigmentation; males show female basitarsal bristles among sex- comb teeth and the presence of sixth sternite bristles.
l(2)mat: lethal (2) maternal
Homozygous females produce 1 daughter to 5.5 sons. Abnormal sex ratio caused by inviability of females. l(2)mat does not seem to be allelic to da, which has a similar effect. RK3.
Summary (Interactive Fly)

CH zinc finger transcription factor - plays a permissive role in sex determination and differentiation - required for female sexual differentiation

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\her 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 New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VJJ6)

If you don't see the viewer to the right, 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.

Comments on Gene Model

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
her-RA
FBtr0080883
NM_057224
2070
487
her-RB
FBtr0335138
NM_001273577
2378
487
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
her-PA
FBpp0080440
57.0
487
7.93
NP_476572
AAF53549
her-PB
FBpp0307137
57.0
487
7.93
NP_001260506
AGB93041
Polypeptides with Identical Sequences

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

487 aa isoforms: her-PA, her-PB
Additional Polypeptide Data and Comments
Reported size (kDa)

487 (aa)

(Li and Baker, 1998)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

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

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
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 | faint | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | faint | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | faint | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | faint | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
larval ventral nerve cord
(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage -- adult stage
(Li and Baker, 1998)
Additional Descriptive Data

her transcript is expressed in all developmental stages.

(Li and Baker, 1998)
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

GBrowse - Visual display of RNA-Seq signals

View Dmel\her in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
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 ( 12 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of her
Transgenic constructs containing regulatory region of her
Aberrations (Deficiencies and Duplications) ( 14 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal
lethal, with Scer\GAL4pnr-MD237
lethal (with her3)
lethal (with her8)
lethal | female
lethal | female | maternal effect | heat sensitive
lethal | male
lethal | maternal effect | heat sensitive
lethal | recessive | heat sensitive
lethal - all die during embryonic stage | maternal effect
lethal - all die during embryonic stage | maternal effect (with her1)
lethal - all die during embryonic stage | maternal effect (with hermat-1)
lethal - all die during P-stage, with Scer\GAL4Mef2.PR
partially lethal - majority die | female
partially lethal - majority die | male
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
Sterility
Allele
female semi-sterile
female sterile
fertile
male fertile
Other Phenotypes
Allele
abnormal neuroanatomy | larval stage
abnormal sex-determination | recessive
abnormal sex-determination | recessive | heat sensitive
some die during embryonic stage | maternal effect
some die during embryonic stage | maternal effect (with her1)
some die during embryonic stage | maternal effect (with hermat-1)
visible, with Scer\GAL4Bx-MS1096
visible | male limited, with Scer\GAL4Bx-MS1096
wild-type
Phenotype manifest in
Allele
abdominal sternite 6
epiproct
female terminalia
female terminalia | maternal effect
ganglion mother cell | larval stage
larval neuroblast | larval stage
male terminalia
male terminalia | maternal effect
muscle cell of male abdominal 5 muscle (with her1)
muscle cell of male abdominal 5 muscle (with her3)
sex comb | maternal effect
wing, with Scer\GAL4Bx-MS1096
wing | male limited, with Scer\GAL4Bx-MS1096
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Hsap\REST
1 of 15
Yes
No
Hsap\ZNF341
1 of 15
Yes
Yes
Hsap\ZNF513
1 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
eggNOG
Hieranoid
Homologene
Inparanoid
Isobase
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
RoundUp
TreeFam
ZFIN
Alignment
Complementation?
Transgene?
Mmus\Rest
1 of 15
Yes
Yes
Mmus\Zfp341
1 of 15
Yes
Yes
Mmus\Zfp513
1 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Zfp341
1 of 13
Yes
Yes
Rnor\Zfp513
1 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (0)
No records found.
Danio rerio (Zebrafish) (2)
Drer\znf341
1 of 15
Yes
Yes
Drer\znf513a
1 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\CRZ1
1 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (21)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
Cf2
1 of 10
CG1792
1 of 10
CG2116
1 of 10
CG2202
1 of 10
CG4820
1 of 10
CG7386
1 of 10
CG8159
1 of 10
CG10274
1 of 10
CG10959
1 of 10
CG11906
1 of 10
cg
1 of 10
D19A
1 of 10
D19B
1 of 10
Kah
1 of 10
M1BP
1 of 10
Nnk
1 of 10
nom
1 of 10
ouib
1 of 10
prg
1 of 10
ranshi
1 of 10
sna
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
    Disease Associations of Human Orthologs (via DIOPT v8.0 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
    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.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    2L
    Recombination map
    2-52
    Cytogenetic map
    36A10-36A10
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    36A10-36A10
    Limits computationally determined from genome sequence between P{PZ}dacP and P{EP}grpEP921&P{lacW}l(2)k13905k13905
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location

    2-52

    (FlyBase, 2016)

    2-50.7

    (Comeron et al., 2012)

    2-52 +/- 1

    (Pultz et al., 1994)

    2-52.9

    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (14)
    Genomic Clones (20)
    cDNA Clones (26)
     

    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 sequenced
    BDGP DGC clones
    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
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
       
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of

      Source for identity of: her CG4694

      (Zhong, 1999.11)
      Source for database merge of
      Additional comments
      Other Comments

      Genetic characterisation demonstrates her is expressed sex non-specifically and independently of other known sex determination genes and acts together with the last genes in the determination hierarchy, dsx and ix, to control female sexual differentiation.

      (Li and Baker, 1998)

      Maternal and zygotic functions of her are needed at two distinctly different levels of the sex determination regulatory hierarchy. Zygotic her function is important for sexual differentiation and maternal her function for daughter viability. Maternal and zygotic her function is required for viability of both sexes. The wild type maternal function of her may be participating in the same process as sisA during female development and maternal her function is needed for the initiation of Sxl function. When daughters lack her function a duplication of sc can improve prospects but be made worse by a single mutation of sisA. Males with extra wild type sisA or sc genes have an increased chance of survival when maternal her function is defective.

      (Pultz and Baker, 1995)

      her encodes a component of the sex determination cascade, and has zygotic and maternal functions. Zygotically her is required for female sexual differentiation, and possibly plays a role in male sexual differentiation. Maternally her is required for the viability of female offspring. The zygotic and maternal components of her function are differentially mutable.

      (Pultz et al., 1994)
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 42 )
      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.
      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.
      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.
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      modMine - A data warehouse for the modENCODE project
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      FlyMine - An integrated database for Drosophila genomics
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (7)
      Datasets (8)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (8)
      Result
      Result Type
      Title
      scRNAseq_2020_Cattenoz_NI_seq_clustering
      Clustering analysis of hemocytes from non-infested third instar larvae
      scRNAseq_2020_Cattenoz_WI_seq_clustering
      Clustering analysis of hemocytes from wasp-infested third instar larvae
      scRNAseq_2020_Cho_NI72LG_seq_clustering
      Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
      scRNAseq_2020_Cho_NI96LG_seq_clustering
      Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
      scRNAseq_2020_Cho_NI120LG_seq_clustering
      Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
      scRNAseq_2020_Cho_WI96LG_seq_clustering
      Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
      scRNAseq_2020_Cho_NI96HL_seq_clustering
      Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
      scRNAseq_2020_Cho_NI120HL_seq_clustering
      Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
      References (73)