FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Ssb-c31a
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General Information
Symbol
Dmel\Ssb-c31a
Species
D. melanogaster
Name
Single stranded-binding protein c31A
Annotation Symbol
CG8396
Feature Type
protein_coding_gene
FlyBase ID
FBgn0015299
Gene Model Status
Current
Stock Availability
12 publicly available
Gene Summary
General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. Binds single-stranded DNA (By similarity). Binds specifically to the NssBF element, a short nucleotide sequence of the 1731 retrotransposon, to repress promoter activity. (UniProt, Q9VLR5)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

C31A

Key Links
Genomic Location
Cytogenetic map
28F3-28F3
Sequence location
Recombination map
2-30
RefSeq locus
NT_033779 REGION:8211347..8211938
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
Gene Ontology (GO) Annotations (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables single-stranded DNA binding
inferred from direct assay
(Lacoste et al., 1995)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables DNA binding
inferred from electronic annotation with InterPro:IPR003173, InterPro:IPR009044
(InterPro Project Members, 2004-)
enables transcription coactivator activity
inferred from electronic annotation with InterPro:IPR045125
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000325022
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in negative regulation of DNA-templated transcription
inferred from direct assay
(Lacoste et al., 1995)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in positive regulation of transcription initiation by RNA polymerase II
inferred from electronic annotation with InterPro:IPR045125
(InterPro Project Members, 2004-)
involved_in regulation of DNA-templated transcription
inferred from electronic annotation with InterPro:IPR003173, InterPro:IPR009044
(InterPro Project Members, 2004-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Lacoste et al., 1995)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000325022
(GO Reference Genome Project, 2011-)
part_of transcription regulator complex
inferred from biological aspect of ancestor with PANTHER:PTN000325022
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the transcriptional coactivator PC4 family. (Q9VLR5)
Protein Signatures (InterPro)
Summaries
Protein Function (UniProtKB)
General coactivator that functions cooperatively with TAFs and mediates functional interactions between upstream activators and the general transcriptional machinery. Binds single-stranded DNA (By similarity). Binds specifically to the NssBF element, a short nucleotide sequence of the 1731 retrotransposon, to repress promoter activity.
(UniProt, Q9VLR5)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Ssb-c31a 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 Q9VLR5)

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 5.45

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Ssb-c31a-RA
FBtr0079590
NM_057788
536
110
Additional Transcript Data and Comments
Reported size (kB)

0.5 (northern blot)

(Lacoste 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
Ssb-c31a-PA
FBpp0079211
12.2
110
9.89
Q9VLR5
NP_477136
AAF52619
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)

98 (aa); 14 (kD observed); 11 (kD predicted)

(Lacoste et al., 1995)
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\Ssb-c31a 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
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).

3.01

Transcript Expression
Polypeptide Expression
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
(Lacoste et al., 1995)
oogenesis & adult stage | female
ovary
(Lacoste et al., 1995)
Additional Descriptive Data

Ssb-c31a protein is detected in embryos and ovaries and weakly in pupae on western blots.

(Lacoste et al., 1995)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Lacoste et al., 1995)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ssb-c31a in JBrowse
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
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Ssb-c31a
Transgenic constructs containing regulatory region of Ssb-c31a
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
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
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
Other Phenotypes
Allele
visible, with Scer\GAL4pnr-MD237
Phenotype manifest in
Allele
trichogen cell, with Scer\GAL4pnr-MD237
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
Hsap\SUB1
11 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Sub1
11 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Sub1
10 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\sub1
9 of 13
Yes
Yes
Danio rerio (Zebrafish) (2)
Drer\sub1a
11 of 14
Yes
Yes
Drer\sub1b
11 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\T13F2.2
11 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP012041
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (5)
Atha\KELP
9 of 13
Yes
Yes
Atha\KIWI
9 of 13
Yes
Yes
Atha\AT5G09240
7 of 13
No
Yes
Atha\AT1G64490
1 of 13
No
Yes
Atha\AT5G42060
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\SUB1
5 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\sub1
10 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Ssb-c31a. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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?
    SUB1; SUB1 regulator of transcription
    11 of 14
    600503
        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
        protein-protein
        Physical Interaction
        Assay
        References
        Ssb-c31a - ApepP
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Arglu1
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - CG10265
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - CG10657
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - CG3107
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - CG4119
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - CG7668
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Df31
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Fkbp12
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Gtpx
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Hr78
        two hybrid array
        (Shokri et al., 2019)
        Ssb-c31a - Nkap
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Prp40
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Raf
        anti tag coimmunoprecipitation, peptide massfingerprinting
        (Friedman et al., 2011)
        Ssb-c31a - S6kII
        anti tag coimmunoprecipitation, Identification by mass spectrometry
        (Vinayagam et al., 2016)
        Ssb-c31a - Srrm234
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - Ubx
        bimolecular fluorescence complementation, fluorescence microscopy
        (Bischof et al., 2018)
        Ssb-c31a - abd-A
        bimolecular fluorescence complementation, fluorescence microscopy
        (Bischof et al., 2018)
        Ssb-c31a - abs
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - eIF1A
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - hfp
        experimental knowledge based
        (Guruharsha et al., 2011)
        Ssb-c31a - retn
        two hybrid array
        (Shokri et al., 2019)
        Ssb-c31a - snRNP-U1-70K
        experimental knowledge based
        (Guruharsha et al., 2011)
        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
        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
        FlyBase
        External Links
        External Data
        Linkouts
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2L
        Recombination map
        2-30
        Cytogenetic map
        28F3-28F3
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        28F3-28F3
        Limits computationally determined from genome sequence between P{lacW}l(2)k16919k16919&P{lacW}Bsgk09030 and P{lacW}Btk29Ak00206&P{EP}Btk29AEP715
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        28E-28F
        (Lacoste, 1994.12.21)
        Experimentally Determined Recombination Data
        Location

        2-30

        (FlyBase, 2016)

        2-27.3

        (Comeron et al., 2012)

        2-

        (Lacoste, 1994.12.21)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (12)
        Genomic Clones (20)
        cDNA Clones (31)
         

        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
        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
          Antibody Information
          Laboratory Generated Antibodies
           

          polyclonal

          (Lacoste et al., 1995)
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments

              Expression is enriched in embryonic gonads.

              (Shigenobu et al., 2006)

              Isolated from a Drosophila Kc cell expression library, using an oligonucleotide containing two NssBF elements as a probe.

              (Lacoste et al., 1995)

              A Ssb-c31a cDNA has been cloned and sequenced. Ssb-c31a encodes a nuclear DNA binding protein that binds specifically to the NssBF element. Overexpression of Ssb-c31a in transfected cells represses the 1731 element promoter.

              (Lacoste 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 (8)
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 30 )
              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/Swiss-Prot - Manually annotated and reviewed 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
              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
              FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
              FlyMine - An integrated database for Drosophila genomics
              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)
              Linkouts
              BioGRID - A database of protein and genetic interactions.
              Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
              DroID - A comprehensive database of gene and protein interactions.
              DRSC - Results frm RNAi screens
              Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
              FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
              FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
              Flygut - An atlas of the Drosophila adult midgut
              iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
              MIST (protein-protein) - An integrated Molecular Interaction Database
              References (56)