FB2025_01 , released February 20, 2025
Gene: Dmel\scaf6
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General Information
Symbol
Dmel\scaf6
Species
D. melanogaster
Name
SR-related CTD associated factor 6
Annotation Symbol
CG33522
Feature Type
protein_coding_gene
FlyBase ID
FBgn0261872
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

BP1047, BP1040

Key Links
Genomic Location
Cytogenetic map
73E5-73E5
Sequence location
Recombination map
3-45
RefSeq locus
NT_037436 REGION:17036859..17042574
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 (5 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables nucleic acid binding
inferred from electronic annotation with InterPro:IPR000467
(InterPro Project Members, 2004-)
enables RNA binding
inferred from electronic annotation with InterPro:IPR000061, InterPro:IPR035967
(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 intracellular calcium ion homeostasis
inferred from biological aspect of ancestor with PANTHER:PTN000268863
(GO Reference Genome Project, 2011-)
involved_in RNA processing
inferred from electronic annotation with InterPro:IPR000061, InterPro:IPR035967
(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 perinuclear region of cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000268863
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
SPLICEOSOME COMPLEX A -
Nuclear pre-mRNA splicing is catalyzed by the spliceosome which assembles in a step-wise manner. Complex A, the pre-spliceosome, is composed of U1 and U2 snRNPs and proteins involved in recognition of the 5' splice site and branch point. (Adapted from PMID:24452469 and PMID:23118483).
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\scaf6 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 Q59E33)

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 5.41

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

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.46

Gene model reviewed during 5.55

Multiphase exon postulated: exon reading frame differs in alternative transcripts.

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
scaf6-RA
FBtr0091474
NM_001014589
3071
960
scaf6-RC
FBtr0301554
NM_001169986
1415
182
scaf6-RE
FBtr0345067
NM_001038939
2998
251
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
scaf6-PA
FBpp0075048
107.6
960
9.71
Q59E33
NP_001014589
AAX52741
scaf6-PC
FBpp0290769
20.4
182
6.68
Q86MQ9
NP_001163457
ACZ94728
scaf6-PE
FBpp0311297
28.0
251
6.01
A0A023GQ04
NP_001034028
ABC66164
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

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
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\scaf6 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).

-0.86

Transcript Expression
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\scaf6 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
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of scaf6
Transgenic constructs containing regulatory region of scaf6
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3L)ED4674
(Hayashi et al., 2014)
Inferred from location ( 4 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
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) (2)
Hsap\CHERP
11 of 14
Yes
Yes
Hsap\SF3A1
2 of 14
No
No
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) (2)
Rnor\Cherp
11 of 14
Yes
Yes
Rnor\Sf3a1
2 of 14
No
No
Mus musculus (laboratory mouse) (2)
Mmus\Cherp
10 of 14
Yes
Yes
Mmus\Sf3a1
2 of 14
No
No
Xenopus tropicalis (Western clawed frog) (3)
Xtro\cherp
7 of 13
Yes
Yes
Xtro\otub1
1 of 13
No
No
Xtro\sf3a1
1 of 13
No
No
Danio rerio (Zebrafish) (2)
Drer\cherp
11 of 14
Yes
Yes
Drer\sf3a1
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\tag-65
12 of 14
Yes
Yes
Cele\prp-21
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP005953
12 of 12
Yes
Yes
Agam\AgaP_AGAP011328
2 of 12
No
No
Arabidopsis thaliana (thale-cress) (11)
Atha\AT4G31200
6 of 13
Yes
Yes
Atha\AT1G14640
2 of 13
No
No
Atha\AT1G14650
2 of 13
No
No
Atha\AT1G18050
2 of 13
No
Yes
Atha\AT3G27600
2 of 13
No
No
Atha\AT4G16200
2 of 13
No
No
Atha\AT5G06520
2 of 13
No
No
Atha\AT5G06890
2 of 13
No
Yes
Atha\AT5G12280
2 of 13
No
No
Atha\AT2G43960
1 of 13
No
No
Atha\AT3G49130
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\PRP21
1 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\sap114
1 of 12
Yes
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:scaf6. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
Sf3a1
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 ( 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?
    CHERP; calcium homeostasis endoplasmic reticulum protein
    11 of 14
    618539
        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:
        Show/hide secondary interactors 
        (data from AllianceMine provided by esyN)
        Select Layout:
        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
        scaf6 - S6kII
        anti tag coimmunoprecipitation, Identification by mass spectrometry
        (Vinayagam et al., 2016)
        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
        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
        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.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-45
        Cytogenetic map
        73E5-73E5
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        73E5-73E5
        Limits computationally determined from genome sequence between P{PZ}Baldspot02281 and P{PZ}blot01658
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        73E1-73E4
        (Sampson, 2002.8.9)
        Experimentally Determined Recombination Data
        Location

        3-45

        (FlyBase, 2016)

        3-39.8

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (5)
        Genomic Clones (11)
         

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

        cDNA Clones (49)
         

        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
           
          Commercially Available Antibodies
           
          Cell Line Information
          Publicly Available Cell Lines
           
            Other Stable Cell Lines
             
              Other Comments
              Relationship to Other Genes
              Source for database merge of

              Source for merge of: CG6615 CG32168

              (FlyBase, 1996-)

              Source for merge of: CG14058 CG6626

              (FlyBase Genome Annotators, 2002-2003)

              Source for merge of: scaf6 BP1047

              (FlyBase, 1996-)
              Additional comments

              Annotations CG32168 and CG6615 merged as CG33522 (which corresponds to scaf6) in release 4.1 of the genome annotation.

              (FlyBase Genome Annotators, 2005)

              Annotations CG14058 and CG6626 merged as CG32168 in release 3 of the genome annotation.

              (FlyBase Genome Annotators, 2002-2003)

              Source for merge of CG6615 CG32168 was sequence comparison ( date:021216 ).

              (FlyBase, 1996-)
              Nomenclature History
              Source for database identify of

              Source for identity of: scaf6 BP1040

              (FlyBase Genome Annotators, 2005)
              Nomenclature comments
              Etymology
              Synonyms and Secondary IDs (9)
              Reported As
              Symbol Synonym
              BP1040
              (Yandell et al., 2005)
              BP1047
              CG14058
              CG32168
              CG33522
              (Ni et al., 2010.12.1, Keleman et al., 2009.8.5)
              CG6615
              (Yano et al., 2012, Giot et al., 2003)
              CG6626
              scaf6
              (Van Bortle et al., 2015, Hayashi et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Mackay et al., 2012, Yano et al., 2012, Friedman et al., 2011)
              Name Synonyms
              BP1047
              SR-related CTD associated factor 6
              scaf6
              Secondary FlyBase IDs
              • FBgn0053522
              • FBgn0036692
              • FBgn0036693
              • FBgn0036694
              • FBgn0052168
              • FBgn0082866
              • FBgn0082859
              Datasets (0)
              Study focus (0)
              Experimental Role
              Project
              Project Type
              Title
              Study result (0)
              Result
              Result Type
              Title
              External Crossreferences and Linkouts ( 57 )
              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
              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
              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
              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
              Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
              FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
              iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
              KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
              MIST (protein-protein) - An integrated Molecular Interaction Database
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              References (40)