FB2020_06, released Dec 22, 2020

Gene: Dmel\Samuel

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General Information
Symbol
Dmel\Samuel
Species
D. melanogaster
Name
SAM-motif ubiquitously expressed punctatedly localized protein
Annotation Symbol
CG31868
Feature Type
protein_coding_gene
FlyBase ID
FBgn0032330
Gene Model Status
Current
Stock Availability
13 publicly available
Gene Snapshot
SAM-motif ubiquitously expressed punctatedly localized protein (Samuel) encodes a protein that binds to the nuclear receptor encoded by Hr78 and acts as a corepressor. It regulates chromatin silencing and larval growth. [Date last reviewed: 2018-11-15]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
32C1-32D1
Sequence location
2L:11,013,206..11,066,998 [-]
Recombination map

2-44

RefSeq locus
NT_033779 REGION:11013206..11066998
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 (7 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 chromatin binding
inferred from biological aspect of ancestor with PANTHER:PTN002284114
(assigned by GO_Central )
(Gaudet et al., 2011)
enables histone binding
inferred from biological aspect of ancestor with PANTHER:PTN002284114
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in regulation of chromatin silencing
inferred from mutant phenotype
(Schneiderman et al., 2010)
involved_in regulation of growth
inferred from mutant phenotype
(Baker et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in negative regulation of transcription, DNA-templated
inferred from biological aspect of ancestor with PANTHER:PTN002284114
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN002284114
(assigned by GO_Central )
(Gaudet et al., 2011)
part_of PRC1 complex
inferred from biological aspect of ancestor with PANTHER:PTN001745158
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Samuel 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
Comments on Gene Model

Gene model reviewed during 5.52

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 5.44

Gene model reviewed during 6.02

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Samuel-RA
FBtr0080161
NM_080362
4457
968
Samuel-RB
FBtr0331197
NM_001273443
5056
968
Samuel-RD
FBtr0343624
NM_001298899
3166
846
Samuel-RE
FBtr0347160
NM_001273444
3765
846
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
Samuel-PA
FBpp0079750
96.7
968
9.70
NP_525101
AAF53057
Samuel-PB
FBpp0303624
96.7
968
9.70
NP_001260372
AGB92907
Samuel-PD
FBpp0310219
85.6
846
10.05
NP_001285828
AHN54342
Samuel-PE
FBpp0312491
85.6
846
10.05
NP_001260373
AGB92908
Polypeptides with Identical Sequences

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

968 aa isoforms: Samuel-PA, Samuel-PB
846 aa isoforms: Samuel-PD, Samuel-PE
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\Samuel 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
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

GBrowse - Visual display of RNA-Seq signals

View Dmel\Samuel 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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 31 )
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 Samuel
Transgenic constructs containing regulatory region of Samuel
Deletions and Duplications ( 2 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (11)
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\SAMD11
5 of 15
Yes
Yes
Hsap\SAMD7
2 of 15
No
Yes
Hsap\DEAF1
1 of 15
No
No
Hsap\GMEB1
1 of 15
No
Yes
Hsap\GMEB2
1 of 15
No
Yes
Hsap\GPRIN1
1 of 15
No
Yes
Hsap\PHC1
1 of 15
No
No
Hsap\PHC2
1 of 15
No
No
Hsap\PHC3
1 of 15
No
No
Hsap\SAMD1
1 of 15
No
No
Hsap\SAMD13
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (10)
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\Samd11
5 of 15
Yes
Yes
Mmus\Samd7
2 of 15
No
Yes
Mmus\Deaf1
1 of 15
No
No
Mmus\Gmeb1
1 of 15
No
Yes
Mmus\Gmeb2
1 of 15
No
Yes
Mmus\Phc1
1 of 15
No
No
Mmus\Phc2
1 of 15
No
No
Mmus\Phc3
1 of 15
No
No
Mmus\Samd1
1 of 15
No
No
Mmus\Samd13
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (8)
Rnor\Samd11
3 of 13
Yes
Yes
Rnor\Samd7
2 of 13
No
Yes
Rnor\Deaf1
1 of 13
No
No
Rnor\Gmeb1
1 of 13
No
Yes
Rnor\Gmeb2
1 of 13
No
Yes
Rnor\Phc1
1 of 13
No
No
Rnor\Phc2
1 of 13
No
No
Rnor\Phc3
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (7)
Xtro\gmeb1
1 of 12
Yes
Yes
Xtro\gmeb2
1 of 12
Yes
Yes
Xtro\phc1
1 of 12
Yes
No
Xtro\phc2
1 of 12
Yes
No
Xtro\phc3
1 of 12
Yes
No
Xtro\samd7
1 of 12
Yes
No
Xtro\samd11
1 of 12
Yes
Yes
Danio rerio (Zebrafish) (14)
Drer\samd11
5 of 15
Yes
Yes
Drer\samd7
2 of 15
No
Yes
Drer\deaf1
1 of 15
No
No
Drer\gmeb1
1 of 15
No
Yes
Drer\phc1
1 of 15
No
No
Drer\phc2a
1 of 15
No
No
Drer\phc2b
1 of 15
No
No
Drer\phc3
1 of 15
No
No
Drer\samd1a
1 of 15
No
No
Drer\samd1b
1 of 15
No
No
Drer\samd13
1 of 15
No
No
Drer\si:ch73-302a13.2
1 of 15
No
Yes
Drer\si:ch211-230g15.5
1 of 15
No
No
Drer\sp100.3
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\gmeb-1
1 of 15
Yes
Yes
Cele\gmeb-2
1 of 15
Yes
Yes
Cele\gmeb-3
1 of 15
Yes
No
Cele\spe-44
1 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG09190BW9 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila simulans
Dsim\GD22201
Drosophila sechellia
Dsec\GM11188
Drosophila erecta
Dere\GG10332
Drosophila yakuba
Dyak\GE13066
Drosophila ananassae
Dana\GF14234
Drosophila pseudoobscura pseudoobscura
Dpse\GA25710
Drosophila persimilis
Dper\GL18597
Drosophila willistoni
Dwil\GK21247
Drosophila virilis
Dvir\GJ17177
Drosophila mojavensis
Dmoj\GI16650
Drosophila grimshawi
Dgri\GH11444
Drosophila grimshawi
Dgri\GH11445
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091507HF )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17012426
Glossina morsitans
Tsetse fly
Gmor\GMOY008806
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_03597
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W07TS )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_06865
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( None identified )
No non-Insect Arthropod orthologies identified
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( None identified )
No non-Arthropod Metazoa orthologies identified
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (7)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG2662
1 of 10
Deaf1
1 of 10
l(3)mbt
1 of 10
ph-d
1 of 10
ph-p
1 of 10
Scm
1 of 10
Sfmbt
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?
    SAMD11; sterile alpha motif domain containing 11
    5 of 15
    616765
        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:
        Select Layout:
        Legend:
        Protein
        RNA
        Selected Interactor(s)
        Interactions Browser
        View in Interactions Browser
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        Samuel
        pull down, autoradiography
        (Baker et al., 2007)
        Samuel - Hr78
        two hybrid, pull down, autoradiography
        (Baker et al., 2007)
        Summary of Genetic Interactions
        esyN Network Diagram
        esyN Network Key:
        Suppression
        Enhancement
        View in Interactions Browser
        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
        bw
        enhanceable
        Samuel
        (Schneiderman et al., 2010)
        External Data
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        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

        2-44

        Cytogenetic map
        32C1-32D1
        Sequence location
        2L:11,013,206..11,066,998 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        32C1-32D1
        Limits computationally determined from genome sequence between P{lacW}l(2)k05812k05812&P{lacW}l(2)k09104k09104 and P{EP}ppoEP2478&P{lacW}l(2)k15817k15817
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-44

        (FlyBase, 2016)

        2-37.5

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (13)
        Genomic Clones (43)
        cDNA Clones (17)
         

        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 database merge of

                Source for merge of: Samuel CG14918 CG14917 CG12291

                (Kose, 2001.3.7)
                Additional comments

                Annotations CG12291, CG14917, CG14918 merged as CG31868 in release 3 of the genome annotation.

                (FlyBase Genome Annotators, 2002-2003)
                Other Comments

                Hr78 protein is an obligate partner for Samuel protein, a cofactor that requires Hr78 protein for its stability.

                (Baker et al., 2007)

                RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells.

                (Boutros et al., 2004)

                Over-expression of Samuel protein causes severe defects in photoreceptor cell and wing bristle development. Loss of function mutant animals die during first instar larva.

                (Kose et al., 2001)
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 43 )
                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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
                Other crossreferences
                Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
                Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
                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.
                modMine - A data warehouse for the modENCODE project
                Linkouts
                DroID - A comprehensive database of gene and protein interactions.
                DRSC - Results frm RNAi screens
                FLIGHT - Cell culture data for RNAi and other high-throughput technologies
                FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                FlyMine - An integrated database for Drosophila genomics
                InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
                MIST (protein-protein) - An integrated Molecular Interaction Database
                Synonyms and Secondary IDs (12)
                Reported As
                Symbol Synonym
                78BP
                (Baker et al., 2007)
                CG12291
                CG14917
                (Boutros et al., 2004)
                CG14918
                CG31868
                (Meadows, 2019.11.20, Meadows, 2018.10.31, Schneiderman et al., 2010, Wagstaff and Begun, 2005, Peterson et al., 2004)
                Moses
                (Baker et al., 2005)
                Samuel
                (Lee et al., 2018, Clandinin and Owens, 2016-, Gene Disruption Project members, 2016-, Luck et al., 2014, Japanese National Institute of Genetics, 2012.5.21, Schneiderman et al., 2010, Schneiderman et al., 2010, Zhang et al., 2007)
                mdcds_1002
                (FlyBase Genome Annotators, 2014)
                moses
                (Baker et al., 2007)
                Name Synonyms
                Middleman of seventy-eight signaling
                (Baker et al., 2007)
                SAM-motif ubiquitously expressed punctatedly localized protein
                (Kose et al., 2001)
                middleman of seventy-eight signaling
                (Baker et al., 2005)
                Secondary FlyBase IDs
                • FBgn0032332
                • FBgn0032333
                • FBgn0051868
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                References (37)