FB2019_06, released Dec 19, 2019

Gene: Dmel\santa-maria

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General Information
Symbol
Dmel\santa-maria
Species
D. melanogaster
Name
scavenger receptor acting in neural tissue and majority of rhodopsin is absent
Annotation Symbol
CG12789
Feature Type
protein_coding_gene
FlyBase ID
FBgn0025697
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Snapshot
scavenger receptor acting in neural tissue and majority of rhodopsin is absent (santa-maria) encodes a class B scavenger receptor that contributes to the conversion of carotenoids to vitamin A. It is involved in phototransduction and thermotaxis. [Date last reviewed: 2019-09-26]
Other Summaries
Also Known As
santa maria, BEST:CK01577
Key Links
Genomic Location
Cytogenetic map
28A1-28A1
Sequence location
2L:7,445,355..7,451,244 [-]
Recombination map
2-27
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
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Molecular Function (GO)
[Detailed GO annotations]
Experimental Evidence
-
Predictions / Assertions
-
Summaries
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\santa-maria or the JBrowse view of Dmel\santa-maria 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 5.45
Gene model reviewed during 5.56
Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
santa-maria-RA
FBtr0079464
NM_164752
2302
563
santa-maria-RC
FBtr0346571
NM_135277
5563
563
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
santa-maria-PA
FBpp0079088
62.9
563
5.35
NP_723277
AAF52518
santa-maria-PC
FBpp0312169
62.9
563
5.35
NP_609121
AAN10632
Polypeptides with Identical Sequences

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

563 aa isoforms: santa-maria-PA, santa-maria-PC
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\santa-maria using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (5 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (4 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
carotenoid metabolic process
inferred from mutant phenotype
(Wang et al., 2007)
phototransduction
inferred from mutant phenotype
(Wang et al., 2007)
rhodopsin biosynthetic process
inferred from mutant phenotype
(Wang et al., 2007)
thermotaxis
inferred from mutant phenotype
(Shen et al., 2011)
Terms Based on Predictions or Assertions (0 terms)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
membrane
inferred from electronic annotation with InterPro:IPR002159
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
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
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
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\santa-maria in GBrowse 2
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, and Transgenic Constructs
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 santa-maria
Transgenic constructs containing regulatory region of santa-maria
Deletions and Duplications ( 2 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
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\SCARB1
6 of 15
Yes
No
 
Hsap\CD36
4 of 15
No
No
Hsap\SCARB2
3 of 15
No
No
 
Model Organism Orthologs (via DIOPT v7.1)
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\Scarb1
6 of 15
Yes
No
Mmus\Cd36
3 of 15
No
No
Mmus\Scarb2
3 of 15
No
No
Rattus norvegicus (Norway rat) (6)
Rnor\Scarb1
6 of 13
Yes
No
Rnor\LOC103690020
3 of 13
No
No
Rnor\Scarb2
3 of 13
No
No
Rnor\RGD1565355
2 of 13
No
No
Rnor\Cd36
1 of 13
No
No
Rnor\LOC100365047
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
Xtro\scarb1
5 of 12
Yes
No
Xtro\cd36
2 of 12
No
No
Xtro\scarb2
2 of 12
No
No
Xtro\cd36l
1 of 12
No
Yes
Danio rerio (Zebrafish) (5)
Drer\scarb1
5 of 15
Yes
No
Drer\cd36
4 of 15
No
Yes
Drer\scarb2a
3 of 15
No
No
Drer\scarb2b
3 of 15
No
No
Drer\wu:fj81e10
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (9)
Cele\scav-2
8 of 15
Yes
Yes
Cele\scav-1
7 of 15
No
Yes
Cele\scav-3
7 of 15
No
No
Cele\scav-4
5 of 15
No
No
Cele\scav-5
4 of 15
No
No
Cele\scav-6
3 of 15
No
No
Cele\clec-254
1 of 15
No
Yes
Cele\srz-60
1 of 15
No
Yes
Cele\Y51A2A.4
1 of 15
No
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.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091905DN )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\santa-maria
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00001514
Drosophila simulans
Dsim\GD22494
Drosophila sechellia
Dsec\GM13558
Drosophila erecta
Dere\GG23532
Drosophila yakuba
Dyak\GE18358
Drosophila ananassae
Dana\GF14024
Drosophila pseudoobscura pseudoobscura
Dpse\GA25196
Drosophila persimilis
Dper\GL25933
Drosophila willistoni
Dwil\GK24723
Drosophila virilis
Dvir\GJ17608
Drosophila mojavensis
Dmoj\GI17783
Drosophila grimshawi
Dgri\GH13144
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091504DL )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17007752
Musca domestica
House fly
Mdoa\17006165
Musca domestica
House fly
Mdoa\17012546
Glossina morsitans
Tsetse fly
Gmor\GMOY006344
Glossina morsitans
Tsetse fly
Gmor\GMOY006345
Glossina morsitans
Tsetse fly
Gmor\GMOY006342
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_14325
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_14422
Mayetiola destructor
Hessian fly
Mdes\Mdes008797
Aedes aegypti
Yellow fever mosquito
Aaeg\SCRB17
Anopheles darlingi
American malaria mosquito
Adar\ADAC006794
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ017039
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W046S )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA010477
Danaus plexippus
Monarch butterfly
Dple\DPOGS202827-PA
Danaus plexippus
Monarch butterfly
Dple\DPOGS203890-PA
Heliconius melpomene
Postman butterfly
Hmel\SCR-like7
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_08065
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_08064
Tribolium castaneum
Red flour beetle
Tcas\TC012757
Tribolium castaneum
Red flour beetle
Tcas\TC012758
Tribolium castaneum
Red flour beetle
Tcas\TC012756
Pediculus humanus
Human body louse
Phum\PHUM512380
Pediculus humanus
Human body louse
Phum\PHUM351640
Rhodnius prolixus
Kissing bug
Rpro\RPRC015150
Rhodnius prolixus
Kissing bug
Rpro\RPRC009306
Cimex lectularius
Bed bug
Clec\CLEC004179
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01929
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_17151
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X08YJ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR010651
Strigamia maritima
European centipede
Smar\SMAR002938
Ixodes scapularis
Black-legged tick
Isca\ISCW010934
Ixodes scapularis
Black-legged tick
Isca\ISCW002412
Ixodes scapularis
Black-legged tick
Isca\ISCW023721
Stegodyphus mimosarum
African social velvet spider
Smim\KFM77785.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM63982.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM69030.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM60893.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur10g02420
Tetranychus urticae
Two-spotted spider mite
Turt\tetur03g08040
Tetranychus urticae
Two-spotted spider mite
Turt\tetur04g08760
Tetranychus urticae
Two-spotted spider mite
Turt\tetur13g00340
Tetranychus urticae
Two-spotted spider mite
Turt\tetur09g00840
Tetranychus urticae
Two-spotted spider mite
Turt\tetur11g04660
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_120417
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_303164
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_303163
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_237864
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0E0V )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000015724
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (13)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
CG3829
7 of 10
CG7227
6 of 10
CG40006
6 of 10
dsb
6 of 10
emp
6 of 10
CG10345
5 of 10
crq
5 of 10
Snmp1
5 of 10
CG2736
4 of 10
CG31741
4 of 10
ninaD
4 of 10
pes
4 of 10
Snmp2
4 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 v7.1 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?
    SCARB1; scavenger receptor class B member 1
    6 of 15
    601040
       
      CD36; CD36 molecule
      4 of 15
      173510
      SCARB2; scavenger receptor class B member 2
      3 of 15
      602257
       
      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
      RNA-RNA
      Physical Interaction
      Assay
      References
      santa-maria - mir-184
      luminiscence technology
      (Iovino et al., 2009, Kertesz et al., 2007)
      protein-protein
      Physical Interaction
      Assay
      References
      santa-maria - CG8560
      experimental knowledge based
      (Guruharsha et al., 2011)
      santa-maria - Hk
      experimental knowledge based
      (Guruharsha et al., 2011)
      santa-maria - Tango2
      experimental knowledge based
      (Guruharsha et al., 2011)
      santa-maria - nwk
      experimental knowledge based
      (Guruharsha et al., 2011)
      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
      Ras85D
      suppressible
      santa-maria
      (Hauling et al., 2014)
      Ras85D
      enhanceable
      santa-maria
      (Hauling et al., 2014)
      External Data
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      2L
      Recombination map
      2-27
      Cytogenetic map
      28A1-28A1
      Sequence location
      2L:7,445,355..7,451,244 [-]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      28A1-28A1
      Limits computationally determined from genome sequence between P{PZ}cuc10607 and P{EP}EP2419EP2419&P{EP}EP575
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location
      2-27
      (FlyBase, 2016)
      2-24.3
      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (7)
      Genomic Clones (16)
       

      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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

      cDNA clones, fully sequences
      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: CG12789 santa-maria
      (Wang et al., 2007)
      Source for database merge of
      Source for merge of: BEST:CK01577 CG12789
      (Bayraktaroglu, 2000.11.2)
      Additional comments
      Other Comments
      santa-maria acts as a modifier of Ras85D-induced tissue abnormalities and this affects the survival of mutant larvae.
      (Hauling et al., 2014)
      The santa-maria protein functions in neurons and glia.
      (Wang et al., 2007)
      dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.
      (Kiger et al., 2003)
      Identification: cDNA screen for secreted and transmembrane proteins expressed during embryogenesis.
      (Kopczynski et al., 1998)
      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 47 )
      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
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      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.
      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
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      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
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DPiM - Drosophila Protein interaction map
      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 (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      Synonyms and Secondary IDs (8)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (56)