A Database of Drosophila Genes & Genomes

FB2008_07, released August 8, 2008
 

Gene Dmel\Spt6

General Information
SymbolDmel\Spt6SpeciesD. melanogaster
NameSpt6Annotation symbolCG12225
Feature typeprotein_coding_geneFlyBase IDFBgn0028982
Created / Updated2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)XRecombination map
Cytogenetic map5E4-5E4Sequence locationX:6,161,847..6,169,019 [+]
Map ( GBrowse ) detailed view
hide Summary Information
Automatically generated summary

See sections below for more information
This gene is referred to in FlyBase by the symbol Spt6 (CG12225, FBgn0028982). It has the cytological map location 5E4. Its sequence location is X:6161847..6169019. Its molecular function is described as: chromatin binding; transcription elongation regulator activity; hydrolase activity, acting on ester bonds; RNA binding; protein binding. It is involved in the biological processes: RNA elongation; regulation of transcription from RNA polymerase II promoter. 7 alleles are reported. No phenotypic data is available. It has one annotated transcript and one annotated polypeptide.

External Summaries

hide Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
5E4-5E4  
Limits computationally determined from genome sequence between P{EP}EP1457EP1457&P{EP}CG5928EP1083 and P{EP}EP1311&P{EP}EP1384  
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
5E1-5E2
(determined by in situ hybridisation)  
(Peter et al., 2002)
5E6-5E8
 
(Chiang, 1998.11.4)
5E1-5E8
 
(Chiang et al., 1999)
5E1-5E7
(determined by in situ hybridisation)  
(Schaefer et al., 1999.6.15)
5E1-5E2
(determined by in situ hybridisation)  
(Schaefer et al., 1999.3.29)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology)
References
Gene Order (overall orientation not stated)
References
hide Gene Model & Products
Please see the GBrowse view of Dmel\Spt6 for information on other features
detailed view FBtr0070938 FBtr0070937 FBtr0070896 FBtr0089869 FBtr0089870 FBtr0070933 FBpp0070898 FBpp0070899 FBpp0070861 FBpp0088809 FBpp0088808 FBti0013918 FBti0038406 FBti0038405 FBti0038407 FBti0012826 FBti0015633 FBti0018603 FBti0037241 FBti0059628 FBti0047266 FBti0012825 FBti0099858 FBti0039296
Comments on Gene Model
DGC clone LD47893 appears problematic: incomplete CDS
hide Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Associated CDS (aa)
Spt6-RA
FBtr0070896
 NM_143705
  6151
  1831
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
hide Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kD)
Length (aa)
Theoretical pI
RefSeq ID
GenBank protein
Spt6-PA  
FBpp0070861  
208.6  
1831  
4.96  
  NP_651962
  AAF46140
Additional Polypeptide Data & Comments
Reported size (kD)
Comments
External Data
Linkouts
PANTHER - Protein classification by function, families, and pathways
•
Crossreferences
InterPro domains - A database of protein families, domains, and functional sites
•
SH2 motif (IPR000980)
S1, RNA binding (IPR003029)
Resolvase, RNase H-like fold (IPR006641)
Nucleic acid-binding, OB-fold (IPR012340)
Nucleic acid-binding, OB-fold-like (IPR016027)
Transcription elongation factor Spt6 (IPR017072)
hide Sequences Consistent with the Gene Model
DDBJ /
EMBL /
GenBank
DNA sequence
Protein sequence
Name
AA202206
 
AA202705
 
AA391792
 
AA392166
 
AA539528
 
AA539582
 
AA539603
 
AA540589
 
AA540894
 
AA567281
 
AA695350
 
AA802947
 
AA803404
 
AA820152
 
AA940994
 
AA941412
 
AA941430
 
AA948960
 
AA949736
 
AA951018
 
AE003437
AAF46140
 
AF104400
AAF14114
 
AF104401
AAF14115
 
AI259265
 
AI295118
 
AI455021
 
AI512258
 
AI513035
 
AI514494
 
AI514504
 
AI516547
 
AI533804
 
AI546339
 
AJ426714
 
AW943932
 
AY052030
AAK93454
 
BG633583
 
BG637978
 
BG638372
 
BG638505
 
BG639776
 
BI166941
 
BI169795
 
BI242364
 
BI352860
 
BI353787
 
BI356698
 
BI484946
 
BI580110
 
BI636908
 
CO196097
 
CO196272
 
CO196480
 
CO261872
 
CO288150
 
CO289173
 
CO290040
 
CO297934
 
EC064988
 
EC068199
 
EC078901
 
EC081529
 
EC083444
 
EC085375
 
EC198004
 
EC209396
 
EC219069
 
EC228681
 
EC231295
 
EC232460
 
EC242201
 
ES689995
 
GM02265
 
LD23621
 
LD27675
 
SD05767
 
 
UniProtKB/Swiss-Prot
    UniProtKB/TrEMBL
    Maps to
    Does NOT map to
    Identified with
    (Andrulis et al., 2002)
    (Kaplan et al., 2000)
    (BDGP Project Members, 2000-)
    hide Mapped Features & Mutations
    Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here
    Type
    Symbol & Location
    Additional Notes
    References
    hide External Data
    Linkouts
    DEDB - Drosophila exon database: splicing graphs
    •
    Crossreferences
    hide Expression Data
    FlyBase-Curated Data
    Transcript and
    Protein data     		Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
    hide Summary of Transcript Expression
    Stage
    Tissue/Position
    Reference
    Marker for
      Subcellular Localization
      CV Term
      hide Summary of Polypeptide Expression
      Stage
      Tissue/Position
      Reference
      Marker for
        Subcellular Localization
        CV Term
        hide Microarray Data
        Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)
        Untitled Document detailed view FBtr0070938 FBtr0070937 FBtr0070896 FBtr0089869 FBtr0089870 FBtr0070933
        AI513035
        AA948960
        AI533804
        AI546339
        hide External Data & Images
        Linkouts
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        •
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        •
        GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies
        •
        hide Alleles & Phenotypes
        hide Summary of Allele Phenotypes
        Lethality
        Allele
        viable
        lethal | recessive
        lethal | embryonic stage
        Phenotype manifest in
        Allele
        hide Classical Alleles ( 5 )
        For All Classical Alleles Show

        Allele of Spt6ClassMutagenStocksKnown lesion
        Spt6B1-260 Yes
        Spt6CA076920 Yes
        Spt6D1-100 --
        Spt6G00631 --
        Spt6PL830 --
        hide Alleles Carried on Transgenic Constructs ( 2 )
        For All Alleles Carried on Transgenic Constructs Show

        Allele of Spt6ClassMutagenStocksKnown lesion
        Spt6Act5C.T:Zzzz\FLAG,T:Zzzz\His60 Yes
        Spt6GD75362 Yes
        hide Aneuploid Aberrations
        Useful deficiency
         
        Disrupted in
        (Petruk et al., 2006)
        Duplicated in
        (Petruk et al., 2006)
        hide Transgenic Constructs & Insertions
        Transgenic Constructs
        Type of construct
        Name
        Expression data
        UAS construct
        P{GD7536}
        NA
        Insertions
        Type of insertions
        Name
        Expression data
        miscellaneous insertions
        P{PTT-GA}Spt6CA07692
        NA
        insertion of enhancer trap
        P{lacW}Spt6G0063
        No
        P{lacW}Spt6PL83
        No
        hide Related Comments
        Please look at the allele reports for the complete phenotype data
        hide Gene Ontology: Function, Process & Cellular Component ( 9 )
        hide Molecular Function
        CV term
        Evidence
        References
        RNA binding
        inferred from electronic annotation with InterPro:IPR003029
        (FlyBase Curators et al., 2004-)
        chromatin binding
        inferred from sequence or structural similarity
        (Chiang, 1998.11.4)
        inferred from sequence or structural similarity with SGD_LOCUS:SPT6; SGD:S0003348
        (FlyBase, 1992-)
        hydrolase activity, acting on ester bonds
        inferred from electronic annotation with InterPro:IPR006641
        (FlyBase Curators et al., 2004-)
        protein binding
        inferred from electronic annotation with InterPro:IPR000980
        (FlyBase Curators et al., 2004-)
        transcription elongation regulator activity
        non-traceable author statement
        (Andrulis et al., 2002)
        inferred from electronic annotation with InterPro:IPR017072
        (FlyBase Curators et al., 2004-)
        hide Biological Process
        CV term
        Evidence
        References
        RNA elongation
        non-traceable author statement
        (Andrulis et al., 2002)
        regulation of transcription from RNA polymerase II promoter
        inferred from electronic annotation with InterPro:IPR017072
        (FlyBase Curators et al., 2004-)
        hide Cellular Component
        CV term
        Evidence
        References
        nuclear exosome (RNase complex)
        inferred from physical interaction
        (Andrulis et al., 2002)
        polytene chromosome
        inferred from direct assay
        (Andrulis et al., 2002)
        hide Sequence Ontology: Class of Gene
        protein_coding_gene
         
        nuclear_gene
         
        hide Interactions & Pathways
        hide Summary of Genetic Interactions
        Interacts with
        Please look at the allele data for full details of the genetic interactions
        Spt6 allele
        Gene
        References
        hide External Data
        Linkouts
        BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions
        •
        hide Orthologs
        Genome-wide drosophilid orthologs
        Curated drosophilid orthologs
         
        Linkouts
        InParanoid orthologs - Eukaryotic orthologs
        •
        hide Functional Complementation between Species
        hide Inter-Species Misexpression Data
        Produces phenotype in
        Produces NO phenotype in
        hide Stocks & Reagents
        hide Stocks Listed in FlyBase ( 3 )
        VDRC
        v31701
        w1118; P{GD7536}v31701/TM3
        v31703
        w1118; P{GD7536}v31703/TM3
        Bloomington
        11680
        w67c23 P{lacW}Spt6G0063/FM7c
        hide Genomic Clones ( 2 )
        hide cDNA Clones ( 47 )
        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
        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        hide RNAi & Array Information
        Affy Oligo
        Linkouts
        DRSC - RNAi screening (Harvard): high-throughput cell culture data and design
        •
        GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data
        •
        hide Antibody Information
        hide Other Information
        hide Discoverer
        hide Etymology
        hide Identification
        hide Position Effect Variegation Data
        hide Relationship to Other Genes
        Source for database identity of
        Source for database merge of
        Source for merge of: Spt6 l(1)G0063
        (Peter et al., 2002)
        Additional comments
        hide Comments About Role
        Spt6 may be involved in promoter-associated pausing and transcriptional elongation.
        (Andrulis et al., 2000)
        hide Comments About Molecular Function
        hide Other Comments
        hide External Crossreferences & Linkouts
        Sequence Crossreferences
        RefSeq (Transcripts)
        •
        RefSeq (Proteins)
        •
        DDBJ / EMBL / GenBank
        •