FB2021_01, released Feb 18, 2021

Gene: Dmel\TH1

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General Information
Symbol
Dmel\TH1
Species
D. melanogaster
Name
TH1
Annotation Symbol
CG9984
Feature Type
protein_coding_gene
FlyBase ID
FBgn0010416
Gene Model Status
Current
Stock Availability
8 publicly available
Gene Snapshot
TH1 (TH1) encodes one of four subunits that constitutes the NELF complex. The NELF complex along with DSIF causes RNA polymerase II to pause 20 to 50 nucleotides downstream from the transcription start site of most and possibly all actively transcribed genes in a process commonly called promoter proximal pausing. [Date last reviewed: 2019-03-14]
Other Summaries
Also Known As

NELF-D, NELF

Key Links
Genomic Location
Cytogenetic map
14C2-14C3
Sequence location
X:16,388,820..16,391,438 [-]
Recombination map

1-53

RefSeq locus
NC_004354 REGION:16388820..16391438
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 (9 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables RNA binding
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables RNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000254315
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in negative regulation of transcription by RNA polymerase II
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
involved_in negative regulation of transcription elongation from RNA polymerase II promoter
inferred from direct assay
(Missra and Gilmour, 2010)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in negative regulation of transcription elongation from RNA polymerase II promoter
inferred from biological aspect of ancestor with PANTHER:PTN000254315
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
part_of NELF complex
inferred from physical interaction with FLYBASE:Nelf-E; FB:FBgn0017430
(Missra and Gilmour, 2010)
inferred from physical interaction with FLYBASE:NELF-B; FB:FBgn0027553
(Missra and Gilmour, 2010)
inferred from physical interaction with FLYBASE:Nelf-A; FB:FBgn0038872
(Missra and Gilmour, 2010)
located_in nucleus
inferred from direct assay
(Missra and Gilmour, 2010)
located_in polytene chromosome interband
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
located_in polytene chromosome puff
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
part_of transcription elongation factor complex
inferred from physical interaction with UniProtKB:P92204
(assigned by UniProt )
(Wu et al., 2003)
part_of transcription repressor complex
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of NELF complex
inferred from biological aspect of ancestor with PANTHER:PTN000254315
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the NELF-D family. (Q24134)
Protein Signatures (InterPro)
Summaries
Protein Function (UniProtKB)
Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex, causes transcriptional pausing.
(UniProt, Q24134)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\TH1 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

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

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
TH1-RA
FBtr0074305
NM_132895
2297
578
TH1-RB
FBtr0340315
NM_001298397
1967
578
Additional Transcript Data and Comments
Reported size (kB)

2.2 (northern blot)

(Banga et al., 1995)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
TH1-PA
FBpp0074080
65.8
578
4.72
NP_573123
AAF48603
TH1-PB
FBpp0309276
65.8
578
4.72
NP_001285326
AHN59796
Polypeptides with Identical Sequences

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

578 aa isoforms: TH1-PA, TH1-PB
Additional Polypeptide Data and Comments
Reported size (kDa)

384 (aa); 43 (kD)

(Banga et al., 1995)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the NELF complex, which is at least composed of TH1/NELF-D and NELF-E.

(UniProt, Q24134)
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\TH1 using the Feature Mapper tool.

External Data
Crossreferences
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
pole plasm

Comment: maternally deposited

(Fisher et al., 2012)
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
anlage in statu nascendi
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
anterior endoderm anlage
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior endoderm
(Fisher et al., 2012)
embryonic stage 9 -- 10
anterior endoderm
(Fisher et al., 2012)
head mesoderm
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior endoderm
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
central brain primordium
(Fisher et al., 2012)
head mesoderm
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
ventral nerve cord primordium
(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic brain
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
organism | faint | ubiquitous
(Fisher et al., 2012)
ventral nerve cord
(Fisher et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
(Banga et al., 1995)
adult stage | female
(Banga et al., 1995)
Additional Descriptive Data

TH1 transcripts are detected in RNA from embryos and adult females.

(Banga et al., 1995)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of NELF complex
inferred from physical interaction with FLYBASE:Nelf-E; FB:FBgn0017430
(Missra and Gilmour, 2010)
inferred from physical interaction with FLYBASE:NELF-B; FB:FBgn0027553
(Missra and Gilmour, 2010)
inferred from physical interaction with FLYBASE:Nelf-A; FB:FBgn0038872
(Missra and Gilmour, 2010)
located_in nucleus
inferred from direct assay
(Missra and Gilmour, 2010)
located_in polytene chromosome interband
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
located_in polytene chromosome puff
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
part_of transcription elongation factor complex
inferred from physical interaction with UniProtKB:P92204
(assigned by UniProt )
(Wu et al., 2003)
part_of transcription repressor complex
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2003)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\TH1 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
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) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
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 ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of TH1
Transgenic constructs containing regulatory region of TH1
Aberrations (Deficiencies and Duplications) ( 0 )
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
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\NELFCD
14 of 15
Yes
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (1)
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\Nelfcd
13 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
Rnor\Nelfcd
4 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\nelfcd
8 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\nelfcd
10 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
No records found.
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) ( EOG091904WU )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00007315
Drosophila simulans
Dsim\GD15751
Drosophila sechellia
Dsec\GM13403
Drosophila erecta
Dere\GG19326
Drosophila yakuba
Dyak\GE15972
Drosophila ananassae
Dana\GF19568
Drosophila pseudoobscura pseudoobscura
Dpse\GA22166
Drosophila persimilis
Dper\GL15890
Drosophila persimilis
Dper\GL15394
Drosophila willistoni
Dwil\GK25710
Drosophila virilis
Dvir\GJ19362
Drosophila mojavensis
Dmoj\GI14305
Drosophila grimshawi
Dgri\GH22626
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915031P )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17021217
Glossina morsitans
Tsetse fly
Gmor\GMOY000907
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_06496
Mayetiola destructor
Hessian fly
Mdes\Mdes006191
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL002450
Anopheles darlingi
American malaria mosquito
Adar\ADAC004906
Anopheles gambiae
Malaria mosquito
Agam\AGAP000391
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013659
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ011793
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02TS )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA003465
Danaus plexippus
Monarch butterfly
Dple\DPOGS203670-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL013344
Apis florea
Little honeybee
Aflo\3222308692
Apis mellifera
Western honey bee
Amel\TH1
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP21763
Bombus terrestris
Buff-tailed bumblebee
Bter\15211437
Linepithema humile
Argentine ant
Lhum\LH23923
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:002b81
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:0028e4
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG007054
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_02772
Tribolium castaneum
Red flour beetle
Tcas\TC003474
Pediculus humanus
Human body louse
Phum\PHUM539310
Rhodnius prolixus
Kissing bug
Rpro\RPRC012040
Rhodnius prolixus
Kissing bug
Rpro\RPRC012111
Cimex lectularius
Bed bug
Clec\CLEC000173
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI005588
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_17570
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X02QS )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR007640
Ixodes scapularis
Black-legged tick
Isca\ISCW017834
Stegodyphus mimosarum
African social velvet spider
Smim\KFM83205.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur09g01470
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_313834
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G046Y )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Th1L
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Th1L_1
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000001124
Gallus gallus
Domestic chicken
Ggal\TH1L
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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?
    NELFCD; negative elongation factor complex member C/D
    14 of 15
    605297
        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
        TH1 - Hsp22
        anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
        (Rhee et al., 2014)
        TH1 - Hsp23
        anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
        (Rhee et al., 2014)
        TH1 - NELF-B
        anti tag coimmunoprecipitation, peptide massfingerprinting, experimental knowledge based
        (Rhee et al., 2014)
        Summary of Genetic Interactions
        esyN Network Diagram
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        External Data
        Subunit Structure (UniProtKB)
        Component of the NELF complex, which is at least composed of TH1/NELF-D and NELF-E.
        (UniProt, Q24134 )
        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 (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        X
        Recombination map

        1-53

        Cytogenetic map
        14C2-14C3
        Sequence location
        X:16,388,820..16,391,438 [-]
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        14C2-14C3
        Limits computationally determined from genome sequence between P{EP}EP1493EP1493 and P{EP}EP1547EP1547
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        14C3-14C6
        (Oliveri, 1992)
        Experimentally Determined Recombination Data
        Location

        1-53

        (FlyBase, 2016)

        1-54.5

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (8)
        Genomic Clones (9)
         

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

        cDNA Clones (62)
         

        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
        Additional comments
        Other Comments

        The NELF complex (including TH1 and Nelf-E) and DSIF (including Spt5) may cause polymerase to pause in the proximal promoter region of hsp70.

        (Wu et al., 2003)

        Identified during a molecular analysis of the mei-41 gene region.

        (Banga et al., 1995)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 42 )
        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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        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
        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
        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 (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (5)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (56)