FB2025_02 , released April 17, 2025
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
10 publicly available
Gene Summary
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] (FlyBase Gene Snapshot)
All Summaries
Also Known As

NELF-D, NELF

Key Links
Genomic Location
Cytogenetic map
14C2-14C3
Sequence location
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
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables RNA binding
inferred from direct assay
(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
(GO Reference Genome Project, 2011-)
Biological Process (3 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
(Wu et al., 2003)
involved_in negative regulation of transcription elongation by RNA polymerase II
inferred from direct assay
(Missra and Gilmour, 2010)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in negative regulation of DNA-templated transcription
inferred from electronic annotation with InterPro:IPR006942
(InterPro Project Members, 2004-)
involved_in negative regulation of transcription elongation by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN000254315
(GO Reference Genome Project, 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
(Wu et al., 2003)
located_in polytene chromosome puff
inferred from direct assay
(Wu et al., 2003)
part_of transcription elongation factor complex
inferred from physical interaction with UniProtKB:P92204
(Wu et al., 2003)
part_of transcription repressor complex
inferred from direct assay
(Wu et al., 2003)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of NELF complex
inferred from biological aspect of ancestor with PANTHER:PTN000254315
(GO Reference Genome Project, 2011-)
located_in nucleus
inferred from electronic annotation with InterPro:IPR006942
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the NELF-D family. (Q24134)
Protein Signatures (InterPro)
Summaries
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]
Gene Group (FlyBase)
NEGATIVE ELONGATION FACTOR -
The negative elongation factor (NELF) is a multisubunit transcription regulator complex. It binds with DRB sensitivity-inducing factor (DSIF) complex and RNA polymerase II elongation complex and induces transcriptional pausing. P-TEFb phosphorylates the repressive DSIF-NELF complex, causing NELF to dissociate from Pol II and promotes RNA polymerase II elongation. (Adapted from FBrf0211126, FBrf0203142 and FBrf0184223).
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
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q24134)

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

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

Gene model reviewed during 5.50

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
UniProt
RefSeq ID
GenBank
TH1-PA
FBpp0074080
65.8
578
4.72
Q24134
NP_573123
AAF48603
TH1-PB
FBpp0309276
65.8
578
4.72
Q24134
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
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).

-0.04

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)
larval 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
(Wu et al., 2003)
located_in polytene chromosome puff
inferred from direct assay
(Wu et al., 2003)
part_of transcription elongation factor complex
inferred from physical interaction with UniProtKB:P92204
(Wu et al., 2003)
part_of transcription repressor complex
inferred from direct assay
(Wu et al., 2003)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\TH1 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
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 )
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) (1)
Hsap\NELFCD
13 of 14
Yes
Yes
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) (1)
Rnor\Nelfcd
12 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Nelfcd
12 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\nelfcd
7 of 13
Yes
Yes
Xtro\gnas
5 of 13
No
Yes
Danio rerio (Zebrafish) (1)
Drer\nelfcd
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (0)
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP000391
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:TH1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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?
    NELFCD; negative elongation factor complex member C/D
    13 of 14
    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
        Summary of Genetic Interactions
        Interaction Browsers
        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.
        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)
        X
        Recombination map
        1-53
        Cytogenetic map
        14C2-14C3
        Sequence location
        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 (10)
        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 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

            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)
            Relationship to Other Genes
            Source for database merge of
            Additional comments
            Nomenclature History
            Source for database identify of
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (6)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 50 )
            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/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
            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
            FlyMine - An integrated database for Drosophila genomics
            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
            BioGRID - A database of protein and genetic interactions.
            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
            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
            Flygut - An atlas of the Drosophila adult midgut
            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 (64)