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    NELFCD negative elongation factor complex member C/D [ Homo sapiens (human) ]

    Gene ID: 51497, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NELFCDprovided by HGNC
    Official Full Name
    negative elongation factor complex member C/Dprovided by HGNC
    Primary source
    HGNC:HGNC:15934
    See related
    Ensembl:ENSG00000101158 MIM:605297; AllianceGenome:HGNC:15934
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TH1; TH1L; NELF-C; NELF-D; HSPC130
    Summary
    The NELF complex of proteins interacts with the DSIF protein complex to repress transcriptional elongation by RNA polymerase II. The protein encoded by this gene is an essential part of the NELF complex. Alternative translation initiation site usage results in the formation of two isoforms with different N-termini. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 29.3), thyroid (RPKM 23.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NELFCD in Genome Data Viewer
    Location:
    20q13.32
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (58981256..58995113)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (60764380..60778214)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (57556311..57570168)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene GNAS complex locus Neighboring gene uncharacterized LOC101927932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13084 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:57470438-57471032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57471033-57471626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57474225-57474776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18180 Neighboring gene uncharacterized LOC107985382 Neighboring gene small integral membrane protein 30-like Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:57540701-57541253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:57556569-57557069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18183 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57581561-57582372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18186 Neighboring gene cathepsin Z Neighboring gene tubulin beta 1 class VI Neighboring gene ATP synthase F1 subunit epsilon

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Negative role of trihydrophobin 1 in breast cancer growth and migration. Zou W, et al. Cancer Sci, 2010 Oct. PMID 20735431, Free PMC Article
    2. Human negative elongation factor activates transcription and regulates alternative transcription initiation. Sun J, et al. J Biol Chem, 2010 Feb 26. PMID 20028984, Free PMC Article
    3. [Maternal serum Th1 and Th2 cytokines in preterm and term delivery]. Jarocki S, et al. Ginekol Pol, 2007 Apr. PMID 17621989
    4. TH1L involvement in colorectal cancer pathogenesis by regulation of CCL20 through the NF-κB signalling pathway. Wang S, et al. J Cell Mol Med, 2024 May. PMID 38809918, Free PMC Article
    5. Trihydrophobin 1 phosphorylation by c-Src regulates MAPK/ERK signaling and cell migration. Wu W, et al. PLoS One, 2012. PMID 22238675, Free PMC Article

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TH1L involvement in colorectal cancer pathogenesis by regulation of CCL20 through the NF-kappaB signalling pathway.
      Title: TH1L involvement in colorectal cancer pathogenesis by regulation of CCL20 through the NF-κB signalling pathway.
    2. Structural basis of the human negative elongation factor NELF-B/C/E ternary complex.
      Title: Structural basis of the human negative elongation factor NELF-B/C/E ternary complex.
    3. NELFCD polymorphisms are associated with jaundice-stage progression in primary biliary cholangitis.
      Title: NELFCD and CTSZ loci are associated with jaundice-stage progression in primary biliary cholangitis in the Japanese population.
    4. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo.
      Title: Architecture and RNA binding of the human negative elongation factor.
    5. data show that NELF subunits exhibit highly specific subcellular localizations, such as in NELF bodies or in midbodies, and some shuttle actively between the nucleus and cytoplasm; loss of NELF from cells can lead to enlarged and/or multiple nuclei
      Title: Cellular dynamics of the negative transcription elongation factor NELF.
    6. Trihydrophobin 1 phosphorylation by c-Src regulates MAPK/ERK signaling and cell migration.
      Title: Trihydrophobin 1 phosphorylation by c-Src regulates MAPK/ERK signaling and cell migration.
    7. TH1 might play an important role in regulation of proliferation and invasion in human breast cancer.
      Title: Negative role of trihydrophobin 1 in breast cancer growth and migration.
    8. These results indicate that TH1 is a novel regulator to control the duration and magnitude of androgen signal transduction and might be directly involved in androgen-related developmental, physiological, and pathological processes.
      Title: Trihydrophobin 1 attenuates androgen signal transduction through promoting androgen receptor degradation.
    9. diverse transcriptional consequence of NELF-mediated RNAPII pausing in the human genome
      Title: Human negative elongation factor activates transcription and regulates alternative transcription initiation.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of tagging single nucleotide polymorphisms on 8 candidate genes in dopaminergic pathway with schizophrenia in Croatian population.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genomic association analysis of common variants influencing antihypertensive response to hydrochlorothiazide.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat NELF represses HIV-1 transcription by pausing the RNA polymerase II complex PubMed
    tat NELF associates with HIV-1 Tat as part of the HIV-1 transcription elongation complex PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of transcription elongation by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription elongation by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of NELF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of NELF complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of NELF complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    negative elongation factor C/D
    Names
    NELF-C/D
    TH1 drosophila homolog
    TH1-like protein
    negative elongation factor proteins C and D
    trihydrophobin 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_198976.4 → NP_945327.3  negative elongation factor C/D

      Status: REVIEWED

      Source sequence(s)
      AK293410, BQ022435
      Consensus CDS
      CCDS13473.3
      UniProtKB/Swiss-Prot
      B4DE06, Q8IXH7, Q9BYL2, Q9H405, Q9H888, Q9H8T3, Q9NVX5, Q9P029, Q9UGN1, Q9UGN2, Q9UGN3
      Related
      ENSP00000499018.1, ENST00000652272.2
      Conserved Domains (1) summary
      pfam04858
      Location:2 → 578
      TH1; TH1 protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      58981256..58995113
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440188.1 → XP_047296144.1  negative elongation factor C/D isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      60764380..60778214
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323481.1 → XP_054179456.1  negative elongation factor C/D isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016397.2: Suppressed sequence

      Description
      NM_016397.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IXH7.2 GenPept UniProtKB/Swiss-Prot:Q8IXH7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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