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

Gene ID: 51497, updated on 3-Apr-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
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Genomic context

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Location:
20q13.32
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (58981256..58995113)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (60764380..60778214)
105.20220307 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
  • 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
  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. NELFCD and CTSZ loci are associated with jaundice-stage progression in primary biliary cholangitis in the Japanese population. Nishida N, et al. Sci Rep, 2018 May 23. PMID 29795304, 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 (71) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. diverse transcriptional consequence of NELF-mediated RNAPII pausing in the human genome
    Title: Human negative elongation factor activates transcription and regulates alternative transcription initiation.
  9. 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.
  10. TH1 interacts with PAK1 and specifically restricts the activation of MAPK modules through the upstream region of the MAPK pathway, thereby influencing cell migration.
    Title: Trihydrophobin 1 Interacts with PAK1 and Regulates ERK/MAPK Activation and Cell Migration.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

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_2023_10

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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