NELFCD Gene (Protein Coding)

Negative Elongation Factor Complex Member C/D

GC20P058981
GIFtS:
36
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] See more...

Aliases for NELFCD Gene

Aliases for NELFCD Gene

  • Negative Elongation Factor Complex Member C/D 2 3 5
  • Negative Elongation Factor C/D 3 4
  • Trihydrophobin 1 2 3
  • TH1-Like Protein 3 4
  • NELF-C/D 3 4
  • TH1L 3 4
  • TH1 3 4
  • Negative Elongation Factor Proteins C And D 3
  • TH1-Like (Drosophila Homolog) 2
  • TH1 Drosophila Homolog 3
  • TH1-Like (Drosophila) 2
  • HSPC130 3
  • NELF-C 3
  • NELF-D 3
  • NELFD 4

External Ids for NELFCD Gene

Previous HGNC Symbols for NELFCD Gene

  • TH1L

Previous GeneCards Identifiers for NELFCD Gene

  • GC20P057557

Summaries for NELFCD Gene

Entrez Gene Summary for NELFCD Gene

  • 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]

GeneCards Summary for NELFCD Gene

NELFCD (Negative Elongation Factor Complex Member C/D) is a Protein Coding gene. Diseases associated with NELFCD include Hyperlucent Lung and Glanders. Among its related pathways are Formation of HIV-1 elongation complex containing HIV-1 Tat and HIV Life Cycle.

UniProtKB/Swiss-Prot Summary for NELFCD Gene

  • Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II (PubMed:12612062). The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex (PubMed:10199401).
  • (Microbial infection) The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II.

Gene Wiki entry for NELFCD Gene

Additional gene information for NELFCD Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NELFCD Gene

Genomics for NELFCD Gene

GeneHancer (GH) Regulatory Elements for NELFCD Gene

Promoters and enhancers for NELFCD Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NELFCD on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NELFCD

Genomic Locations for NELFCD Gene

Genomic Locations for NELFCD Gene
chr20:58,981,208-58,995,134
(GRCh38/hg38)
Size:
13,927 bases
Orientation:
Plus strand
chr20:57,556,263-57,570,188
(GRCh37/hg19)
Size:
13,926 bases
Orientation:
Plus strand

Genomic View for NELFCD Gene

Genes around NELFCD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NELFCD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NELFCD Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for NELFCD Gene

Proteins for NELFCD Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for NELFCD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IXH7-NELFD_HUMAN
    Recommended name:
    Negative elongation factor C/D
    Protein Accession:
    Q8IXH7
    Secondary Accessions:
    • B4DE06
    • Q9BYL2
    • Q9H405
    • Q9H888
    • Q9H8T3
    • Q9NVX5
    • Q9P029
    • Q9UGN1
    • Q9UGN2
    • Q9UGN3

    Protein attributes for NELFCD Gene

    Size:
    590 amino acids
    Molecular mass:
    66247 Da
    Quaternary structure:
    • The NELF complex is composed of NELFA, NELFB, NELFCD (isoform NELF-C or isoform NELF-D) and NELFE; NELFA and NELFCD form a stable subcomplex that binds primarily through NELFCD to the N-terminus of NELFB (PubMed:27282391, PubMed:12612062). Binds RNA which may help to stabilize the NELF complex on nucleic acid (PubMed:27282391). In vitro, the NELFA:NELFCD subcomplex binds to ssDNA and ssRNA in a sequence- and structure-dependent manner (PubMed:27282391). Interacts with ARAF1 (PubMed:11952167). Interacts with PCF11 (PubMed:23884411). Interacts with KAT8 (By similarity).
    Miscellaneous:
    • [Isoform NELF-D]: Produced by alternative initiation at Met-10 of isoform NELF-C.
    SequenceCaution:
    • Sequence=AAF29094.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAA91618.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB14519.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAB64339.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NELFCD Gene

    Alternative splice isoforms for NELFCD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NELFCD Gene

Protein Expression for NELFCD Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for NELFCD Gene

  • Ubiquitination at Lys67, Lys125, and Lys272
  • Modification sites at PhosphoSitePlus

Other Protein References for NELFCD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NELFCD Gene

Domains & Families for NELFCD Gene

Gene Families for NELFCD Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NELFCD Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NELFCD Gene

GenScript: Design optimal peptide antigens:
  • TH1-like (Drosophila), isoform CRA_b (E1P5H4_HUMAN)
  • TH1-like protein (NELFD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IXH7

UniProtKB/Swiss-Prot:

NELFD_HUMAN :
  • Belongs to the NELF-D family.
Family:
  • Belongs to the NELF-D family.
genes like me logo Genes that share domains with NELFCD: view

Function for NELFCD Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for NELFCD Gene

UniProtKB/Swiss-Prot Function:
Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II (PubMed:12612062). The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex (PubMed:10199401).
UniProtKB/Swiss-Prot Function:
(Microbial infection) The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II.

Phenotypes From GWAS Catalog for NELFCD Gene

Gene Ontology (GO) - Molecular Function for NELFCD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA 21873635
GO:0005515 protein binding IPI 12612062
genes like me logo Genes that share ontologies with NELFCD: view
genes like me logo Genes that share phenotypes with NELFCD: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NELFCD

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NELFCD Gene

Localization for NELFCD Gene

Subcellular locations from UniProtKB/Swiss-Prot for NELFCD Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NELFCD gene
Compartment Confidence
nucleus 5
extracellular 3
cytosol 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
lysosome 2
peroxisome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleoplasm (3)
  • Cytosol (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NELFCD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0016020 membrane HDA 19946888
GO:0032021 NELF complex IDA,IBA 12612062
genes like me logo Genes that share ontologies with NELFCD: view

Pathways & Interactions for NELFCD Gene

genes like me logo Genes that share pathways with NELFCD: view

Gene Ontology (GO) - Biological Process for NELFCD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription by RNA polymerase II TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
GO:0034244 negative regulation of transcription elongation from RNA polymerase II promoter IBA 21873635
GO:0045892 negative regulation of transcription, DNA-templated IEA --
GO:0050434 positive regulation of viral transcription TAS --
genes like me logo Genes that share ontologies with NELFCD: view

No data available for SIGNOR curated interactions for NELFCD Gene

Drugs & Compounds for NELFCD Gene

Products:

  1. Drug

(3) Drugs for NELFCD Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Hydrochlorothiazide Approved, Vet_approved Pharma Inhibition, Inhibitor 447
diuretics Pharma 1711
Thiazides, plain Pharma 0
genes like me logo Genes that share compounds with NELFCD: view

Transcripts for NELFCD Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for NELFCD Gene

2 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NELFCD

Alternative Splicing Database (ASD) splice patterns (SP) for NELFCD Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a ·
SP1: - - - - - -
SP2: - -
SP3: -
SP4: - - -
SP5: - -
SP6: -
SP7:
SP8:
SP9: -
SP10:

ExUns: 15b ^ 16a · 16b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for NELFCD Gene

GeneLoc Exon Structure for
NELFCD

Expression for NELFCD Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NELFCD Gene

mRNA expression in normal human tissues for NELFCD Gene
mRNA expression by BioGPS for NELFCD GenemRNA expression by GTEx for NELFCD Gene

Protein differential expression in normal tissues from HIPED for NELFCD Gene

This gene is overexpressed in Bone (31.7) and Breast (15.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for NELFCD Gene



Protein tissue co-expression partners for NELFCD Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NELFCD

SOURCE GeneReport for Unigene cluster for NELFCD Gene:

Hs.517148

mRNA Expression by UniProt/SwissProt for NELFCD Gene:

Q8IXH7-NELFD_HUMAN
Tissue specificity: Widely expressed. Expressed in heart, brain, lung, placenta, liver, skeletal and cardiac muscle, adrenal, thyroid, kidney and pancreas.

Evidence on tissue expression from TISSUES for NELFCD Gene

  • Nervous system(4.8)
  • Blood(4.6)
  • Skin(4.6)
  • Thyroid gland(4.3)
  • Lung(3.3)
  • Intestine(3.1)
  • Lymph node(2.7)
  • Spleen(2.7)
  • Eye(2)
  • Liver(2)
genes like me logo Genes that share expression patterns with NELFCD: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NELFCD Gene

Orthologs for NELFCD Gene

This gene was present in the common ancestor of animals.

Orthologs for NELFCD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TH1L 31 30
  • 99.72 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia NELFCD 31
  • 99 (a)
 OneToOne
LOC477276 30
  • 90.63 (n)
cow
(Bos Taurus)
 Mammalia NELFCD 31
  • 98 (a)
 OneToOne
LOC514958 30
  • 89.19 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia NELFCD 31
  • 96 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia NELFCD 31
  • 96 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Nelfcd 30
  • 87.8 (n)
mouse
(Mus musculus)
 Mammalia Nelfcd 17 31 30
  • 87.51 (n)
chicken
(Gallus gallus)
 Aves TH1L 31 30
  • 81.14 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia NELFCD 31
  • 96 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia nelfcd 30
  • 79.89 (n)
Str.10276 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.3030 30
zebrafish
(Danio rerio)
 Actinopterygii nelfcd 31 30
  • 78.7 (n)
 OneToOne
zgc55482 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP000391 30
  • 60.31 (n)
fruit fly
(Drosophila melanogaster)
 Insecta TH1 31 30
  • 58.38 (n)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 60 (a)
 OneToOne
Cin.4834 30
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.4834 30
Species where no ortholog for NELFCD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NELFCD Gene

ENSEMBL:
Gene Tree for NELFCD (if available)
TreeFam:
Gene Tree for NELFCD (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NELFCD: view image

Paralogs for NELFCD Gene

(1) SIMAP similar genes for NELFCD Gene using alignment to 1 proteins:

  • NELFD_HUMAN
genes like me logo Genes that share paralogs with NELFCD: view

No data available for Paralogs for NELFCD Gene

Variants for NELFCD Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NELFCD Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
784412 Benign: not provided 58,993,122(+) C/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for NELFCD Gene

Structural Variations from Database of Genomic Variants (DGV) for NELFCD Gene

Variant ID Type Subtype PubMed ID
nsv525118 CNV loss 19592680

Variation tolerance for NELFCD Gene

Residual Variation Intolerance Score: 8.68% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.70; 14.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NELFCD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NELFCD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NELFCD Gene

Disorders for NELFCD Gene

MalaCards: The human disease database

(10) MalaCards diseases for NELFCD Gene - From: DISEASES

Disorder Aliases PubMed IDs
hyperlucent lung
  • lung, hyperlucent
glanders
  • farcy pipes
pericardial tuberculosis
  • tuberculous pericarditis
tuberculoid leprosy
  • smooth leprosy
mucocutaneous leishmaniasis
  • american cutaneous leishmaniasis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for NELFCD

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with NELFCD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NELFCD Gene

Publications for NELFCD Gene

  1. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang QH … Chen Z (Genome research 2000) 2 3 4 54
  2. Characterization of TH1 and CTSZ, two non-imprinted genes downstream of GNAS1 in chromosome 20q13. (PMID: 11030415) Bonthron DT … Strain L (Human genetics 2000) 2 3 4 54
  3. Architecture and RNA binding of the human negative elongation factor. (PMID: 27282391) Vos SM … Cramer P (eLife 2016) 3 4 54
  4. Trihydrophobin 1 attenuates androgen signal transduction through promoting androgen receptor degradation. (PMID: 20069563) Yang Y … Gu J (Journal of cellular biochemistry 2010) 3 23 54
  5. Trihydrophobin 1 Interacts with PAK1 and Regulates ERK/MAPK Activation and Cell Migration. (PMID: 19136554) Cheng C … Gu J (The Journal of biological chemistry 2009) 3 23 54

ExternalLinks

View latest publications for NELFCD gene in Mastermind

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