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    NELFB negative elongation factor complex member B [ Homo sapiens (human) ]

    Gene ID: 25920, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NELFBprovided by HGNC
    Official Full Name
    negative elongation factor complex member Bprovided by HGNC
    Primary source
    HGNC:HGNC:24324
    See related
    Ensembl:ENSG00000188986 MIM:611180; AllianceGenome:HGNC:24324
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    COBRA1; NELF-B
    Summary
    NELFB is a subunit of negative elongation factor (NELF), which also includes NELFA (WHSC2; MIM 606026), either NELFC or NELFD (TH1L; MIM 605297), and NELFE (RDBP; MIM 154040). NELF acts with DRB sensitivity-inducing factor (DSIF), a heterodimer of SPT4 (SUPT4H1; MIM 603555) and SPT5 (SUPT5H; MIM 602102), to cause transcriptional pausing of RNA polymerase II (see MIM 180660) (Narita et al., 2003 [PubMed 12612062]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in testis (RPKM 16.5), fat (RPKM 16.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NELFB in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137255327..137273542)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149492996..149511192)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140149779..140167994)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ciliary microtubule inner protein 2A Neighboring gene uncharacterized LOC124902316 Neighboring gene STPG3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140149187-140150134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140150135-140151082 Neighboring gene sperm-tail PG-rich repeat containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140157448-140158007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140165697-140166196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20606 Neighboring gene torsin family 4 member A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29350 Neighboring gene 9q34.3 TOR4A distal recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140191021-140191688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140193329-140194222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140196022-140196940 Neighboring gene NOTCH regulated ankyrin repeat protein

    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. Knockdown of COBRA1 decreases the proliferation and migration of hepatocellular carcinoma cells. El Zeneini E, et al. Oncol Rep, 2017 Mar. PMID 28112367
    2. Deregulation of cofactor of BRCA1 expression in breast cancer cells. Sun J, et al. J Cell Biochem, 2008 Apr 15. PMID 17910036, Free PMC Article
    3. Cofactor of BRCA1 modulates androgen-dependent transcription and alternative splicing. Sun J, et al. J Steroid Biochem Mol Biol, 2007 Nov-Dec. PMID 17659869, Free PMC Article
    4. Cofactor of BRCA1: a novel transcription factor regulator in upper gastrointestinal adenocarcinomas. McChesney PA, et al. Cancer Res, 2006 Feb 1. PMID 16452188
    5. Characterization of COBRA1 in human breast cancer cell lines using a new polyclonal antibody against COBRA1. Zhu J, et al. IUBMB Life, 2004 Mar. PMID 15185750

    See all (98) 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. NSUN6, an RNA methyltransferase of 5-mC controls glioblastoma response to temozolomide (TMZ) via NELFB and RPS6KB2 interaction.
      Title: NSUN6, an RNA methyltransferase of 5-mC controls glioblastoma response to temozolomide (TMZ) via NELFB and RPS6KB2 interaction.
    3. BRCA1 Interacting Protein COBRA1 Facilitates Adaptation to Castrate-Resistant Growth Conditions.
      Title: BRCA1 Interacting Protein COBRA1 Facilitates Adaptation to Castrate-Resistant Growth Conditions.
    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. High COBRA1 expression is associated with hepatocellular carcinoma.
      Title: Knockdown of COBRA1 decreases the proliferation and migration of hepatocellular carcinoma cells.
    6. both human and mouse NELF-B proteins are translated from a non-AUG codon upstream of the annotated AUG.
      Title: Translational Initiation at a Non-AUG Start Codon for Human and Mouse Negative Elongation Factor-B.
    7. These studies allow us to position the actions of two new modulators of GR-regulated transactivation, NELF-A and NELF-B, relative to other factors in the overall gene induction sequence.
      Title: A conserved protein motif is required for full modulatory activity of negative elongation factor subunits NELF-A and NELF-B in modifying glucocorticoid receptor-regulated gene induction properties.
    8. 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.
    9. a lack of COBRA1 expression in breast carcinoma may serve as a useful indicator for poor prognosis.
      Title: Deregulation of cofactor of BRCA1 expression in breast cancer cells.
    10. COBRA1 and BRCA1 may engage in common gene regulatory pathways to suppress breast cancer progression.
      Title: Concerted transcriptional regulation by BRCA1 and COBRA1 in breast cancer cells.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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

    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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    Replication interactions

    Interaction Pubs
    Knockdown of NELF-B by shRNA enhances HIV-1 transcription in latently infected cells PubMed

    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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    Homology

    Clone Names

    • KIAA1182, DKFZp586B0519

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of stem cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 
    involved_in negative regulation of transcription elongation by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in stem cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    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 B
    Names
    cofactor of BRCA1
    negative elongation factor protein B

    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_015456.5 → NP_056271.3  negative elongation factor B

      Status: VALIDATED

      Source sequence(s)
      AK022651, AL050280, BC019029, DA210427
      Consensus CDS
      CCDS7040.2
      UniProtKB/TrEMBL
      A0A5H1ZRP4
      Related
      ENSP00000339495.6, ENST00000343053.6
      Conserved Domains (1) summary
      pfam06209
      Location:155 → 626
      COBRA1; Cofactor of BRCA1 (COBRA1)

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      137255327..137273542
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      149492996..149511192
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WX92.1 GenPept UniProtKB/Swiss-Prot:Q8WX92

    Gene LinkOut

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

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