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NELFE negative elongation factor complex member E [ Homo sapiens (human) ]

Gene ID: 7936, updated on 9-Dec-2018

Summary

Official Symbol
NELFEprovided by HGNC
Official Full Name
negative elongation factor complex member Eprovided by HGNC
Primary source
HGNC:HGNC:13974
See related
Ensembl:ENSG00000204356 MIM:154040
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
RD; RDP; RDBP; D6S45; NELF-E
Summary
The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 52.1), ovary (RPKM 20.1) and 25 other tissues See more
Orthologs

Genomic context

See NELFE in Genome Data Viewer
Location:
6p21.33
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (31952087..31959087, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31919864..31926864, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene complement C2 Neighboring gene C2 antisense RNA 1 Neighboring gene complement factor B Neighboring gene microRNA 1236 Neighboring gene Ski2 like RNA helicase Neighboring gene serine/threonine kinase 19 Neighboring gene decapping exoribonuclease Neighboring gene complement C4A (Rodgers blood group)

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of NELF-E 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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
NELF complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
negative elongation factor E
Names
RD RNA-binding protein
RNA-binding protein RD
major histocompatibility complex gene RD
negative elongation factor polypeptide E
nuclear protein

NCBI Reference Sequences (RefSeq)

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_002904.6NP_002895.3  negative elongation factor E

    See identical proteins and their annotated locations for NP_002895.3

    Status: REVIEWED

    Source sequence(s)
    BC050617, BU935034, CD579634
    Consensus CDS
    CCDS4730.1
    UniProtKB/Swiss-Prot
    P18615
    UniProtKB/TrEMBL
    A0A1U9X830
    Related
    ENSP00000364578.3, ENST00000375429.7
    Conserved Domains (1) summary
    cd12305
    Location:258332
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    31952087..31959087 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011299.2XP_016866788.1  negative elongation factor E isoform X3

  2. XM_011514913.3XP_011513215.1  negative elongation factor E isoform X2

    See identical proteins and their annotated locations for XP_011513215.1

    Conserved Domains (1) summary
    cd12305
    Location:203277
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins
  3. XM_006715205.3XP_006715268.1  negative elongation factor E isoform X1

    See identical proteins and their annotated locations for XP_006715268.1

    Related
    ENSP00000388400.2, ENST00000444811.6
    Conserved Domains (1) summary
    cd12305
    Location:253327
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

    Range
    3429514..3436514 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

    Range
    3199867..3206862 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

    Range
    3294123..3301123 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

    Range
    3208062..3215057 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p12 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p12 ALT_REF_LOCI_7

    Range
    3253276..3260276 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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