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

    Gene ID: 7936, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:13974
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NELFE in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31952087..31958971, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31805292..31812176, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31919864..31926748, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene complement C2 Neighboring gene C2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31915103-31915602 Neighboring gene complement factor B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:31929542-31930741 Neighboring gene microRNA 1236 Neighboring gene SKI2 subunit of superkiller complex Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31939702-31940412 Neighboring gene serine/threonine kinase 19 Neighboring gene decapping exoribonuclease

    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 Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis.
    EBI GWAS 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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    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 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear body 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
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in 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)

    NEW Try the new Transcript table

    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
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839
      Related
      ENSP00000364578.3, ENST00000375429.8
      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: 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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      31952087..31958971 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715205.4XP_006715268.1  negative elongation factor E isoform X2

      See identical proteins and their annotated locations for XP_006715268.1

      UniProtKB/TrEMBL
      A0A1U9X839
      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
    2. XM_047419356.1XP_047275312.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_047419354.1XP_047275310.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839
    4. XM_047419355.1XP_047275311.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839
      Related
      ENSP00000364574.5, ENST00000375425.9
    5. XM_011514913.4XP_011513215.1  negative elongation factor E isoform X3

      See identical proteins and their annotated locations for XP_011513215.1

      UniProtKB/TrEMBL
      A0A1U9X839
      Conserved Domains (1) summary
      cd12305
      Location:203277
      RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3429514..3436398 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329906.1XP_054185881.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    2. XM_054329907.1XP_054185882.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_054329905.1XP_054185880.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      3199867..3206746 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330398.1XP_054186373.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    2. XM_054330399.1XP_054186374.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_054330397.1XP_054186372.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      3294123..3301007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330890.1XP_054186865.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    2. XM_054330891.1XP_054186866.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_054330889.1XP_054186864.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3208062..3214941 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331174.1XP_054187149.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    2. XM_054331175.1XP_054187150.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_054331173.1XP_054187148.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      3253276..3260160 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331413.1XP_054187388.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    2. XM_054331414.1XP_054187389.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_054331412.1XP_054187387.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31805292..31812176 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356410.1XP_054212385.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    2. XM_054356411.1XP_054212386.1  negative elongation factor E isoform X2

      UniProtKB/TrEMBL
      A0A1U9X839
    3. XM_054356409.1XP_054212384.1  negative elongation factor E isoform X1

      UniProtKB/Swiss-Prot
      A2BE08, B4DUN1, B4DYX9, P18615, Q5JP74, Q5JP75, Q96F56, Q9NPK2
      UniProtKB/TrEMBL
      A0A1U9X830, A0A1U9X839