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Nelfe negative elongation factor complex member E, Rdbp [ Mus musculus (house mouse) ]

Gene ID: 27632, updated on 11-Apr-2024

Summary

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Official Symbol
Nelfeprovided by MGI
Official Full Name
negative elongation factor complex member E, Rdbpprovided by MGI
Primary source
MGI:MGI:102744
See related
Ensembl:ENSMUSG00000024369 AllianceGenome:MGI:102744
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
RD; Rdbp; NELF-E; D17H6S45
Summary
Predicted to enable chromatin binding activity. Acts upstream of or within negative regulation of transcription elongation from RNA polymerase II promoter. Predicted to be located in nuclear body and plasma membrane. Predicted to be part of NELF complex. Is expressed in brain and early conceptus. Orthologous to human NELFE (negative elongation factor complex member E). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 47.2), CNS E11.5 (RPKM 20.2) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
17 B1; 17 18.4 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (35069367..35075348)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (34850391..34856372)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene SKI2 subunit of superkiller complex Neighboring gene microRNA 6971 Neighboring gene microRNA 6970 Neighboring gene STARR-positive B cell enhancer ABC_E5597 Neighboring gene microRNA 6972 Neighboring gene complement factor B Neighboring gene complement C2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Murine D17H6S45 (Rd) gene: polymorphism and overlap with complement factor B. Taylor PR, et al. Mamm Genome, 1997 Oct. PMID 9321489
  2. A Population Study of Common Ocular Abnormalities in C57BL/6N rd8 Mice. Moore BA, et al. Invest Ophthalmol Vis Sci, 2018 May 1. PMID 29847629, Free PMC Article
  3. cDNA cloning and characterization of the protein encoded by RD, a gene located in the class III region of the human major histocompatibility complex. Cheng J, et al. Biochem J, 1993 Sep 1. PMID 8373374, Free PMC Article
  4. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. Etchegaray JP, et al. Mol Cell, 2019 Aug 22. PMID 31399344, Free PMC Article
  5. Distinct patterns of RNA polymerase II and transcriptional elongation characterize mammalian genome activation. Abe K, et al. Cell Rep, 2022 Dec 27. PMID 36577375

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1) 

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 MGI

Function Evidence Code Pubs
enables RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables mRNA binding ISO
Inferred from Sequence Orthology
more info
  
enables nucleic acid 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 negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
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 
acts_upstream_of_or_within negative regulation of transcription elongation by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription elongation by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of ERK1 and ERK2 cascade ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of protein modification process ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of NELF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of NELF complex ISO
Inferred from Sequence Orthology
more info
  
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
negative elongation factor E
Names
RD RNA-binding protein
RNA-binding protein RD

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_001045863.1 → NP_001039328.1  negative elongation factor E

    See identical proteins and their annotated locations for NP_001039328.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AI325150, AK147011, CX203833
    Consensus CDS
    CCDS28662.1
    UniProtKB/Swiss-Prot
    P19426, P97485, P97486, Q9CZN3
    UniProtKB/TrEMBL
    Q3UIA1
    Related
    ENSMUSP00000134272.2, ENSMUST00000173357.8
    Conserved Domains (1) summary
    cd12305
    Location:254 → 328
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

  2. NM_001045864.1 → NP_001039329.1  negative elongation factor E

    See identical proteins and their annotated locations for NP_001039329.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein.
    Source sequence(s)
    AI325150, CN525174, CT025759, DV662511
    Consensus CDS
    CCDS28662.1
    UniProtKB/Swiss-Prot
    P19426, P97485, P97486, Q9CZN3
    UniProtKB/TrEMBL
    Q3UIA1
    Related
    ENSMUSP00000094956.5, ENSMUST00000097343.11
    Conserved Domains (1) summary
    cd12305
    Location:254 → 328
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

  3. NM_138580.2 → NP_613046.2  negative elongation factor E

    See identical proteins and their annotated locations for NP_613046.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript. All variants encode the same protein.
    Source sequence(s)
    AI325150, AK131947, CX203833
    Consensus CDS
    CCDS28662.1
    UniProtKB/Swiss-Prot
    P19426, P97485, P97486, Q9CZN3
    UniProtKB/TrEMBL
    Q3UIA1
    Related
    ENSMUSP00000131195.3, ENSMUST00000165953.3
    Conserved Domains (1) summary
    cd12305
    Location:254 → 328
    RRM_NELFE; RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    35069367..35075348
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P19426.2 GenPept UniProtKB/Swiss-Prot:P19426

Gene LinkOut

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