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    RTF1 RTF1 homolog, Paf1/RNA polymerase II complex component [ Homo sapiens (human) ]

    Gene ID: 23168, updated on 9-Dec-2024

    Summary

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    Official Symbol
    RTF1provided by HGNC
    Official Full Name
    RTF1 homolog, Paf1/RNA polymerase II complex componentprovided by HGNC
    Primary source
    HGNC:HGNC:28996
    See related
    Ensembl:ENSG00000137815 MIM:611633; AllianceGenome:HGNC:28996
    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
    GTL7; KIAA0252
    Summary
    This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]
    Expression
    Ubiquitous expression in thyroid (RPKM 16.0), testis (RPKM 15.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RTF1 in Genome Data Viewer
    Location:
    15q15.1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (41417095..41483563)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (39223257..39289730)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (41709293..41775761)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:41628937-41629558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:41629559-41630180 Neighboring gene nucleolar and spindle associated protein 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:41675757-41676295 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41723973-41724473 Neighboring gene RNA, U6 small nuclear 1169, pseudogene Neighboring gene uncharacterized LOC105370790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9282 Neighboring gene Sharpr-MPRA regulatory region 6351 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:41784974-41785474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:41785475-41785975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6359 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6360 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:41804857-41805604 Neighboring gene inositol-trisphosphate 3-kinase A Neighboring gene leukocyte receptor tyrosine kinase

    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
    • 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. Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Vos SM, et al. Nat Struct Mol Biol, 2020 Jul. PMID 32541898
    2. Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex. Cao QF, et al. Mol Cell Biol, 2015 Oct. PMID 26217014, Free PMC Article
    3. Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Žumer K, et al. Mol Cell, 2021 Aug 5. PMID 34146481
    4. Structure and DNA binding of the human Rtf1 Plus3 domain. de Jong RN, et al. Structure, 2008 Jan. PMID 18184592
    5. Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Wier AD, et al. Proc Natl Acad Sci U S A, 2013 Oct 22. PMID 24101474, Free PMC Article

    See all (79) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo.
      Title: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo.
    2. Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
      Title: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation.
    3. Human Rtf1 as a transcription elongation factor.
      Title: Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex.
    4. Data indicate that the Plus3 domain of the Rtf1 subunit mediates Paf1C recruitment to genes by binding a repeating domain within the phosphorylated elongation factor Spt5.
      Title: Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N 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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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in blastocyst growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endodermal cell fate commitment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in stem cell population maintenance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transcription elongation by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cdc73/Paf1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    RNA polymerase-associated protein RTF1 homolog
    Names
    Rtf1, Paf1/RNA polymerase II complex component, homolog
    ortholog of mouse gene trap locus 7

    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.

    Genomic

    1. NG_027680.1 RefSeqGene

      Range
      4992..71460
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015138.5 → NP_055953.3  RNA polymerase-associated protein RTF1 homolog

      See identical proteins and their annotated locations for NP_055953.3

      Status: REVIEWED

      Source sequence(s)
      AC087721
      Consensus CDS
      CCDS32200.2
      UniProtKB/Swiss-Prot
      Q92541, Q96BX6
      Related
      ENSP00000374280.4, ENST00000389629.9
      Conserved Domains (2) summary
      COG5296
      Location:189 → 623
      COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
      pfam03126
      Location:359 → 459
      Plus-3; Plus-3 domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      41417095..41483563
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      39223257..39289730
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92541.4 GenPept UniProtKB/Swiss-Prot:Q92541

    Gene LinkOut

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

    Chemical Information
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