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    RUNDC3B RUN domain containing 3B [ Homo sapiens (human) ]

    Gene ID: 154661, updated on 17-Sep-2024

    Summary

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    Official Symbol
    RUNDC3Bprovided by HGNC
    Official Full Name
    RUN domain containing 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:30286
    See related
    Ensembl:ENSG00000105784 MIM:617295; AllianceGenome:HGNC:30286
    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
    RPIB9; RPIP9
    Expression
    Broad expression in adrenal (RPKM 7.8), brain (RPKM 4.9) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RUNDC3B in Genome Data Viewer
    Location:
    7q21.12
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (87628398..87832296)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (88878278..89082221)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (87257714..87461611)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 9 Neighboring gene ATP binding cassette subfamily B member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:87218704-87219204 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:87228303-87229502 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 13989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18351 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:87363145-87363320 Neighboring gene NANOG hESC enhancer GRCh37_chr7:87368534-87369080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:87376668-87377257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:87377258-87377846 Neighboring gene NANOG hESC enhancer GRCh37_chr7:87448246-87448747 Neighboring gene solute carrier family 25 member 40 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:87505271-87505780 Neighboring gene origin of replication in promoter of DBF4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26234 Neighboring gene DBF4-CDC7 kinase regulatory subunit

    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. Cloning, expression, and genomic structure of a novel human Rap2 interacting gene (RPIP9). Wang S, et al. Biochem Genet, 2003 Feb. PMID 12645870
    2. Expression of RPIP9 (Rap2 interacting protein 9) is activated in breast carcinoma and correlates with a poor prognosis. Raguz S, et al. Int J Cancer, 2005 Dec 20. PMID 15986426
    3. Dual regulation of P-glycoprotein expression by trichostatin A in cancer cell lines. Balaguer TM, et al. BMC Mol Biol, 2012 Jul 30. PMID 22846052, Free PMC Article
    4. The expression of RUNDC3B is associated with promoter methylation in lymphoid malignancies. Burmeister DW, et al. Hematol Oncol, 2017 Mar. PMID 26011749, Free PMC Article
    5. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. Deng X, et al. PLoS One, 2013. PMID 24324551, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RUNDC3B expression has a role in promoter methylation in lymphoid malignancies
      Title: The expression of RUNDC3B is associated with promoter methylation in lymphoid malignancies.
    2. The ABCB1 nested gene RUNDC3B expression, although upregulated by TSA, is independent of the ABCB1 alternative promoter used.
      Title: Dual regulation of P-glycoprotein expression by trichostatin A in cancer cell lines.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    5. activation of Rap2-binding protein 9 (RPIP9) occurs during the malignant breast epithelial transformation and increases with progression toward an invasive phenotype
      Title: Expression of RPIP9 (Rap2 interacting protein 9) is activated in breast carcinoma and correlates with a poor prognosis.
    6. During a large-scale screen of a human fetal brain cDNA library, a full-length cDNA encoding a novel Rap2-interacting protein was isolated and sequenced. The gene was mapped to human chromosome 7q21-q22 and has 9 exons and 8 introns.
      Title: Cloning, expression, and genomic structure of a novel human Rap2 interacting gene (RPIP9).
    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
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30671, MGC26655

    General protein information

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    Preferred Names
    RUN domain-containing protein 3B
    Names
    Rap2 binding protein 9
    Rap2-interacting protein 9
    rap2-binding protein 9

    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_001134405.2 → NP_001127877.1  RUN domain-containing protein 3B isoform b

      See identical proteins and their annotated locations for NP_001127877.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC002457, AC003083, AK055233, AK294039
      Consensus CDS
      CCDS47635.1
      UniProtKB/TrEMBL
      B4DEG0
      Related
      ENSP00000378149.3, ENST00000394654.4
      Conserved Domains (2) summary
      TIGR00618
      Location:250 → 395
      sbcc; exonuclease SbcC
      pfam02759
      Location:65 → 186
      RUN; RUN domain

    2. NM_001134406.2 → NP_001127878.1  RUN domain-containing protein 3B isoform c

      See identical proteins and their annotated locations for NP_001127878.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC002457, AC003083, AK055233, AK294039, BC022520
      Consensus CDS
      CCDS47636.1
      UniProtKB/TrEMBL
      B4DEG0
      Related
      ENSP00000420394.1, ENST00000493037.5
      Conserved Domains (1) summary
      pfam02759
      Location:65 → 186
      RUN; RUN domain

    3. NM_001394224.1 → NP_001381153.1  RUN domain-containing protein 3B isoform d

      Status: VALIDATED

      Source sequence(s)
      AC002457, AC003083
      UniProtKB/TrEMBL
      B4DEG0
      Conserved Domains (1) summary
      pfam02759
      Location:65 → 203
      RUN; RUN domain

    4. NM_001394225.1 → NP_001381154.1  RUN domain-containing protein 3B isoform e

      Status: VALIDATED

      Source sequence(s)
      AC002457, AC003083
      UniProtKB/TrEMBL
      B4DEG0
      Conserved Domains (2) summary
      TIGR00618
      Location:249 → 394
      sbcc; exonuclease SbcC
      smart00593
      Location:125 → 186
      RUN; domain involved in Ras-like GTPase signaling

    5. NM_001394226.1 → NP_001381155.1  RUN domain-containing protein 3B isoform f

      Status: VALIDATED

      Source sequence(s)
      AC002457, AC003083
      UniProtKB/TrEMBL
      B4DEG0
      Conserved Domains (1) summary
      pfam02759
      Location:65 → 186
      RUN; RUN domain

    6. NM_001394227.1 → NP_001381156.1  RUN domain-containing protein 3B isoform g

      Status: VALIDATED

      Source sequence(s)
      AC002457, AC003083
      UniProtKB/TrEMBL
      B4DEG0
      Conserved Domains (1) summary
      pfam02759
      Location:65 → 203
      RUN; RUN domain

    7. NM_001394228.1 → NP_001381157.1  RUN domain-containing protein 3B isoform h

      Status: VALIDATED

      Source sequence(s)
      AC002457, AC003083
      Conserved Domains (1) summary
      pfam02759
      Location:1 → 72
      RUN; RUN domain

    8. NM_138290.3 → NP_612147.1  RUN domain-containing protein 3B isoform a

      See identical proteins and their annotated locations for NP_612147.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC002457, AC003083, AK055233, DC304423
      Consensus CDS
      CCDS5609.1
      UniProtKB/Swiss-Prot
      B4DFD0, E9PBR4, Q8IWW5, Q8NB55, Q8TBG7, Q96NL0
      UniProtKB/TrEMBL
      B4DEG0
      Related
      ENSP00000337732.3, ENST00000338056.7
      Conserved Domains (1) summary
      pfam02759
      Location:65 → 203
      RUN; RUN 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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      87628398..87832296
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      88878278..89082221
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96NL0.1 GenPept UniProtKB/Swiss-Prot:Q96NL0

    Gene LinkOut

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

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