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

Gene ID: 154661, updated on 5-Mar-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
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Genomic context

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Location:
7q21.12
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (87628398..87832296)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (88878278..89082221)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. Cloning, expression, and genomic structure of a novel human Rap2 interacting gene (RPIP9). Wang S, et al. Biochem Genet, 2003 Feb. PMID 12645870
  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_2023_10

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

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