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    RAD9B RAD9 checkpoint clamp component B [ Homo sapiens (human) ]

    Gene ID: 144715, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RAD9Bprovided by HGNC
    Official Full Name
    RAD9 checkpoint clamp component Bprovided by HGNC
    Primary source
    HGNC:HGNC:21700
    See related
    Ensembl:ENSG00000151164 MIM:608368; AllianceGenome:HGNC:21700
    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
    Summary
    Predicted to be involved in DNA integrity checkpoint signaling; DNA repair; and cellular response to ionizing radiation. Located in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in testis (RPKM 7.5), bone marrow (RPKM 6.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RAD9B in Genome Data Viewer
    Location:
    12q24.11
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110502331..110533556)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110480028..110511250)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110940136..110971361)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903016 Neighboring gene family with sequence similarity 216 member A Neighboring gene uncharacterized LOC124903015 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene Sharpr-MPRA regulatory region 4252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7006 Neighboring gene VPS29 retromer complex component Neighboring gene ReSE screen-validated silencer GRCh37_chr12:110953094-110953337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978258-110978758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110978759-110979259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7008 Neighboring gene protein phosphatase targeting COQ7 Neighboring gene HNF4 motif-containing MPRA enhancer 250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7013 Neighboring gene RNA, 7SL, cytoplasmic 387, pseudogene Neighboring gene tectonic family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:111099215-111099717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7016 Neighboring gene uncharacterized LOC124903017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7018 Neighboring gene hydrogen voltage gated channel 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7019

    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. Loss of RAD9B impairs early neural development and contributes to the risk for human spina bifida. Cao X, et al. Hum Mutat, 2020 Apr. PMID 31898828, Free PMC Article
    2. Rad9B responds to nucleolar stress through ATR and JNK signalling, and delays the G1-S transition. Pérez-Castro AJ, et al. J Cell Sci, 2012 Mar 1. PMID 22399810
    3. Expression of RAD9B in the mesostriatal system of rats and humans: Overexpression in a 6-OHDA rat model of Parkinson's disease. Barroso-Chinea P, et al. Ann Anat, 2023 Oct. PMID 37460044
    4. Clamping down on mammalian meiosis. Lyndaker AM, et al. Cell Cycle, 2013 Oct 1. PMID 24013428, Free PMC Article
    5. Rad9, an evolutionarily conserved gene with multiple functions for preserving genomic integrity. Lieberman HB. J Cell Biochem, 2006 Mar 1. PMID 16365875

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of RAD9B in the mesostriatal system of rats and humans: Overexpression in a 6-OHDA rat model of Parkinson's disease.
      Title: Expression of RAD9B in the mesostriatal system of rats and humans: Overexpression in a 6-OHDA rat model of Parkinson's disease.
    2. Loss of RAD9B impairs early neural development and contributes to the risk for human spina bifida.
      Title: Loss of RAD9B impairs early neural development and contributes to the risk for human spina bifida.
    3. Rad9B responds to nucleolar stress after the activation of JNK-dependent stress signalling and ATR-dependent DNA damage response pathways, and actively accumulates within nucleoli, where it does not cause a transcription block.
      Title: Rad9B responds to nucleolar stress through ATR and JNK signalling, and delays the G1-S transition.
    4. The encoded mammalian proteins participate in promoting resistance to DNA damage, cell cycle checkpoint control, DNA repair, and apoptosis.
      Title: Rad9, an evolutionarily conserved gene with multiple functions for preserving genomic integrity.
    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

    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

    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

    Clone Names

    • FLJ40346, MGC75426

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA replication checkpoint signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to ionizing radiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic intra-S DNA damage checkpoint signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of checkpoint clamp complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    cell cycle checkpoint control protein RAD9B
    Names
    DNA repair exonuclease rad9 homolog B
    RAD9 homolog B
    NP_001273460.1
    NP_001273461.1
    NP_001273462.1
    NP_001273463.1
    NP_001273464.1
    NP_001273465.1
    NP_001354980.1
    NP_001354981.1
    NP_001354982.1
    NP_001354983.1
    NP_001354984.1
    NP_001354985.1
    NP_689655.3
    XP_005253906.1
    XP_011536274.1
    XP_024304628.1
    XP_047284349.1
    XP_054227183.1
    XP_054227184.1
    XP_054227185.1
    XP_054227186.1

    NCBI Reference Sequences (RefSeq)

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    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_001286531.2 → NP_001273460.1  cell cycle checkpoint control protein RAD9B isoform b

      See identical proteins and their annotated locations for NP_001273460.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks a portion of the 5' coding region and differs in the exon structure in the 3' coding region, compared to variant 1. It initiates translation from a downstream in-frame start codon. The encoded isoform (b) has a shorter N-terminus and a distinct C-terminus, and is shorter than isoform a. Variants 2, 3, and 8 all encode the same isoform (b).
      Source sequence(s)
      AC002350
      Consensus CDS
      CCDS73527.1
      Related
      ENSP00000387329.1, ENST00000409246.5
      Conserved Domains (1) summary
      pfam04139
      Location:5 → 204
      Rad9; Rad9

    2. NM_001286532.2 → NP_001273461.1  cell cycle checkpoint control protein RAD9B isoform b

      See identical proteins and their annotated locations for NP_001273461.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks a portion of the 5' coding region and differs in the exon structure in the 3' coding region, compared to variant 1. It initiates translation from a downstream in-frame start codon. The encoded isoform (b) has a shorter N-terminus and a distinct C-terminus, and is shorter than isoform a. Variants 2, 3, and 8 all encode the same isoform (b).
      Source sequence(s)
      AC002350
      Consensus CDS
      CCDS73527.1
      Related
      ENSP00000386629.1, ENST00000409425.5
      Conserved Domains (1) summary
      pfam04139
      Location:5 → 204
      Rad9; Rad9

    3. NM_001286533.2 → NP_001273462.1  cell cycle checkpoint control protein RAD9B isoform c

      See identical proteins and their annotated locations for NP_001273462.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains multiple differences in both the 5' and 3' coding regions, compared to variant 1, including initiation of translation from a downstream in-frame start codon. The encoded isoform (c) has a shorter N-terminus and a distinct C-terminus, and is shorter than isoform a. Variants 4 and 5 encode the same isoform (c).
      Source sequence(s)
      AC002350
      Conserved Domains (1) summary
      pfam04139
      Location:1 → 118
      Rad9; Rad9

    4. NM_001286534.2 → NP_001273463.1  cell cycle checkpoint control protein RAD9B isoform c

      See identical proteins and their annotated locations for NP_001273463.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and contains multiple differences in both the 5' and 3' coding regions, compared to variant 1, including initiation of translation from a downstream in-frame start codon. The encoded isoform (c) has a shorter N-terminus and a distinct C-terminus, and is shorter than isoform a. Variants 4 and 5 encode the same isoform (c).
      Source sequence(s)
      AC002350
      Conserved Domains (1) summary
      pfam04139
      Location:1 → 118
      Rad9; Rad9

    5. NM_001286535.2 → NP_001273464.1  cell cycle checkpoint control protein RAD9B isoform d

      See identical proteins and their annotated locations for NP_001273464.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the exon structure in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AC002350
      Consensus CDS
      CCDS73526.1
      UniProtKB/Swiss-Prot
      Q5U5K0, Q6NVJ1, Q6WBX8, Q6ZVT7, Q8N7T9, Q96LI8
      UniProtKB/TrEMBL
      B4DX60
      Related
      ENSP00000386434.1, ENST00000409300.6
      Conserved Domains (2) summary
      cd00577
      Location:9 → 278
      PCNA; Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the ...
      pfam04139
      Location:17 → 276
      Rad9; Rad9

    6. NM_001286536.2 → NP_001273465.1  cell cycle checkpoint control protein RAD9B isoform e

      See identical proteins and their annotated locations for NP_001273465.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks three alternate exons, which results in a frameshift, compared to variant 1. The encoded isoform (e) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AC002350
      Consensus CDS
      CCDS66469.1
      UniProtKB/TrEMBL
      B4DYM6
      Related
      ENSP00000386697.3, ENST00000409778.7
      Conserved Domains (2) summary
      pfam04139
      Location:17 → 207
      Rad9; Rad9
      cl24017
      Location:9 → 209
      PCNA; Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the ...

    7. NM_001368051.1 → NP_001354980.1  cell cycle checkpoint control protein RAD9B isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variants 2 and 3, encodes isoform b.
      Source sequence(s)
      AC002350
      Consensus CDS
      CCDS73527.1

    8. NM_001368052.1 → NP_001354981.1  cell cycle checkpoint control protein RAD9B isoform f

      Status: VALIDATED

      Source sequence(s)
      AC002350
      UniProtKB/Swiss-Prot
      Q5U5K0, Q6NVJ1, Q6WBX8, Q6ZVT7, Q8N7T9, Q96LI8

    9. NM_001368053.1 → NP_001354982.1  cell cycle checkpoint control protein RAD9B isoform g

      Status: VALIDATED

      Source sequence(s)
      AC002350

    10. NM_001368054.1 → NP_001354983.1  cell cycle checkpoint control protein RAD9B isoform h

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11), as well as variant 12, encodes isoform h.
      Source sequence(s)
      AC002350

    11. NM_001368055.1 → NP_001354984.1  cell cycle checkpoint control protein RAD9B isoform h

      Status: VALIDATED

      Description
      Transcript Variant: This variant (12), as well as variant 11, encodes isoform h.
      Source sequence(s)
      AC002350

    12. NM_001368056.1 → NP_001354985.1  cell cycle checkpoint control protein RAD9B isoform i

      Status: VALIDATED

      Source sequence(s)
      AC002350

    13. NM_152442.4 → NP_689655.3  cell cycle checkpoint control protein RAD9B isoform a

      See identical proteins and their annotated locations for NP_689655.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC002350
      Consensus CDS
      CCDS9148.2
      UniProtKB/Swiss-Prot
      Q5U5K0, Q6NVJ1, Q6WBX8, Q6ZVT7, Q8N7T9, Q96LI8
      UniProtKB/TrEMBL
      J3KPN7
      Related
      ENSP00000376440.4, ENST00000392672.8
      Conserved Domains (2) summary
      cd00577
      Location:9 → 278
      PCNA; Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the ...
      pfam04139
      Location:17 → 276
      Rad9; Rad9

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      110502331..110533556
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024448860.2 → XP_024304628.1  cell cycle checkpoint control protein RAD9B isoform X3

      Conserved Domains (1) summary
      pfam04139
      Location:5 → 204
      Rad9; Rad9

    2. XM_005253849.6 → XP_005253906.1  cell cycle checkpoint control protein RAD9B isoform X2

      Conserved Domains (2) summary
      pfam04139
      Location:17 → 207
      Rad9; Rad9
      cl24017
      Location:9 → 209
      PCNA; Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the ...

    3. XM_011537972.4 → XP_011536274.1  cell cycle checkpoint control protein RAD9B isoform X1

      UniProtKB/Swiss-Prot
      Q5U5K0, Q6NVJ1, Q6WBX8, Q6ZVT7, Q8N7T9, Q96LI8
      Conserved Domains (2) summary
      cd00577
      Location:9 → 254
      PCNA; Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the ...
      pfam04139
      Location:17 → 252
      Rad9; Rad9

    4. XM_047428393.1 → XP_047284349.1  cell cycle checkpoint control protein RAD9B isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      110480028..110511250
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371209.1 → XP_054227184.1  cell cycle checkpoint control protein RAD9B isoform X2

    2. XM_054371208.1 → XP_054227183.1  cell cycle checkpoint control protein RAD9B isoform X1

    3. XM_054371210.1 → XP_054227185.1  cell cycle checkpoint control protein RAD9B isoform X3

    4. XM_054371211.1 → XP_054227186.1  cell cycle checkpoint control protein RAD9B isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6WBX8.2 GenPept UniProtKB/Swiss-Prot:Q6WBX8

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