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

Gene ID: 144715, updated on 3-Apr-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, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 7.5), bone marrow (RPKM 6.0) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110502331..110533556)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110480028..110511250)
105.20220307 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
  • 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. Clamping down on mammalian meiosis. Lyndaker AM, et al. Cell Cycle, 2013 Oct 1. PMID 24013428, Free PMC Article
  4. Rad9, an evolutionarily conserved gene with multiple functions for preserving genomic integrity. Lieberman HB. J Cell Biochem, 2006 Mar 1. PMID 16365875
  5. Identification and characterization of RAD9B, a paralog of the RAD9 checkpoint gene. Dufault VM, et al. Genomics, 2003 Dec. PMID 14611806

See all (15) 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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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_2023_10

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

Gene LinkOut

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