Human Gene CHAF1B (ENST00000314103.6_4) from GENCODE V47lift37
  Description: chromatin assembly factor 1 subunit B (from RefSeq NM_005441.3)
Gencode Transcript: ENST00000314103.6_4
Gencode Gene: ENSG00000159259.8_8
Transcript (Including UTRs)
   Position: hg19 chr21:37,757,690-37,791,313 Size: 33,624 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr21:37,758,435-37,788,664 Size: 30,230 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:37,757,690-37,791,313)mRNA (may differ from genome)Protein (559 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAF1B_HUMAN
DESCRIPTION: RecName: Full=Chromatin assembly factor 1 subunit B; Short=CAF-1 subunit B; AltName: Full=Chromatin assembly factor I p60 subunit; Short=CAF-I 60 kDa subunit; Short=CAF-I p60; AltName: Full=M-phase phosphoprotein 7;
FUNCTION: Complex that is thought to mediate chromatin assembly in DNA replication and DNA repair. Assembles histone octamers onto replicating DNA in vitro. CAF-1 performs the first step of the nucleosome assembly process, bringing newly synthesized histones H3 and H4 to replicating DNA; histones H2A/H2B can bind to this chromatin precursor subsequent to DNA replication to complete the histone octamer. The CCR4-NOT complex functions as general transcription regulation complex.
SUBUNIT: Subunit of the CAF-1 complex that contains RBBP4, CHAF1B and CHAF1A. CHAF1A binds directly to CHAF1B. Only minor amounts of RBBP4 are complexed with CHAF1A and CHAF1B in G1 phase. In G2 and S phase also monomeric CHAF1B is detected. Subunit of the CCR4-NOT core complex that contains CHAF1A, CHAF1B, CNOT1, CNOT2, CNOT3, CNOT4, CNOT6 and CNOT8.
INTERACTION: Q96LI5:CNOT6L; NbExp=2; IntAct=EBI-1052944, EBI-1046635;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=DNA replication foci. Cytoplasmic in M phase.
DEVELOPMENTAL STAGE: Active complex is found in G1, S and G2 phases.
PTM: Differentially phosphorylated during cell cycle. During mitosis the p60 subunit of inactive CAF-1 is hyperphosphorylated and displaced into the cytosol. Progressivly dephosphorylated from G1 to S and G2 phase. Phosphorylated p60 is recruited to chromatin undergoing DNA repair after UV irradiation in G1, S or G2 phases.
SIMILARITY: Belongs to the WD repeat HIR1 family.
SIMILARITY: Contains 7 WD repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D010634 Phenobarbital
  • D013749 Tetrachlorodibenzodioxin
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C009505 4,4'-diaminodiphenylmethane
  • C065250 4-hydroxy-equilenin
  • C547126 AZM551248
  • D016604 Aflatoxin B1
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.33 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 59.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -52.10137-0.380 Picture PostScript Text
3' UTR -1187.202649-0.448 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001632 - Gprotein_B
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF12894 - Anaphase-promoting complex subunit 4 WD40 domain
PF15512 - Chromatin assembly factor complex 1 subunit p60, C-terminal

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q13112
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0042393 histone binding
GO:0051082 unfolded protein binding

Biological Process:
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006335 DNA replication-dependent nucleosome assembly
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006974 cellular response to DNA damage stimulus
GO:0007049 cell cycle
GO:0031497 chromatin assembly

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0032991 macromolecular complex
GO:0033186 CAF-1 complex
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF385150 - JP 2014500723-A/192653: Polycomb-Associated Non-Coding RNAs.
AK313152 - Homo sapiens cDNA, FLJ93645, highly similar to Homo sapiens chromatin assembly factor 1, subunit B (p60) (CHAF1B),mRNA.
BC001143 - Homo sapiens, Similar to chromatin assembly factor 1, subunit B (p60), clone IMAGE:3534467, mRNA.
BC021218 - Homo sapiens chromatin assembly factor 1, subunit B (p60), mRNA (cDNA clone MGC:12639 IMAGE:4302243), complete cds.
U20980 - Human chromatin assembly factor-I p60 subunit mRNA, complete cds.
JF432525 - Synthetic construct Homo sapiens clone IMAGE:100073747 chromatin assembly factor 1, subunit B (p60) (CHAF1B) gene, encodes complete protein.
KJ892476 - Synthetic construct Homo sapiens clone ccsbBroadEn_01870 CHAF1B gene, encodes complete protein.
X98262 - H.sapiens mRNA for M-phase phosphoprotein, mpp7.
AK092781 - Homo sapiens cDNA FLJ35462 fis, clone SMINT2005174.
JD315060 - Sequence 296084 from Patent EP1572962.
JD315061 - Sequence 296085 from Patent EP1572962.
JD178917 - Sequence 159941 from Patent EP1572962.
AJ001856 - Homo Sapiens partial mRNA for human chromatin assembly factor-I (CAF1P60), clone t23f17clone.
JD441811 - Sequence 422835 from Patent EP1572962.
JD236293 - Sequence 217317 from Patent EP1572962.
JD052118 - Sequence 33142 from Patent EP1572962.
JD267844 - Sequence 248868 from Patent EP1572962.
JD475610 - Sequence 456634 from Patent EP1572962.
JD143677 - Sequence 124701 from Patent EP1572962.
JD066881 - Sequence 47905 from Patent EP1572962.
JD321949 - Sequence 302973 from Patent EP1572962.
JD308136 - Sequence 289160 from Patent EP1572962.
JD435431 - Sequence 416455 from Patent EP1572962.
JD254670 - Sequence 235694 from Patent EP1572962.
JD159026 - Sequence 140050 from Patent EP1572962.
JD159027 - Sequence 140051 from Patent EP1572962.
JD258432 - Sequence 239456 from Patent EP1572962.
JD411928 - Sequence 392952 from Patent EP1572962.
MA620727 - JP 2018138019-A/192653: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_btg2Pathway - BTG family proteins and cell cycle regulation

-  Other Names for This Gene
  Alternate Gene Symbols: CAF1A, CAF1B_HUMAN, CAF1P60, CHAF1B , ENST00000314103.1, ENST00000314103.2, ENST00000314103.3, ENST00000314103.4, ENST00000314103.5, MPHOSPH7, MPP7, NM_005441, Q13112, Q99548, uc317pnt.1, uc317pnt.2
UCSC ID: ENST00000314103.6_4
RefSeq Accession: NM_005441.3
Protein: Q13112 (aka CAF1B_HUMAN or CAFB_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.