Mouse Gene Fancd2 (ENSMUST00000036340.11) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus Fanconi anemia, complementation group D2 (Fancd2), transcript variant q, mRNA. (from RefSeq NM_001033244)
Gencode Transcript: ENSMUST00000036340.11
Gencode Gene: ENSMUSG00000034023.16
Transcript (Including UTRs)
   Position: mm10 chr6:113,531,682-113,597,017 Size: 65,336 Total Exon Count: 44 Strand: +
Coding Region
   Position: mm10 chr6:113,533,808-113,595,959 Size: 62,152 Coding Exon Count: 43 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:113,531,682-113,597,017)mRNA (may differ from genome)Protein (1450 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: FACD2_MOUSE
DESCRIPTION: RecName: Full=Fanconi anemia group D2 protein homolog; Short=Protein FACD2;
FUNCTION: Required for maintenance of chromosomal stability. Promotes accurate and efficient pairing of homologs during meiosis. Involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing. May participate in S phase and G2 phase checkpoint activation upon DNA damage. Plays a role in preventing breakage and loss of missegregating chromatin at the end of cell division, particularly after replication stress (By similarity). Promotes BRCA2/FANCD1 loading onto damaged chromatin. May also be involved in B-cell immunoglobulin isotype switching.
SUBUNIT: Interacts directly with FANCE and FANCI. Interacts with USP1 and MEN1. The ubiquitinated form specifically interacts with BRCA1 and BLM. Both the nonubiquitinated and the monoubiquitinated forms interact with BRCA2; this interaction is mediated by phosphorylated FANCG and the complex also includes XCCR3 (By similarity). The ubiquitinated form specifically interacts with MTMR15/FAN1 (via UBZ-type zinc finger), leading to recruit MTMR15/FAN1 to sites of DNA damage. Interacts with DCLRE1B/Apollo (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=Concentrates in nuclear foci during S phase and upon genotoxic stress (By similarity).
PTM: Monoubiquitinated on Lys-559 during S phase and upon genotoxic stress by FANCL in complex with E2 ligases UBE2T or UBE2W. Deubiquitinated by USP1 as cells enter G2/M, or once DNA repair is completed. Monoubiquitination requires the joint intervention of the FANC core complex, including FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL and FANCM, and proteins involved in cell cycle checkpoints and DNA repair, including RPA1, ATR, CHEK1 and BRCA1. Ubiquitination is required for binding to chromatin, interaction with BRCA1, BRCA2 and MTMR15/FAN1, DNA repair, and normal cell cycle progression (By similarity).
PTM: Phosphorylated on several sites including Ser-220 and Ser- 1399 in response to genotoxic stress (By similarity).
DISRUPTION PHENOTYPE: Mice display delayed pre- and postnatal development, defects in germ-cell development, and increase incidence of microphthalmia and tumors of epithelial cell origin.

-  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           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -22.70101-0.225 Picture PostScript Text
3' UTR -299.401058-0.283 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
  Pfam Domains:
PF14631 - Fanconi anaemia protein FancD2 nuclease

SCOP Domains:
48371 - ARM repeat

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3S4W - X-ray


ModBase Predicted Comparative 3D Structure on Q80V62
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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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsemblEnsembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0070182 DNA polymerase binding

Biological Process:
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0007049 cell cycle
GO:0007129 synapsis
GO:0007275 multicellular organism development
GO:0007276 gamete generation
GO:0010332 response to gamma radiation
GO:0034599 cellular response to oxidative stress
GO:0045589 regulation of regulatory T cell differentiation
GO:0048854 brain morphogenesis
GO:0050727 regulation of inflammatory response
GO:0051090 regulation of sequence-specific DNA binding transcription factor activity
GO:0097150 neuronal stem cell population maintenance
GO:2000348 regulation of CD40 signaling pathway

Cellular Component:
GO:0000793 condensed chromosome
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  BC139004 - Mus musculus Fanconi anemia, complementation group D2, mRNA (cDNA clone MGC:170631 IMAGE:8862026), complete cds.
AK142384 - Mus musculus 13 days embryo lung cDNA, RIKEN full-length enriched library, clone:D430030I24 product:Fanconi anemia, complementation group D2, full insert sequence.
AK019136 - Mus musculus ES cells cDNA, RIKEN full-length enriched library, clone:2410150O07 product:hypothetical protein, full insert sequence.
AK166411 - Mus musculus mammary gland RCB-0527 Jyg-MC(B) cDNA, RIKEN full-length enriched library, clone:G930012L19 product:Fanconi anemia, complementation group D2, full insert sequence.
AK155602 - Mus musculus B6-derived CD11 +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F730015H14 product:Fanconi anemia, complementation group D2, full insert sequence.
BC040776 - Mus musculus Fanconi anemia, complementation group D2, mRNA (cDNA clone IMAGE:4948653), partial cds.
BC042619 - Mus musculus Fanconi anemia, complementation group D2, mRNA (cDNA clone IMAGE:4948653), partial cds.
BC042870 - Mus musculus Fanconi anemia, complementation group D2, mRNA (cDNA clone IMAGE:5353374), partial cds.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
m_atrbrcaPathway - Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility

Reactome (by CSHL, EBI, and GO)

Protein Q80V62 (Reactome details) participates in the following event(s):

R-MMU-6785594 FANCD2 binds FANCI
R-MMU-6785342 FANCD2:FANCI complex and UBE2T bind ICL-DNA associated with the FA core complex
R-MMU-6786171 FANCD2 deubiquitination by USP1:WDR48
R-MMU-6788385 The complex of ATR and ATRIP is recruited to ICL-DNA
R-MMU-6785361 Monoubiquitination of FANCD2:FANCI
R-MMU-6788392 ATR phosphorylates RPA2, FANCI, FANCD2 and FANCM at ICL-DNA
R-MMU-6785732 DNA nucleases bind monoubiquitinated ID2 complex
R-MMU-6786155 POLN binds ICL-DNA
R-MMU-6783310 Fanconi Anemia Pathway
R-MMU-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: FACD2_MOUSE, NM_001033244, Q80V62, Q9CWC7, uc009dgx.1, uc009dgx.2, uc009dgx.3
UCSC ID: uc009dgx.3
RefSeq Accession: NM_001347350
Protein: Q80V62 (aka FACD2_MOUSE)
CCDS: CCDS20426.1, CCDS85123.1

-  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.