Human Gene RAD1 (uc003jiy.3)
  Description: Homo sapiens RAD1 homolog (S. pombe) (RAD1), transcript variant 1, mRNA.
RefSeq Summary (NM_002853): This gene encodes a component of a heterotrimeric cell cycle checkpoint complex, known as the 9-1-1 complex, that is activated to stop cell cycle progression in response to DNA damage or incomplete DNA replication. The 9-1-1 complex is recruited by RAD17 to affected sites where it may attract specialized DNA polymerases and other DNA repair effectors. Alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jan 2009].
Transcript (Including UTRs)
   Position: hg19 chr5:34,905,366-34,918,383 Size: 13,018 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr5:34,908,870-34,914,997 Size: 6,128 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:34,905,366-34,918,383)mRNA (may differ from genome)Protein (282 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RAD1_HUMAN
DESCRIPTION: RecName: Full=Cell cycle checkpoint protein RAD1; Short=hRAD1; EC=3.1.11.2; AltName: Full=DNA repair exonuclease rad1 homolog; AltName: Full=Rad1-like DNA damage checkpoint protein;
FUNCTION: Component of the 9-1-1 cell-cycle checkpoint response complex that plays a major role in DNA repair. The 9-1-1 complex is recruited to DNA lesion upon damage by the RAD17-replication factor C (RFC) clamp loader complex. Acts then as a sliding clamp platform on DNA for several proteins involved in long-patch base excision repair (LP-BER). The 9-1-1 complex stimulates DNA polymerase beta (POLB) activity by increasing its affinity for the 3'-OH end of the primer-template and stabilizes POLB to those sites where LP-BER proceeds; endonuclease FEN1 cleavage activity on substrates with double, nick, or gap flaps of distinct sequences and lengths; and DNA ligase I (LIG1) on long-patch base excision repair substrates. The 9-1-1 complex is necessary for the recruitment of RHNO1 to sites of double-stranded breaks (DSB) occurring during the S phase. Isoform 1 possesses 3'->5' double stranded DNA exonuclease activity.
CATALYTIC ACTIVITY: Exonucleolytic cleavage in the 3'- to 5'- direction to yield nucleoside 5'-phosphates.
SUBUNIT: Component of the toroidal 9-1-1 (RAD9-RAD1-HUS1) complex, composed of RAD9A, RAD1 and HUS1. The 9-1-1 complex associates with LIG1, POLB, FEN1, RAD17, HDAC1, RPA1 and RPA2. The 9-1-1 complex associates with the RAD17-RFC complex. RAD1 interacts with POLB, FEN1, HUS1, HUS1B, RAD9A and RAD9B. Interacts with DNAJC7.
INTERACTION: O60921:HUS1; NbExp=4; IntAct=EBI-721835, EBI-1056174; Q99638:RAD9A; NbExp=2; IntAct=EBI-721835, EBI-2606224;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in testis, uterus, bladder, spleen, ovaries, lung, brain and muscle (at protein level).
SIMILARITY: Belongs to the rad1 family.
SEQUENCE CAUTION: Sequence=AAC35550.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAC35550.1; Type=Frameshift; Positions=103; Sequence=CAA06249.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAA06249.1; Type=Frameshift; Positions=103;
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rad1/";

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RAD1
CDC HuGE Published Literature: RAD1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 9.80 RPKM in Cells - Cultured fibroblasts
Total median expression: 210.05 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 -189.30412-0.459 Picture PostScript Text
3' UTR -1153.763504-0.329 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
IPR003011 - Cell_cycle_checkpoint_Rad1
IPR003021 - Rad1_Rec1_Rad17

Pfam Domains:
PF02144 - Repair protein Rad1/Rec1/Rad17

SCOP Domains:
55979 - DNA clamp

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3A1J - X-ray MuPIT 3G65 - X-ray MuPIT 3GGR - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O60671
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
   Gene DetailsGene Details 
   Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003684 damaged DNA binding
GO:0004518 nuclease activity
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0008408 3'-5' exonuclease activity
GO:0008853 exodeoxyribonuclease III activity
GO:0016787 hydrolase activity

Biological Process:
GO:0000077 DNA damage checkpoint
GO:0006281 DNA repair
GO:0006974 cellular response to DNA damage stimulus
GO:0021762 substantia nigra development
GO:0051598 meiotic recombination checkpoint
GO:0071479 cellular response to ionizing radiation
GO:0090305 nucleic acid phosphodiester bond hydrolysis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0030896 checkpoint clamp complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  LF210228 - JP 2014500723-A/17731: Polycomb-Associated Non-Coding RNAs.
BC035771 - Homo sapiens RAD1 homolog (S. pombe), mRNA (cDNA clone IMAGE:5582524), with apparent retained intron.
AK096960 - Homo sapiens cDNA FLJ39641 fis, clone SMINT2003423.
JD414700 - Sequence 395724 from Patent EP1572962.
AF030933 - Homo sapiens exonuclease homolog RAD1 (RAD1) mRNA, complete cds.
BC006837 - Homo sapiens RAD1 homolog (S. pombe), mRNA (cDNA clone MGC:5110 IMAGE:3450321), complete cds.
JD125717 - Sequence 106741 from Patent EP1572962.
JD055243 - Sequence 36267 from Patent EP1572962.
JD306380 - Sequence 287404 from Patent EP1572962.
JD125716 - Sequence 106740 from Patent EP1572962.
JD055242 - Sequence 36266 from Patent EP1572962.
JD306379 - Sequence 287403 from Patent EP1572962.
JD169727 - Sequence 150751 from Patent EP1572962.
JD135983 - Sequence 117007 from Patent EP1572962.
JD233041 - Sequence 214065 from Patent EP1572962.
JD052747 - Sequence 33771 from Patent EP1572962.
JD451312 - Sequence 432336 from Patent EP1572962.
JD473595 - Sequence 454619 from Patent EP1572962.
JD194775 - Sequence 175799 from Patent EP1572962.
JD274709 - Sequence 255733 from Patent EP1572962.
JD194774 - Sequence 175798 from Patent EP1572962.
JD144554 - Sequence 125578 from Patent EP1572962.
JD394621 - Sequence 375645 from Patent EP1572962.
JD410076 - Sequence 391100 from Patent EP1572962.
JD410075 - Sequence 391099 from Patent EP1572962.
JD438897 - Sequence 419921 from Patent EP1572962.
JD264179 - Sequence 245203 from Patent EP1572962.
JD105345 - Sequence 86369 from Patent EP1572962.
JD036732 - Sequence 17756 from Patent EP1572962.
JD329105 - Sequence 310129 from Patent EP1572962.
JD434361 - Sequence 415385 from Patent EP1572962.
JD043108 - Sequence 24132 from Patent EP1572962.
JD420224 - Sequence 401248 from Patent EP1572962.
JD420225 - Sequence 401249 from Patent EP1572962.
JD329106 - Sequence 310130 from Patent EP1572962.
JD441388 - Sequence 422412 from Patent EP1572962.
JD564332 - Sequence 545356 from Patent EP1572962.
JD441387 - Sequence 422411 from Patent EP1572962.
JD556339 - Sequence 537363 from Patent EP1572962.
JD319314 - Sequence 300338 from Patent EP1572962.
JD340831 - Sequence 321855 from Patent EP1572962.
JD171558 - Sequence 152582 from Patent EP1572962.
JD238119 - Sequence 219143 from Patent EP1572962.
JD279117 - Sequence 260141 from Patent EP1572962.
JD231946 - Sequence 212970 from Patent EP1572962.
JD283409 - Sequence 264433 from Patent EP1572962.
JD233300 - Sequence 214324 from Patent EP1572962.
JD223824 - Sequence 204848 from Patent EP1572962.
JD348991 - Sequence 330015 from Patent EP1572962.
AF011905 - Homo sapiens putative checkpoint control protein HRAD1 mRNA, complete cds.
AF076841 - Homo sapiens Rad1-like protein (RAD1) mRNA, complete cds.
AK002112 - Homo sapiens cDNA FLJ11250 fis, clone PLACE1008808, highly similar to Cell cycle checkpoint protein RAD1 (EC 3.1.11.2).
BC009804 - Homo sapiens RAD1 homolog (S. pombe), mRNA (cDNA clone MGC:13690 IMAGE:4109436), complete cds.
AJ004974 - Homo sapiens mRNA for cell cycle checkpoint protein rad1A.
AJ004975 - Homo sapiens mRNA for cell cycle checkpoint protein rad1B.
AF084513 - Homo sapiens DNA repair exonuclease (REC1) mRNA, alternatively spliced product, complete cds.
AF073524 - Homo sapiens RAD1 mRNA, complete cds.
AF090170 - Homo sapiens Rad1-like protein (RAD1) mRNA, complete cds.
AF084512 - Homo sapiens DNA repair exonuclease (REC1) mRNA, complete cds.
JD502941 - Sequence 483965 from Patent EP1572962.
BC037857 - Homo sapiens RAD1 homolog (S. pombe), mRNA (cDNA clone MGC:43773 IMAGE:5272408), complete cds.
LF336011 - JP 2014500723-A/143514: Polycomb-Associated Non-Coding RNAs.
JD422103 - Sequence 403127 from Patent EP1572962.
JD348419 - Sequence 329443 from Patent EP1572962.
AF074717 - Homo sapiens Rad1-like DNA damage checkpoint protein (RAD1) mRNA, complete cds.
JD080595 - Sequence 61619 from Patent EP1572962.
AF058392 - Homo sapiens cell cycle checkpoint protein Hrad1 mRNA, complete cds.
AF058393 - Homo sapiens cell cycle checkpoint protein Hrad1 mRNA, alternatively spliced.
KJ891953 - Synthetic construct Homo sapiens clone ccsbBroadEn_01347 RAD1 gene, encodes complete protein.
BT006908 - Homo sapiens RAD1 homolog (S. pombe) mRNA, complete cds.
CU675471 - Synthetic construct Homo sapiens gateway clone IMAGE:100018718 5' read RAD1 mRNA.
DQ891144 - Synthetic construct clone IMAGE:100003774; FLH169712.01X; RZPDo839F0496D RAD1 homolog (S. pombe) (RAD1) gene, encodes complete protein.
DQ894324 - Synthetic construct Homo sapiens clone IMAGE:100008784; FLH169708.01L; RZPDo839F0495D RAD1 homolog (S. pombe) (RAD1) gene, encodes complete protein.
AB528352 - Synthetic construct DNA, clone: pF1KB6324, Homo sapiens RAD1 gene for RAD1 homolog, without stop codon, in Flexi system.
LF336008 - JP 2014500723-A/143511: Polycomb-Associated Non-Coding RNAs.
JD027170 - Sequence 8194 from Patent EP1572962.
JD028455 - Sequence 9479 from Patent EP1572962.
JD023302 - Sequence 4326 from Patent EP1572962.
JD033473 - Sequence 14497 from Patent EP1572962.
JD177309 - Sequence 158333 from Patent EP1572962.
DL491683 - Novel nucleic acids.
JD193159 - Sequence 174183 from Patent EP1572962.
JD069275 - Sequence 50299 from Patent EP1572962.
JD443479 - Sequence 424503 from Patent EP1572962.
DL490267 - Novel nucleic acids.
JD379491 - Sequence 360515 from Patent EP1572962.
JD476675 - Sequence 457699 from Patent EP1572962.
JD560663 - Sequence 541687 from Patent EP1572962.
JD414698 - Sequence 395722 from Patent EP1572962.
JD560662 - Sequence 541686 from Patent EP1572962.
JD206173 - Sequence 187197 from Patent EP1572962.
JD277373 - Sequence 258397 from Patent EP1572962.
JD309143 - Sequence 290167 from Patent EP1572962.
JD566018 - Sequence 547042 from Patent EP1572962.
JD081739 - Sequence 62763 from Patent EP1572962.
JD413829 - Sequence 394853 from Patent EP1572962.
JD463296 - Sequence 444320 from Patent EP1572962.
JD100768 - Sequence 81792 from Patent EP1572962.
JD247137 - Sequence 228161 from Patent EP1572962.
JD247561 - Sequence 228585 from Patent EP1572962.
MA445805 - JP 2018138019-A/17731: Polycomb-Associated Non-Coding RNAs.
MA571588 - JP 2018138019-A/143514: Polycomb-Associated Non-Coding RNAs.
MA571585 - JP 2018138019-A/143511: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O60671 (Reactome details) participates in the following event(s):

R-HSA-176264 Recruitment of the Rad9-Hus1-Rad1 complex to DNA
R-HSA-5685011 ATR activation at DNA DSBs
R-HSA-5686657 ERCC1:XPF cleaves flaps generated by SSA
R-HSA-5693561 RAD51 binds BRCA2 at resected DNA DSBs
R-HSA-5684887 Activation of CHEK1 at resected DNA DSBs
R-HSA-5684882 CHEK1 is recruited to resected DNA DSBs
R-HSA-5685156 ATR phosphorylates RPA2
R-HSA-5693580 Association of RAD52 with the RPA complex at resected DNA DSBs
R-HSA-6799332 ATR phosphorylates TP53
R-HSA-5693564 Association of RAD51 with RAD52:DNA double-strand break ends
R-HSA-5686642 RAD52 promotes single strand annealing at resected DNA DSBs
R-HSA-176187 Activation of ATR in response to replication stress
R-HSA-5693607 Processing of DNA double-strand break ends
R-HSA-5685938 HDR through Single Strand Annealing (SSA)
R-HSA-5693616 Presynaptic phase of homologous DNA pairing and strand exchange
R-HSA-69481 G2/M Checkpoints
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693579 Homologous DNA Pairing and Strand Exchange
R-HSA-69473 G2/M DNA damage checkpoint
R-HSA-6804756 Regulation of TP53 Activity through Phosphorylation
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-5693538 Homology Directed Repair
R-HSA-5685942 HDR through Homologous Recombination (HRR)
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-1640170 Cell Cycle
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-73894 DNA Repair
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: AF030933, NM_002853, NP_002844, O60671, O75572, O95304, Q1W161, Q5KSM0, Q5KSM1, Q9UEP1, RAD1_HUMAN, REC1
UCSC ID: uc003jiy.3
RefSeq Accession: NM_002853
Protein: O60671 (aka RAD1_HUMAN)
CCDS: CCDS3905.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF030933.1
exon count: 8CDS single in 3' UTR: no RNA size: 1884
ORF size: 849CDS single in intron: no Alignment % ID: 99.73
txCdsPredict score: 1749.00frame shift in genome: no % Coverage: 97.51
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.