Human Gene RFC5 (uc001twq.3) Description and Page Index
  Description: Homo sapiens replication factor C (activator 1) 5, 36.5kDa (RFC5), transcript variant 1, mRNA.
RefSeq Summary (NM_007370): This gene encodes the smallest subunit of the replication factor C complex, which consists of five distinct subunits (140, 40, 38, 37, and 36 kDa) and is required for DNA replication. This subunit interacts with the C-terminal region of proliferating cell nuclear antigen and is required to open and load proliferating cell nuclear antigen onto DNA during S phase. It is a member of the AAA+ (ATPases associated with various cellular activities) ATPase family and forms a core complex with the 38 and 40 kDa subunits that possesses DNA-dependent ATPase activity. A related pseudogene has been identified on chromosome 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016].
Transcript (Including UTRs)
   Position: hg19 chr12:118,454,506-118,470,042 Size: 15,537 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr12:118,454,633-118,469,083 Size: 14,451 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:118,454,506-118,470,042)mRNA (may differ from genome)Protein (340 aa)
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RFC5_HUMAN
DESCRIPTION: RecName: Full=Replication factor C subunit 5; AltName: Full=Activator 1 36 kDa subunit; Short=A1 36 kDa subunit; AltName: Full=Activator 1 subunit 5; AltName: Full=Replication factor C 36 kDa subunit; Short=RF-C 36 kDa subunit; Short=RFC36;
FUNCTION: The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins proliferating cell nuclear antigen (PCNA) and activator 1.
SUBUNIT: Heterotetramer of subunits RFC2, RFC3, RFC4 and RFC5 that can form a complex either with RFC1 or with RAD17. The former interacts with PCNA in the presence of ATP, while the latter has ATPase activity but is not stimulated by PCNA.
INTERACTION: P35249:RFC4; NbExp=6; IntAct=EBI-712376, EBI-476655;
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Belongs to the activator 1 small subunits family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/rfc5/";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RFC5
CDC HuGE Published Literature: RFC5

-  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: 15.89 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 204.44 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 -43.90127-0.346 Picture PostScript Text
3' UTR -268.35959-0.280 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
IPR003593 - AAA+_ATPase
IPR003959 - ATPase_AAA_core
IPR008921 - DNA_pol3_clamp-load_cplx_C
IPR013748 - Rep_factorC_C_dom

Pfam Domains:
PF00004 - ATPase family associated with various cellular activities (AAA)
PF03215 - Rad17 cell cycle checkpoint protein
PF05496 - Holliday junction DNA helicase ruvB N-terminus
PF08542 - Replication factor C C-terminal domain
PF13177 - DNA polymerase III, delta subunit
PF13479 - AAA domain

SCOP Domains:
48019 - DNA polymerase III clamp loader subunits, C-terminal domain
52540 - P-loop containing nucleoside triphosphate hydrolases

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

1LFS
- Model


ModBase Predicted Comparative 3D Structure on P40937
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
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 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0019899 enzyme binding
GO:0003689 DNA clamp loader activity
GO:0043142 single-stranded DNA-dependent ATPase activity

Biological Process:
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006283 transcription-coupled nucleotide-excision repair
GO:0006296 nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0019985 translesion synthesis
GO:0032201 telomere maintenance via semi-conservative replication
GO:0033683 nucleotide-excision repair, DNA incision
GO:0042276 error-prone translesion synthesis
GO:0042769 DNA damage response, detection of DNA damage
GO:0070987 error-free translesion synthesis
GO:1900264 positive regulation of DNA-directed DNA polymerase activity

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005663 DNA replication factor C complex
GO:0031390 Ctf18 RFC-like complex


-  Descriptions from all associated GenBank mRNAs
  AK291107 - Homo sapiens cDNA FLJ77120 complete cds, highly similar to Homo sapiens replication factor C (activator 1) 5, 36.5kDa (RFC5), transcript variant 2, mRNA.
AK094575 - Homo sapiens cDNA FLJ37256 fis, clone BRAMY2009612, highly similar to Replication factor C subunit 5.
AK290685 - Homo sapiens cDNA FLJ76127 complete cds, highly similar to Homo sapiens replication factor C (activator 1) 5, 36.5kDa (RFC5), transcript variant 1, mRNA.
BC001866 - Homo sapiens replication factor C (activator 1) 5, 36.5kDa, mRNA (cDNA clone MGC:1155 IMAGE:3544137), complete cds.
BC013961 - Homo sapiens replication factor C (activator 1) 5, 36.5kDa, mRNA (cDNA clone MGC:4451 IMAGE:2960023), complete cds.
AB208992 - Homo sapiens mRNA for replication factor C 5 isoform 1 variant protein.
BC020440 - Homo sapiens replication factor C (activator 1) 5, 36.5kDa, mRNA (cDNA clone IMAGE:3447174).
L07540 - Human replication factor C, 36-kDa subunit mRNA, complete cds.
AB464140 - Synthetic construct DNA, clone: pF1KB3490, Homo sapiens RFC5 gene for replication factor C, without stop codon, in Flexi system.
CU674898 - Synthetic construct Homo sapiens gateway clone IMAGE:100019008 5' read RFC5 mRNA.
HQ447800 - Synthetic construct Homo sapiens clone IMAGE:100071143; CCSB003772_01 replication factor C (activator 1) 5, 36.5kDa (RFC5) gene, encodes complete protein.
KJ891997 - Synthetic construct Homo sapiens clone ccsbBroadEn_01391 RFC5 gene, encodes complete protein.
CR407651 - Homo sapiens full open reading frame cDNA clone RZPDo834G122D for gene RFC5, replication factor C (activator 1) 5, 36.5kDa complete cds, without stopcodon.
JD097060 - Sequence 78084 from Patent EP1572962.
JD181705 - Sequence 162729 from Patent EP1572962.
JD272570 - Sequence 253594 from Patent EP1572962.
JD054711 - Sequence 35735 from Patent EP1572962.
JD239668 - Sequence 220692 from Patent EP1572962.
JD185834 - Sequence 166858 from Patent EP1572962.
JD255634 - Sequence 236658 from Patent EP1572962.
JD495623 - Sequence 476647 from Patent EP1572962.
JD097988 - Sequence 79012 from Patent EP1572962.
JD082313 - Sequence 63337 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03030 - DNA replication
hsa03420 - Nucleotide excision repair
hsa03430 - Mismatch repair

Reactome (by CSHL, EBI, and GO)

Protein P40937 (Reactome details) participates in the following event(s):

R-HSA-69053 RFC binding displaces Pol Alpha
R-HSA-174452 RFC binding displaces Pol Alpha on the C-strand of the telomere
R-HSA-5690213 DNA polymerases delta, epsilon or kappa bind the GG-NER site
R-HSA-6782211 DNA polymerases delta, epsilon or kappa bind the TC-NER site
R-HSA-69068 RFC dissociates after sliding clamp formation
R-HSA-174447 RFC dissociates after sliding clamp formation on the C-strand of the telomere
R-HSA-176101 Recruitment of Rad17-RFC 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-69063 Loading of PCNA - Sliding Clamp Formation
R-HSA-174439 Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere
R-HSA-110364 PCNA:POLD,POLE:RPA:RFC and FEN1 bind APEX1
R-HSA-5651992 PCNA-containing replication complex binds damaged dsDNA
R-HSA-5651809 LIG1, APEX1 and PCNA:POLD,POLE:RPA:RFC dissociate from repaired DNA
R-HSA-5653840 POLD,POLE complete replication of damaged DNA after TLS
R-HSA-5653766 USP10 binds monoUb:K164,ISG:K164,ISG:K168-PCNA
R-HSA-5653754 UBE2L6:TRIM25 ISGylates monoUb:K164-PCNA
R-HSA-5653780 USP43 binds ISG:K164,ISG:K168-PCNA
R-HSA-5653770 USP10 deubiquitinates monoUb:K164,ISG:K164,ISG:K168-PCNA
R-HSA-5653838 POLD,POLE binds deISGylated PCNA after TLS
R-HSA-5653786 USP43 deISGylates ISG:K164,ISG:K168-PCNA
R-HSA-5655466 USP1:WDR48 deubiquitinates monoUb:K164-PCNA
R-HSA-5690997 Ligation of newly synthesized repair patch to incised DNA in GG-NER
R-HSA-6782227 Ligation of newly synthesized repair patch to incised DNA in TC-NER
R-HSA-176264 Recruitment of the Rad9-Hus1-Rad1 complex to DNA
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-110368 POLD,POLE-mediated DNA strand displacement synthesis
R-HSA-110371 LIG1 binds APEX1 and PCNA at SSB
R-HSA-110363 FEN1 bound to PCNA and APEX1 cleaves flap ssDNA
R-HSA-5651805 LIG1 bound to APEX1 and PCNA ligates SSB
R-HSA-5652005 RAD18:UBE2B or RBX1:CUL4:DDB1:DTL ubiquitin ligase complex binds PCNA:POLD,POLE:RPA:RFC associated with damaged dsDNA
R-HSA-5655481 USP1:WDR48 binds monoUb:K164-PCNA
R-HSA-5652009 RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA
R-HSA-110307 REV1 binds AP-dsDNA
R-HSA-110311 POLZ extends translesion synthesis
R-HSA-5653756 TRIM25 binds monoUb:164-PCNA
R-HSA-110316 POLH binds monoUb:K164-PCNA at damaged TT-CPD-DNA template
R-HSA-5654986 SPRTN binds monoUb:K164-PCNA associated with POLH
R-HSA-110319 Elongation by POLH
R-HSA-5654989 SPRTN:VCP-mediated release of POLH from monoUb:K164-PCNA
R-HSA-5655835 POLK forms a quaternary complex with REV1 and POLZ on damaged DNA template
R-HSA-5656105 POLI simultaneously binds REV1 and monoUb:K164-PCNA at damaged DNA
R-HSA-110317 Insertion of correct bases opposite the lesion by POLH
R-HSA-5690988 3'-incision of DNA by ERCC5 (XPG) in GG-NER
R-HSA-5691001 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in GG-NER
R-HSA-6782224 3' incision by ERCC5 (XPG) in TC-NER
R-HSA-6782208 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER
R-HSA-6799332 ATR phosphorylates TP53
R-HSA-5693564 Association of RAD51 with RAD52:DNA double-strand break ends
R-HSA-5693593 D-loop extension by DNA polymerases
R-HSA-5652151 REV1 recruits POLZ to (AP:Cyt)-DNA Template
R-HSA-110308 REV1 inserts dCMP opposite to AP sites in DNA
R-HSA-5654985 SPRTN recruits VCP to monoUb:K164-PCNA associated with POLH
R-HSA-5655892 POLK incorporates dNMP opposite to damaged DNA base
R-HSA-5655965 POLK and POLZ cooperate in elongation of mispaired primer termini
R-HSA-5656148 POLI incorporates dNMP opposite to damaged DNA base
R-HSA-5656158 POLZ elongates POLI-incorporated dNMP
R-HSA-5686642 RAD52 promotes single strand annealing at resected DNA DSBs
R-HSA-69091 Polymerase switching
R-HSA-174411 Polymerase switching on the C-strand of the telomere
R-HSA-5696400 Dual Incision in GG-NER
R-HSA-6782135 Dual incision in TC-NER
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-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-HSA-110314 Recognition of DNA damage by PCNA-containing replication complex
R-HSA-5656169 Termination of translesion DNA synthesis
R-HSA-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-69109 Leading Strand Synthesis
R-HSA-69186 Lagging Strand Synthesis
R-HSA-174417 Telomere C-strand (Lagging Strand) Synthesis
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
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-110373 Resolution of AP sites via the multiple-nucleotide patch replacement pathway
R-HSA-73893 DNA Damage Bypass
R-HSA-110313 Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template
R-HSA-110312 Translesion synthesis by REV1
R-HSA-110320 Translesion Synthesis by POLH
R-HSA-5655862 Translesion synthesis by POLK
R-HSA-5656121 Translesion synthesis by POLI
R-HSA-69190 DNA strand elongation
R-HSA-180786 Extension of Telomeres
R-HSA-5696398 Nucleotide Excision Repair
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-73933 Resolution of Abasic Sites (AP sites)
R-HSA-73894 DNA Repair
R-HSA-69239 Synthesis of DNA
R-HSA-157579 Telomere Maintenance
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-1640170 Cell Cycle
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-73884 Base Excision Repair
R-HSA-69242 S Phase
R-HSA-69306 DNA Replication
R-HSA-73886 Chromosome Maintenance
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-69278 Cell Cycle (Mitotic)
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: A8MZ62, B3KSX8, NM_007370, NP_001123584, P40937, RFC5_HUMAN
UCSC ID: uc001twq.3
RefSeq Accession: NM_007370
Protein: P40937 (aka RFC5_HUMAN)
CCDS: CCDS9185.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007370.5
exon count: 11CDS single in 3' UTR: no RNA size: 2122
ORF size: 1023CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2246.00frame shift in genome: no % Coverage: 99.39
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.