Human Gene PIF1 (ENST00000559239.2_7) from GENCODE V47lift37
  Description: PIF1 5'-to-3' DNA helicase, transcript variant 1 (from RefSeq NM_001286499.2)
Gencode Transcript: ENST00000559239.2_7
Gencode Gene: ENSG00000140451.13_9
Transcript (Including UTRs)
   Position: hg19 chr15:65,107,831-65,117,846 Size: 10,016 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr15:65,108,497-65,116,534 Size: 8,038 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:65,107,831-65,117,846)mRNA (may differ from genome)Protein (641 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PIF1_HUMAN
DESCRIPTION: RecName: Full=ATP-dependent DNA helicase PIF1; EC=3.6.4.12; AltName: Full=PIF1/RRM3 DNA helicase-like protein;
FUNCTION: DNA-dependent ATPase and DNA helicase inhibiting telomerase activity by unwinding DNA/RNA duplex formed by telomerase RNA and telomeric DNA in a 5' to 3' polarity. Negatively regulates telomere length and such inhibition requires its ATPase activity. Tightly cell cycle regulated and expressed in late S/G2 phase.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Interacts with telomerase.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Weak ubiquitous expression.
SIMILARITY: Belongs to the helicase family.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PIF1
Diseases sorted by gene-association score: cataract 7 (6)

-  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: 16.99 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 57.63 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -29.3098-0.299 Picture PostScript Text
3' UTR -246.30666-0.370 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
IPR003840 - DNA_helicase
IPR010285 - DNA_helicase_PIF1

Pfam Domains:
PF05970 - PIF1-like helicase
PF13245 - AAA domain
PF13604 - AAA domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like

ModBase Predicted Comparative 3D Structure on Q9H611
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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0010521 telomerase inhibitor activity
GO:0016787 hydrolase activity
GO:0017116 single-stranded DNA-dependent ATP-dependent DNA helicase activity
GO:0033682 ATP-dependent 5'-3' DNA/RNA helicase activity
GO:0042162 telomeric DNA binding
GO:0043141 ATP-dependent 5'-3' DNA helicase activity

Biological Process:
GO:0000002 mitochondrial genome maintenance
GO:0000723 telomere maintenance
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006974 cellular response to DNA damage stimulus
GO:0032204 regulation of telomere maintenance
GO:0032211 negative regulation of telomere maintenance via telomerase
GO:0032508 DNA duplex unwinding
GO:0044806 G-quadruplex DNA unwinding
GO:0051974 negative regulation of telomerase activity

Cellular Component:
GO:0000784 nuclear chromosome, telomeric region
GO:0005634 nucleus
GO:0005657 replication fork
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  KJ899610 - Synthetic construct Homo sapiens clone ccsbBroadEn_09004 PIF1 gene, encodes complete protein.
BC033254 - Homo sapiens chromosome 15 open reading frame 20, mRNA (cDNA clone IMAGE:5445559).
AF108138 - Homo sapiens DNA helicase homolog (PIF1) mRNA, partial cds.
EU084033 - Homo sapiens PIF1 DNA helicase transcript variant 1 (PIF1) mRNA, complete cds.
AB185926 - Homo sapiens PIF1 mRNA for PIF1 DNA helicase isoform alpha, complete cds.
AB185927 - Homo sapiens PIF1 mRNA for PIF1 DNA helicase isoform beta, complete cds.
AY498716 - Homo sapiens PIF1/RRM3 DNA helicase-like protein (PIF1) mRNA, complete cds.
JD091688 - Sequence 72712 from Patent EP1572962.
JD386794 - Sequence 367818 from Patent EP1572962.
JD456939 - Sequence 437963 from Patent EP1572962.
JD232676 - Sequence 213700 from Patent EP1572962.
JD427264 - Sequence 408288 from Patent EP1572962.
BC137503 - Homo sapiens PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae), mRNA (cDNA clone MGC:169126 IMAGE:9021503), complete cds.
BC137504 - Homo sapiens PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae), mRNA (cDNA clone MGC:169127 IMAGE:9021504), complete cds.
JD540994 - Sequence 522018 from Patent EP1572962.
JD442499 - Sequence 423523 from Patent EP1572962.
JD391926 - Sequence 372950 from Patent EP1572962.
JD133627 - Sequence 114651 from Patent EP1572962.
JD180649 - Sequence 161673 from Patent EP1572962.
JD199958 - Sequence 180982 from Patent EP1572962.
JD539618 - Sequence 520642 from Patent EP1572962.
JD098083 - Sequence 79107 from Patent EP1572962.
JD385444 - Sequence 366468 from Patent EP1572962.
JD163049 - Sequence 144073 from Patent EP1572962.
JD072677 - Sequence 53701 from Patent EP1572962.
JD319755 - Sequence 300779 from Patent EP1572962.
JD325578 - Sequence 306602 from Patent EP1572962.
DQ437529 - Homo sapiens DNA helicase PIF1 (PIF1) mRNA, complete cds.
JD143250 - Sequence 124274 from Patent EP1572962.
JD254128 - Sequence 235152 from Patent EP1572962.
JD168900 - Sequence 149924 from Patent EP1572962.
JD324199 - Sequence 305223 from Patent EP1572962.
AK026345 - Homo sapiens cDNA: FLJ22692 fis, clone HSI11184.
JD135020 - Sequence 116044 from Patent EP1572962.
BC018978 - Homo sapiens chromosome 15 open reading frame 20, mRNA (cDNA clone IMAGE:3139288), partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RPL7, C15orf20, ENST00000559239.1, NM_001286499, PIF1 , PIF1_HUMAN, Q1W5B6, Q330H5, Q33E24, Q9H611, uc325mnr.1, uc325mnr.2
UCSC ID: ENST00000559239.2_7
RefSeq Accession: NM_001286499.2
Protein: Q9H611 (aka PIF1_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.