Human Gene PHF13 (ENST00000377648.5) from GENCODE V44
  Description: Homo sapiens PHD finger protein 13 (PHF13), mRNA. (from RefSeq NM_153812)
Gencode Transcript: ENST00000377648.5
Gencode Gene: ENSG00000116273.6
Transcript (Including UTRs)
   Position: hg38 chr1:6,613,731-6,624,030 Size: 10,300 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr1:6,614,067-6,621,637 Size: 7,571 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:6,613,731-6,624,030)mRNA (may differ from genome)Protein (300 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=PHD finger protein 13; AltName: Full=Survival time-associated PHD finger protein in ovarian cancer 1; Short=SPOC1;
FUNCTION: Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.
SUBUNIT: Interacts with histone H3 that is trimethylated at 'Lys- 4' (H3K4me3). Interacts with GSK3B.
SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleoplasm. Note=Predominantly bound to chromatin, but a minor proportion is also detected in the nucleoplasm.
INDUCTION: Expression levels are tightly regulated during the cell cycle. Strongly up-regulated during late G2 phase and M phase of the mitotic cell cycle. Down-regulated at the G1-S phase transition of the cell cycle.
PTM: Subject to proteasomal degradation. Stable when bound to chromatin. The soluble form is rapidly degraded.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAH32792.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAD92781.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.21 RPKM in Testis
Total median expression: 442.19 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 -141.80336-0.422 Picture PostScript Text
3' UTR -854.202393-0.357 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
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger

Pfam Domains:
PF00628 - PHD-finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3O70 - X-ray MuPIT 3O7A - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q86YI8
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0035064 methylated histone binding
GO:0046872 metal ion binding

Biological Process:
GO:0000278 mitotic cell cycle
GO:0006325 chromatin organization
GO:0007049 cell cycle
GO:0007059 chromosome segregation
GO:0007076 mitotic chromosome condensation
GO:0030261 chromosome condensation
GO:0051301 cell division

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm

-  Descriptions from all associated GenBank mRNAs
  BC038516 - Homo sapiens PHD finger protein 13, mRNA (cDNA clone MGC:43399 IMAGE:5266750), complete cds.
JD020584 - Sequence 1608 from Patent EP1572962.
AK097715 - Homo sapiens cDNA FLJ40396 fis, clone TESTI2036969, highly similar to PHD finger protein 13.
AK315110 - Homo sapiens cDNA, FLJ96070, highly similar to Homo sapiens PHD finger protein 13 (PHF13), mRNA.
JD489519 - Sequence 470543 from Patent EP1572962.
JD020620 - Sequence 1644 from Patent EP1572962.
JD392626 - Sequence 373650 from Patent EP1572962.
JD134709 - Sequence 115733 from Patent EP1572962.
JD029985 - Sequence 11009 from Patent EP1572962.
JD187222 - Sequence 168246 from Patent EP1572962.
JD405827 - Sequence 386851 from Patent EP1572962.
AB209544 - Homo sapiens mRNA for PHD finger protein 13 variant protein.
JD149165 - Sequence 130189 from Patent EP1572962.
JD458444 - Sequence 439468 from Patent EP1572962.
HQ448030 - Synthetic construct Homo sapiens clone IMAGE:100071405; CCSB010444_01 PHD finger protein 13 (PHF13) gene, encodes complete protein.
KJ900263 - Synthetic construct Homo sapiens clone ccsbBroadEn_09657 PHF13 gene, encodes complete protein.
CU691588 - Synthetic construct Homo sapiens gateway clone IMAGE:100020833 5' read PHF13 mRNA.
AB464011 - Synthetic construct DNA, clone: pF1KB4637, Homo sapiens PHF13 gene for PHD finger protein 13, without stop codon, in Flexi system.
AY069975 - Homo sapiens PHD finger protein SPOC1 (SPOC1) mRNA, complete cds.
AK027492 - Homo sapiens cDNA FLJ14586 fis, clone NT2RM4001710.
AL121733 - Novel human gene mapping to chomosome 1.
BC032792 - Homo sapiens PHD finger protein 13, mRNA (cDNA clone IMAGE:3878461), partial cds.
DQ600530 - Homo sapiens piRNA piR-38596, complete sequence.
DQ574492 - Homo sapiens piRNA piR-42604, complete sequence.
JD428104 - Sequence 409128 from Patent EP1572962.
JD348493 - Sequence 329517 from Patent EP1572962.
JD558645 - Sequence 539669 from Patent EP1572962.
JD152843 - Sequence 133867 from Patent EP1572962.
JD360133 - Sequence 341157 from Patent EP1572962.
BC007931 - Homo sapiens PHD finger protein 13, mRNA (cDNA clone IMAGE:4122428), partial cds.
JD354409 - Sequence 335433 from Patent EP1572962.
JD336895 - Sequence 317919 from Patent EP1572962.
JD543424 - Sequence 524448 from Patent EP1572962.
JD072673 - Sequence 53697 from Patent EP1572962.
JD196808 - Sequence 177832 from Patent EP1572962.
JD553540 - Sequence 534564 from Patent EP1572962.
JD290866 - Sequence 271890 from Patent EP1572962.
JD278754 - Sequence 259778 from Patent EP1572962.
JD263042 - Sequence 244066 from Patent EP1572962.
JD455940 - Sequence 436964 from Patent EP1572962.
JD552492 - Sequence 533516 from Patent EP1572962.
JD431643 - Sequence 412667 from Patent EP1572962.
JD502118 - Sequence 483142 from Patent EP1572962.
BC048202 - Homo sapiens PHD finger protein 13, mRNA (cDNA clone IMAGE:3641223), partial cds.
DQ572478 - Homo sapiens piRNA piR-40590, complete sequence.
JD233385 - Sequence 214409 from Patent EP1572962.
DQ595526 - Homo sapiens piRNA piR-61638, complete sequence.
JD262998 - Sequence 244022 from Patent EP1572962.
JD193913 - Sequence 174937 from Patent EP1572962.
DQ582404 - Homo sapiens piRNA piR-32516, complete sequence.
JD284256 - Sequence 265280 from Patent EP1572962.
JD230478 - Sequence 211502 from Patent EP1572962.
JD485160 - Sequence 466184 from Patent EP1572962.
JD481683 - Sequence 462707 from Patent EP1572962.
JD445953 - Sequence 426977 from Patent EP1572962.
JD106684 - Sequence 87708 from Patent EP1572962.
JD116408 - Sequence 97432 from Patent EP1572962.
JD562554 - Sequence 543578 from Patent EP1572962.
DQ574924 - Homo sapiens piRNA piR-43036, complete sequence.
JD137703 - Sequence 118727 from Patent EP1572962.
JD279079 - Sequence 260103 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KUQ7, ENST00000377648.1, ENST00000377648.2, ENST00000377648.3, ENST00000377648.4, NM_153812, PHF13_HUMAN, Q59FB6, Q5TH65, Q86YI8, Q8N551, Q9UJP2, uc001aob.1, uc001aob.2, uc001aob.3, uc001aob.4, uc001aob.5, uc001aob.6
UCSC ID: ENST00000377648.5
RefSeq Accession: NM_153812
Protein: Q86YI8 (aka PHF13_HUMAN or PHFD_HUMAN)

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