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Protein

PHD finger protein 13

Gene

PHF13

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Modulates chromatin structure. Required for normal chromosome condensation during the early stages of mitosis. Required for normal chromosome separation during mitosis.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri232 – 280PHD-typeAdd BLAST49

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • methylated histone binding Source: UniProtKB

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • chromatin organization Source: UniProtKB-KW
  • chromosome segregation Source: UniProtKB
  • mitotic cell cycle Source: UniProtKB
  • mitotic chromosome condensation Source: UniProtKB

Keywordsi

Molecular functionChromatin regulator
Biological processCell cycle, Cell division, DNA condensation, Mitosis
LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 13
Alternative name(s):
Survival time-associated PHD finger protein in ovarian cancer 1
Short name:
SPOC1
Gene namesi
Name:PHF13
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi

Organism-specific databases

EuPathDBiHostDB:ENSG00000116273.5
HGNCiHGNC:22983 PHF13
neXtProtiNX_Q86YI8

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi148479
OpenTargetsiENSG00000116273
PharmGKBiPA134901883

Chemistry databases

ChEMBLiCHEMBL1764945

Polymorphism and mutation databases

BioMutaiPHF13
DMDMi229462750

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000593041 – 300PHD finger protein 13Add BLAST300

Post-translational modificationi

Subject to proteasomal degradation. Stable when bound to chromatin. The soluble form is rapidly degraded.

Proteomic databases

EPDiQ86YI8
PaxDbiQ86YI8
PeptideAtlasiQ86YI8
PRIDEiQ86YI8

PTM databases

iPTMnetiQ86YI8
PhosphoSitePlusiQ86YI8

Expressioni

Inductioni

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.1 Publication

Gene expression databases

BgeeiENSG00000116273
CleanExiHS_PHF13
ExpressionAtlasiQ86YI8 baseline and differential
GenevisibleiQ86YI8 HS

Organism-specific databases

HPAiHPA026830

Interactioni

Subunit structurei

Interacts with histone H3 that is trimethylated at 'Lys-4' (H3K4me3). Interacts with GSK3B.2 Publications

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi127151, 4 interactors
IntActiQ86YI8, 1 interactor

Chemistry databases

BindingDBiQ86YI8

Structurei

Secondary structure

1300
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi246 – 248Combined sources3
Turni250 – 252Combined sources3
Beta strandi255 – 257Combined sources3
Turni258 – 262Combined sources5
Helixi265 – 267Combined sources3
Helixi275 – 278Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3O70X-ray1.85A232-281[»]
3O7AX-ray1.67A229-280[»]
ProteinModelPortaliQ86YI8
SMRiQ86YI8
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ86YI8

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni241 – 248Interaction with trimethylated histone H3 (H3K4)8

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi110 – 127Nuclear localization signalCuratedAdd BLAST18

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri232 – 280PHD-typeAdd BLAST49

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG410IMXF Eukaryota
ENOG4111YY1 LUCA
GeneTreeiENSGT00530000063882
HOGENOMiHOG000010286
HOVERGENiHBG071437
InParanoidiQ86YI8
OMAiCFGHLQP
OrthoDBiEOG091G0FTQ
PhylomeDBiQ86YI8
TreeFamiTF331373

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit

Sequencei

Sequence statusi: Complete.

Q86YI8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDSDSCAAAF HPEEYSPSCK RRRTVEDFNK FCTFVLAYAG YIPYPKEELP
60 70 80 90 100
LRSSPSPANS TAGTIDSDGW DAGFSDIASS VPLPVSDRCF SHLQPTLLQR
110 120 130 140 150
AKPSNFLLDR KKTDKLKKKK KRKRRDSDAP GKEGYRGGLL KLEAADPYVE
160 170 180 190 200
TPTSPTLQDI PQAPSDPCSG WDSDTPSSGS CATVSPDQVK EIKTEGKRTI
210 220 230 240 250
VRQGKQVVFR DEDSTGNDED IMVDSDDDSW DLVTCFCMKP FAGRPMIECN
260 270 280 290 300
ECHTWIHLSC AKIRKSNVPE VFVCQKCRDS KFDIRRSNRS RTGSRKLFLD
Length:300
Mass (Da):33,582
Last modified:May 5, 2009 - v2
Checksum:i197663A113B995F2
GO

Sequence cautioni

The sequence AAH32792 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAD92781 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti111K → R in BAG53519 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05528520K → E1 PublicationCorresponds to variant dbSNP:rs17853850Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK315110 mRNA Translation: BAG37568.1
AK097715 mRNA Translation: BAG53519.1
AB209544 mRNA Translation: BAD92781.1 Different initiation.
AL031447 Genomic DNA No translation available.
CH471130 Genomic DNA Translation: EAW71561.1
BC032792 mRNA Translation: AAH32792.2 Different initiation.
BC038516 mRNA Translation: AAH38516.1
AL121733 mRNA Translation: CAB57324.1
CCDSiCCDS85.1
RefSeqiNP_722519.2, NM_153812.2
UniGeneiHs.516079

Genome annotation databases

EnsembliENST00000377648; ENSP00000366876; ENSG00000116273
GeneIDi148479
KEGGihsa:148479
UCSCiuc001aob.5 human

Keywords - Coding sequence diversityi

Polymorphism

Entry informationi

Entry nameiPHF13_HUMAN
AccessioniPrimary (citable) accession number: Q86YI8
Secondary accession number(s): B3KUQ7
, Q59FB6, Q5TH65, Q8N551, Q9UJP2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 15, 2003
Last sequence update: May 5, 2009
Last modified: April 25, 2018
This is version 121 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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