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Protein

PHD finger protein 13

Gene

PHF13

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
  • methylated histone binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • chromatin modification Source: UniProtKB-KW
  • chromosome segregation Source: UniProtKB
  • mitotic cell cycle Source: UniProtKB
  • mitotic chromosome condensation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

Cell cycle, Cell division, DNA condensation, Mitosis

Keywords - Ligandi

Metal-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
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:22983. PHF13.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB
Complete GO annotation...

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.
STRINGi9606.ENSP00000366876.

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

Sequence similaritiesi

Contains 1 PHD-type zinc finger.Curated

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.
OMAiRAMIECN.
OrthoDBiEOG091G0FTQ.
PhylomeDBiQ86YI8.
TreeFamiTF331373.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
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 → E.1 PublicationCorresponds to variant rs17853850dbSNPEnsembl.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. Translation: CAI19471.1.
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

Cross-referencesi

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. Translation: CAI19471.1.
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.

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...

Protein-protein interaction databases

BioGridi127151. 4 interactors.
IntActiQ86YI8. 1 interactor.
STRINGi9606.ENSP00000366876.

Chemistry databases

BindingDBiQ86YI8.
ChEMBLiCHEMBL1764945.

PTM databases

iPTMnetiQ86YI8.
PhosphoSitePlusiQ86YI8.

Polymorphism and mutation databases

BioMutaiPHF13.
DMDMi229462750.

Proteomic databases

EPDiQ86YI8.
PaxDbiQ86YI8.
PeptideAtlasiQ86YI8.
PRIDEiQ86YI8.

Protocols and materials databases

DNASUi148479.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi148479.
DisGeNETi148479.
GeneCardsiPHF13.
H-InvDBHIX0000084.
HGNCiHGNC:22983. PHF13.
HPAiHPA026830.
neXtProtiNX_Q86YI8.
OpenTargetsiENSG00000116273.
PharmGKBiPA134901883.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IMXF. Eukaryota.
ENOG4111YY1. LUCA.
GeneTreeiENSGT00530000063882.
HOGENOMiHOG000010286.
HOVERGENiHBG071437.
InParanoidiQ86YI8.
OMAiRAMIECN.
OrthoDBiEOG091G0FTQ.
PhylomeDBiQ86YI8.
TreeFamiTF331373.

Miscellaneous databases

ChiTaRSiPHF13. human.
EvolutionaryTraceiQ86YI8.
GenomeRNAii148479.
PROiQ86YI8.

Gene expression databases

BgeeiENSG00000116273.
CleanExiHS_PHF13.
ExpressionAtlasiQ86YI8. baseline and differential.
GenevisibleiQ86YI8. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPHF13_HUMAN
AccessioniPrimary (citable) accession number: Q86YI8
Secondary accession number(s): B3KUQ7
, Q59FB6, Q5TH65, Q8N551, Q9UJP2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 15, 2003
Last sequence update: May 5, 2009
Last modified: November 30, 2016
This is version 114 of the entry and version 2 of the sequence. [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
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.