Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Zinc finger protein with KRAB and SCAN domains 3

Gene

ZKSCAN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional factor that binds to the consensus sequence 5'-[GT][AG][AGT]GGGG-3' and acts as a repressor of autophagy. Specifically represses expression of genes involved in autophagy and lysosome biogenesis/function such as MAP1LC3B, ULK1 or WIPI2. Associates with chromatin at the ITGB4 and VEGF promoters. Also acts as a transcription activator and promotes cancer cell progression and/or migation in various tumors and myelomas.4 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri314 – 336C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri342 – 364C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri370 – 392C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri398 – 420C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri426 – 448C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri480 – 502C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri508 – 530C2H2-type 7PROSITE-ProRule annotationAdd BLAST23

GO - Molecular functioni

  • chromatin binding Source: UniProtKB
  • DNA binding Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: NTNU_SB
  • sequence-specific DNA binding Source: UniProtKB
  • transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: NTNU_SB
  • transcription factor activity, sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • autophagy Source: UniProtKB-KW
  • lysosome organization Source: UniProtKB
  • negative regulation of autophagy Source: UniProtKB
  • negative regulation of cellular senescence Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Autophagy, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000137184-MONOMER.
ReactomeiR-HSA-212436. Generic Transcription Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc finger protein with KRAB and SCAN domains 3
Alternative name(s):
Zinc finger and SCAN domain-containing protein 13
Zinc finger protein 306
Zinc finger protein 309
Zinc finger protein 47 homolog
Short name:
Zf47
Short name:
Zfp-47
Gene namesi
Name:ZKSCAN3
Synonyms:ZFP47, ZNF306, ZNF309, ZSCAN13
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:13853. ZKSCAN3.

Subcellular locationi

  • Nucleus
  • Cytoplasm

  • Note: Mainly localizes in the nucleus. Under starvation conditions translocates to the cytoplasm, allowing expression of target genes involved in autophagy and lysosome biogenesis/function.

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi80317.
OpenTargetsiENSG00000189298.
PharmGKBiPA37821.

Polymorphism and mutation databases

BioMutaiZKSCAN3.
DMDMi116242859.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000475241 – 538Zinc finger protein with KRAB and SCAN domains 3Add BLAST538

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei42PhosphoserineBy similarity1
Modified residuei207PhosphothreonineCombined sources1
Modified residuei449PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9BRR0.
MaxQBiQ9BRR0.
PaxDbiQ9BRR0.
PeptideAtlasiQ9BRR0.
PRIDEiQ9BRR0.

PTM databases

iPTMnetiQ9BRR0.
PhosphoSitePlusiQ9BRR0.

Expressioni

Inductioni

Overexpressed in various tumors, such as multiple myeloma, colorectal and prostate cancers (at protein level).3 Publications

Gene expression databases

BgeeiENSG00000189298.
CleanExiHS_ZKSCAN3.
GenevisibleiQ9BRR0. HS.

Organism-specific databases

HPAiHPA009637.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
LZTS2Q9BRK43EBI-1965777,EBI-741037

Protein-protein interaction databases

BioGridi123230. 12 interactors.
IntActiQ9BRR0. 6 interactors.
STRINGi9606.ENSP00000252211.

Structurei

3D structure databases

ProteinModelPortaliQ9BRR0.
SMRiQ9BRR0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini46 – 128SCAN boxPROSITE-ProRule annotationAdd BLAST83
Domaini214 – 274KRABAdd BLAST61

Sequence similaritiesi

Contains 7 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 KRAB domain.Curated
Contains 1 SCAN box domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri314 – 336C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri342 – 364C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri370 – 392C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri398 – 420C2H2-type 4PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri426 – 448C2H2-type 5PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri480 – 502C2H2-type 6PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri508 – 530C2H2-type 7PROSITE-ProRule annotationAdd BLAST23

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00760000118881.
HOGENOMiHOG000234619.
HOVERGENiHBG018163.
InParanoidiQ9BRR0.
KOiK09229.
OMAiQGEAWKS.
OrthoDBiEOG091G040B.
PhylomeDBiQ9BRR0.
TreeFamiTF350830.

Family and domain databases

CDDicd07765. KRAB_A-box. 1 hit.
Gene3Di3.30.160.60. 7 hits.
InterProiIPR001909. KRAB.
IPR008916. Retrov_capsid_C.
IPR003309. SCAN_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF01352. KRAB. 1 hit.
PF02023. SCAN. 1 hit.
PF00096. zf-C2H2. 2 hits.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00431. SCAN. 1 hit.
SM00355. ZnF_C2H2. 7 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
SSF47353. SSF47353. 1 hit.
PROSITEiPS50804. SCAN_BOX. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 7 hits.
PS50157. ZINC_FINGER_C2H2_2. 7 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BRR0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MARELSESTA LDAQSTEDQM ELLVIKVEEE EAGFPSSPDL GSEGSRERFR
60 70 80 90 100
GFRYPEAAGP REALSRLREL CRQWLQPEMH SKEQILELLV LEQFLTILPG
110 120 130 140 150
NLQSWVREQH PESGEEVVVL LEYLERQLDE PAPQVSGVDQ GQELLCCKMA
160 170 180 190 200
LLTPAPGSQS SQFQLMKALL KHESVGSQPL QDRVLQVPVL AHGGCCREDK
210 220 230 240 250
VVASRLTPES QGLLKVEDVA LTLTPEWTQQ DSSQGNLCRD EKQENHGSLV
260 270 280 290 300
SLGDEKQTKS RDLPPAEELP EKEHGKISCH LREDIAQIPT CAEAGEQEGR
310 320 330 340 350
LQRKQKNATG GRRHICHECG KSFAQSSGLS KHRRIHTGEK PYECEECGKA
360 370 380 390 400
FIGSSALVIH QRVHTGEKPY ECEECGKAFS HSSDLIKHQR THTGEKPYEC
410 420 430 440 450
DDCGKTFSQS CSLLEHHRIH TGEKPYQCSM CGKAFRRSSH LLRHQRIHTG
460 470 480 490 500
DKNVQEPEQG EAWKSRMESQ LENVETPMSY KCNECERSFT QNTGLIEHQK
510 520 530
IHTGEKPYQC NACGKGFTRI SYLVQHQRSH VGKNILSQ
Length:538
Mass (Da):60,641
Last modified:October 17, 2006 - v2
Checksum:i0D8F706F1B2F888F
GO
Isoform 2 (identifier: Q9BRR0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-148: Missing.

Note: No experimental confirmation available.
Show »
Length:390
Mass (Da):43,793
Checksum:iBE2B599E4BE6A684
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti206 – 207LT → IP in AAB16813 (PubMed:10520746).Curated2
Sequence conflicti348 – 350GKA → AKP in AAB16813 (PubMed:10520746).Curated3
Sequence conflicti437R → D in AAB16813 (PubMed:10520746).Curated1
Sequence conflicti459 – 479QGEAW…ETPMS → TGRGWKVGWKASWKMLKLPC P in AAB16813 (PubMed:10520746).CuratedAdd BLAST21

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0242083R → T.Corresponds to variant rs733743dbSNPEnsembl.1
Natural variantiVAR_02831333G → V.Corresponds to variant rs3857554dbSNPEnsembl.1
Natural variantiVAR_02831434F → L.Corresponds to variant rs3857555dbSNPEnsembl.1
Natural variantiVAR_028315189V → M.1 PublicationCorresponds to variant rs17856167dbSNPEnsembl.1
Natural variantiVAR_059950200K → A Requires 2 nucleotide substitutions. 3 PublicationsCorresponds to variant rs13201752dbSNPEnsembl.1
Natural variantiVAR_028316200K → E.1 PublicationCorresponds to variant rs45505399dbSNPEnsembl.1
Natural variantiVAR_028317200K → T.Corresponds to variant rs13201753dbSNPEnsembl.1
Natural variantiVAR_028318246H → Q.Corresponds to variant rs213227dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0459081 – 148Missing in isoform 2. 1 PublicationAdd BLAST148

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT007427 mRNA. Translation: AAP36095.1.
AK122790 mRNA. Translation: BAG53732.1.
AK313532 mRNA. Translation: BAG36309.1.
AL358785, AL021997 Genomic DNA. Translation: CAH71668.1.
AL021997, AL358785 Genomic DNA. Translation: CAI23088.1.
CH471081 Genomic DNA. Translation: EAX03157.1.
BC006118 mRNA. Translation: AAH06118.1.
U71601 mRNA. Translation: AAB16813.1.
CCDSiCCDS4650.1. [Q9BRR0-1]
CCDS56408.1. [Q9BRR0-2]
RefSeqiNP_001229823.1. NM_001242894.1. [Q9BRR0-1]
NP_001229824.1. NM_001242895.1. [Q9BRR0-2]
NP_077819.2. NM_024493.3. [Q9BRR0-1]
XP_006715278.1. XM_006715215.2. [Q9BRR0-1]
XP_006715281.1. XM_006715218.3. [Q9BRR0-2]
UniGeneiHs.380930.
Hs.485004.

Genome annotation databases

EnsembliENST00000252211; ENSP00000252211; ENSG00000189298. [Q9BRR0-1]
ENST00000341464; ENSP00000341883; ENSG00000189298. [Q9BRR0-2]
ENST00000377255; ENSP00000366465; ENSG00000189298. [Q9BRR0-1]
GeneIDi80317.
KEGGihsa:80317.
UCSCiuc003nle.4. human. [Q9BRR0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT007427 mRNA. Translation: AAP36095.1.
AK122790 mRNA. Translation: BAG53732.1.
AK313532 mRNA. Translation: BAG36309.1.
AL358785, AL021997 Genomic DNA. Translation: CAH71668.1.
AL021997, AL358785 Genomic DNA. Translation: CAI23088.1.
CH471081 Genomic DNA. Translation: EAX03157.1.
BC006118 mRNA. Translation: AAH06118.1.
U71601 mRNA. Translation: AAB16813.1.
CCDSiCCDS4650.1. [Q9BRR0-1]
CCDS56408.1. [Q9BRR0-2]
RefSeqiNP_001229823.1. NM_001242894.1. [Q9BRR0-1]
NP_001229824.1. NM_001242895.1. [Q9BRR0-2]
NP_077819.2. NM_024493.3. [Q9BRR0-1]
XP_006715278.1. XM_006715215.2. [Q9BRR0-1]
XP_006715281.1. XM_006715218.3. [Q9BRR0-2]
UniGeneiHs.380930.
Hs.485004.

3D structure databases

ProteinModelPortaliQ9BRR0.
SMRiQ9BRR0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123230. 12 interactors.
IntActiQ9BRR0. 6 interactors.
STRINGi9606.ENSP00000252211.

PTM databases

iPTMnetiQ9BRR0.
PhosphoSitePlusiQ9BRR0.

Polymorphism and mutation databases

BioMutaiZKSCAN3.
DMDMi116242859.

Proteomic databases

EPDiQ9BRR0.
MaxQBiQ9BRR0.
PaxDbiQ9BRR0.
PeptideAtlasiQ9BRR0.
PRIDEiQ9BRR0.

Protocols and materials databases

DNASUi80317.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000252211; ENSP00000252211; ENSG00000189298. [Q9BRR0-1]
ENST00000341464; ENSP00000341883; ENSG00000189298. [Q9BRR0-2]
ENST00000377255; ENSP00000366465; ENSG00000189298. [Q9BRR0-1]
GeneIDi80317.
KEGGihsa:80317.
UCSCiuc003nle.4. human. [Q9BRR0-1]

Organism-specific databases

CTDi80317.
DisGeNETi80317.
GeneCardsiZKSCAN3.
HGNCiHGNC:13853. ZKSCAN3.
HPAiHPA009637.
MIMi612791. gene.
neXtProtiNX_Q9BRR0.
OpenTargetsiENSG00000189298.
PharmGKBiPA37821.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00760000118881.
HOGENOMiHOG000234619.
HOVERGENiHBG018163.
InParanoidiQ9BRR0.
KOiK09229.
OMAiQGEAWKS.
OrthoDBiEOG091G040B.
PhylomeDBiQ9BRR0.
TreeFamiTF350830.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000137184-MONOMER.
ReactomeiR-HSA-212436. Generic Transcription Pathway.

Miscellaneous databases

ChiTaRSiZKSCAN3. human.
GenomeRNAii80317.
PROiQ9BRR0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000189298.
CleanExiHS_ZKSCAN3.
GenevisibleiQ9BRR0. HS.

Family and domain databases

CDDicd07765. KRAB_A-box. 1 hit.
Gene3Di3.30.160.60. 7 hits.
InterProiIPR001909. KRAB.
IPR008916. Retrov_capsid_C.
IPR003309. SCAN_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF01352. KRAB. 1 hit.
PF02023. SCAN. 1 hit.
PF00096. zf-C2H2. 2 hits.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
SM00431. SCAN. 1 hit.
SM00355. ZnF_C2H2. 7 hits.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
SSF47353. SSF47353. 1 hit.
PROSITEiPS50804. SCAN_BOX. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 7 hits.
PS50157. ZINC_FINGER_C2H2_2. 7 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiZKSC3_HUMAN
AccessioniPrimary (citable) accession number: Q9BRR0
Secondary accession number(s): B2R8W2
, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9H4T3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: October 17, 2006
Last modified: November 30, 2016
This is version 143 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  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.