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Protein

Zinc finger protein with KRAB and SCAN domains 3

Gene

ZKSCAN3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 migration 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
  • DNA binding transcription factor activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • RNA polymerase II proximal promoter sequence-specific DNA binding Source: NTNU_SB
  • RNA polymerase II transcription factor activity, sequence-specific DNA binding Source: NTNU_SB
  • sequence-specific DNA binding Source: UniProtKB
  • transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding Source: NTNU_SB

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 by RNA polymerase II Source: NTNU_SB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processAutophagy, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000189298.13
HGNCiHGNC:13853 ZKSCAN3
MIMi612791 gene
neXtProtiNX_Q9BRR0

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

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
Cross-linki171Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei207PhosphothreonineCombined sources1
Modified residuei449PhosphothreonineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9BRR0
MaxQBiQ9BRR0
PaxDbiQ9BRR0
PeptideAtlasiQ9BRR0
PRIDEiQ9BRR0
ProteomicsDBi78810

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
HPA060116

Interactioni

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi123230, 14 interactors
IntActiQ9BRR0, 10 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

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
OMAiNVETPMS
OrthoDBiEOG091G040B
PhylomeDBiQ9BRR0
TreeFamiTF350830

Family and domain databases

CDDicd07765 KRAB_A-box, 1 hit
cd07936 SCAN, 1 hit
Gene3Di1.10.4020.10, 1 hit
InterProiView protein in InterPro
IPR001909 KRAB
IPR036051 KRAB_dom_sf
IPR003309 SCAN_dom
IPR038269 SCAN_sf
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF01352 KRAB, 1 hit
PF02023 SCAN, 1 hit
SMARTiView protein in SMART
SM00349 KRAB, 1 hit
SM00431 SCAN, 1 hit
SM00355 ZnF_C2H2, 7 hits
SUPFAMiSSF109640 SSF109640, 1 hit
SSF57667 SSF57667, 4 hits
PROSITEiView protein in PROSITE
PS50804 SCAN_BOX, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 7 hits
PS50157 ZINC_FINGER_C2H2_2, 7 hits

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 dbSNP:rs733743Ensembl.1
Natural variantiVAR_02831333G → V. Corresponds to variant dbSNP:rs3857554Ensembl.1
Natural variantiVAR_02831434F → L. Corresponds to variant dbSNP:rs3857555Ensembl.1
Natural variantiVAR_028315189V → M1 PublicationCorresponds to variant dbSNP:rs17856167Ensembl.1
Natural variantiVAR_059950200K → A Requires 2 nucleotide substitutions. 3 PublicationsCorresponds to variant dbSNP:rs371085669Ensembl.1
Natural variantiVAR_028316200K → E1 PublicationCorresponds to variant dbSNP:rs13201752Ensembl.1
Natural variantiVAR_028317200K → T. Corresponds to variant dbSNP:rs13201753Ensembl.1
Natural variantiVAR_028318246H → Q. Corresponds to variant dbSNP:rs213227Ensembl.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 Genomic DNA No translation available.
AL021997 Genomic DNA No translation available.
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

Similar proteinsi

Entry informationi

Entry nameiZKSC3_HUMAN
AccessioniPrimary (citable) accession number: Q9BRR0
Secondary accession number(s): B2R8W2
, B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9H4T3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: October 17, 2006
Last modified: July 18, 2018
This is version 159 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

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

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