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Q9BRR0 (ZKSC3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:ZKSCAN3
Synonyms:ZFP47, ZNF306, ZNF309, ZSCAN13
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length538 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.8 Ref.9 Ref.10 Ref.11

Subcellular location

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. Ref.8 Ref.11

Induction

Overexpressed in various tumors, such as multiple myeloma, colorectal and prostate cancers (at protein level). Ref.8 Ref.9 Ref.10

Sequence similarities

Belongs to the krueppel C2H2-type zinc-finger protein family.

Contains 7 C2H2-type zinc fingers.

Contains 1 KRAB domain.

Contains 1 SCAN box domain.

Ontologies

Keywords
   Biological processAutophagy
Transcription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainRepeat
Zinc-finger
   LigandDNA-binding
Metal-binding
Zinc
   Molecular functionRepressor
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processautophagy

Inferred from electronic annotation. Source: UniProtKB-KW

lysosome organization

Inferred from mutant phenotype Ref.11. Source: UniProtKB

negative regulation of autophagy

Inferred from mutant phenotype Ref.11. Source: UniProtKB

negative regulation of cellular senescence

Inferred from mutant phenotype Ref.11. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from direct assay Ref.11. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from direct assay Ref.8. Source: UniProtKB

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from direct assay Ref.11. Source: UniProtKB

nucleus

Inferred from direct assay Ref.8Ref.11. Source: UniProtKB

   Molecular_functionDNA binding

Inferred from direct assay Ref.8. Source: UniProtKB

chromatin binding

Inferred from direct assay Ref.8. Source: UniProtKB

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

sequence-specific DNA binding

Inferred from direct assay Ref.11. Source: UniProtKB

sequence-specific DNA binding transcription factor activity

Inferred from direct assay Ref.11. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9BRR0-1)

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.
Isoform 2 (identifier: Q9BRR0-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-148: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 538538Zinc finger protein with KRAB and SCAN domains 3
PRO_0000047524

Regions

Domain46 – 12883SCAN box
Domain214 – 27461KRAB
Zinc finger314 – 33623C2H2-type 1
Zinc finger342 – 36423C2H2-type 2
Zinc finger370 – 39223C2H2-type 3
Zinc finger398 – 42023C2H2-type 4
Zinc finger426 – 44823C2H2-type 5
Zinc finger480 – 50223C2H2-type 6
Zinc finger508 – 53023C2H2-type 7

Natural variations

Alternative sequence1 – 148148Missing in isoform 2.
VSP_045908
Natural variant31R → T.
Corresponds to variant rs733743 [ dbSNP | Ensembl ].
VAR_024208
Natural variant331G → V.
Corresponds to variant rs3857554 [ dbSNP | Ensembl ].
VAR_028313
Natural variant341F → L.
Corresponds to variant rs3857555 [ dbSNP | Ensembl ].
VAR_028314
Natural variant1891V → M. Ref.1
Corresponds to variant rs17856167 [ dbSNP | Ensembl ].
VAR_028315
Natural variant2001K → A Requires 2 nucleotide substitutions. Ref.1 Ref.2 Ref.5
Corresponds to variant rs13201752 [ dbSNP | Ensembl ].
VAR_059950
Natural variant2001K → E. Ref.2
Corresponds to variant rs45505399 [ dbSNP | Ensembl ].
VAR_028316
Natural variant2001K → T.
Corresponds to variant rs13201753 [ dbSNP | Ensembl ].
VAR_028317
Natural variant2461H → Q.
Corresponds to variant rs213227 [ dbSNP | Ensembl ].
VAR_028318

Experimental info

Sequence conflict206 – 2072LT → IP in AAB16813. Ref.6
Sequence conflict348 – 3503GKA → AKP in AAB16813. Ref.6
Sequence conflict4371R → D in AAB16813. Ref.6
Sequence conflict459 – 47921QGEAW…ETPMS → TGRGWKVGWKASWKMLKLPC P in AAB16813. Ref.6

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 17, 2006. Version 2.
Checksum: 0D8F706F1B2F888F

FASTA53860,641
        10         20         30         40         50         60 
MARELSESTA LDAQSTEDQM ELLVIKVEEE EAGFPSSPDL GSEGSRERFR GFRYPEAAGP 

        70         80         90        100        110        120 
REALSRLREL CRQWLQPEMH SKEQILELLV LEQFLTILPG NLQSWVREQH PESGEEVVVL 

       130        140        150        160        170        180 
LEYLERQLDE PAPQVSGVDQ GQELLCCKMA LLTPAPGSQS SQFQLMKALL KHESVGSQPL 

       190        200        210        220        230        240 
QDRVLQVPVL AHGGCCREDK VVASRLTPES QGLLKVEDVA LTLTPEWTQQ DSSQGNLCRD 

       250        260        270        280        290        300 
EKQENHGSLV SLGDEKQTKS RDLPPAEELP EKEHGKISCH LREDIAQIPT CAEAGEQEGR 

       310        320        330        340        350        360 
LQRKQKNATG GRRHICHECG KSFAQSSGLS KHRRIHTGEK PYECEECGKA FIGSSALVIH 

       370        380        390        400        410        420 
QRVHTGEKPY ECEECGKAFS HSSDLIKHQR THTGEKPYEC DDCGKTFSQS CSLLEHHRIH 

       430        440        450        460        470        480 
TGEKPYQCSM CGKAFRRSSH LLRHQRIHTG DKNVQEPEQG EAWKSRMESQ LENVETPMSY 

       490        500        510        520        530 
KCNECERSFT QNTGLIEHQK IHTGEKPYQC NACGKGFTRI SYLVQHQRSH VGKNILSQ 

« Hide

Isoform 2 [UniParc].

Checksum: BE2B599E4BE6A684
Show »

FASTA39043,793

References

« Hide 'large scale' references
[1]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANTS MET-189 AND ALA-200.
[2]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANTS ALA-200 AND GLU-200.
Tissue: Testis.
[3]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT ALA-200.
Tissue: Placenta.
[6]"Computer sequence analysis of human highly conserved zinc finger modules."
Petroni D., Bartolini E., Chiaramonte R., Ottolenghi S., Comi P.
DNA Seq. 9:163-169(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 206-538 (ISOFORM 1/2).
[7]"The previously undescribed ZKSCAN3 (ZNF306) is a novel 'driver' of colorectal cancer progression."
Yang L., Hamilton S.R., Sood A., Kuwai T., Ellis L., Sanguino A., Lopez-Berestein G., Boyd D.D.
Cancer Res. 68:4321-4330(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
[8]"Unbiased screening for transcriptional targets of ZKSCAN3 identifies integrin beta 4 and vascular endothelial growth factor as downstream targets."
Yang L., Zhang L., Wu Q., Boyd D.D.
J. Biol. Chem. 283:35295-35304(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, DNA-BINDING, INDUCTION.
[9]"Evidence of a role for the novel zinc-finger transcription factor ZKSCAN3 in modulating Cyclin D2 expression in multiple myeloma."
Yang L., Wang H., Kornblau S.M., Graber D.A., Zhang N., Matthews J.A., Wang M., Weber D.M., Thomas S.K., Shah J.J., Zhang L., Lu G., Zhao M., Muddasani R., Yoo S.Y., Baggerly K.A., Orlowski R.Z.
Oncogene 30:1329-1340(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INDUCTION.
[10]"The zinc finger transcription factor ZKSCAN3 promotes prostate cancer cell migration."
Zhang X., Jing Y., Qin Y., Hunsucker S., Meng H., Sui J., Jiang Y., Gao L., An G., Yang N., Orlowski R.Z., Yang L.
Int. J. Biochem. Cell Biol. 44:1166-1173(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INDUCTION.
[11]"ZKSCAN3 is a master transcriptional repressor of autophagy."
Chauhan S., Goodwin J.G., Chauhan S., Manyam G., Wang J., Kamat A.M., Boyd D.D.
Mol. Cell 50:16-28(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DNA-BINDING, SUBCELLULAR LOCATION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS4650.1. [Q9BRR0-1]
CCDS56408.1. [Q9BRR0-2]
RefSeqNP_001229823.1. NM_001242894.1. [Q9BRR0-1]
NP_001229824.1. NM_001242895.1. [Q9BRR0-2]
NP_077819.2. NM_024493.3. [Q9BRR0-1]
XP_005249481.1. XM_005249424.1. [Q9BRR0-2]
XP_006715278.1. XM_006715215.1. [Q9BRR0-1]
XP_006715281.1. XM_006715218.1. [Q9BRR0-2]
XP_006715282.1. XM_006715219.1. [Q9BRR0-2]
UniGeneHs.380930.
Hs.485004.

3D structure databases

ProteinModelPortalQ9BRR0.
SMRQ9BRR0. Positions 37-129, 289-533.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9BRR0. 1 interaction.
STRING9606.ENSP00000252211.

PTM databases

PhosphoSiteQ9BRR0.

Polymorphism databases

DMDM116242859.

Proteomic databases

MaxQBQ9BRR0.
PaxDbQ9BRR0.
PRIDEQ9BRR0.

Protocols and materials databases

DNASU80317.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000252211; ENSP00000252211; ENSG00000189298. [Q9BRR0-1]
ENST00000341464; ENSP00000341883; ENSG00000189298. [Q9BRR0-2]
ENST00000377255; ENSP00000366465; ENSG00000189298. [Q9BRR0-1]
GeneID80317.
KEGGhsa:80317.
UCSCuc003nle.4. human. [Q9BRR0-1]

Organism-specific databases

CTD80317.
GeneCardsGC06P028317.
HGNCHGNC:13853. ZKSCAN3.
HPAHPA009637.
MIM612791. gene.
neXtProtNX_Q9BRR0.
PharmGKBPA37821.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5048.
HOGENOMHOG000234619.
HOVERGENHBG018163.
InParanoidQ9BRR0.
KOK09229.
OMAQGEAWKS.
OrthoDBEOG79GT5W.
PhylomeDBQ9BRR0.
TreeFamTF350830.

Enzyme and pathway databases

ReactomeREACT_71. Gene Expression.

Gene expression databases

BgeeQ9BRR0.
CleanExHS_ZKSCAN3.
GenevestigatorQ9BRR0.

Family and domain databases

Gene3D3.30.160.60. 7 hits.
InterProIPR001909. Krueppel-associated_box.
IPR008916. Retrov_capsid_C.
IPR003309. Tscrpt_reg_SCAN.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamPF01352. KRAB. 1 hit.
PF02023. SCAN. 1 hit.
[Graphical view]
SMARTSM00349. KRAB. 1 hit.
SM00431. SCAN. 1 hit.
SM00355. ZnF_C2H2. 7 hits.
[Graphical view]
SUPFAMSSF109640. SSF109640. 1 hit.
SSF47353. SSF47353. 1 hit.
PROSITEPS50804. SCAN_BOX. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 7 hits.
PS50157. ZINC_FINGER_C2H2_2. 7 hits.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi80317.
NextBio70823.
PROQ9BRR0.
SOURCESearch...

Entry information

Entry nameZKSC3_HUMAN
AccessionPrimary (citable) accession number: Q9BRR0
Secondary accession number(s): B2R8W2 expand/collapse secondary AC list , B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9H4T3
Entry history
Integrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: October 17, 2006
Last modified: July 9, 2014
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM