Q9BRR0 (ZKSC3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	ZKSCAN3
Synonyms:	ZFP47, ZNF306, ZNF309, ZSCAN13

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	538 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Autophagy Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Repeat Zinc-finger
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	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-dependent Inferred from direct assay Ref.11. Source: UniProtKB positive regulation of transcription, DNA-dependent Inferred from direct assay Ref.8. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW viral reproduction Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from direct assay Ref.11. Source: UniProtKB nucleus Inferred from direct assay Ref.8Ref.11. Source: UniProtKB
Molecular_function	chromatin binding Inferred from direct assay Ref.8. Source: UniProtKB sequence-specific DNA binding Inferred from physical interaction Ref.11. Source: UniProtKB sequence-specific DNA binding transcription factor activity Inferred from direct assay Ref.11. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 538	538	Zinc finger protein with KRAB and SCAN domains 3		PRO_0000047524
Regions
	Domain	46 – 128	83	SCAN box
	Domain	214 – 274	61	KRAB
	Zinc finger	314 – 336	23	C2H2-type 1
	Zinc finger	342 – 364	23	C2H2-type 2
	Zinc finger	370 – 392	23	C2H2-type 3
	Zinc finger	398 – 420	23	C2H2-type 4
	Zinc finger	426 – 448	23	C2H2-type 5
	Zinc finger	480 – 502	23	C2H2-type 6
	Zinc finger	508 – 530	23	C2H2-type 7
Natural variations
	Alternative sequence	1 – 148	148	Missing in isoform 2.		VSP_045908
	Natural variant	3	1	R → T. Corresponds to variant rs733743 [ dbSNP | Ensembl ].		VAR_024208
	Natural variant	33	1	G → V. Corresponds to variant rs3857554 [ dbSNP | Ensembl ].		VAR_028313
	Natural variant	34	1	F → L. Corresponds to variant rs3857555 [ dbSNP | Ensembl ].		VAR_028314
	Natural variant	189	1	V → M. Ref.1 Corresponds to variant rs17856167 [ dbSNP | Ensembl ].		VAR_028315
	Natural variant	200	1	K → A Requires 2 nucleotide substitutions. Ref.1 Ref.2 Ref.5 Corresponds to variant rs13201752 [ dbSNP | Ensembl ].		VAR_059950
	Natural variant	200	1	K → E. Ref.2 Corresponds to variant rs45505399 [ dbSNP | Ensembl ].		VAR_028316
	Natural variant	200	1	K → T. Corresponds to variant rs13201753 [ dbSNP | Ensembl ].		VAR_028317
	Natural variant	246	1	H → Q. Corresponds to variant rs213227 [ dbSNP | Ensembl ].		VAR_028318
Experimental info
	Sequence conflict	206 – 207	2	LT → IP in AAB16813. Ref.6
	Sequence conflict	348 – 350	3	GKA → AKP in AAB16813. Ref.6
	Sequence conflict	437	1	R → D in AAB16813. Ref.6
	Sequence conflict	459 – 479	21	QGEAW…ETPMS → TGRGWKVGWKASWKMLKLPC P in AAB16813. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 17, 2006. Version 2. Checksum: 0D8F706F1B2F888F	FASTA	538	60,641
	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
	Isoform 2 [UniParc]. Checksum: BE2B599E4BE6A684	FASTA	390	43,793
	10 20 30 40 50 60 MALLTPAPGS QSSQFQLMKA LLKHESVGSQ PLQDRVLQVP VLAHGGCCRE DKVVASRLTP 70 80 90 100 110 120 ESQGLLKVED VALTLTPEWT QQDSSQGNLC RDEKQENHGS LVSLGDEKQT KSRDLPPAEE 130 140 150 160 170 180 LPEKEHGKIS CHLREDIAQI PTCAEAGEQE GRLQRKQKNA TGGRRHICHE CGKSFAQSSG 190 200 210 220 230 240 LSKHRRIHTG EKPYECEECG KAFIGSSALV IHQRVHTGEK PYECEECGKA FSHSSDLIKH 250 260 270 280 290 300 QRTHTGEKPY ECDDCGKTFS QSCSLLEHHR IHTGEKPYQC SMCGKAFRRS SHLLRHQRIH 310 320 330 340 350 360 TGDKNVQEPE QGEAWKSRME SQLENVETPM SYKCNECERS FTQNTGLIEH QKIHTGEKPY 370 380 390 QCNACGKGFT RISYLVQHQR SHVGKNILSQ

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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 0:0-0(2013) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DNA-BINDING, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

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.
IPI	IPI00010069.
RefSeq	NP_001229823.1. NM_001242894.1. NP_001229824.1. NM_001242895.1. NP_077819.2. NM_024493.3.
UniGene	Hs.380930. Hs.485004.
3D structure databases
ProteinModelPortal	Q9BRR0.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9BRR0. 1 interaction.
STRING	9606.ENSP00000252211.
PTM databases
PhosphoSite	Q9BRR0.
Polymorphism databases
DMDM	116242859.
Proteomic databases
PaxDb	Q9BRR0.
PRIDE	Q9BRR0.
Protocols and materials databases
DNASU	80317.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000252211; ENSP00000252211; ENSG00000189298. ENST00000341464; ENSP00000341883; ENSG00000189298. ENST00000377255; ENSP00000366465; ENSG00000189298.
GeneID	80317.
KEGG	hsa:80317.
UCSC	uc003nle.4. human.
Organism-specific databases
CTD	80317.
GeneCards	GC06P028317.
HGNC	HGNC:13853. ZKSCAN3.
HPA	HPA009637.
MIM	612791. gene.
neXtProt	NX_Q9BRR0.
PharmGKB	PA37821.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG5048.
HOGENOM	HOG000234619.
HOVERGEN	HBG018163.
InParanoid	Q9BRR0.
KO	K09229.
OMA	TRISYLV.
OrthoDB	EOG4H19VD.
PhylomeDB	Q9BRR0.
Enzyme and pathway databases
Reactome	REACT_71. Gene Expression.
Gene expression databases
ArrayExpress	Q9BRR0.
Bgee	Q9BRR0.
CleanEx	HS_ZKSCAN3.
Genevestigator	Q9BRR0.
GermOnline	ENSG00000189298. Homo sapiens.
Family and domain databases
Gene3D	3.30.160.60. 7 hits.
InterPro	IPR001909. 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]
Pfam	PF01352. KRAB. 1 hit. PF02023. SCAN. 1 hit. [Graphical view]
SMART	SM00349. KRAB. 1 hit. SM00431. SCAN. 1 hit. SM00355. ZnF_C2H2. 7 hits. [Graphical view]
SUPFAM	SSF109640. Krueppel-associated_box. 1 hit. SSF47353. Retrov_capsid_C. 1 hit.
PROSITE	PS50805. KRAB. False negative. PS50804. SCAN_BOX. 1 hit. PS00028. ZINC_FINGER_C2H2_1. 7 hits. PS50157. ZINC_FINGER_C2H2_2. 7 hits. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	80317.
NextBio	70823.
SOURCE	Search...

Entry information

Entry name

ZKSC3_HUMAN

Accession

Primary (citable) accession number: Q9BRR0
Secondary accession number(s): B2R8W2 , B3KVC0, H7BXX1, Q5VXH3, Q92972, Q9H4T3

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2002
Last sequence update:	October 17, 2006
Last modified:	May 1, 2013
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.