ZN540_HUMAN
ID ZN540_HUMAN Reviewed; 660 AA.
AC Q8NDQ6; A0AVS5; A8K371; Q05D58; Q3LIC5; Q6ZN36; Q7Z3C8; Q86T31;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Zinc finger protein 540;
GN Name=ZNF540; ORFNames=Nbla10512;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 4), AND VARIANT
RP VAL-53.
RC TISSUE=Hippocampus;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Brain, and Heart;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 318-660.
RC TISSUE=Neuroblastoma;
RX PubMed=12880961; DOI=10.1016/s0304-3835(03)00085-5;
RA Ohira M., Morohashi A., Nakamura Y., Isogai E., Furuya K., Hamano S.,
RA Machida T., Aoyama M., Fukumura M., Miyazaki K., Suzuki Y., Sugano S.,
RA Hirato J., Nakagawara A.;
RT "Neuroblastoma oligo-capping cDNA project: toward the understanding of the
RT genesis and biology of neuroblastoma.";
RL Cancer Lett. 197:63-68(2003).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH MVP, AND TISSUE
RP SPECIFICITY.
RX PubMed=16815308; DOI=10.1016/j.bbrc.2006.06.076;
RA Xiang Z., Yuan W., Luo N., Wang Y., Tan K., Deng Y., Zhou X., Zhu C.,
RA Li Y., Liu M., Wu X., Li Y.;
RT "A novel human zinc finger protein ZNF540 interacts with MVP and inhibits
RT transcriptional activities of the ERK signal pathway.";
RL Biochem. Biophys. Res. Commun. 347:288-296(2006).
RN [6]
RP VARIANT [LARGE SCALE ANALYSIS] ILE-275.
RX PubMed=16959974; DOI=10.1126/science.1133427;
RA Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D.,
RA Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P.,
RA Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V.,
RA Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H.,
RA Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W.,
RA Velculescu V.E.;
RT "The consensus coding sequences of human breast and colorectal cancers.";
RL Science 314:268-274(2006).
RN [7]
RP VARIANT ARG-340.
RX PubMed=23033978; DOI=10.1056/nejmoa1206524;
RA de Ligt J., Willemsen M.H., van Bon B.W., Kleefstra T., Yntema H.G.,
RA Kroes T., Vulto-van Silfhout A.T., Koolen D.A., de Vries P., Gilissen C.,
RA del Rosario M., Hoischen A., Scheffer H., de Vries B.B., Brunner H.G.,
RA Veltman J.A., Vissers L.E.;
RT "Diagnostic exome sequencing in persons with severe intellectual
RT disability.";
RL N. Engl. J. Med. 367:1921-1929(2012).
CC -!- FUNCTION: May act as a transcriptional repressor.
CC {ECO:0000269|PubMed:16815308}.
CC -!- SUBUNIT: May interact with MVP.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16815308}. Cytoplasm
CC {ECO:0000269|PubMed:16815308}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q8NDQ6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8NDQ6-2; Sequence=VSP_016037;
CC Name=4;
CC IsoId=Q8NDQ6-4; Sequence=VSP_016036;
CC -!- TISSUE SPECIFICITY: Expressed in several fetal tissues, including gut,
CC heart, brain, muscle, lung, testis and liver.
CC {ECO:0000269|PubMed:16815308}.
CC -!- SIMILARITY: Belongs to the krueppel C2H2-type zinc-finger protein
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAH17940.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};
CC Sequence=CAD97942.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AK131388; BAD18539.1; -; mRNA.
DR EMBL; AK290486; BAF83175.1; -; mRNA.
DR EMBL; AL832100; CAD91161.1; -; mRNA.
DR EMBL; AL832315; CAD38611.1; -; mRNA.
DR EMBL; BX537980; CAD97942.1; ALT_FRAME; mRNA.
DR EMBL; BC017940; AAH17940.1; ALT_SEQ; mRNA.
DR EMBL; BC126478; AAI26479.1; -; mRNA.
DR EMBL; BC126480; AAI26481.1; -; mRNA.
DR EMBL; AB074186; BAE45743.1; -; mRNA.
DR CCDS; CCDS12506.1; -. [Q8NDQ6-1]
DR CCDS; CCDS54258.1; -. [Q8NDQ6-2]
DR RefSeq; NP_001165696.1; NM_001172225.2. [Q8NDQ6-1]
DR RefSeq; NP_001165697.1; NM_001172226.2. [Q8NDQ6-2]
DR RefSeq; NP_689819.1; NM_152606.4. [Q8NDQ6-1]
DR AlphaFoldDB; Q8NDQ6; -.
DR SMR; Q8NDQ6; -.
DR IntAct; Q8NDQ6; 1.
DR STRING; 9606.ENSP00000466274; -.
DR iPTMnet; Q8NDQ6; -.
DR PhosphoSitePlus; Q8NDQ6; -.
DR BioMuta; ZNF540; -.
DR DMDM; 74762556; -.
DR jPOST; Q8NDQ6; -.
DR MassIVE; Q8NDQ6; -.
DR PaxDb; Q8NDQ6; -.
DR PeptideAtlas; Q8NDQ6; -.
DR PRIDE; Q8NDQ6; -.
DR Antibodypedia; 836; 92 antibodies from 16 providers.
DR DNASU; 163255; -.
DR Ensembl; ENST00000316433.9; ENSP00000324598.3; ENSG00000171817.17. [Q8NDQ6-1]
DR Ensembl; ENST00000343599.5; ENSP00000343768.5; ENSG00000171817.17. [Q8NDQ6-1]
DR Ensembl; ENST00000589117.5; ENSP00000467118.1; ENSG00000171817.17. [Q8NDQ6-2]
DR Ensembl; ENST00000592533.5; ENSP00000466274.1; ENSG00000171817.17. [Q8NDQ6-1]
DR GeneID; 163255; -.
DR KEGG; hsa:163255; -.
DR MANE-Select; ENST00000316433.9; ENSP00000324598.3; NM_001172225.3; NP_001165696.1.
DR UCSC; uc002ogq.5; human. [Q8NDQ6-1]
DR CTD; 163255; -.
DR DisGeNET; 163255; -.
DR GeneCards; ZNF540; -.
DR HGNC; HGNC:25331; ZNF540.
DR HPA; ENSG00000171817; Tissue enhanced (retina).
DR MIM; 613903; gene.
DR neXtProt; NX_Q8NDQ6; -.
DR OpenTargets; ENSG00000171817; -.
DR PharmGKB; PA134980975; -.
DR VEuPathDB; HostDB:ENSG00000171817; -.
DR eggNOG; KOG1721; Eukaryota.
DR GeneTree; ENSGT00940000164340; -.
DR HOGENOM; CLU_002678_44_5_1; -.
DR InParanoid; Q8NDQ6; -.
DR OMA; VFYFKEH; -.
DR OrthoDB; 1318335at2759; -.
DR PhylomeDB; Q8NDQ6; -.
DR PathwayCommons; Q8NDQ6; -.
DR Reactome; R-HSA-212436; Generic Transcription Pathway.
DR BioGRID-ORCS; 163255; 16 hits in 1094 CRISPR screens.
DR ChiTaRS; ZNF540; human.
DR GenomeRNAi; 163255; -.
DR Pharos; Q8NDQ6; Tbio.
DR PRO; PR:Q8NDQ6; -.
DR Proteomes; UP000005640; Chromosome 19.
DR RNAct; Q8NDQ6; protein.
DR Bgee; ENSG00000171817; Expressed in middle temporal gyrus and 130 other tissues.
DR ExpressionAtlas; Q8NDQ6; baseline and differential.
DR Genevisible; Q8NDQ6; HS.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000900; F:mRNA regulatory element binding translation repressor activity; IMP:UniProtKB.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:UniProtKB.
DR GO; GO:0017148; P:negative regulation of translation; IMP:UniProtKB.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR CDD; cd07765; KRAB_A-box; 1.
DR InterPro; IPR001909; KRAB.
DR InterPro; IPR036051; KRAB_dom_sf.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR Pfam; PF01352; KRAB; 1.
DR Pfam; PF00096; zf-C2H2; 14.
DR SMART; SM00349; KRAB; 1.
DR SMART; SM00355; ZnF_C2H2; 17.
DR SUPFAM; SSF109640; SSF109640; 1.
DR SUPFAM; SSF57667; SSF57667; 9.
DR PROSITE; PS50805; KRAB; 1.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 17.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 17.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; DNA-binding; Isopeptide bond;
KW Metal-binding; Nucleus; Reference proteome; Repeat; Repressor;
KW Transcription; Transcription regulation; Ubl conjugation; Zinc;
KW Zinc-finger.
FT CHAIN 1..660
FT /note="Zinc finger protein 540"
FT /id="PRO_0000047641"
FT DOMAIN 6..77
FT /note="KRAB"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00119"
FT ZN_FING 187..209
FT /note="C2H2-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 215..237
FT /note="C2H2-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 243..265
FT /note="C2H2-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 271..293
FT /note="C2H2-type 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 299..321
FT /note="C2H2-type 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 327..349
FT /note="C2H2-type 6"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 355..377
FT /note="C2H2-type 7"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 383..405
FT /note="C2H2-type 8"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 411..433
FT /note="C2H2-type 9"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 439..461
FT /note="C2H2-type 10"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 467..489
FT /note="C2H2-type 11"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 495..517
FT /note="C2H2-type 12"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 523..545
FT /note="C2H2-type 13"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 551..573
FT /note="C2H2-type 14"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 579..601
FT /note="C2H2-type 15"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 607..629
FT /note="C2H2-type 16"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 635..657
FT /note="C2H2-type 17"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT CROSSLNK 109
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q9Y2G7"
FT VAR_SEQ 1..77
FT /note="MAHALVTFRDVAIDFSQKEWECLDTTQRKLYRDVMLENYNNLVSLGYSGSKP
FT DVITLLEQGKEPCVVARDVTGRQCP -> MLPNFKLYNFIEIFFKPLTPSKNRFHFVSY
FT FENVNFMLCWLQENNFCLLLCFLS (in isoform 4)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_016036"
FT VAR_SEQ 46..77
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:17974005"
FT /id="VSP_016037"
FT VARIANT 53
FT /note="D -> V (in dbSNP:rs1975937)"
FT /evidence="ECO:0000269|PubMed:14702039"
FT /id="VAR_033575"
FT VARIANT 275
FT /note="K -> I (in a colorectal cancer sample; somatic
FT mutation)"
FT /evidence="ECO:0000269|PubMed:16959974"
FT /id="VAR_035586"
FT VARIANT 340
FT /note="G -> R (in dbSNP:rs571893947)"
FT /evidence="ECO:0000269|PubMed:23033978"
FT /id="VAR_069366"
FT CONFLICT 127
FT /note="E -> G (in Ref. 2; CAD97942)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 660 AA; 77094 MW; 9115ABB3B056D9B3 CRC64;
MAHALVTFRD VAIDFSQKEW ECLDTTQRKL YRDVMLENYN NLVSLGYSGS KPDVITLLEQ
GKEPCVVARD VTGRQCPGLL SRHKTKKLSS EKDIHEISLS KESIIEKSKT LRLKGSIFRN
EWQNKSEFEG QQGLKERSIS QKKIVSKKMS TDRKRPSFTL NQRIHNSEKS CDSHLVQHGK
IDSDVKHDCK ECGSTFNNVY QLTLHQKIHT GEKSCKCEKC GKVFSHSYQL TLHQRFHTGE
KPYECQECGK TFTLYPQLNR HQKIHTGKKP YMCKKCDKGF FSRLELTQHK RIHTGKKSYE
CKECGKVFQL IFYFKEHERI HTGKKPYECK ECGKAFSVCG QLTRHQKIHT GVKPYECKEC
GKTFRLSFYL TEHRRTHAGK KPYECKECGK SFNVRGQLNR HKTIHTGIKP FACKVCEKAF
SYSGDLRVHS RIHTGEKPYE CKECGKAFML RSVLTEHQRL HTGVKPYECK ECGKTFRVRS
QISLHKKIHT DVKPYKCVRC GKTFRFGFYL TEHQRIHTGE KPYKCKECGK AFIRRGNLKE
HLKIHSGLKP YDCKECGKSF SRRGQFTEHQ KIHTGVKPYK CKECGKAFSR SVDLRIHQRI
HTGEKPYECK QCGKAFRLNS HLTEHQRIHT GEKPYECKVC RKAFRQYSHL YQHQKTHNVI
