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   27-MAR-2024, entry version 170.
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; 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   BioGRID; 127861; 2.
DR   IntAct; Q8NDQ6; 1.
DR   STRING; 9606.ENSP00000324598; -.
DR   iPTMnet; Q8NDQ6; -.
DR   PhosphoSitePlus; Q8NDQ6; -.
DR   BioMuta; ZNF540; -.
DR   DMDM; 74762556; -.
DR   jPOST; Q8NDQ6; -.
DR   MassIVE; Q8NDQ6; -.
DR   PaxDb; 9606-ENSP00000466274; -.
DR   PeptideAtlas; Q8NDQ6; -.
DR   Antibodypedia; 836; 98 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   AGR; HGNC:25331; -.
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; SWRGQFT; -.
DR   OrthoDB; 3776076at2759; -.
DR   PhylomeDB; Q8NDQ6; -.
DR   PathwayCommons; Q8NDQ6; -.
DR   Reactome; R-HSA-212436; Generic Transcription Pathway.
DR   BioGRID-ORCS; 163255; 18 hits in 1170 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 132 other cell types or tissues.
DR   ExpressionAtlas; Q8NDQ6; baseline and differential.
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 DNA-templated transcription; 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   Gene3D; 6.10.140.140; -; 1.
DR   Gene3D; 3.30.160.60; Classic Zinc Finger; 17.
DR   InterPro; IPR001909; KRAB.
DR   InterPro; IPR036051; KRAB_dom_sf.
DR   InterPro; IPR036236; Znf_C2H2_sf.
DR   InterPro; IPR013087; Znf_C2H2_type.
DR   PANTHER; PTHR24390; ZINC FINGER PROTEIN; 1.
DR   PANTHER; PTHR24390:SF245; ZINC FINGER PROTEIN 383-RELATED; 1.
DR   Pfam; PF01352; KRAB; 1.
DR   Pfam; PF00096; zf-C2H2; 16.
DR   Pfam; PF13912; zf-C2H2_6; 1.
DR   SMART; SM00349; KRAB; 1.
DR   SMART; SM00355; ZnF_C2H2; 17.
DR   SUPFAM; SSF57667; beta-beta-alpha zinc fingers; 9.
DR   SUPFAM; SSF109640; KRAB domain (Kruppel-associated box); 1.
DR   PROSITE; PS50805; KRAB; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 17.
DR   PROSITE; PS50157; ZINC_FINGER_C2H2_2; 17.
DR   Genevisible; Q8NDQ6; HS.
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
//