Q8NDQ6 (ZN540_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Zinc finger protein 540

Gene names

Name:	ZNF540
ORF Names:	Nbla10512

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	660 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	May act as a transcriptional repressor. Ref.5
Subunit structure	May interact with MVP.
Subcellular location	Nucleus. Cytoplasm Ref.5.
Tissue specificity	Expressed in several fetal tissues, including gut, heart, brain, muscle, lung, testis and liver. Ref.5
Sequence similarities	Belongs to the krueppel C2H2-type zinc-finger protein family. Contains 17 C2H2-type zinc fingers. Contains 1 KRAB domain.
Sequence caution	The sequence AAH17940.1 differs from that shown. Reason: Contaminating sequence. Potential poly-A sequence. The sequence CAD97942.1 differs from that shown. Reason: Frameshift at position 580.

Ontologies

Keywords
Biological process	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	negative regulation of transcription, DNA-dependent Inferred from direct assay Ref.5. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from direct assay Ref.5. Source: UniProtKB nucleus Inferred from direct assay Ref.5. Source: UniProtKB
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW translation repressor activity, nucleic acid binding Inferred from mutant phenotype Ref.5. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q8NDQ6-1)

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: Q8NDQ6-2)

The sequence of this isoform differs from the canonical sequence as follows:
     46-77: Missing.

Note: No experimental confirmation available.

Isoform 4 (identifier: Q8NDQ6-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-77: MAHALVTFRD...ARDVTGRQCP → MLPNFKLYNF...NFCLLLCFLS

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 660	660	Zinc finger protein 540		PRO_0000047641
Regions
	Domain	6 – 77	72	KRAB
	Zinc finger	187 – 209	23	C2H2-type 1
	Zinc finger	215 – 237	23	C2H2-type 2
	Zinc finger	243 – 265	23	C2H2-type 3
	Zinc finger	271 – 293	23	C2H2-type 4
	Zinc finger	299 – 321	23	C2H2-type 5
	Zinc finger	327 – 349	23	C2H2-type 6
	Zinc finger	355 – 377	23	C2H2-type 7
	Zinc finger	383 – 405	23	C2H2-type 8
	Zinc finger	411 – 433	23	C2H2-type 9
	Zinc finger	439 – 461	23	C2H2-type 10
	Zinc finger	467 – 489	23	C2H2-type 11
	Zinc finger	495 – 517	23	C2H2-type 12
	Zinc finger	523 – 545	23	C2H2-type 13
	Zinc finger	551 – 573	23	C2H2-type 14
	Zinc finger	579 – 601	23	C2H2-type 15
	Zinc finger	607 – 629	23	C2H2-type 16
	Zinc finger	635 – 657	23	C2H2-type 17
Natural variations
	Alternative sequence	1 – 77	77	MAHAL…GRQCP → MLPNFKLYNFIEIFFKPLTP SKNRFHFVSYFENVNFMLCW LQENNFCLLLCFLS in isoform 4.		VSP_016036
	Alternative sequence	46 – 77	32	Missing in isoform 2.		VSP_016037
	Natural variant	53	1	D → V. Ref.1 Corresponds to variant rs1975937 [ dbSNP | Ensembl ].		VAR_033575
	Natural variant	275	1	K → I in a colorectal cancer sample; somatic mutation. Ref.6		VAR_035586
Experimental info
	Sequence conflict	127	1	E → G in CAD97942. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 1, 2002. Version 1. Checksum: 9115ABB3B056D9B3	FASTA	660	77,094
	10 20 30 40 50 60 MAHALVTFRD VAIDFSQKEW ECLDTTQRKL YRDVMLENYN NLVSLGYSGS KPDVITLLEQ 70 80 90 100 110 120 GKEPCVVARD VTGRQCPGLL SRHKTKKLSS EKDIHEISLS KESIIEKSKT LRLKGSIFRN 130 140 150 160 170 180 EWQNKSEFEG QQGLKERSIS QKKIVSKKMS TDRKRPSFTL NQRIHNSEKS CDSHLVQHGK 190 200 210 220 230 240 IDSDVKHDCK ECGSTFNNVY QLTLHQKIHT GEKSCKCEKC GKVFSHSYQL TLHQRFHTGE 250 260 270 280 290 300 KPYECQECGK TFTLYPQLNR HQKIHTGKKP YMCKKCDKGF FSRLELTQHK RIHTGKKSYE 310 320 330 340 350 360 CKECGKVFQL IFYFKEHERI HTGKKPYECK ECGKAFSVCG QLTRHQKIHT GVKPYECKEC 370 380 390 400 410 420 GKTFRLSFYL TEHRRTHAGK KPYECKECGK SFNVRGQLNR HKTIHTGIKP FACKVCEKAF 430 440 450 460 470 480 SYSGDLRVHS RIHTGEKPYE CKECGKAFML RSVLTEHQRL HTGVKPYECK ECGKTFRVRS 490 500 510 520 530 540 QISLHKKIHT DVKPYKCVRC GKTFRFGFYL TEHQRIHTGE KPYKCKECGK AFIRRGNLKE 550 560 570 580 590 600 HLKIHSGLKP YDCKECGKSF SRRGQFTEHQ KIHTGVKPYK CKECGKAFSR SVDLRIHQRI 610 620 630 640 650 660 HTGEKPYECK QCGKAFRLNS HLTEHQRIHT GEKPYECKVC RKAFRQYSHL YQHQKTHNVI
	Isoform 2 [UniParc]. Checksum: 9F9A840C17682706	FASTA	628	73,708
	10 20 30 40 50 60 MAHALVTFRD VAIDFSQKEW ECLDTTQRKL YRDVMLENYN NLVSLGLLSR HKTKKLSSEK 70 80 90 100 110 120 DIHEISLSKE SIIEKSKTLR LKGSIFRNEW QNKSEFEGQQ GLKERSISQK KIVSKKMSTD 130 140 150 160 170 180 RKRPSFTLNQ RIHNSEKSCD SHLVQHGKID SDVKHDCKEC GSTFNNVYQL TLHQKIHTGE 190 200 210 220 230 240 KSCKCEKCGK VFSHSYQLTL HQRFHTGEKP YECQECGKTF TLYPQLNRHQ KIHTGKKPYM 250 260 270 280 290 300 CKKCDKGFFS RLELTQHKRI HTGKKSYECK ECGKVFQLIF YFKEHERIHT GKKPYECKEC 310 320 330 340 350 360 GKAFSVCGQL TRHQKIHTGV KPYECKECGK TFRLSFYLTE HRRTHAGKKP YECKECGKSF 370 380 390 400 410 420 NVRGQLNRHK TIHTGIKPFA CKVCEKAFSY SGDLRVHSRI HTGEKPYECK ECGKAFMLRS 430 440 450 460 470 480 VLTEHQRLHT GVKPYECKEC GKTFRVRSQI SLHKKIHTDV KPYKCVRCGK TFRFGFYLTE 490 500 510 520 530 540 HQRIHTGEKP YKCKECGKAF IRRGNLKEHL KIHSGLKPYD CKECGKSFSR RGQFTEHQKI 550 560 570 580 590 600 HTGVKPYKCK ECGKAFSRSV DLRIHQRIHT GEKPYECKQC GKAFRLNSHL TEHQRIHTGE 610 620 KPYECKVCRK AFRQYSHLYQ HQKTHNVI
	Isoform 4 [UniParc]. Checksum: 7A0FCC9ED61BDE68	FASTA	637	74,993
	10 20 30 40 50 60 MLPNFKLYNF IEIFFKPLTP SKNRFHFVSY FENVNFMLCW LQENNFCLLL CFLSGLLSRH 70 80 90 100 110 120 KTKKLSSEKD IHEISLSKES IIEKSKTLRL KGSIFRNEWQ NKSEFEGQQG LKERSISQKK 130 140 150 160 170 180 IVSKKMSTDR KRPSFTLNQR IHNSEKSCDS HLVQHGKIDS DVKHDCKECG STFNNVYQLT 190 200 210 220 230 240 LHQKIHTGEK SCKCEKCGKV FSHSYQLTLH QRFHTGEKPY ECQECGKTFT LYPQLNRHQK 250 260 270 280 290 300 IHTGKKPYMC KKCDKGFFSR LELTQHKRIH TGKKSYECKE CGKVFQLIFY FKEHERIHTG 310 320 330 340 350 360 KKPYECKECG KAFSVCGQLT RHQKIHTGVK PYECKECGKT FRLSFYLTEH RRTHAGKKPY 370 380 390 400 410 420 ECKECGKSFN VRGQLNRHKT IHTGIKPFAC KVCEKAFSYS GDLRVHSRIH TGEKPYECKE 430 440 450 460 470 480 CGKAFMLRSV LTEHQRLHTG VKPYECKECG KTFRVRSQIS LHKKIHTDVK PYKCVRCGKT 490 500 510 520 530 540 FRFGFYLTEH QRIHTGEKPY KCKECGKAFI RRGNLKEHLK IHSGLKPYDC KECGKSFSRR 550 560 570 580 590 600 GQFTEHQKIH TGVKPYKCKE CGKAFSRSVD LRIHQRIHTG EKPYECKQCG KAFRLNSHLT 610 620 630 EHQRIHTGEK PYECKVCRKA FRQYSHLYQH QKTHNVI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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 4), VARIANT VAL-53. Tissue: Hippocampus.
[2]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Brain and Heart.
[3]	"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). Tissue: Brain.
[4]	"Neuroblastoma oligo-capping cDNA project: toward the understanding of the genesis and biology of neuroblastoma." Ohira M., Morohashi A., Nakamura Y., Isogai E., Furuya K., Hamano S., Machida T., Aoyama M., Fukumura M., Miyazaki K., Suzuki Y., Sugano S., Hirato J., Nakagawara A. Cancer Lett. 197:63-68(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 318-660. Tissue: Neuroblastoma.
[5]	"A novel human zinc finger protein ZNF540 interacts with MVP and inhibits transcriptional activities of the ERK signal pathway." Xiang Z., Yuan W., Luo N., Wang Y., Tan K., Deng Y., Zhou X., Zhu C., Li Y., Liu M., Wu X., Li Y. Biochem. Biophys. Res. Commun. 347:288-296(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH MVP, TISSUE SPECIFICITY.
[6]	"The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] ILE-275.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AK131388 mRNA. Translation: BAD18539.1. AK290486 mRNA. Translation: BAF83175.1. AL832100 mRNA. Translation: CAD91161.1. AL832315 mRNA. Translation: CAD38611.1. BX537980 mRNA. Translation: CAD97942.1. Frameshift. BC017940 mRNA. Translation: AAH17940.1. Sequence problems. BC126478 mRNA. Translation: AAI26479.1. BC126480 mRNA. Translation: AAI26481.1. AB074186 mRNA. Translation: BAE45743.1.
IPI	IPI00168568. IPI00383994. IPI00442104.
RefSeq	NP_001165696.1. NM_001172225.2. NP_001165697.1. NM_001172226.2. NP_689819.1. NM_152606.4.
UniGene	Hs.728927.
3D structure databases
ProteinModelPortal	Q8NDQ6.
ModBase	Search...
PTM databases
PhosphoSite	Q8NDQ6.
Polymorphism databases
DMDM	74762556.
Proteomic databases
PaxDb	Q8NDQ6.
PRIDE	Q8NDQ6.
Protocols and materials databases
DNASU	163255.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000316433; ENSP00000324598; ENSG00000171817. ENST00000343599; ENSP00000343768; ENSG00000171817. ENST00000589117; ENSP00000467118; ENSG00000171817. ENST00000592533; ENSP00000466274; ENSG00000171817.
GeneID	163255.
KEGG	hsa:163255.
UCSC	uc002ogq.3. human. uc010efq.3. human.
Organism-specific databases
CTD	163255.
GeneCards	GC19P038086.
HGNC	HGNC:25331. ZNF540.
HPA	HPA003444.
MIM	613903. gene.
neXtProt	NX_Q8NDQ6.
PharmGKB	PA134980975.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG5048.
HOVERGEN	HBG018163.
InParanoid	Q8NDQ6.
KO	K09228.
OMA	SFYLTEH.
OrthoDB	EOG4HHP1T.
PhylomeDB	Q8NDQ6.
Enzyme and pathway databases
Reactome	REACT_71. Gene Expression.
Gene expression databases
Bgee	Q8NDQ6.
CleanEx	HS_ZNF540.
Genevestigator	Q8NDQ6.
GermOnline	ENSG00000171817. Homo sapiens.
Family and domain databases
Gene3D	3.30.160.60. 17 hits.
InterPro	IPR001909. Krueppel-associated_box. IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. [Graphical view]
Pfam	PF01352. KRAB. 1 hit. [Graphical view]
SMART	SM00349. KRAB. 1 hit. SM00355. ZnF_C2H2. 17 hits. [Graphical view]
SUPFAM	SSF109640. Krueppel-associated_box. 1 hit.
PROSITE	PS50805. KRAB. 1 hit. PS00028. ZINC_FINGER_C2H2_1. 17 hits. PS50157. ZINC_FINGER_C2H2_2. 17 hits. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	163255.
NextBio	88343.
SOURCE	Search...

Entry information

Entry name

ZN540_HUMAN

Accession

Primary (citable) accession number: Q8NDQ6
Secondary accession number(s): A0AVS5 , A8K371, Q05D58, Q3LIC5, Q6ZN36, Q7Z3C8, Q86T31

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2005
Last sequence update:	October 1, 2002
Last modified:	May 1, 2013
This is version 90 of the entry and version 1 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.