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Q96T68 (SETB2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 111. 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:
Histone-lysine N-methyltransferase SETDB2

EC=2.1.1.43
Alternative name(s):
Chronic lymphocytic leukemia deletion region gene 8 protein
Lysine N-methyltransferase 1F
SET domain bifurcated 2
Gene names
Name:SETDB2
Synonyms:C13orf4, CLLD8, KMT1F
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length719 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone methyltransferase involved in left-right axis specification in early development and mitosis. Specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). H3K9me3 is a specific tag for epigenetic transcriptional repression that recruits HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Contributes to H3K9me3 in both the interspersed repetitive elements and centromere-associated repeats. Plays a role in chromosome condensation and segregation during mitosis. Ref.5

Catalytic activity

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].

Subcellular location

Nucleus. Chromosome Probable Ref.5.

Tissue specificity

Ubiquitous. Highest expression in heart, testis and ovary.

Domain

In the pre-SET domain, Cys residues bind 3 zinc ions that are arranged in a triangular cluster; some of these Cys residues contribute to the binding of two zinc ions within the cluster By similarity.

Sequence similarities

Belongs to the class V-like SAM-binding methyltransferase superfamily.

Contains 1 MBD (methyl-CpG-binding) domain.

Contains 1 pre-SET domain.

Contains 1 SET domain.

Sequence caution

The sequence CAH56265.1 differs from that shown. Reason: Contaminating sequence. Potential poly-A sequence.

The sequence CAI10818.2 differs from that shown. Reason: Erroneous gene model prediction.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q96T68-1)

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: Q96T68-2)

The sequence of this isoform differs from the canonical sequence as follows:
     70-81: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q96T68-3)

The sequence of this isoform differs from the canonical sequence as follows:
     523-523: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 719719Histone-lysine N-methyltransferase SETDB2
PRO_0000186088

Regions

Domain157 – 22973MBD
Domain291 – 36474Pre-SET
Domain367 – 694328SET
Region377 – 3793S-adenosyl-L-methionine binding By similarity
Region651 – 6522S-adenosyl-L-methionine binding By similarity

Sites

Metal binding2931Zinc 1 By similarity
Metal binding2931Zinc 2 By similarity
Metal binding2951Zinc 1 By similarity
Metal binding2991Zinc 1 By similarity
Metal binding2991Zinc 3 By similarity
Metal binding3051Zinc 1 By similarity
Metal binding3071Zinc 2 By similarity
Metal binding3451Zinc 2 By similarity
Metal binding3451Zinc 3 By similarity
Metal binding3491Zinc 2 By similarity
Metal binding3511Zinc 3 By similarity
Metal binding3561Zinc 3 By similarity
Metal binding6541Zinc 4 By similarity
Metal binding7071Zinc 4 By similarity
Metal binding7091Zinc 4 By similarity
Metal binding7141Zinc 4 By similarity
Binding site4181S-adenosyl-L-methionine By similarity
Binding site6481S-adenosyl-L-methionine By similarity

Natural variations

Alternative sequence70 – 8112Missing in isoform 2.
VSP_008413
Alternative sequence5231Missing in isoform 3.
VSP_024034
Natural variant1171E → G. Ref.1 Ref.6
Corresponds to variant rs7998427 [ dbSNP | Ensembl ].
VAR_031282
Natural variant4731V → M. Ref.3 Ref.4 Ref.6
Corresponds to variant rs2057413 [ dbSNP | Ensembl ].
VAR_016976

Sequences

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

Last modified April 3, 2007. Version 2.
Checksum: 01CD2CFE5C1D9067

FASTA71981,894
        10         20         30         40         50         60 
MGEKNGDAKT FWMELEDDGK VDFIFEQVQN VLQSLKQKIK DGSATNKEYI QAMILVNEAT 

        70         80         90        100        110        120 
IINSSTSIKG ASQKEVNAQS SDPMPVTQKE QENKSNAFPS TSCENSFPED CTFLTTENKE 

       130        140        150        160        170        180 
ILSLEDKVVD FREKDSSSNL SYQSHDCSGA CLMKMPLNLK GENPLQLPIK CHFQRRHAKT 

       190        200        210        220        230        240 
NSHSSALHVS YKTPCGRSLR NVEEVFRYLL ETECNFLFTD NFSFNTYVQL ARNYPKQKEV 

       250        260        270        280        290        300 
VSDVDISNGV ESVPISFCNE IDSRKLPQFK YRKTVWPRAY NLTNFSSMFT DSCDCSEGCI 

       310        320        330        340        350        360 
DITKCACLQL TARNAKTSPL SSDKITTGYK YKRLQRQIPT GIYECSLLCK CNRQLCQNRV 

       370        380        390        400        410        420 
VQHGPQVRLQ VFKTEQKGWG VRCLDDIDRG TFVCIYSGRL LSRANTEKSY GIDENGRDEN 

       430        440        450        460        470        480 
TMKNIFSKKR KLEVACSDCE VEVLPLGLET HPRTAKTEKC PPKFSNNPKE LTVETKYDNI 

       490        500        510        520        530        540 
SRIQYHSVIR DPESKTAIFQ HNGKKMEFVS SESVTPEDND GFKPPREHLN SKTKGAQKDS 

       550        560        570        580        590        600 
SSNHVDEFED NLLIESDVID ITKYREETPP RSRCNQATTL DNQNIKKAIE VQIQKPQEGR 

       610        620        630        640        650        660 
STACQRQQVF CDEELLSETK NTSSDSLTKF NKGNVFLLDA TKEGNVGRFL NHSCCPNLLV 

       670        680        690        700        710 
QNVFVETHNR NFPLVAFFTN RYVKARTELT WDYGYEAGTV PEKEIFCQCG VNKCRKKIL 

« Hide

Isoform 2 [UniParc].

Checksum: 631679B2687F6FBD
Show »

FASTA70780,707
Isoform 3 [UniParc].

Checksum: FCBD4B8D5A1A3506
Show »

FASTA71881,766

References

« Hide 'large scale' references
[1]"Cloning and characterization of CLLD6, CLLD7, and CLLD8, novel candidate genes for leukemogenesis at chromosome 13q14, a region commonly deleted in B-cell chronic lymphocytic leukemia."
Mabuchi H., Fujii H., Calin G., Alder H., Negrini M., Rassenti L., Kipps T.J., Bullrich F., Croce C.M.
Cancer Res. 61:2870-2877(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT GLY-117.
[2]"The DNA sequence and analysis of human chromosome 13."
Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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 2), VARIANT MET-473.
Tissue: Colon and Testis.
[4]"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] OF 332-719 (ISOFORM 3), VARIANT MET-473.
Tissue: Amygdala.
[5]"CLLD8/KMT1F is a lysine methyltransferase that is important for chromosome segregation."
Falandry C., Fourel G., Galy V., Ristriani T., Horard B., Bensimon E., Salles G., Gilson E., Magdinier F.
J. Biol. Chem. 285:20234-20241(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[6]"Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma."
Zhang Y., Leaves N.I., Anderson G.G., Ponting C.P., Broxholme J., Holt R., Edser P., Bhattacharyya S., Dunham A., Adcock I.M., Pulleyn L., Barnes P.J., Harper J.I., Abecasis G., Cardon L., White M., Burton J., Matthews L. expand/collapse author list , Mott R., Ross M., Cox R., Moffatt M.F., Cookson W.O.C.M.
Nat. Genet. 34:181-186(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS GLY-117 AND MET-473.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF334407 mRNA. Translation: AAK38373.1.
AL139321, AL136218 Genomic DNA. Translation: CAH71048.1.
AL136218, AL139321 Genomic DNA. Translation: CAI10817.1.
AL136218 Genomic DNA. Translation: CAI10818.2. Sequence problems.
BC017078 mRNA. Translation: AAH17078.1.
BC047434 mRNA. Translation: AAH47434.1.
AL831937 mRNA. Translation: CAH56265.1. Sequence problems.
CCDSCCDS53868.1. [Q96T68-2]
CCDS9417.1. [Q96T68-1]
RefSeqNP_001153780.1. NM_001160308.1. [Q96T68-2]
NP_114121.2. NM_031915.2. [Q96T68-1]
XP_005266625.1. XM_005266568.2. [Q96T68-2]
UniGeneHs.631789.

3D structure databases

ProteinModelPortalQ96T68.
SMRQ96T68. Positions 243-408, 567-715.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid123768. 2 interactions.
IntActQ96T68. 1 interaction.
STRING9606.ENSP00000326477.

PTM databases

PhosphoSiteQ96T68.

Polymorphism databases

DMDM143811459.

Proteomic databases

PaxDbQ96T68.
PRIDEQ96T68.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000317257; ENSP00000326477; ENSG00000136169. [Q96T68-1]
ENST00000354234; ENSP00000346175; ENSG00000136169. [Q96T68-2]
GeneID83852.
KEGGhsa:83852.
UCSCuc001vcz.3. human. [Q96T68-1]
uc001vda.3. human. [Q96T68-2]

Organism-specific databases

CTD83852.
GeneCardsGC13P050018.
H-InvDBHIX0011315.
HGNCHGNC:20263. SETDB2.
HPACAB012190.
MIM607865. gene.
neXtProtNX_Q96T68.
PharmGKBPA134956285.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG2940.
HOVERGENHBG106688.
InParanoidQ96T68.
KOK11421.
OMAKCHFQRR.
OrthoDBEOG7ZD1TG.
PhylomeDBQ96T68.
TreeFamTF106411.

Gene expression databases

ArrayExpressQ96T68.
BgeeQ96T68.
CleanExHS_SETDB2.
GenevestigatorQ96T68.

Family and domain databases

Gene3D3.30.890.10. 1 hit.
InterProIPR016177. DNA-bd_dom.
IPR001739. Methyl_CpG_DNA-bd.
IPR007728. Pre-SET_dom.
IPR001214. SET_dom.
[Graphical view]
PfamPF01429. MBD. 1 hit.
PF05033. Pre-SET. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
SMARTSM00317. SET. 1 hit.
[Graphical view]
SUPFAMSSF54171. SSF54171. 1 hit.
PROSITEPS50982. MBD. 1 hit.
PS50867. PRE_SET. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi83852.
NextBio72831.
PROQ96T68.
SOURCESearch...

Entry information

Entry nameSETB2_HUMAN
AccessionPrimary (citable) accession number: Q96T68
Secondary accession number(s): Q5TC65 expand/collapse secondary AC list , Q5TC66, Q5W0A7, Q659A7, Q86UD6, Q96AI6
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2003
Last sequence update: April 3, 2007
Last modified: July 9, 2014
This is version 111 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 13

Human chromosome 13: entries, gene names and cross-references to MIM