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Protein

Probable histone-lysine N-methyltransferase PRDM7

Gene

PRDM7

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Probable histone methyltransferase.By similarity

Catalytic activityi

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

ReactomeiR-HSA-212436. Generic Transcription Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable histone-lysine N-methyltransferase PRDM7 (EC:2.1.1.43)
Alternative name(s):
PR domain zinc finger protein 7
PR domain-containing protein 7
Gene namesi
Name:PRDM7
Synonyms:PFM4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:9351. PRDM7.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33719.

Polymorphism and mutation databases

BioMutaiPRDM7.
DMDMi223590134.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 492492Probable histone-lysine N-methyltransferase PRDM7PRO_0000047763Add
BLAST

Proteomic databases

PaxDbiQ9NQW5.
PRIDEiQ9NQW5.

PTM databases

iPTMnetiQ9NQW5.
PhosphoSiteiQ9NQW5.

Expressioni

Gene expression databases

BgeeiQ9NQW5.
CleanExiHS_PRDM7.
ExpressionAtlasiQ9NQW5. baseline and differential.

Organism-specific databases

HPAiHPA059555.
HPA059944.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
TRAF1Q130773EBI-10312471,EBI-359224

Protein-protein interaction databases

BioGridi116286. 1 interaction.
IntActiQ9NQW5. 1 interaction.
STRINGi9606.ENSP00000396732.

Structurei

3D structure databases

ProteinModelPortaliQ9NQW5.
SMRiQ9NQW5. Positions 195-368.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini23 – 8664KRAB-relatedPROSITE-ProRule annotationAdd
BLAST
Domaini244 – 358115SETPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 KRAB-related domain.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2461. Eukaryota.
ENOG410ZFVU. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000115687.
InParanoidiQ9NQW5.
OMAiVWNEASH.
OrthoDBiEOG7MH10H.
PhylomeDBiQ9NQW5.
TreeFamiTF337915.

Family and domain databases

InterProiIPR001909. KRAB.
IPR003655. Krueppel-associated_box-rel.
IPR001214. SET_dom.
IPR019041. SSXRD_motif.
[Graphical view]
PfamiPF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NQW5-3) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSPERSQEES PEGDTERTER KPMVKDAFKD ISIYFTKEEW AEMGDWEKTR
60 70 80 90 100
YRNVKMNYNA LITVGLRATR PAFMCHRRQA IKLQVDDTED SDEEWTPRQQ
110 120 130 140 150
VKPPWMAFRG EQSKHQKGMP KASFNNESSL RELSGTPNLL NTSDSEQAQK
160 170 180 190 200
PVSPPGEAST SGQHSRLKLE LRRKETEGKM YSLRERKGHA YKEISEPQDD
210 220 230 240 250
DYLYCEMCQN FFIDSCAAHG PPTFVKDSAV DKGHPNRSAL SLPPGLRIGP
260 270 280 290 300
SGIPQAGLGV WNEASDLPLG LHFGPYEGRI TEDEEAANSG YSWLITKGRN
310 320 330 340 350
CYEYVDGKDK SSANWMRYVN CARDDEEQNL VAFQYHRQIF YRTCRVIRPG
360 370 380 390 400
CELLVWSGDE YGQELGIRSS IEPAESLGQA VNCWSGMGMS MARNWASSGA
410 420 430 440 450
ASGRKSSWQG ENQSQRSIHV PHAVWPFQVK NFSVNMWNAI TPLRTSQDHL
460 470 480 490
QENFSNQRIP AQGIRIRSGN ILIHAAVMTK PKVKRSKKGP NS
Length:492
Mass (Da):55,777
Last modified:February 10, 2009 - v2
Checksum:i0C80D8DE8BA65DC5
GO
Isoform 2 (identifier: Q9NQW5-2) [UniParc]FASTAAdd to basket

Also known as: B

The sequence of this isoform differs from the canonical sequence as follows:
     1-206: Missing.
     318-377: YVNCARDDEE...RSSIEPAESL → TKARDPSMSL...RGSESGAAIF
     378-492: Missing.

Show »
Length:171
Mass (Da):18,442
Checksum:iF4F63783520C0072
GO
Isoform 3 (identifier: Q9NQW5-1) [UniParc]FASTAAdd to basket

Also known as: A

The sequence of this isoform differs from the canonical sequence as follows:
     1-206: Missing.
     368-492: RSSIEPAESL...VKRSKKGPNS → KWGSKWKKEL...GEAPVCRKDE

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Show »
Length:407
Mass (Da):45,890
Checksum:iD09E7D983CFA4426
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti357 – 3571S → Y in AAF78084 (PubMed:10668202).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti90 – 901D → E.1 Publication
Corresponds to variant rs12925933 [ dbSNP | Ensembl ].
VAR_057461
Natural varianti131 – 1311R → K.
Corresponds to variant rs2078478 [ dbSNP | Ensembl ].
VAR_057462
Natural varianti435 – 4351N → K.
Corresponds to variant rs7206111 [ dbSNP | Ensembl ].
VAR_057463

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 206206Missing in isoform 2 and isoform 3. 2 PublicationsVSP_036349Add
BLAST
Alternative sequencei318 – 37760YVNCA…PAESL → TKARDPSMSLMLSGLFKSKI SQSTCGTQSLLSELPRTICK KTSPTRESLPRGSESGAAIF in isoform 2. 2 PublicationsVSP_006930Add
BLAST
Alternative sequencei368 – 492125RSSIE…KGPNS → KWGSKWKKELMAGREPKPEI HPCPSCCLAFSSQKFLSQHV ERNHSSQNFPGPSARKLLQP ENPCPGDQNQERQYSDPRCC NDKTKGQEIKERSKLLNKRT WQREISRAFSSPPKGQMGSS RVGERMMEEESRTGQKVNPG NTGKLFVGVGISRIAKVKYG ECGQGFSDKSDVITHQRTHT GGKPYVCRECGEGFSRKSDL LSHQRTHTGEKPYVCRECER GFSRKSVLLIHQRTHRGEAP VCRKDE in isoform 3. 1 PublicationVSP_036350Add
BLAST
Alternative sequencei378 – 492115Missing in isoform 2. 2 PublicationsVSP_006931Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM690991 mRNA. Translation: CAM84449.1.
AF274347 mRNA. Translation: AAF78084.1.
AF274348 mRNA. Translation: AAF78085.1.
CH471184 Genomic DNA. Translation: EAW66654.1.
BC107033 mRNA. Translation: AAI07034.1.
CCDSiCCDS45557.1. [Q9NQW5-3]
RefSeqiNP_001091643.1. NM_001098173.1. [Q9NQW5-3]
XP_005256331.1. XM_005256274.3. [Q9NQW5-3]
UniGeneiHs.406695.

Genome annotation databases

EnsembliENST00000449207; ENSP00000396732; ENSG00000126856. [Q9NQW5-3]
GeneIDi11105.
KEGGihsa:11105.
UCSCiuc010cje.4. human. [Q9NQW5-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM690991 mRNA. Translation: CAM84449.1.
AF274347 mRNA. Translation: AAF78084.1.
AF274348 mRNA. Translation: AAF78085.1.
CH471184 Genomic DNA. Translation: EAW66654.1.
BC107033 mRNA. Translation: AAI07034.1.
CCDSiCCDS45557.1. [Q9NQW5-3]
RefSeqiNP_001091643.1. NM_001098173.1. [Q9NQW5-3]
XP_005256331.1. XM_005256274.3. [Q9NQW5-3]
UniGeneiHs.406695.

3D structure databases

ProteinModelPortaliQ9NQW5.
SMRiQ9NQW5. Positions 195-368.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116286. 1 interaction.
IntActiQ9NQW5. 1 interaction.
STRINGi9606.ENSP00000396732.

PTM databases

iPTMnetiQ9NQW5.
PhosphoSiteiQ9NQW5.

Polymorphism and mutation databases

BioMutaiPRDM7.
DMDMi223590134.

Proteomic databases

PaxDbiQ9NQW5.
PRIDEiQ9NQW5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000449207; ENSP00000396732; ENSG00000126856. [Q9NQW5-3]
GeneIDi11105.
KEGGihsa:11105.
UCSCiuc010cje.4. human. [Q9NQW5-3]

Organism-specific databases

CTDi11105.
GeneCardsiPRDM7.
HGNCiHGNC:9351. PRDM7.
HPAiHPA059555.
HPA059944.
MIMi609759. gene.
neXtProtiNX_Q9NQW5.
PharmGKBiPA33719.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2461. Eukaryota.
ENOG410ZFVU. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000115687.
InParanoidiQ9NQW5.
OMAiVWNEASH.
OrthoDBiEOG7MH10H.
PhylomeDBiQ9NQW5.
TreeFamiTF337915.

Enzyme and pathway databases

ReactomeiR-HSA-212436. Generic Transcription Pathway.

Miscellaneous databases

GenomeRNAii11105.
PROiQ9NQW5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NQW5.
CleanExiHS_PRDM7.
ExpressionAtlasiQ9NQW5. baseline and differential.

Family and domain databases

InterProiIPR001909. KRAB.
IPR003655. Krueppel-associated_box-rel.
IPR001214. SET_dom.
IPR019041. SSXRD_motif.
[Graphical view]
PfamiPF01352. KRAB. 1 hit.
PF09514. SSXRD. 1 hit.
[Graphical view]
SMARTiSM00349. KRAB. 1 hit.
[Graphical view]
SUPFAMiSSF109640. SSF109640. 1 hit.
PROSITEiPS50806. KRAB_RELATED. 1 hit.
PS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates."
    Fumasoni I., Meani N., Rambaldi D., Scafetta G., Alcalay M., Ciccarelli F.D.
    BMC Evol. Biol. 7:187-187(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT GLU-90.
  2. "The yin-yang of PR-domain family genes in tumorigenesis."
    Jiang G.L., Huang S.
    Histol. Histopathol. 15:109-117(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3).
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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).
  5. Cited for: SPLICE ISOFORM(S) THAT ARE POTENTIAL NMD TARGET(S).

Entry informationi

Entry nameiPRDM7_HUMAN
AccessioniPrimary (citable) accession number: Q9NQW5
Secondary accession number(s): A4Q9G8, Q08EM4, Q9NQW4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 16, 2001
Last sequence update: February 10, 2009
Last modified: June 8, 2016
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Miscellaneous

The mouse orthologous protein seems not to exist. According to PubMed:17916234, human PRDM7 and PRDM9 genes, a pair of close paralogs corresponding to a single mouse gene Prdm9, were generated by a recent gene duplication event after the divergence of the ancestors of human and mouse.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.