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Protein

PR domain zinc finger protein 8

Gene

PRDM8

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

Functioni

Probable histone methyltransferase, preferentially acting on 'Lys-9' of histone H3 (By similarity). Involved in the control of steroidogenesis through transcriptional repression of steroidogenesis marker genes such as CYP17A1 and LHCGR (By similarity). Forms with BHLHE22 a transcriptional repressor complex controlling genes involved in neural development and neuronal differentiation (By similarity). In the retina, it is required for rod bipolar and type 2 OFF-cone bipolar cell survival (By similarity).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri155 – 18329C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri625 – 64824C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri666 – 68823C2H2-type 3PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 8 (EC:2.1.1.-)
Alternative name(s):
PR domain-containing protein 8
Gene namesi
Name:PRDM8
Synonyms:PFM5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:13993. PRDM8.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Epilepsy, progressive myoclonic 10 (EPM10)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA progressive myoclonus epilepsy characterized by progressive dysarthria, myoclonus, ataxia, cognitive decline, psychosis, dementia and spasticity, with onset in childhood. There is variability between patients.
See also OMIM:616640
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti261 – 2611F → L in EPM10; does not affect interaction with EPM2A and NHLRC1. 1 Publication
VAR_075044

Keywords - Diseasei

Disease mutation, Epilepsy

Organism-specific databases

MalaCardsiPRDM8.
MIMi616640. phenotype.
Orphaneti324290. Early-onset Lafora body disease.
PharmGKBiPA33720.

Polymorphism and mutation databases

BioMutaiPRDM8.
DMDMi212276495.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 689689PR domain zinc finger protein 8PRO_0000047764Add
BLAST

Proteomic databases

PaxDbiQ9NQV8.
PRIDEiQ9NQV8.

PTM databases

PhosphoSiteiQ9NQV8.

Expressioni

Tissue specificityi

Expressed in brain, heart, skeletal muscle, testes, prostate.1 Publication

Gene expression databases

BgeeiQ9NQV8.
CleanExiHS_PRDM8.
ExpressionAtlasiQ9NQV8. baseline and differential.
GenevisibleiQ9NQV8. HS.

Organism-specific databases

HPAiHPA044298.

Interactioni

Subunit structurei

Interacts with EPM2A and NHLRC1. This interaction sequesters EPM2A and NHLRC1 to the nucleus (PubMed:22961547). Interacts with BHLHE22 (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi121296. 1 interaction.
STRINGi9606.ENSP00000339764.

Structurei

3D structure databases

ProteinModelPortaliQ9NQV8.
SMRiQ9NQV8. Positions 24-184, 623-649, 663-688.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini16 – 131116SETPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi137 – 1404Poly-Leu
Compositional biasi194 – 491298Gly-richAdd
BLAST
Compositional biasi212 – 2176Poly-Gln
Compositional biasi238 – 28952Ser-richAdd
BLAST
Compositional biasi565 – 5684Poly-Gly
Compositional biasi578 – 59821Ala-richAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 3 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri155 – 18329C2H2-type 1; atypicalPROSITE-ProRule annotationAdd
BLAST
Zinc fingeri625 – 64824C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri666 – 68823C2H2-type 3PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
KOG2461. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00520000055673.
HOGENOMiHOG000060226.
HOVERGENiHBG053674.
InParanoidiQ9NQV8.
OMAiAFTSVPQ.
OrthoDBiEOG77T142.
PhylomeDBiQ9NQV8.
TreeFamiTF327090.

Family and domain databases

InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 3 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 2 hits.
PS50157. ZINC_FINGER_C2H2_2. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NQV8-1) [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
MEDTGIQRGI WDGDAKAVQQ CLTDIFTSVY TTCDIPENAI FGPCVLSHTS
60 70 80 90 100
LYDSIAFIAL KSTDKRTVPY IFRVDTSAAN GSSEGLMWLR LVQSARDKEE
110 120 130 140 150
QNLEAYIKNG QLFYRSLRRI AKDEELLVWY GKELTELLLL CPSRSHNKMN
160 170 180 190 200
GSSPYTCLEC SQRFQFEFPY VAHLRFRCPK RLHSADISPQ DEQGGGVGTK
210 220 230 240 250
DHGGGGGGGK DQQQQQQEAP LGPGPKFCKA GPLHHYPSPS PESSNPSAAA
260 270 280 290 300
GGSSAKPSTD FHNLARELEN SRGGSSCSPA QSLSSGSGSG GGGGHQEAEL
310 320 330 340 350
SPDGIATGGG KGKRKFPEEA AEGGGGAGLV GGRGRFVERP LPASKEDLVC
360 370 380 390 400
TPQQYRASGS YFGLEENGRL FAPPSPETGE AKRSAFVEVK KAARAASLQE
410 420 430 440 450
EGTADGAGVA SEDQDAGGGG GSSTPAAASP VGAEKLLAPR PGGPLPSRLE
460 470 480 490 500
GGSPARGSAF TSVPQLGSAG STSGGGGTGA GAAGGAGGGQ GAASDERKSA
510 520 530 540 550
FSQPARSFSQ LSPLVLGQKL GALEPCHPAD GVGPTRLYPA AADPLAVKLQ
560 570 580 590 600
GAADLNGGCG SLPSGGGGLP KQSPFLYATA FWPKSSAAAA AAAAAAAAGP
610 620 630 640 650
LQLQLPSALT LLPPSFTSLC LPAQNWCAKC NASFRMTSDL VYHMRSHHKK
660 670 680
EYAMEPLVKR RREEKLKCPI CNESFRERHH LSRHMTSHN
Length:689
Mass (Da):71,663
Last modified:November 4, 2008 - v3
Checksum:i4D8E3EA8B463682A
GO
Isoform 2 (identifier: Q9NQV8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     332-334: GRG → AAL
     335-689: Missing.

Show »
Length:334
Mass (Da):35,470
Checksum:i2BB470D9E2EB4529
GO

Sequence cautioni

The sequence AAF87241.1 differs from that shown. Reason: Frameshift at position 287. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti323 – 3231G → A in AAF87241 (Ref. 1) Curated
Sequence conflicti354 – 3541Q → R in AAH71584 (PubMed:15489334).Curated
Sequence conflicti640 – 6401L → M in AAH71584 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti261 – 2611F → L in EPM10; does not affect interaction with EPM2A and NHLRC1. 1 Publication
VAR_075044

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei332 – 3343GRG → AAL in isoform 2. 1 PublicationVSP_035602
Alternative sequencei335 – 689355Missing in isoform 2. 1 PublicationVSP_035603Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF275815 mRNA. Translation: AAF87241.1. Frameshift.
AK292137 mRNA. Translation: BAF84826.1.
CH471057 Genomic DNA. Translation: EAX05851.1.
BC071584 mRNA. Translation: AAH71584.1.
CCDSiCCDS43243.1. [Q9NQV8-1]
RefSeqiNP_001092873.1. NM_001099403.1. [Q9NQV8-1]
NP_064611.3. NM_020226.3. [Q9NQV8-1]
XP_005263203.1. XM_005263146.3. [Q9NQV8-1]
UniGeneiHs.373642.

Genome annotation databases

EnsembliENST00000339711; ENSP00000339764; ENSG00000152784. [Q9NQV8-1]
ENST00000415738; ENSP00000406998; ENSG00000152784. [Q9NQV8-1]
ENST00000504452; ENSP00000423985; ENSG00000152784. [Q9NQV8-1]
GeneIDi56978.
KEGGihsa:56978.
UCSCiuc003hmb.5. human. [Q9NQV8-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF275815 mRNA. Translation: AAF87241.1. Frameshift.
AK292137 mRNA. Translation: BAF84826.1.
CH471057 Genomic DNA. Translation: EAX05851.1.
BC071584 mRNA. Translation: AAH71584.1.
CCDSiCCDS43243.1. [Q9NQV8-1]
RefSeqiNP_001092873.1. NM_001099403.1. [Q9NQV8-1]
NP_064611.3. NM_020226.3. [Q9NQV8-1]
XP_005263203.1. XM_005263146.3. [Q9NQV8-1]
UniGeneiHs.373642.

3D structure databases

ProteinModelPortaliQ9NQV8.
SMRiQ9NQV8. Positions 24-184, 623-649, 663-688.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121296. 1 interaction.
STRINGi9606.ENSP00000339764.

PTM databases

PhosphoSiteiQ9NQV8.

Polymorphism and mutation databases

BioMutaiPRDM8.
DMDMi212276495.

Proteomic databases

PaxDbiQ9NQV8.
PRIDEiQ9NQV8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000339711; ENSP00000339764; ENSG00000152784. [Q9NQV8-1]
ENST00000415738; ENSP00000406998; ENSG00000152784. [Q9NQV8-1]
ENST00000504452; ENSP00000423985; ENSG00000152784. [Q9NQV8-1]
GeneIDi56978.
KEGGihsa:56978.
UCSCiuc003hmb.5. human. [Q9NQV8-1]

Organism-specific databases

CTDi56978.
GeneCardsiPRDM8.
HGNCiHGNC:13993. PRDM8.
HPAiHPA044298.
MalaCardsiPRDM8.
MIMi616639. gene.
616640. phenotype.
neXtProtiNX_Q9NQV8.
Orphaneti324290. Early-onset Lafora body disease.
PharmGKBiPA33720.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
KOG2461. Eukaryota.
COG5048. LUCA.
GeneTreeiENSGT00520000055673.
HOGENOMiHOG000060226.
HOVERGENiHBG053674.
InParanoidiQ9NQV8.
OMAiAFTSVPQ.
OrthoDBiEOG77T142.
PhylomeDBiQ9NQV8.
TreeFamiTF327090.

Miscellaneous databases

GenomeRNAii56978.
NextBioi62633.
PROiQ9NQV8.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NQV8.
CleanExiHS_PRDM8.
ExpressionAtlasiQ9NQV8. baseline and differential.
GenevisibleiQ9NQV8. HS.

Family and domain databases

InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 3 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 2 hits.
PS50157. ZINC_FINGER_C2H2_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A family of novel PR-domain (PRDM) genes as candidate tumor suppressors."
    Yang X.-H., Huang S.
    Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
  2. "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] (ISOFORM 1).
    Tissue: Synovium.
  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 1).
    Tissue: Brain.
  5. Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH EPM2A AND NHLRC1, LACK OF HISTONE METHYLTRANSFERASE ACTIVITY, INVOLVEMENT IN EPM10, VARIANT EPM10 LEU-261, CHARACTERIZATION OF VARIANT EPM10 LEU-261.

Entry informationi

Entry nameiPRDM8_HUMAN
AccessioniPrimary (citable) accession number: Q9NQV8
Secondary accession number(s): A8K7X2, Q6IQ36
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: November 4, 2008
Last modified: May 11, 2016
This is version 129 of the entry and version 3 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

Caution

In disagreement with experimental results in mouse, PubMed:22961547 reports lack of histone methyltransferase activity on core histones generally, and on histone H3 specifically.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: 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.