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Protein

PR domain-containing protein 11

Gene

PRDM11

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

Functioni

May be involved in transcription regulation.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciZFISH:ENSG00000019485-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain-containing protein 11 (EC:2.1.1.-)
Gene namesi
Name:PRDM11
Synonyms:PFM8
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

HGNCiHGNC:13996. PRDM11.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi56981.
OpenTargetsiENSG00000019485.
PharmGKBiPA33709.

Polymorphism and mutation databases

DMDMi308153475.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477681 – 511PR domain-containing protein 11Add BLAST511

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei63PhosphoserineCombined sources1
Cross-linki214Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ9NQV5.
PaxDbiQ9NQV5.
PeptideAtlasiQ9NQV5.
PRIDEiQ9NQV5.

PTM databases

iPTMnetiQ9NQV5.
PhosphoSitePlusiQ9NQV5.

Expressioni

Tissue specificityi

Highly expressed in lung, including bronchial epithelial cells and airway smooth muscle cells, as well as in peripheral blood mononuclear cells. In tonsils, expressed in B-cell types, including naive B-cells, centroblasts, centrocytes and memory B-cells (at protein level). In benign hyperplastic lymph nodes, expressed in germinal center cells in both the dark and light zones, as well as in scattered cells in the mantle zone and the interfollicular area (at protein level).2 Publications

Developmental stagei

Differential expressed during pseudoglandular and canalicular stages of lung development.1 Publication

Gene expression databases

BgeeiENSG00000019485.
CleanExiHS_PRDM11.
ExpressionAtlasiQ9NQV5. baseline and differential.
GenevisibleiQ9NQV5. HS.

Organism-specific databases

HPAiHPA057072.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000263765.

Structurei

Secondary structure

1511
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi108 – 110Combined sources3
Turni111 – 114Combined sources4
Beta strandi115 – 121Combined sources7
Turni122 – 124Combined sources3
Beta strandi128 – 130Combined sources3
Helixi142 – 145Combined sources4
Beta strandi151 – 155Combined sources5
Beta strandi161 – 165Combined sources5
Beta strandi174 – 176Combined sources3
Beta strandi181 – 184Combined sources4
Beta strandi194 – 198Combined sources5
Beta strandi204 – 208Combined sources5
Turni212 – 214Combined sources3
Helixi217 – 220Combined sources4
Turni227 – 229Combined sources3
Beta strandi232 – 237Combined sources6
Beta strandi240 – 247Combined sources8
Beta strandi256 – 259Combined sources4
Helixi261 – 267Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RAYX-ray1.73A79-314[»]
ProteinModelPortaliQ9NQV5.
SMRiQ9NQV5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini149 – 260SETPROSITE-ProRule annotationAdd BLAST112

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IN44. Eukaryota.
ENOG410ZHQ1. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000231445.
HOVERGENiHBG053665.
InParanoidiQ9NQV5.
OMAiWMRYVII.
PhylomeDBiQ9NQV5.
TreeFamiTF316279.

Family and domain databases

InterProiIPR001214. SET_dom.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9NQV5-1) [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
MLKMAEPIAS LMIVECRACL RCSPLFLYQR EKDRMTENMK ECLAQTNAAV
60 70 80 90 100
GDMVTVVKTE VCSPLRDQEY GQPCSRRPDS SAMEVEPKKL KGKRDLIVPK
110 120 130 140 150
SFQQVDFWFC ESCQEYFVDE CPNHGPPVFV SDTPVPVGIP DRAALTIPQG
160 170 180 190 200
MEVVKDTSGE SDVRCVNEVI PKGHIFGPYE GQISTQDKSA GFFSWLIVDK
210 220 230 240 250
NNRYKSIDGS DETKANWMRY VVISREEREQ NLLAFQHSER IYFRACRDIR
260 270 280 290 300
PGEWLRVWYS EDYMKRLHSM SQETIHRNLA RGEKRLQREK SEQVLDNPED
310 320 330 340 350
LRGPIHLSVL RQGKSPYKRG FDEGDVHPQA KKKKIDLIFK DVLEASLESA
360 370 380 390 400
KVEAHQLALS TSLVIRKVPK YQDDAYSQCA TTMTHGVQNI GQTQGEGDWK
410 420 430 440 450
VPQGVSKEPG QLEDEEEEPS SFKADSPAEA SLASDPHELP TTSFCPNCIR
460 470 480 490 500
LKKKVRELQA ELDMLKSGKL PEPPVLPPQV LELPEFSDPA GKLVWMRLLS
510
EGRVRSGLCG G
Length:511
Mass (Da):57,863
Last modified:October 5, 2010 - v2
Checksum:i81DCAA502315EA5B
GO
Isoform 2 (identifier: Q9NQV5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-34: Missing.

Note: No experimental confirmation available.
Show »
Length:477
Mass (Da):53,865
Checksum:i70133F1E616A817D
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti48A → V in BAC04425 (PubMed:14702039).Curated1
Sequence conflicti58 – 67KTEVCSPLRD → NPS in AAF87244 (Ref. 1) Curated10
Sequence conflicti214K → E in AAF87244 (Ref. 1) Curated1

Polymorphismi

A genome-wide association analysis shows PRDM11 association with forced vital capacity (FVC), a spirometric measure of pulmonary function, that reflects lung volume and is used to diagnose and monitor lung diseases.1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073689200K → E in a patient with diffuse large B-cell lymphoma; unknown pathological significance. 1 PublicationCorresponds to variant rs139870847dbSNPEnsembl.1
Natural variantiVAR_073690285R → S in a patient with diffuse large B-cell lymphoma; unknown pathological significance. 1 PublicationCorresponds to variant rs35090414dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0398361 – 34Missing in isoform 2. 1 PublicationAdd BLAST34

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF275818 mRNA. Translation: AAF87244.1.
AK094792 mRNA. Translation: BAC04425.1.
AC103681 Genomic DNA. No translation available.
CCDSiCCDS58130.1. [Q9NQV5-2]
RefSeqiNP_001243624.1. NM_001256695.1.
NP_001243625.1. NM_001256696.1. [Q9NQV5-2]
XP_011518533.1. XM_011520231.2. [Q9NQV5-2]
UniGeneiHs.178715.

Genome annotation databases

EnsembliENST00000424263; ENSP00000394314; ENSG00000019485. [Q9NQV5-2]
ENST00000530656; ENSP00000435976; ENSG00000019485. [Q9NQV5-1]
GeneIDi56981.
KEGGihsa:56981.
UCSCiuc031qaa.2. human. [Q9NQV5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF275818 mRNA. Translation: AAF87244.1.
AK094792 mRNA. Translation: BAC04425.1.
AC103681 Genomic DNA. No translation available.
CCDSiCCDS58130.1. [Q9NQV5-2]
RefSeqiNP_001243624.1. NM_001256695.1.
NP_001243625.1. NM_001256696.1. [Q9NQV5-2]
XP_011518533.1. XM_011520231.2. [Q9NQV5-2]
UniGeneiHs.178715.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RAYX-ray1.73A79-314[»]
ProteinModelPortaliQ9NQV5.
SMRiQ9NQV5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000263765.

PTM databases

iPTMnetiQ9NQV5.
PhosphoSitePlusiQ9NQV5.

Polymorphism and mutation databases

DMDMi308153475.

Proteomic databases

MaxQBiQ9NQV5.
PaxDbiQ9NQV5.
PeptideAtlasiQ9NQV5.
PRIDEiQ9NQV5.

Protocols and materials databases

DNASUi56981.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000424263; ENSP00000394314; ENSG00000019485. [Q9NQV5-2]
ENST00000530656; ENSP00000435976; ENSG00000019485. [Q9NQV5-1]
GeneIDi56981.
KEGGihsa:56981.
UCSCiuc031qaa.2. human. [Q9NQV5-1]

Organism-specific databases

CTDi56981.
DisGeNETi56981.
GeneCardsiPRDM11.
HGNCiHGNC:13996. PRDM11.
HPAiHPA057072.
MIMi616347. gene.
neXtProtiNX_Q9NQV5.
OpenTargetsiENSG00000019485.
PharmGKBiPA33709.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IN44. Eukaryota.
ENOG410ZHQ1. LUCA.
GeneTreeiENSGT00830000128341.
HOGENOMiHOG000231445.
HOVERGENiHBG053665.
InParanoidiQ9NQV5.
OMAiWMRYVII.
PhylomeDBiQ9NQV5.
TreeFamiTF316279.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000019485-MONOMER.

Miscellaneous databases

GenomeRNAii56981.
PROiQ9NQV5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000019485.
CleanExiHS_PRDM11.
ExpressionAtlasiQ9NQV5. baseline and differential.
GenevisibleiQ9NQV5. HS.

Family and domain databases

InterProiIPR001214. SET_dom.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRD11_HUMAN
AccessioniPrimary (citable) accession number: Q9NQV5
Secondary accession number(s): Q8N9F1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: October 5, 2010
Last modified: November 2, 2016
This is version 108 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.