JMJD6

Protein identityUniProt · HPA

UniProt accession

Q6NYC1

Gene

JMJD6

Ensembl

ENSG00000070495

Chromosome

17

Canonical length

403 aa

Protein class

Predicted intracellular proteins

Subcellular location

Nucleoplasm

Quaternary structure

Homooligomer

OverviewNCBI Gene

This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that it does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

403 residues, UniProt reviewed canonical sequence.

>Q6NYC1|JMJD6
     1  MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESFSLSPA AVADNVERAD ALQLSVEEFV
    61  ERYERPYKPV VLLNAQEGWS AQEKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYIEY
   121  MESTRDDSPL YIFDSSYGEH PKRRKLLEDY KVPKFFTDDL FQYAGEKRRP PYRWFVMGPP
   181  RSGTGIHIDP LGTSAWNALV QGHKRWCLFP TSTPRELIKV TRDEGGNQQD EAITWFNVIY
   241  PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK
   301  TVRGRPKLSR KWYRILKQEH PELAVLADSV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE
   361  CESGSEGDGT VHRRKKRRTC SMVGNGDTTS QDDCVSKERS SSR

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against JMJD6 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.3

Highest tissue expression

115 nTPM

Expression across tissuesHPA

ReferencesPubMed · IEDB

Publications for JMJD6 from three distinct lines of evidence, kept separate because they answer different questions: whether antibodies are directed at the protein, whether a B-cell epitope has been mapped on it, and whether a T-cell epitope has. Each is labelled with its source.

Sources: PubMed — antigen-level antibody evidence from a custom retrieval. Records matching a controlled set of autoantibody terms (the MeSH descriptors Autoantibodies and Autoantigens, with title and abstract term variants) were obtained through NCBI E-utilities, and their titles and abstracts parsed for constructions that direct an antibody at a named protein rather than for co-occurrence. Captured names were resolved against UniProt nomenclature and each antigen adjudicated individually against the source text. Bibliographic records from PubMed and MeSH, U.S. National Library of Medicine; citation metrics from NIH iCite (Hutchins et al., PLoS Biology 2016). Titles link to PubMed; abstracts are not reproduced here. The NLM does not endorse this analysis.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.36

gnomAD pLI

0.93

gnomAD missense Z

1.48

DepMap mean gene effect

-0.46

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 8% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• cell surface receptor signaling pathway
• chromatin remodeling
• erythrocyte development
• heart development
• kidney development
• lung development
• macrophage activation
• membraneless organelle assembly
• mRNA processing
• negative regulation of protein homooligomerization
• oxidative RNA demethylation
• phagocytosis
• positive regulation of DNA-templated transcription
• positive regulation of transcription by RNA polymerase II
• protein homooligomerization
• recognition of apoptotic cell
• regulation of mRNA splicing, via spliceosome
• retina development in camera-type eye
• RNA splicing
• sprouting angiogenesis
• T cell differentiation in thymus
• peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine

Molecular functions

• histone demethylase activity
• identical protein binding
• iron ion binding
• oxidative RNA demethylase activity
• P-TEFb complex binding
• protein demethylase activity
• RNA binding
• signaling receptor activity
• single-stranded RNA binding
• transcription regulator activator activity
• histone H3R2 demethylase activity
• histone H4R3 demethylase activity
• peptidyl-lysine 5-dioxygenase activity

Cellular components

• cytoplasm
• cytosol
• nucleolus
• nucleoplasm
• nucleus
• plasma membrane
• ribonucleoprotein complex

Protein domainsUniProt · Pfam · InterPro

• JmjC domain
• JMJD6 family arginine demethylases/lysyl-hydroxylases
• JmjC domain, hydroxylase

KeywordsUniProt

• Chromatin regulator
• Cytoplasm
• Developmental protein
• Differentiation
• Dioxygenase
• Iron
• Metal-binding
• mRNA processing
• mRNA splicing
• Nucleus
• Oxidoreductase
• Phosphoprotein
• RNA-binding
• Transcription
• Transcription regulation

InteractionsUniProt · HPA

Protein binding partners of JMJD6 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• ARGLU1
• CCNT1
• CDK9
• LUC7L2
• LUC7L3
• LIAT1
• BRD4
• CCNL1
• CPSF6
• FAM9A
• PRPF38A
• RSRC1
• U2AF1
• ZCCHC17