Gene/Proteome Database (LMPD)

LMPD ID
LMP005684
Gene ID
107817
Species
Mus musculus (Mouse)
Gene Name
jumonji domain containing 6
Gene Symbol
Jmjd6
Synonyms
5730436I23Rik; D11Ertd195e; PSR; PtdSerR; Ptdsr; mKIAA0585
Alternate Names
bifunctional arginine demethylase and lysyl-hydroxylase JMJD6; lysyl-hydroxylase JMJD6; phosphatidylserine receptor; jmjC domain-containing protein 6; histone arginine demethylase JMJD6; peptide-lysine 5-dioxygenase JMJD6; jumonji domain-containing protein 6; apoptotic cell clearance receptor PtdSerR
Chromosome
11
Map Location
11 E2|11 81.49 cM
EC Number
1.14.11.-
Summary
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 functions in differentiation of multiple tissues during development, and in anti-inflammatory cytokine signaling. It was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that this protein does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. [provided by RefSeq, Jul 2008]
Orthologs
View orthologs and multiple alignments for Jmjd6

Proteins

bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
Refseq ID NP_203971
Protein GI 125988379
UniProt ID Q9ERI5
mRNA ID NM_033398
Length 403
RefSeq Status REVIEWED
MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESYPLNPAAVPDNVERADALQLSVKEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTNTPRELIKVTREEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADAVDLQESTGIASDSSSDSSSSSSSSSSDSDSECESGSEGDGTTHRRKKRRTCSMVGNGDTTSQDDCVSKERSSSR

Gene Information

Entrez Gene ID
107817
Gene Name
jumonji domain containing 6
Gene Symbol
Jmjd6
Species
Mus musculus

Gene Ontology (GO Annotations)

GO ID Source Type Description
GO:0005730 ISS:UniProtKB C nucleolus
GO:0005654 ISS:UniProtKB C nucleoplasm
GO:0005634 IDA:UniProtKB C nucleus
GO:0005886 IDA:MGI C plasma membrane
GO:0033746 ISS:UniProtKB F histone demethylase activity (H3-R2 specific)
GO:0033749 ISS:UniProtKB F histone demethylase activity (H4-R3 specific)
GO:0005506 IEA:Ensembl F iron ion binding
GO:0070815 ISS:UniProtKB F peptidyl-lysine 5-dioxygenase activity
GO:0004872 IDA:MGI F receptor activity
GO:0003727 ISS:UniProtKB F single-stranded RNA binding
GO:0008380 IEA:UniProtKB-KW P RNA splicing
GO:0033077 IMP:MGI P T cell differentiation in thymus
GO:0043277 IMP:MGI P apoptotic cell clearance
GO:0001568 IMP:MGI P blood vessel development
GO:0007166 IDA:MGI P cell surface receptor signaling pathway
GO:0048821 IMP:MGI P erythrocyte development
GO:0007507 IMP:MGI P heart development
GO:0001822 IMP:MGI P kidney development
GO:0030324 IMP:MGI P lung development
GO:0006397 IEA:UniProtKB-KW P mRNA processing
GO:0042116 IMP:MGI P macrophage activation
GO:0018395 ISS:UniProtKB P peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine
GO:0043654 IDA:MGI P recognition of apoptotic cell
GO:0048024 IMP:UniProtKB P regulation of mRNA splicing, via spliceosome
GO:0006355 IEA:UniProtKB-KW P regulation of transcription, DNA-templated
GO:0060041 IMP:MGI P retina development in camera-type eye
GO:0002040 IMP:UniProtKB P sprouting angiogenesis
GO:0006351 IEA:UniProtKB-KW P transcription, DNA-templated

Domain Information

InterPro Annotations

Accession Description
IPR003347 JmjC domain

UniProt Annotations

Entry Information

Gene Name
jumonji domain containing 6
Protein Entry
JMJD6_MOUSE
UniProt ID
Q9ERI5
Species
Mouse

Comments

Comment Type Description
Alternative Products Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q9ERI5-1; Sequence=Displayed; Name=2; IsoId=Q9ERI5-2; Sequence=VSP_014024, VSP_014025; Note=No experimental confirmation available.;
Caution Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition of phosphatidylserine, a specific marker only present at the surface of apoptotic cells. Phosphatidylserine receptor probably participates in apoptotic cell phagocytosis. This protein was identified using phage display expressing mAb 217, an antibody that specifically recognizes phosphatidylserine receptor. However, its nuclear localization and the fact that mAb 217 antibody still recognizes the phosphatidylserine receptor in mice lacking Jmjd6, strongly suggest that it does not constitute the receptor for phosphatidylserine and is not involved in apoptotic cell removal. {ECO:0000305}.
Cofactor Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250}; Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
Developmental Stage Expressed early in development. Expressed from embryonic stem cells and throughout embryogenesis. {ECO:0000269|PubMed:14645847, ECO:0000269|PubMed:15345036}.
Disruption Phenotype Mice display perinatal lethality, growth retardation, severe anemia and a delay in terminal differentiation of the kidney, intestine, liver and lungs during embryogenesis. Moreover, eye development can be severely disturbed, ranging from defects in retinal differentiation to complete unilateral or bilateral absence of eyes. According to PubMed:14645847, mice are defective in removing apoptotic cells, especially in the lung and brain, in which dead cells accumulate, causing abnormal development and leading to neonatal lethality. According to PubMed:14715629, mice lacking Jmjd6 display a reduced number of macrophages and apoptotic cells in fetal liver. In contrast, according to PubMed:15345036, mice show a normal engulfment of apoptotic cells. The contradictory results concerning apoptosis and macrophage function may be explained by the fact that the protein plays a key role in hematopoietic differentiation. {ECO:0000269|PubMed:14645847, ECO:0000269|PubMed:14715629, ECO:0000269|PubMed:15345036}.
Domain The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus. {ECO:0000250}.
Function Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity, may act as an RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo. Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis. Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine responses (By similarity). {ECO:0000250}.
Sequence Caution Sequence=BAC65599.1; Type=Erroneous initiation; Evidence={ECO:0000305};
Similarity Belongs to the JMJD6 family. {ECO:0000305}.
Similarity Contains 1 JmjC domain. {ECO:0000255|PROSITE- ProRule:PRU00538}.
Subcellular Location Nucleus, nucleoplasm {ECO:0000269|PubMed:14729065}. Nucleus, nucleolus {ECO:0000250}. Note=Mainly found throughout the nucleoplasm outside of regions containing heterochromatic DNA, with some localization in nucleolus. During mitosis, excluded from the nucleus and reappears in the telophase of the cell cycle (By similarity). {ECO:0000250}.
Subunit Interacts with LUC7L2 and LUC7L3. Interacts with BRD4 (By similarity). Interacts with U2AF2/U2AF65. {ECO:0000250, ECO:0000269|PubMed:21300889}.
Tissue Specificity Widely expressed. Expressed in brain, eye, spinal chord, thymus, lung, liver, kidney and intestine. {ECO:0000269|PubMed:14645847, ECO:0000269|PubMed:15345036}.

Identical and Related Proteins

Unique RefSeq proteins for LMP005684 (as displayed in Record Overview)

Protein GI Database Accession Length Protein Name
125988379 RefSeq NP_203971 403 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

Identical Sequences to LMP005684 proteins

Reference Database Accession Length Protein Name
GI:125988379 GenBank EDL34598.1 403 phosphatidylserine receptor, isoform CRA_c [Mus musculus]
GI:125988379 SwissProt Q9ERI5.2 403 RecName: Full=Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6; AltName: Full=Histone arginine demethylase JMJD6; AltName: Full=JmjC domain-containing protein 6; AltName: Full=Jumonji domain-containing protein 6; AltName: Full=Lysyl-hydroxylase JMJD6; AltName: Full=Peptide-lysine 5-dioxygenase JMJD6; AltName: Full=Phosphatidylserine receptor; Short=Protein PTDSR [Mus musculus]

Related Sequences to LMP005684 proteins

Reference Database Accession Length Protein Name
GI:125988379 GenBank AAG27719.1 403 apoptotic cell clearance receptor PtdSerR [Mus musculus]
GI:125988379 GenBank AAH56629.1 403 Jumonji domain containing 6 [Mus musculus]
GI:125988379 GenBank AAR65242.1 403 Sequence 5 from patent US 6630313
GI:125988379 GenBank EDM06699.1 403 rCG35128, isoform CRA_d [Rattus norvegicus]
GI:125988379 RefSeq NP_001012143.2 403 bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Rattus norvegicus]
GI:125988379 SwissProt Q6AYK2.2 403 RecName: Full=Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6; AltName: Full=Histone arginine demethylase JMJD6; AltName: Full=JmjC domain-containing protein 6; AltName: Full=Jumonji domain-containing protein 6; AltName: Full=Lysyl-hydroxylase JMJD6; AltName: Full=Peptide-lysine 5-dioxygenase JMJD6; AltName: Full=Phosphatidylserine receptor; Short=Protein PTDSR [Rattus norvegicus]