Gene/Proteome Database (LMPD)
LMPD ID
LMP006324
Gene ID
Species
Homo sapiens (Human)
Gene Name
jumonji domain containing 6
Gene Symbol
Synonyms
PSR; PTDSR; PTDSR1
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
Chromosome
17
Map Location
17q25
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 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]
Orthologs
Proteins
| bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1 | |
|---|---|
| Refseq ID | NP_001074930 |
| Protein GI | 125988395 |
| UniProt ID | Q6NYC1 |
| mRNA ID | NM_001081461 |
| Length | 414 |
| RefSeq Status | REVIEWED |
| MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERADALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTSTPRELIKVTRDEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADSVDLQESTGIASDSSSDSSSSSSSSSSDSDSECESGSEGDGTVHRRKKRRTCSMVGNGDTTSQDDCVSKERSSSRIRDTCGGRAHP | |
| bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 2 | |
|---|---|
| Refseq ID | NP_055982 |
| Protein GI | 125988389 |
| UniProt ID | Q6NYC1 |
| mRNA ID | NM_015167 |
| Length | 403 |
| RefSeq Status | REVIEWED |
| MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERADALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTSTPRELIKVTRDEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADSVDLQESTGIASDSSSDSSSSSSSSSSDSDSECESGSEGDGTVHRRKKRRTCSMVGNGDTTSQDDCVSKERSSSR | |
Gene Information
Gene Ontology (GO Annotations)
| GO ID | Source | Type | Description |
|---|---|---|---|
| GO:0005730 | IDA:UniProtKB | C | nucleolus |
| GO:0005654 | IDA:UniProtKB | C | nucleoplasm |
| GO:0005634 | IDA:UniProtKB | C | nucleus |
| GO:0005886 | IEA:Ensembl | C | plasma membrane |
| GO:0003723 | TAS:UniProtKB | F | RNA binding |
| GO:0033746 | IDA:UniProtKB | F | histone demethylase activity (H3-R2 specific) |
| GO:0033749 | IDA:UniProtKB | F | histone demethylase activity (H4-R3 specific) |
| GO:0042802 | IPI:IntAct | F | identical protein binding |
| GO:0005506 | IDA:UniProtKB | F | iron ion binding |
| GO:0070815 | IDA:UniProtKB | F | peptidyl-lysine 5-dioxygenase activity |
| GO:0004872 | IEA:Ensembl | F | receptor activity |
| GO:0003727 | IDA:UniProtKB | F | single-stranded RNA binding |
| GO:0008380 | IEA:UniProtKB-KW | P | RNA splicing |
| GO:0033077 | IEA:Ensembl | P | T cell differentiation in thymus |
| GO:0007166 | IEA:Ensembl | P | cell surface receptor signaling pathway |
| GO:0048821 | IEA:Ensembl | P | erythrocyte development |
| GO:0007507 | IEA:Ensembl | P | heart development |
| GO:0070078 | IDA:BHF-UCL | P | histone H3-R2 demethylation |
| GO:0070079 | IDA:BHF-UCL | P | histone H4-R3 demethylation |
| GO:0001822 | IEA:Ensembl | P | kidney development |
| GO:0030324 | IEA:Ensembl | P | lung development |
| GO:0006397 | IEA:UniProtKB-KW | P | mRNA processing |
| GO:0042116 | IEA:Ensembl | P | macrophage activation |
| GO:0018395 | IDA:UniProtKB | P | peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine |
| GO:0043654 | IEA:Ensembl | 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 | IEA:Ensembl | P | retina development in camera-type eye |
| GO:0002040 | ISS: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
Comments
| Comment Type | Description |
|---|---|
| Alternative Products | Event=Alternative splicing; Named isoforms=3; Name=1; Synonyms=Alpha; IsoId=Q6NYC1-1; Sequence=Displayed; Name=2; Synonyms=Beta; IsoId=Q6NYC1-2; Sequence=VSP_014022, VSP_014023; Name=3; IsoId=Q6NYC1-3; Sequence=VSP_014023; |
| Biophysicochemical Properties | Kinetic parameters: KM=39 uM for 2-oxoglutarate ; |
| 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. |
| Cofactor | Name=Fe(2+); Xref=ChEBI |
| Domain | The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus. |
| 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. {ECO |
| Induction | Up-regulated upon cytokine treatment, but not upon TNF treatment. |
| Interaction | Self; NbExp=3; IntAct=EBI-8464037, EBI-8464037; O60885:BRD4; NbExp=10; IntAct=EBI-8464037, EBI-723869; P50750:CDK9; NbExp=5; IntAct=EBI-8464037, EBI-1383449; Q8NAV1:PRPF38A; NbExp=2; IntAct=EBI-8464037, EBI-715374; Q01081:U2AF1; NbExp=2; IntAct=EBI-8464037, EBI-632461; Q9NP64:ZCCHC17; NbExp=2; IntAct=EBI-8464037, EBI-746345; |
| Sequence Caution | Sequence=AAH47003.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence= ; Sequence=BAA25511.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence= ; |
| Similarity | Belongs to the JMJD6 family. |
| Similarity | Contains 1 JmjC domain. {ECO |
| Subcellular Location | Nucleus, nucleoplasm. Nucleus, nucleolus. 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. |
| Subunit | Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65. Interacts with BRD4. {ECO |
| Tissue Specificity | Highly expressed in the heart, skeletal muscle and kidney. Expressed at moderate or low level in brain, placenta, lung, liver, pancreas, spleen, thymus, prostate, testis and ovary. Up-regulated in many patients with chronic pancreatitis. Expressed in nursing thymic epithelial cells. {ECO |
Identical and Related Proteins
Unique RefSeq proteins for LMP006324 (as displayed in Record Overview)
| Protein GI | Database | Accession | Length | Protein Name |
|---|---|---|---|---|
| 125988395 | RefSeq | NP_001074930 | 414 | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1 |
| 125988389 | RefSeq | NP_055982 | 403 | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 2 |
Identical Sequences to LMP006324 proteins
| Reference | Database | Accession | Length | Protein Name |
|---|---|---|---|---|
| GI:125988395 | DBBJ | BAG09769.1 | 414 | jmjC domain-containing protein 6, partial [synthetic construct] |
| GI:125988395 | DBBJ | BAG57932.1 | 414 | unnamed protein product [Homo sapiens] |
| GI:125988389 | GenBank | JAA05003.1 | 403 | jumonji domain containing 6 [Pan troglodytes] |
| GI:125988389 | GenBank | JAA14897.1 | 403 | jumonji domain containing 6 [Pan troglodytes] |
| GI:125988389 | GenBank | JAA29493.1 | 403 | jumonji domain containing 6 [Pan troglodytes] |
| GI:125988395 | GenBank | JAA41849.1 | 414 | jumonji domain containing 6 [Pan troglodytes] |
| GI:125988389 | GenBank | JAA41850.1 | 403 | jumonji domain containing 6 [Pan troglodytes] |
| GI:125988389 | GenBank | AIC50928.1 | 403 | JMJD6, partial [synthetic construct] |
| GI:125988389 | RefSeq | NP_001126553.1 | 403 | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Pongo abelii] |
| GI:125988395 | RefSeq | XP_003818343.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Pan paniscus] |
| GI:125988395 | RefSeq | XP_004040953.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Gorilla gorilla gorilla] |
| GI:125988395 | RefSeq | XP_009431521.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1 [Pan troglodytes] |
Related Sequences to LMP006324 proteins
| Reference | Database | Accession | Length | Protein Name |
|---|---|---|---|---|
| GI:125988395 | DBBJ | BAA25511.1 | 416 | KIAA0585 protein, partial [Homo sapiens] |
| GI:125988389 | DBBJ | BAA25511.1 | 416 | KIAA0585 protein, partial [Homo sapiens] |
| GI:125988389 | DBBJ | BAG09769.1 | 414 | jmjC domain-containing protein 6, partial [synthetic construct] |
| GI:125988389 | GenBank | AAH47003.1 | 441 | Jumonji domain containing 6, partial [Homo sapiens] |
| GI:125988395 | GenBank | EHH58375.1 | 414 | hypothetical protein EGM_08207 [Macaca fascicularis] |
| GI:125988389 | GenBank | JAA41849.1 | 414 | jumonji domain containing 6 [Pan troglodytes] |
| GI:125988389 | RefSeq | NP_001074930.1 | 414 | bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1 [Homo sapiens] |
| GI:125988389 | RefSeq | XP_003818343.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Pan paniscus] |
| GI:125988395 | RefSeq | XP_005585134.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Macaca fascicularis] |
| GI:125988395 | RefSeq | XP_008009809.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Chlorocebus sabaeus] |
| GI:125988395 | RefSeq | XP_008063434.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1 [Tarsius syrichta] |
| GI:125988395 | RefSeq | XP_010385812.1 | 414 | PREDICTED: bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 [Rhinopithecus roxellana] |