Jade3 (jade family PHD finger 3) - Rat Genome Database

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Gene: Jade3 (jade family PHD finger 3) Rattus norvegicus
Analyze
Symbol: Jade3
Name: jade family PHD finger 3
RGD ID: 1563945
Description: Predicted to enable metal ion binding activity. Predicted to be involved in regulation of DNA biosynthetic process; regulation of DNA replication; and regulation of cell cycle. Predicted to be located in nucleoplasm. Predicted to be part of histone acetyltransferase complex. Orthologous to human JADE3 (jade family PHD finger 3); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC299305; RGD1563945; similar to mKIAA0215 protein; uncharacterized protein LOC299305
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X4,222,369 - 4,424,164 (-)NCBIGRCr8
mRatBN7.2X1,668,873 - 1,848,781 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX1,669,930 - 1,845,138 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX1,704,728 - 1,871,527 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X5,180,427 - 5,347,241 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X1,495,715 - 1,655,190 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X1,885,927 - 2,038,639 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX1,885,927 - 1,952,111 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X2,678,420 - 2,835,212 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X13,097,957 - 13,199,008 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX2,234,755 - 2,391,006 (-)NCBICelera
Cytogenetic MapXq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16387653  


Genomics

Comparative Map Data
Jade3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X4,222,369 - 4,424,164 (-)NCBIGRCr8
mRatBN7.2X1,668,873 - 1,848,781 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX1,669,930 - 1,845,138 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX1,704,728 - 1,871,527 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X5,180,427 - 5,347,241 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X1,495,715 - 1,655,190 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X1,885,927 - 2,038,639 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX1,885,927 - 1,952,111 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X2,678,420 - 2,835,212 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X13,097,957 - 13,199,008 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX2,234,755 - 2,391,006 (-)NCBICelera
Cytogenetic MapXq11NCBI
JADE3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X46,912,301 - 47,061,242 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX46,912,276 - 47,061,242 (+)EnsemblGRCh38hg38GRCh38
GRCh37X46,771,736 - 46,920,641 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X46,656,680 - 46,805,585 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X46,528,121 - 46,676,894NCBI
CeleraX50,964,282 - 51,112,586 (+)NCBICelera
Cytogenetic MapXp11.3NCBI
HuRefX44,482,963 - 44,631,372 (+)NCBIHuRef
CHM1_1X46,803,849 - 46,952,483 (+)NCBICHM1_1
T2T-CHM13v2.0X46,319,282 - 46,468,244 (+)NCBIT2T-CHM13v2.0
Jade3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X20,291,611 - 20,386,178 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX20,291,927 - 20,386,178 (+)EnsemblGRCm39 Ensembl
GRCm38X20,425,312 - 20,519,939 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX20,425,688 - 20,519,939 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X20,037,653 - 20,095,022 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X19,617,486 - 19,674,855 (+)NCBIMGSCv36mm8
CeleraX18,591,827 - 18,649,001 (+)NCBICelera
Cytogenetic MapXA1.3NCBI
cM MapX15.9NCBI
Jade3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955516998,725 - 1,061,279 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955516998,854 - 1,133,013 (-)NCBIChiLan1.0ChiLan1.0
JADE3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X48,537,574 - 48,686,796 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X48,540,951 - 48,690,168 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X39,347,038 - 39,496,236 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X47,206,925 - 47,354,732 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX47,278,395 - 47,354,732 (+)Ensemblpanpan1.1panPan2
JADE3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X40,545,474 - 40,682,593 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX40,521,569 - 40,680,536 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX14,921,015 - 15,058,046 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X40,679,883 - 40,817,007 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX40,654,112 - 40,815,685 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X40,667,759 - 40,804,843 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X40,655,367 - 40,792,486 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X40,748,457 - 40,885,540 (+)NCBIUU_Cfam_GSD_1.0
Jade3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X32,886,915 - 33,022,330 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650212,727,649 - 12,863,083 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650212,727,685 - 12,863,074 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JADE3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX41,579,764 - 41,714,706 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X41,579,565 - 41,714,705 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X46,416,965 - 46,551,694 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JADE3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X44,119,480 - 44,266,268 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX44,192,385 - 44,266,329 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660769,373,267 - 9,522,588 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Jade3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248873,808,785 - 3,872,416 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248873,712,530 - 3,872,416 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Jade3
389 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:151
Count of miRNA genes:133
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000061140
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144797211374346Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 12 4 6 4 37 19 18 1
Low 3 38 45 37 13 37 8 8 37 16 23 10 8
Below cutoff 1 3

Sequence


RefSeq Acc Id: ENSRNOT00000061140   ⟹   ENSRNOP00000057855
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX1,669,930 - 1,845,138 (-)Ensembl
Rnor_6.0 EnsemblX1,885,927 - 1,952,111 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103250   ⟹   ENSRNOP00000082402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX1,669,930 - 1,845,138 (-)Ensembl
RefSeq Acc Id: NM_001271265   ⟹   NP_001258194
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,224,426 - 4,398,627 (-)NCBI
mRatBN7.2X1,670,930 - 1,845,138 (-)NCBI
Rnor_6.0X1,885,927 - 2,038,639 (-)NCBI
Rnor_5.0X2,678,420 - 2,835,212 (-)NCBI
CeleraX2,234,755 - 2,391,006 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099576   ⟹   XP_038955504
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,401,970 (-)NCBI
mRatBN7.2X1,668,873 - 1,848,489 (-)NCBI
RefSeq Acc Id: XM_039099577   ⟹   XP_038955505
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,424,163 (-)NCBI
mRatBN7.2X1,668,873 - 1,848,780 (-)NCBI
RefSeq Acc Id: XM_039099578   ⟹   XP_038955506
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,401,971 (-)NCBI
mRatBN7.2X1,668,873 - 1,848,490 (-)NCBI
RefSeq Acc Id: XM_039099579   ⟹   XP_038955507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,424,164 (-)NCBI
mRatBN7.2X1,668,873 - 1,848,781 (-)NCBI
RefSeq Acc Id: XM_039099580   ⟹   XP_038955508
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,401,969 (-)NCBI
mRatBN7.2X1,668,873 - 1,848,488 (-)NCBI
RefSeq Acc Id: XM_063279878   ⟹   XP_063135948
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,424,160 (-)NCBI
RefSeq Acc Id: XM_063279879   ⟹   XP_063135949
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X4,222,369 - 4,401,969 (-)NCBI
RefSeq Acc Id: NP_001258194   ⟸   NM_001271265
- UniProtKB: F1M6J5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000057855   ⟸   ENSRNOT00000061140
RefSeq Acc Id: XP_038955507   ⟸   XM_039099579
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZTH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955505   ⟸   XM_039099577
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZTH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955506   ⟸   XM_039099578
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZTH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955504   ⟸   XM_039099576
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZTH1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955508   ⟸   XM_039099580
- Peptide Label: isoform X2
- UniProtKB: F1M6J5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000082402   ⟸   ENSRNOT00000103250
RefSeq Acc Id: XP_063135948   ⟸   XM_063279878
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063135949   ⟸   XM_063279879
- Peptide Label: isoform X2
Protein Domains
PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M6J5-F1-model_v2 AlphaFold F1M6J5 1-785 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563945 AgrOrtholog
BioCyc Gene G2FUF-3177 BioCyc
Ensembl Genes ENSRNOG00000039837 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000061140 ENTREZGENE
  ENSRNOT00000061140.5 UniProtKB/TrEMBL
  ENSRNOT00000103250.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro Enhancer_polycomb-like_N UniProtKB/TrEMBL
  EPHD UniProtKB/TrEMBL
  JADE3_PHD UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:299305 UniProtKB/TrEMBL
NCBI Gene 299305 ENTREZGENE
PANTHER PHD FINGER PROTEINS UniProtKB/TrEMBL
  PROTEIN JADE-3 UniProtKB/TrEMBL
Pfam EPL1 UniProtKB/TrEMBL
  PHD_2 UniProtKB/TrEMBL
  zf-HC5HC2H_2 UniProtKB/TrEMBL
PhenoGen Jade3 PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000039837 RatGTEx
SMART PHD UniProtKB/TrEMBL
Superfamily-SCOP SSF57903 UniProtKB/TrEMBL
UniProt A0A8I5ZTH1 ENTREZGENE, UniProtKB/TrEMBL
  F1M6J5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-25 Jade3  jade family PHD finger 3  RGD1563945  similar to mKIAA0215 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563945  similar to mKIAA0215 protein   RGD1563945_predicted  similar to mKIAA0215 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563945_predicted  similar to mKIAA0215 protein (predicted)  LOC299305  similar to mKIAA0215 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC299305  similar to mKIAA0215 protein      Symbol and Name status set to provisional 70820 PROVISIONAL