Synj2 (synaptojanin 2) - Rat Genome Database

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Gene: Synj2 (synaptojanin 2) Rattus norvegicus
Analyze
Symbol: Synj2
Name: synaptojanin 2
RGD ID: 69436
Description: Enables phosphatase activity and protein domain specific binding activity. Involved in inositol phosphate catabolic process and phosphatidylinositol dephosphorylation. Located in axon terminus; cytoplasmic microtubule; and ruffle membrane. Is active in presynapse. Orthologous to human SYNJ2 (synaptojanin 2); PARTICIPATES IN inositol phosphate metabolic pathway; phosphatidylinositol 3-kinase signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: synaptic inositol 1,4,5-trisphosphate 5-phosphatase 2; synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2; synaptojanin-2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Synj2_v1   Synj2_v3   Synj2_v2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8148,923,742 - 49,027,153 (+)NCBIGRCr8
mRatBN7.2146,518,594 - 46,621,919 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl146,518,709 - 46,633,687 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx147,069,005 - 47,165,022 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0153,056,255 - 53,152,284 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0147,144,430 - 47,240,455 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0146,835,922 - 46,932,544 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl146,835,971 - 46,932,529 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0148,140,566 - 48,236,043 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4140,763,794 - 40,818,491 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1140,766,738 - 40,821,418 (+)NCBI
Celera142,211,492 - 42,305,219 (+)NCBICelera
Cytogenetic Map1q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
belinostat  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
cantharidin  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cypermethrin  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
fluoranthene  (ISO)
furan  (EXP)
gallic acid  (ISO)
genistein  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
maneb  (ISO)
mercury dibromide  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
orphenadrine  (EXP)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
progesterone  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
3. Localization of mRNAs for synaptojanin isoforms in the brain of developing and mature rats. Kudo M, etal., Brain Res Mol Brain Res. 1999 Feb 5;64(2):179-85.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. Recruitment of an alternatively spliced form of synaptojanin 2 to mitochondria by the interaction with the PDZ domain of a mitochondrial outer membrane protein. Nemoto Y and De Camilli P, EMBO J 1999 Jun 1;18(11):2991-3006.
7. Synaptojanin 2, a novel synaptojanin isoform with a distinct targeting domain and expression pattern. Nemoto Y, etal., J Biol Chem 1997 Dec 5;272(49):30817-21.
8. Identification and characterization of a synaptojanin 2 splice isoform predominantly expressed in nerve terminals. Nemoto Y, etal., J Biol Chem 2001 Nov 2;276(44):41133-42.
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:8889548   PMID:9442075  


Genomics

Comparative Map Data
Synj2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8148,923,742 - 49,027,153 (+)NCBIGRCr8
mRatBN7.2146,518,594 - 46,621,919 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl146,518,709 - 46,633,687 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx147,069,005 - 47,165,022 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0153,056,255 - 53,152,284 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0147,144,430 - 47,240,455 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0146,835,922 - 46,932,544 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl146,835,971 - 46,932,529 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0148,140,566 - 48,236,043 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4140,763,794 - 40,818,491 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1140,766,738 - 40,821,418 (+)NCBI
Celera142,211,492 - 42,305,219 (+)NCBICelera
Cytogenetic Map1q11NCBI
SYNJ2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386157,981,296 - 158,099,176 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6157,981,863 - 158,099,176 (+)EnsemblGRCh38hg38GRCh38
GRCh376158,402,895 - 158,520,208 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366158,322,907 - 158,439,556 (+)NCBINCBI36Build 36hg18NCBI36
Build 346158,373,327 - 158,489,977NCBI
Celera6159,051,752 - 159,169,058 (+)NCBICelera
Cytogenetic Map6q25.3NCBI
HuRef6155,875,294 - 155,992,255 (+)NCBIHuRef
CHM1_16158,665,133 - 158,782,434 (+)NCBICHM1_1
T2T-CHM13v2.06159,227,492 - 159,345,318 (+)NCBIT2T-CHM13v2.0
Synj2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39175,991,555 - 6,106,041 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl175,991,555 - 6,094,565 (+)EnsemblGRCm39 Ensembl
GRCm38175,941,280 - 6,055,766 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl175,941,280 - 6,044,290 (+)EnsemblGRCm38mm10GRCm38
MGSCv37175,941,280 - 6,044,290 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36175,932,123 - 6,000,772 (+)NCBIMGSCv36mm8
Celera176,513,365 - 6,582,071 (+)NCBICelera
Cytogenetic Map17A1NCBI
cM Map173.59NCBI
Synj2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554394,290,238 - 4,400,775 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554394,305,630 - 4,400,775 (-)NCBIChiLan1.0ChiLan1.0
SYNJ2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25178,095,787 - 178,228,422 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16175,999,205 - 176,128,735 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06155,881,818 - 156,011,416 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16157,940,846 - 158,058,462 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6157,940,179 - 158,055,662 (+)Ensemblpanpan1.1panPan2
SYNJ2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1147,506,925 - 47,582,353 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl147,483,942 - 47,579,831 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha148,327,920 - 48,426,329 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0147,669,938 - 47,768,899 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl147,669,793 - 47,771,015 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1147,548,877 - 47,647,228 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0147,418,371 - 47,516,811 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0147,977,352 - 48,075,852 (+)NCBIUU_Cfam_GSD_1.0
Synj2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946142,595,865 - 142,659,959 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364899,848,062 - 9,908,760 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364899,848,070 - 9,911,952 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SYNJ2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl19,014,551 - 9,109,103 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.119,014,206 - 9,109,050 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2111,136,293 - 11,232,123 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SYNJ2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11385,579,457 - 85,695,694 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1385,580,392 - 85,692,908 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604057,949,365 - 58,065,977 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Synj2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624785145,228 - 266,022 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624785157,455 - 265,926 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Synj2
617 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:798
Count of miRNA genes:268
Interacting mature miRNAs:331
Transcripts:ENSRNOT00000066798, ENSRNOT00000067661, ENSRNOT00000068476
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat

Markers in Region
D1Got56  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera142,222,525 - 42,222,818UniSTS
RH 2.0 Map1272.9RGD
Cytogenetic Map1q11UniSTS
D1Cebr7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2146,591,603 - 46,591,829 (+)MAPPERmRatBN7.2
Rnor_6.0146,905,371 - 46,905,596NCBIRnor6.0
Rnor_5.0148,208,870 - 48,209,095UniSTSRnor5.0
RGSC_v3.4140,794,071 - 40,794,296UniSTSRGSC3.4
Celera142,280,799 - 42,281,024UniSTS
Cytogenetic Map1q11UniSTS
D1Cebr2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2146,604,732 - 46,604,922 (+)MAPPERmRatBN7.2
Rnor_6.0146,918,500 - 46,918,687NCBIRnor6.0
Rnor_5.0148,221,999 - 48,222,186UniSTSRnor5.0
RGSC_v3.4140,807,200 - 40,807,387UniSTSRGSC3.4
Celera142,293,928 - 42,294,115UniSTS
Cytogenetic Map1q11UniSTS


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 2 28 2 3 24 4 38 11 2
Low 1 15 57 41 19 41 6 8 50 31 3 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001113371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001113372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_032071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092677 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275679 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275686 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275688 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063275732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY034050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY034051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI290811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK653289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FB336982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HH768321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U90312 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066798   ⟹   ENSRNOP00000059744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl146,518,709 - 46,633,687 (+)Ensembl
Rnor_6.0 Ensembl146,835,971 - 46,932,053 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067661   ⟹   ENSRNOP00000062564
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl146,583,330 - 46,616,012 (+)Ensembl
Rnor_6.0 Ensembl146,873,011 - 46,932,529 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000068476   ⟹   ENSRNOP00000063385
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl146,518,709 - 46,616,012 (+)Ensembl
Rnor_6.0 Ensembl146,873,011 - 46,932,529 (+)Ensembl
RefSeq Acc Id: NM_001113371   ⟹   NP_001106842
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,877 - 49,021,131 (+)NCBI
mRatBN7.2146,518,758 - 46,616,027 (+)NCBI
Rnor_6.0146,835,971 - 46,932,544 (+)NCBI
Rnor_5.0148,140,566 - 48,236,043 (+)NCBI
RGSC_v3.4140,763,794 - 40,818,491 (+)RGD
Celera142,211,541 - 42,305,219 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001113372   ⟹   NP_001106843
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,877 - 49,021,131 (+)NCBI
mRatBN7.2146,518,758 - 46,616,027 (+)NCBI
Rnor_6.0146,835,971 - 46,932,544 (+)NCBI
Rnor_5.0148,140,566 - 48,236,043 (+)NCBI
RGSC_v3.4140,763,794 - 40,818,491 (+)RGD
Celera142,211,541 - 42,305,219 (+)NCBI
Sequence:
RefSeq Acc Id: NM_032071   ⟹   NP_114460
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,828 - 49,021,131 (+)NCBI
mRatBN7.2146,518,709 - 46,616,027 (+)NCBI
Rnor_6.0146,835,922 - 46,932,544 (+)NCBI
Rnor_5.0148,140,566 - 48,236,043 (+)NCBI
RGSC_v3.4140,763,794 - 40,818,491 (+)RGD
Celera142,211,492 - 42,305,219 (+)RGD
Sequence:
RefSeq Acc Id: XM_039092677   ⟹   XP_038948605
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,743 - 49,022,603 (+)NCBI
mRatBN7.2146,518,596 - 46,621,356 (+)NCBI
RefSeq Acc Id: XM_039092679   ⟹   XP_038948607
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,742 - 49,027,153 (+)NCBI
mRatBN7.2146,518,594 - 46,621,919 (+)NCBI
RefSeq Acc Id: XM_039092680   ⟹   XP_038948608
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,743 - 49,027,153 (+)NCBI
mRatBN7.2146,518,595 - 46,621,919 (+)NCBI
RefSeq Acc Id: XM_039092684   ⟹   XP_038948612
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,743 - 49,020,046 (+)NCBI
mRatBN7.2146,518,595 - 46,614,943 (+)NCBI
RefSeq Acc Id: XM_039092687   ⟹   XP_038948615
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,420 - 49,022,603 (+)NCBI
mRatBN7.2146,583,313 - 46,621,356 (+)NCBI
RefSeq Acc Id: XM_063275679   ⟹   XP_063131749
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,743 - 49,022,603 (+)NCBI
RefSeq Acc Id: XM_063275683   ⟹   XP_063131753
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,742 - 49,027,153 (+)NCBI
RefSeq Acc Id: XM_063275686   ⟹   XP_063131756
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,743 - 49,027,153 (+)NCBI
RefSeq Acc Id: XM_063275688   ⟹   XP_063131758
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,742 - 49,020,046 (+)NCBI
RefSeq Acc Id: XM_063275699   ⟹   XP_063131769
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,420 - 49,022,603 (+)NCBI
RefSeq Acc Id: XM_063275707   ⟹   XP_063131777
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,420 - 49,022,603 (+)NCBI
RefSeq Acc Id: XM_063275714   ⟹   XP_063131784
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,769 - 49,022,603 (+)NCBI
RefSeq Acc Id: XM_063275718   ⟹   XP_063131788
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,420 - 49,022,603 (+)NCBI
RefSeq Acc Id: XM_063275719   ⟹   XP_063131789
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,420 - 49,027,153 (+)NCBI
RefSeq Acc Id: XM_063275722   ⟹   XP_063131792
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,420 - 49,027,153 (+)NCBI
RefSeq Acc Id: XM_063275725   ⟹   XP_063131795
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,411 - 49,027,153 (+)NCBI
RefSeq Acc Id: XM_063275728   ⟹   XP_063131798
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,988,769 - 49,027,153 (+)NCBI
RefSeq Acc Id: XM_063275732   ⟹   XP_063131802
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8148,923,743 - 49,020,046 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001106842 (Get FASTA)   NCBI Sequence Viewer  
  NP_001106843 (Get FASTA)   NCBI Sequence Viewer  
  NP_114460 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948605 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948607 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948608 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948612 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948615 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131749 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131753 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131756 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131758 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131769 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131777 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131784 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131788 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131789 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131792 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131795 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131798 (Get FASTA)   NCBI Sequence Viewer  
  XP_063131802 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB92481 (Get FASTA)   NCBI Sequence Viewer  
  AAK61722 (Get FASTA)   NCBI Sequence Viewer  
  AAK61723 (Get FASTA)   NCBI Sequence Viewer  
  CAR81447 (Get FASTA)   NCBI Sequence Viewer  
  CBX84909 (Get FASTA)   NCBI Sequence Viewer  
  EDL83727 (Get FASTA)   NCBI Sequence Viewer  
  EDL83728 (Get FASTA)   NCBI Sequence Viewer  
  EDL83729 (Get FASTA)   NCBI Sequence Viewer  
  EDL83730 (Get FASTA)   NCBI Sequence Viewer  
  EDL83731 (Get FASTA)   NCBI Sequence Viewer  
  EDL83732 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059744
  ENSRNOP00000059744.4
  ENSRNOP00000062564
  ENSRNOP00000062564.4
  ENSRNOP00000063385
  ENSRNOP00000063385.4
GenBank Protein O55207 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_114460   ⟸   NM_032071
- Peptide Label: isoform 3
- UniProtKB: F1M2D6 (UniProtKB/TrEMBL),   A6KNZ7 (UniProtKB/TrEMBL),   F1M0S5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106842   ⟸   NM_001113371
- Peptide Label: isoform 1
- UniProtKB: Q91ZD9 (UniProtKB/Swiss-Prot),   Q91ZD8 (UniProtKB/Swiss-Prot),   O55207 (UniProtKB/Swiss-Prot),   A6KNZ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106843   ⟸   NM_001113372
- Peptide Label: isoform 2
- UniProtKB: A6KNZ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062564   ⟸   ENSRNOT00000067661
RefSeq Acc Id: ENSRNOP00000063385   ⟸   ENSRNOT00000068476
RefSeq Acc Id: ENSRNOP00000059744   ⟸   ENSRNOT00000066798
RefSeq Acc Id: XP_038948607   ⟸   XM_039092679
- Peptide Label: isoform X6
- UniProtKB: F1M0S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948608   ⟸   XM_039092680
- Peptide Label: isoform X7
- UniProtKB: F1M0S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948612   ⟸   XM_039092684
- Peptide Label: isoform X8
- UniProtKB: F1M0S5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948605   ⟸   XM_039092677
- Peptide Label: isoform X2
- UniProtKB: A6KNZ5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038948615   ⟸   XM_039092687
- Peptide Label: isoform X11
- UniProtKB: F1LPP1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063131753   ⟸   XM_063275683
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063131758   ⟸   XM_063275688
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063131756   ⟸   XM_063275686
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063131749   ⟸   XM_063275679
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063131802   ⟸   XM_063275732
- Peptide Label: isoform X18
RefSeq Acc Id: XP_063131795   ⟸   XM_063275725
- Peptide Label: isoform X16
RefSeq Acc Id: XP_063131792   ⟸   XM_063275722
- Peptide Label: isoform X15
RefSeq Acc Id: XP_063131789   ⟸   XM_063275719
- Peptide Label: isoform X14
RefSeq Acc Id: XP_063131769   ⟸   XM_063275699
- Peptide Label: isoform X9
RefSeq Acc Id: XP_063131777   ⟸   XM_063275707
- Peptide Label: isoform X10
RefSeq Acc Id: XP_063131788   ⟸   XM_063275718
- Peptide Label: isoform X13
RefSeq Acc Id: XP_063131798   ⟸   XM_063275728
- Peptide Label: isoform X17
RefSeq Acc Id: XP_063131784   ⟸   XM_063275714
- Peptide Label: isoform X12
Protein Domains
RRM   SAC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O55207-F1-model_v2 AlphaFold O55207 1-1496 view protein structure

Transcriptome

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

Promoters
RGD ID:13689606
Promoter ID:EPDNEW_R127
Type:multiple initiation site
Name:Synj2_1
Description:synaptojanin 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0146,836,028 - 46,836,088EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69436 AgrOrtholog
BIND 129613
  129615
  129616
  144351
BioCyc Gene G2FUF-61629 BioCyc
Ensembl Genes ENSRNOG00000017114 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066798.5 UniProtKB/TrEMBL
  ENSRNOT00000067661.4 UniProtKB/TrEMBL
  ENSRNOT00000068476 ENTREZGENE
  ENSRNOT00000068476.5 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.60.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DUF1866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Endo/exonu/phosph_ase_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IP5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SYNJ2_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84018 UniProtKB/Swiss-Prot
NCBI Gene 84018 ENTREZGENE
PANTHER INOSITOL 5-PHOSPHATASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11200:SF148 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF1866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Syja_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Synj2 PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017114 RatGTEx
SMART DUF1866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IPPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56219 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC233057
UniProt A6KNZ4 ENTREZGENE, UniProtKB/TrEMBL
  A6KNZ5 ENTREZGENE, UniProtKB/TrEMBL
  A6KNZ6_RAT UniProtKB/TrEMBL
  A6KNZ7 ENTREZGENE, UniProtKB/TrEMBL
  A6KNZ8_RAT UniProtKB/TrEMBL
  A6KNZ9_RAT UniProtKB/TrEMBL
  F1LPP1 ENTREZGENE, UniProtKB/TrEMBL
  F1M0S5 ENTREZGENE, UniProtKB/TrEMBL
  F1M2D6 ENTREZGENE, UniProtKB/TrEMBL
  O55207 ENTREZGENE
  Q91ZD8 ENTREZGENE
  Q91ZD9 ENTREZGENE
  SYNJ2_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q91ZD8 UniProtKB/Swiss-Prot
  Q91ZD9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Synj2  synaptojanin 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains an N-terminal region homologous to yeast Sac1p, a central inositol 5-phosphatase domain, and a C-terminal region mediating protein-protein interactions 628465
gene_expression ubiquitously expressed 628465
gene_product member of the family of phosphoinositide phosphatases 628465
gene_protein protein contains 1248 aa residues of 140 kDa 69390