Ormdl2 (ORMDL sphingolipid biosynthesis regulator 2) - Rat Genome Database

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Gene: Ormdl2 (ORMDL sphingolipid biosynthesis regulator 2) Rattus norvegicus
Analyze
Symbol: Ormdl2
Name: ORMDL sphingolipid biosynthesis regulator 2
RGD ID: 1305642
Description: Predicted to be involved in ceramide metabolic process; intracellular sphingolipid homeostasis; and sphingolipid biosynthetic process. Predicted to act upstream of or within negative regulation of ceramide biosynthetic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be part of serine palmitoyltransferase complex. Orthologous to human ORMDL2 (ORMDL sphingolipid biosynthesis regulator 2); INTERACTS WITH 2,6-dinitrotoluene; 4,4'-sulfonyldiphenol; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC288783; ORM1-like 2; ORM1-like 2 (S. cerevisiae); ORM1-like protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,832,368 - 1,835,501 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl71,832,368 - 1,836,223 (-)EnsemblGRCr8
mRatBN7.271,247,869 - 1,250,999 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl71,246,479 - 1,250,907 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx74,012,326 - 4,015,404 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.075,887,987 - 5,891,065 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.076,189,261 - 6,192,341 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.073,242,991 - 3,246,085 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl73,242,991 - 3,246,071 (-)Ensemblrn6Rnor6.0
Rnor_5.073,214,561 - 3,217,649 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.472,118,025 - 2,121,105 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera71,118,626 - 1,121,706 (-)NCBICelera
RGSC_v3.172,118,029 - 2,121,070 (-)NCBI
Cytogenetic Map7q11NCBI
JBrowse:




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

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12093374   PMID:20182505   PMID:25691431  


Genomics

Comparative Map Data
Ormdl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,832,368 - 1,835,501 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl71,832,368 - 1,836,223 (-)EnsemblGRCr8
mRatBN7.271,247,869 - 1,250,999 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl71,246,479 - 1,250,907 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx74,012,326 - 4,015,404 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.075,887,987 - 5,891,065 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.076,189,261 - 6,192,341 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.073,242,991 - 3,246,085 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl73,242,991 - 3,246,071 (-)Ensemblrn6Rnor6.0
Rnor_5.073,214,561 - 3,217,649 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.472,118,025 - 2,121,105 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera71,118,626 - 1,121,706 (-)NCBICelera
RGSC_v3.172,118,029 - 2,121,070 (-)NCBI
Cytogenetic Map7q11NCBI
ORMDL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381255,818,041 - 55,821,879 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1255,818,041 - 55,821,879 (+)Ensemblhg38GRCh38
GRCh371256,211,825 - 56,215,663 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,498,073 - 54,501,226 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341254,499,048 - 54,501,224NCBI
Celera1255,864,167 - 55,867,320 (+)NCBICelera
Cytogenetic Map12q13.2NCBI
HuRef1253,250,189 - 53,253,342 (+)NCBIHuRef
CHM1_11256,178,576 - 56,181,729 (+)NCBICHM1_1
T2T-CHM13v2.01255,784,685 - 55,788,525 (+)NCBIT2T-CHM13v2.0
Ormdl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,653,771 - 128,657,498 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,653,771 - 128,657,514 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3810128,817,902 - 128,821,629 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,817,902 - 128,821,645 (-)Ensemblmm10GRCm38
MGSCv3710128,254,513 - 128,258,687 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3610128,220,851 - 128,224,543 (-)NCBIMGSCv36mm8
Celera10131,210,016 - 131,214,206 (-)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1077.16NCBI
Ormdl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,451,021 - 3,457,086 (+)Ensembl
ChiLan1.0NW_0049554583,451,434 - 3,454,259 (+)NCBIChiLan1.0ChiLan1.0
ORMDL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21038,507,967 - 38,510,461 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11238,504,753 - 38,507,231 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01233,091,020 - 33,093,794 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11233,814,895 - 33,818,669 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1233,815,514 - 33,818,669 (-)EnsemblpanPan2panpan1.1
ORMDL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110203,750 - 206,247 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10259,654 - 268,284 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.010204,482 - 213,096 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10210,674 - 217,396 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110182,409 - 191,038 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010425,203 - 433,856 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.010549,440 - 558,070 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ormdl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,586,738 - 58,589,508 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936646280,661 - 287,144 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936646280,745 - 283,488 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ORMDL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,262,193 - 21,264,685 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1521,262,134 - 21,264,689 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2522,742,352 - 22,744,872 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ORMDL2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11151,768,533 - 51,771,461 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1151,768,642 - 51,770,998 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037194,221,943 - 194,225,433 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ormdl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480212,197,114 - 12,199,983 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462480212,197,114 - 12,200,044 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ormdl2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11156,291,584 - 156,294,678 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ormdl2
37 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:194
Count of miRNA genes:139
Interacting mature miRNAs:151
Transcripts:ENSRNOT00000044292
Prediction methods:Microtar, Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7166965846669658Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7123748937Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)7131777942Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)71104117804Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7170952746709527Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)71509236116977875Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7132612984Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)7139960528Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7129716167Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134650782Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7132612984Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000044292   ⟹   ENSRNOP00000047680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl71,832,368 - 1,836,223 (-)Ensembl
mRatBN7.2 Ensembl71,246,479 - 1,250,907 (-)Ensembl
Rnor_6.0 Ensembl73,242,991 - 3,246,071 (-)Ensembl
RefSeq Acc Id: NM_001105940   ⟹   NP_001099410
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,832,368 - 1,835,448 (-)NCBI
mRatBN7.271,247,869 - 1,250,949 (-)NCBI
Rnor_6.073,242,991 - 3,246,071 (-)NCBI
Rnor_5.073,214,561 - 3,217,649 (-)NCBI
RGSC_v3.472,118,025 - 2,121,105 (-)RGD
Celera71,118,626 - 1,121,706 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240753   ⟹   XP_006240815
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,832,373 - 1,835,501 (-)NCBI
mRatBN7.271,247,874 - 1,250,999 (-)NCBI
Rnor_6.073,242,996 - 3,246,085 (-)NCBI
Rnor_5.073,214,561 - 3,217,649 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240754   ⟹   XP_006240816
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr871,832,373 - 1,835,497 (-)NCBI
mRatBN7.271,247,874 - 1,250,996 (-)NCBI
Rnor_6.073,242,996 - 3,246,073 (-)NCBI
Rnor_5.073,214,561 - 3,217,649 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001099410   ⟸   NM_001105940
- Sequence:
RefSeq Acc Id: XP_006240815   ⟸   XM_006240753
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006240816   ⟸   XM_006240754
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000047680   ⟸   ENSRNOT00000044292

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2I4-F1-model_v2 AlphaFold D4A2I4 1-153 view protein structure

Transcriptome

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

Promoters
RGD ID:13694955
Promoter ID:EPDNEW_R5479
Type:initiation region
Name:Ormdl2_1
Description:ORMDL sphingolipid biosynthesis regulator 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_6.073,246,038 - 3,246,098EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305642 AgrOrtholog
BioCyc Gene G2FUF-35329 BioCyc
Ensembl Genes ENSRNOG00000030120 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044292.5 UniProtKB/TrEMBL
InterPro ORMDL UniProtKB/TrEMBL
KEGG Report rno:288783 UniProtKB/TrEMBL
NCBI Gene 288783 ENTREZGENE
PANTHER ORMDL UniProtKB/TrEMBL
Pfam ORMDL UniProtKB/TrEMBL
PhenoGen Ormdl2 PhenoGen
PIRSF ORMDL UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030120 RatGTEx
UniProt A6KSJ5 ENTREZGENE, UniProtKB/TrEMBL
  D4A2I4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-06-25 Ormdl2  ORMDL sphingolipid biosynthesis regulator 2  Ormdl2  ORM1-like 2 (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ormdl2  ORM1-like 2 (S. cerevisiae)   Ormdl2_predicted  ORM1-like 2 (S. cerevisiae) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ormdl2_predicted  ORM1-like 2 (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED