Scd3 (stearoyl-coenzyme A desaturase 3) - Rat Genome Database

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Gene: Scd3 (stearoyl-coenzyme A desaturase 3) Rattus norvegicus
Analyze
Symbol: Scd3 (Ensembl: LOC681458)
Name: stearoyl-coenzyme A desaturase 3 (Ensembl:similar to stearoyl-coenzyme A desaturase 3)
RGD ID: 1595370
Description: Predicted to enable iron ion binding activity; palmitoyl-CoA 9-desaturase activity; and stearoyl-CoA 9-desaturase activity. Predicted to be involved in monounsaturated fatty acid biosynthetic process; response to fatty acid; and unsaturated fatty acid biosynthetic process. Predicted to be active in endoplasmic reticulum membrane. Orthologous to human SCD (stearoyl-CoA desaturase); INTERACTS WITH 1,2-dichloroethane (ortholog); 1,2-dimethylhydrazine (ortholog); 2,2',4,4',5,5'-hexachlorobiphenyl (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: acyl-CoA desaturase 3; LOC681458; similar to stearoyl-coenzyme A desaturase 3
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81253,028,053 - 253,063,662 (+)NCBIGRCr8
mRatBN7.21243,093,057 - 243,114,451 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1243,078,774 - 243,114,229 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01263,968,156 - 264,003,991 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1263,968,134 - 264,004,008 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01271,425,333 - 271,448,208 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1238,895,982 - 238,931,504 (+)NCBICelera
Cytogenetic Map1q54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Scd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81253,028,053 - 253,063,662 (+)NCBIGRCr8
mRatBN7.21243,093,057 - 243,114,451 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1243,078,774 - 243,114,229 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01263,968,156 - 264,003,991 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1263,968,134 - 264,004,008 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01271,425,333 - 271,448,208 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1238,895,982 - 238,931,504 (+)NCBICelera
Cytogenetic Map1q54NCBI
Scd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391944,191,727 - 44,232,455 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1944,191,708 - 44,232,455 (+)EnsemblGRCm39 Ensembl
GRCm381944,203,288 - 44,244,016 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1944,203,269 - 44,244,016 (+)EnsemblGRCm38mm10GRCm38
MGSCv371944,277,778 - 44,318,506 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361944,098,078 - 44,138,928 (+)NCBIMGSCv36mm8
MGSCv361944,256,599 - 44,297,327 (+)NCBIMGSCv36mm8
Celera1944,981,578 - 45,013,768 (+)NCBICelera
Cytogenetic Map19C3NCBI
cM Map1937.98NCBI

Variants

.
Variants in Scd3
130 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:3
Count of miRNA genes:3
Interacting mature miRNAs:3
Transcripts:ENSRNOT00000018090
Prediction methods: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
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1201554356246554356Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1144267353251128347Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1206081677251081677Rat
631836Stl31Serum triglyceride level QTL 314.645e-06blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1201554356246554356Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1150700247252085048Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1183970203243914901Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1191019702246062233Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1201554356246554356Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1213707201252085212Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1201554356246554356Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1150700142252085212Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1206329708251329708Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228985440245907899Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1206329708251329708Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1218753689245907899Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1202069611247069611Rat
2292216Bw80Body weight QTL 803.230.0019body mass (VT:0001259)body weight (CMO:0000012)1213533809243914901Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1164310393243914901Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1224054293243747962Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1224054293243747962Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1183970203243914901Rat
1581544Rf52Renal function QTL 520.05urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1203995416244113296Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1358191Ept10Estrogen-induced pituitary tumorigenesis QTL 103.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)1192825253243914732Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1201554356246554356Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat

Markers in Region
Scd1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21243,112,004 - 243,112,080 (+)MAPPERmRatBN7.2
mRatBN7.21243,273,354 - 243,273,430 (+)MAPPERmRatBN7.2
Rnor_6.01264,163,576 - 264,163,651NCBIRnor6.0
Rnor_6.01264,001,538 - 264,001,613NCBIRnor6.0
Rnor_5.01271,446,710 - 271,446,785UniSTSRnor5.0
Rnor_5.01271,606,495 - 271,606,570UniSTSRnor5.0
RGSC_v3.41249,462,307 - 249,462,382UniSTSRGSC3.4
Celera1239,088,336 - 239,088,411UniSTS
Celera1238,929,123 - 238,929,198UniSTS
Cytogenetic Map1q54UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 10 16 70 61 60 29 25 29 6 130 63 50 21 53 31

Sequence


Ensembl Acc Id: ENSRNOT00000018090   ⟹   ENSRNOP00000018090
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1243,078,774 - 243,114,229 (+)Ensembl
Rnor_6.0 Ensembl1263,968,134 - 264,004,008 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101696   ⟹   ENSRNOP00000080572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1243,092,993 - 243,114,229 (+)Ensembl
RefSeq Acc Id: XM_008760487   ⟹   XP_008758709
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81253,028,053 - 253,063,662 (+)NCBI
mRatBN7.21243,093,057 - 243,114,451 (+)NCBI
Rnor_6.01263,968,156 - 264,003,991 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001419478 (Get FASTA)   NCBI Sequence Viewer  
  XP_008758709 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018090.5
  ENSRNOP00000080572.1
RefSeq Acc Id: XP_008758709   ⟸   XM_008760487
- UniProtKB: A0A8I5ZQY8 (UniProtKB/TrEMBL),   Z4YNJ9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018090   ⟸   ENSRNOT00000018090
Ensembl Acc Id: ENSRNOP00000080572   ⟸   ENSRNOT00000101696
Protein Domains
Fatty acid desaturase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Z4YNJ9-F1-model_v2 AlphaFold Z4YNJ9 1-359 view protein structure

Transcriptome

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

Promoters
RGD ID:13690946
Promoter ID:EPDNEW_R1462
Type:single initiation site
Name:LOC681458_1
Description:similar to stearoyl-coenzyme A desaturase 3
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_6.01263,968,136 - 263,968,196EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595370 AgrOrtholog
BioCyc Gene G2FUF-55604 BioCyc
BioCyc Pathway PWY-5996 [oleate biosynthesis II (animals and fungi)] BioCyc
  PWY3O-1801 [palmitoleate biosynthesis IV (fungi and animals)] BioCyc
BioCyc Pathway Image PWY-5996 BioCyc
  PWY3O-1801 BioCyc
Ensembl Genes ENSRNOG00000013279 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018090.8 UniProtKB/TrEMBL
  ENSRNOT00000101696.1 UniProtKB/TrEMBL
InterPro Fatty_acid_desaturase-1 UniProtKB/TrEMBL
  Fatty_acid_desaturase-1_C UniProtKB/TrEMBL
  Fatty_acid_desaturase-1_core UniProtKB/TrEMBL
KEGG Report rno:681458 UniProtKB/TrEMBL
NCBI Gene 681458 ENTREZGENE
PANTHER ACYL-COA DESATURASE 3 UniProtKB/TrEMBL
  PTHR11351 UniProtKB/TrEMBL
Pfam FA_desaturase UniProtKB/TrEMBL
PhenoGen Scd3 PhenoGen
PRINTS FACDDSATRASE UniProtKB/TrEMBL
PROSITE FATTY_ACID_DESATUR_1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013279 RatGTEx
UniProt A0A8I5ZQY8 ENTREZGENE, UniProtKB/TrEMBL
  Z4YNJ9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-12-27 Scd3  stearoyl-coenzyme A desaturase 3  LOC681458  similar to stearoyl-coenzyme A desaturase 3  Name and Symbol changed 629549 APPROVED
2006-11-20 LOC681458  similar to stearoyl-coenzyme A desaturase 3      Symbol and Name status set to provisional 70820 PROVISIONAL