Sdr16c5 (short chain dehydrogenase/reductase family 16C, member 5) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Sdr16c5 (short chain dehydrogenase/reductase family 16C, member 5) Rattus norvegicus
Analyze
Symbol: Sdr16c5
Name: short chain dehydrogenase/reductase family 16C, member 5
RGD ID: 1565999
Description: Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity; all-trans-retinol dehydrogenase (NAD+) activity; and transcription corepressor activity. Predicted to be involved in keratinocyte proliferation; negative regulation of macromolecule biosynthetic process; and retinoid metabolic process. Predicted to be located in several cellular components, including chromatin; endoplasmic reticulum membrane; and nucleus. Predicted to be part of transcription repressor complex. Predicted to be active in lipid droplet. Orthologous to human SDR16C5 (short chain dehydrogenase/reductase family 16C member 5); INTERACTS WITH alpha-Zearalanol; bisphenol A; cadmium atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: epidermal retinal dehydrogenase 2; epidermal retinol dehydrogenase 2; LOC297805; Rdhe2; retinal short chain dehydrogenase reductase 2; RGD1565999; similar to short chain dehydrogenase reductase 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,816,394 - 21,841,596 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl521,816,394 - 21,838,551 (-)EnsemblGRCr8
mRatBN7.2517,018,813 - 17,043,974 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl517,018,813 - 17,040,970 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx519,259,704 - 19,281,871 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0520,858,201 - 20,880,369 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0520,609,663 - 20,631,775 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0516,904,926 - 16,930,111 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,904,926 - 16,930,075 (-)Ensemblrn6Rnor6.0
Rnor_5.0521,681,674 - 21,706,737 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4517,339,715 - 17,361,781 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera516,384,689 - 16,406,286 (-)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12372410   PMID:16691198   PMID:18926804   PMID:19102727  


Genomics

Comparative Map Data
Sdr16c5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,816,394 - 21,841,596 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl521,816,394 - 21,838,551 (-)EnsemblGRCr8
mRatBN7.2517,018,813 - 17,043,974 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl517,018,813 - 17,040,970 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx519,259,704 - 19,281,871 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0520,858,201 - 20,880,369 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0520,609,663 - 20,631,775 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0516,904,926 - 16,930,111 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,904,926 - 16,930,075 (-)Ensemblrn6Rnor6.0
Rnor_5.0521,681,674 - 21,706,737 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4517,339,715 - 17,361,781 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera516,384,689 - 16,406,286 (-)NCBICelera
Cytogenetic Map5q12NCBI
SDR16C5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38856,300,005 - 56,320,175 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl856,300,005 - 56,320,776 (-)Ensemblhg38GRCh38
GRCh37857,212,564 - 57,232,734 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36857,375,122 - 57,395,795 (-)NCBIBuild 36Build 36hg18NCBI36
Celera853,202,994 - 53,224,037 (-)NCBICelera
Cytogenetic Map8q12.1NCBI
HuRef852,679,741 - 52,700,502 (-)NCBIHuRef
CHM1_1857,264,741 - 57,285,268 (-)NCBICHM1_1
T2T-CHM13v2.0856,677,119 - 56,697,312 (-)NCBIT2T-CHM13v2.0
Sdr16c5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3943,995,942 - 4,019,663 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl43,995,936 - 4,019,663 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3843,995,942 - 4,019,663 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl43,995,936 - 4,019,663 (-)Ensemblmm10GRCm38
MGSCv3743,923,089 - 3,946,810 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3643,923,089 - 3,946,810 (-)NCBIMGSCv36mm8
Celera43,952,520 - 3,977,907 (-)NCBICelera
Cytogenetic Map4A1NCBI
cM Map42.23NCBI
Sdr16c5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545415,339,297 - 15,351,628 (-)Ensembl
ChiLan1.0NW_00495545415,339,353 - 15,349,180 (-)NCBIChiLan1.0ChiLan1.0
SDR16C5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2771,957,777 - 71,980,560 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1847,682,331 - 47,707,254 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0852,746,371 - 52,769,269 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1850,116,544 - 50,137,811 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl850,113,413 - 50,137,717 (-)EnsemblpanPan2panpan1.1
SDR16C5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1297,660,882 - 7,679,705 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl297,661,633 - 7,679,622 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha297,974,333 - 7,992,397 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0297,736,172 - 7,754,244 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl297,736,172 - 7,754,161 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1297,749,727 - 7,768,520 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0297,881,428 - 7,900,176 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0298,159,225 - 8,177,611 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC101970041
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530371,848,195 - 71,865,912 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364962,919,522 - 2,937,274 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364962,919,611 - 2,937,274 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDR16C5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl475,586,525 - 75,598,989 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1475,586,346 - 75,598,985 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2482,505,913 - 82,518,540 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SDR16C5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1852,330,362 - 52,365,253 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl852,330,731 - 52,351,250 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603989,442,391 - 89,462,973 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Sdr16c5
178 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:21
Count of miRNA genes:21
Interacting mature miRNAs:21
Transcripts:ENSRNOT00000011813
Prediction methods: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
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)51373115343590997Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5862723052665523Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51460607859606078Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51757663362576633Rat
1578774Tcas8Tongue tumor susceptibility QTL 83.47tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)51570745160707451Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5692228237468560Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5706553574335773Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51748608062486080Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)51297048025683802Rat
2303577Gluco47Glucose level QTL 473blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51652001961520019Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)51748608062486080Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5862723053627230Rat


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
7 5 49 90 41 50 20 16 20 6 144 78 7 75 37 84 30 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000011813   ⟹   ENSRNOP00000011813
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl521,816,394 - 21,838,551 (-)Ensembl
mRatBN7.2 Ensembl517,018,813 - 17,040,970 (-)Ensembl
Rnor_6.0 Ensembl516,904,926 - 16,927,083 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000085041   ⟹   ENSRNOP00000073208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl516,904,939 - 16,930,075 (-)Ensembl
RefSeq Acc Id: NM_001106634   ⟹   NP_001100104
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8521,816,394 - 21,838,551 (-)NCBI
mRatBN7.2517,018,813 - 17,040,970 (-)NCBI
Rnor_6.0516,904,926 - 16,927,083 (-)NCBI
Rnor_5.0521,681,674 - 21,706,737 (-)NCBI
RGSC_v3.4517,339,715 - 17,361,781 (-)RGD
Celera516,384,689 - 16,406,286 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237836   ⟹   XP_006237898
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8521,816,401 - 21,841,596 (-)NCBI
mRatBN7.2517,018,820 - 17,043,974 (-)NCBI
Rnor_6.0516,904,933 - 16,930,111 (-)NCBI
Rnor_5.0521,681,674 - 21,706,737 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100104 (Get FASTA)   NCBI Sequence Viewer  
  NP_001423573 (Get FASTA)   NCBI Sequence Viewer  
  XP_006237898 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11621 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000011813
  ENSRNOP00000011813.5
RefSeq Acc Id: NP_001100104   ⟸   NM_001106634
- UniProtKB: D3ZS85 (UniProtKB/TrEMBL),   A6JFM5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237898   ⟸   XM_006237836
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000011813   ⟸   ENSRNOT00000011813
Ensembl Acc Id: ENSRNOP00000073208   ⟸   ENSRNOT00000085041
Protein Domains
Ketoreductase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZS85-F1-model_v2 AlphaFold D3ZS85 1-309 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:1565999 AgrOrtholog
BioCyc Gene G2FUF-42110 BioCyc
BioCyc Pathway PWY-6872 [retinoate biosynthesis I] BioCyc
BioCyc Pathway Image PWY-6872 BioCyc
Ensembl Genes ENSRNOG00000008871 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011813 ENTREZGENE
  ENSRNOT00000011813.8 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro Glc/ribitol_DH UniProtKB/TrEMBL
  KR_dom UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
KEGG Report rno:297805 UniProtKB/TrEMBL
NCBI Gene 297805 ENTREZGENE
PANTHER EPIDERMAL RETINOL DEHYDROGENASE 2 UniProtKB/TrEMBL
  PKSB UniProtKB/TrEMBL
Pfam adh_short UniProtKB/TrEMBL
PhenoGen Sdr16c5 PhenoGen
PRINTS GDHRDH UniProtKB/TrEMBL
  SDRFAMILY UniProtKB/TrEMBL
RatGTEx ENSRNOG00000008871 RatGTEx
SMART PKS_KR UniProtKB/TrEMBL
Superfamily-SCOP SSF51735 UniProtKB/TrEMBL
UniProt A6JFM5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZS85 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-29 Sdr16c5  short chain dehydrogenase/reductase family 16C, member 5  Rdhe2  epidermal retinal dehydrogenase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Rdhe2  epidermal retinal dehydrogenase 2  Rdhe2  retinal short chain dehydrogenase reductase 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Rdhe2  retinal short chain dehydrogenase reductase 2  RGD1565999_predicted  similar to short chain dehydrogenase reductase 9 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565999_predicted  similar to short chain dehydrogenase reductase 9 (predicted)  LOC297805  similar to short chain dehydrogenase reductase 9  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC297805  similar to short chain dehydrogenase reductase 9      Symbol and Name status set to provisional 70820 PROVISIONAL