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

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Gene: Sdr16c5 (short chain dehydrogenase/reductase family 16C, member 5) Mus musculus
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Symbol: Sdr16c5
Name: short chain dehydrogenase/reductase family 16C, member 5
RGD ID: 1620562
MGI Page MGI
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 chromatin; endoplasmic reticulum membrane; and nucleus. Predicted to be part of transcription repressor complex. Predicted to be active in lipid droplet. Predicted to colocalize with endoplasmic reticulum and plasma membrane. Orthologous to human SDR16C5 (short chain dehydrogenase/reductase family 16C member 5).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: EPHD-2; epidermal retinal dehydrogenase 2; epidermal retinol dehydrogenase 2; MGC124012; MGC124013; RDH-E2; Rdhe; Rdhe2; retinal short chain dehydrogenase reductase (Rdhe2); retinal short chain dehydrogenase reductase 2; retinal short-chain dehydrogenase reductase 2; retSDR2; Scd; Scdr9; short chain dehydrogenase reductase 9; short-chain dehydrogenase reductase 9; short-chain dehydrogenase/reductase family 16C member 5
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3943,995,942 - 4,019,663 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl43,995,936 - 4,019,663 (-)EnsemblGRCm39 Ensembl
GRCm3843,995,942 - 4,019,663 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl43,995,936 - 4,019,663 (-)EnsemblGRCm38mm10GRCm38
MGSCv3743,923,089 - 3,946,810 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3643,923,089 - 3,946,810 (-)NCBIMGSCv36mm8
Celera43,952,520 - 3,977,907 (-)NCBICelera
Cytogenetic Map4A1NCBI
cM Map42.23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14681479   PMID:16141072   PMID:16141073   PMID:21267068   PMID:21677750   PMID:21873635  
PMID:31562240   PMID:37075844  


Genomics

Comparative Map Data
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 Ensembl
GRCm3843,995,942 - 4,019,663 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl43,995,936 - 4,019,663 (-)EnsemblGRCm38mm10GRCm38
MGSCv3743,923,089 - 3,946,810 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3643,923,089 - 3,946,810 (-)NCBIMGSCv36mm8
Celera43,952,520 - 3,977,907 (-)NCBICelera
Cytogenetic Map4A1NCBI
cM Map42.23NCBI
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 (-)EnsemblGRCh38hg38GRCh38
GRCh37857,212,564 - 57,232,734 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36857,375,122 - 57,395,795 (-)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8521,816,394 - 21,841,596 (-)NCBIGRCr8
mRatBN7.2517,018,813 - 17,043,974 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl517,018,813 - 17,040,970 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx519,259,704 - 19,281,871 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0520,858,201 - 20,880,369 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0520,609,663 - 20,631,775 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0516,904,926 - 16,930,111 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl516,904,926 - 16,930,075 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0521,681,674 - 21,706,737 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4517,339,715 - 17,361,781 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera516,384,689 - 16,406,286 (-)NCBICelera
Cytogenetic Map5q12NCBI
Sdr16c5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545415,339,297 - 15,351,628 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha297,974,333 - 7,992,397 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0297,736,172 - 7,754,244 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1475,586,346 - 75,598,985 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2482,505,913 - 82,518,540 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103236829
(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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603989,442,391 - 89,462,973 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Sdr16c5
629 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:94
Count of miRNA genes:88
Interacting mature miRNAs:90
Transcripts:ENSMUST00000040925, ENSMUST00000126274
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10412079Sm1_msusceptibility to Schistosoma mansoni infection 1 (mouse)Not determined4122955614Mouse
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156268235Mouse
11049579Lmr9b_mleishmaniasis resistance 9b (mouse)4120657234Mouse
11049580Lmr9a_mleishmaniasis resistance 9 (mouse)4120657234Mouse
1301510Bbaa13_mB.burgdorferi-associated arthritis 13 (mouse)Not determined4126395649Mouse
1301274Lmr9_mleishmaniasis resistance 9 (mouse)Not determined4120657234Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000040925   ⟹   ENSMUSP00000046298
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl43,995,936 - 4,019,663 (-)Ensembl
GRCm38.p6 Ensembl43,995,936 - 4,019,663 (-)Ensembl
Ensembl Acc Id: ENSMUST00000126274
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl44,012,341 - 4,016,621 (-)Ensembl
GRCm38.p6 Ensembl44,012,341 - 4,016,621 (-)Ensembl
RefSeq Acc Id: NM_181989   ⟹   NP_871789
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3943,995,942 - 4,019,663 (-)NCBI
GRCm3843,995,942 - 4,019,663 (-)ENTREZGENE
MGSCv3743,923,089 - 3,946,810 (-)RGD
Celera43,952,520 - 3,977,907 (-)RGD
cM Map4 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_871789 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI04135 (Get FASTA)   NCBI Sequence Viewer  
  AAI04136 (Get FASTA)   NCBI Sequence Viewer  
  AAP41074 (Get FASTA)   NCBI Sequence Viewer  
  BAE23016 (Get FASTA)   NCBI Sequence Viewer  
  EDL05702 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000046298
  ENSMUSP00000046298.4
GenBank Protein Q7TQA3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_871789   ⟸   NM_181989
- UniProtKB: Q7TQA3 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000046298   ⟸   ENSMUST00000040925

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7TQA3-F1-model_v2 AlphaFold Q7TQA3 1-309 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2668443 AgrOrtholog
Ensembl Genes ENSMUSG00000028236 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000040925 ENTREZGENE
  ENSMUST00000040925.4 UniProtKB/Swiss-Prot
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/Swiss-Prot
InterPro NAD(P)-bd_dom_sf UniProtKB/Swiss-Prot
  SDR_fam UniProtKB/Swiss-Prot
KEGG Report mmu:242285 UniProtKB/Swiss-Prot
MGD MGI:2668443 ENTREZGENE
NCBI Gene 242285 ENTREZGENE
PANTHER EPIDERMAL RETINOL DEHYDROGENASE 2 UniProtKB/Swiss-Prot
  PKSB UniProtKB/Swiss-Prot
Pfam adh_short UniProtKB/Swiss-Prot
PhenoGen Sdr16c5 PhenoGen
PRINTS GDHRDH UniProtKB/Swiss-Prot
  SDRFAMILY UniProtKB/Swiss-Prot
Superfamily-SCOP SSF51735 UniProtKB/Swiss-Prot
UniProt Q7TQA3 ENTREZGENE, UniProtKB/Swiss-Prot