Sdr42e1 (short chain dehydrogenase/reductase family 42E, member 1) - Rat Genome Database

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Gene: Sdr42e1 (short chain dehydrogenase/reductase family 42E, member 1) Rattus norvegicus
Analyze
Symbol: Sdr42e1
Name: short chain dehydrogenase/reductase family 42E, member 1
RGD ID: 1308481
Description: Predicted to enable oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. Predicted to be involved in steroid biosynthetic process. Predicted to be located in membrane. Orthologous to human SDR42E1 (short chain dehydrogenase/reductase family 42E, member 1); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Hspc105; LOC307897; NAD(P) dependent steroid dehydrogenase-like; RGD1308481; short-chain dehydrogenase/reductase family 42E member 1; similar to RIKEN cDNA 4632417N05
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81962,624,130 - 62,636,652 (-)NCBIGRCr8
mRatBN7.21945,715,366 - 45,727,901 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,715,399 - 45,727,901 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1952,526,898 - 52,539,342 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01953,178,090 - 53,190,532 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01955,422,321 - 55,434,764 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01950,207,960 - 50,220,455 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1950,207,980 - 50,220,455 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,995,923 - 61,008,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,828,669 - 47,841,129 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11947,843,122 - 47,845,871 (+)NCBI
Celera1944,986,239 - 44,997,699 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548  


Genomics

Comparative Map Data
Sdr42e1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81962,624,130 - 62,636,652 (-)NCBIGRCr8
mRatBN7.21945,715,366 - 45,727,901 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,715,399 - 45,727,901 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1952,526,898 - 52,539,342 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01953,178,090 - 53,190,532 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01955,422,321 - 55,434,764 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01950,207,960 - 50,220,455 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1950,207,980 - 50,220,455 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,995,923 - 61,008,283 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,828,669 - 47,841,129 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11947,843,122 - 47,845,871 (+)NCBI
Celera1944,986,239 - 44,997,699 (-)NCBICelera
Cytogenetic Map19q12NCBI
SDR42E1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381681,988,855 - 82,011,470 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1681,988,855 - 82,011,481 (-)EnsemblGRCh38hg38GRCh38
GRCh371682,022,460 - 82,045,075 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361680,588,752 - 80,602,594 (-)NCBINCBI36Build 36hg18NCBI36
Celera1666,329,095 - 66,343,762 (-)NCBICelera
Cytogenetic Map16q23.3NCBI
HuRef1667,784,802 - 67,798,644 (-)NCBIHuRef
CHM1_11683,442,622 - 83,456,464 (-)NCBICHM1_1
T2T-CHM13v2.01688,052,572 - 88,075,187 (-)NCBIT2T-CHM13v2.0
Sdr42e1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398118,388,138 - 118,400,428 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8118,388,138 - 118,400,428 (-)EnsemblGRCm39 Ensembl
GRCm388117,661,399 - 117,673,689 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8117,661,399 - 117,673,689 (-)EnsemblGRCm38mm10GRCm38
MGSCv378120,185,299 - 120,195,415 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368120,547,376 - 120,557,492 (-)NCBIMGSCv36mm8
Celera8121,882,132 - 121,892,250 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map864.69NCBI
Sdr42e1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555642,019,135 - 2,042,905 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555642,019,135 - 2,042,680 (+)NCBIChiLan1.0ChiLan1.0
SDR42E1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21891,739,271 - 91,761,985 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11697,658,901 - 97,681,615 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01662,598,730 - 62,615,766 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11682,024,473 - 82,038,332 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1682,021,008 - 82,038,332 (-)Ensemblpanpan1.1panPan2
SDR42E1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1570,028,685 - 70,035,924 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl570,033,969 - 70,035,729 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha570,027,914 - 70,051,811 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0570,318,528 - 70,342,536 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl570,338,812 - 70,340,573 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1570,261,447 - 70,283,578 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0570,097,651 - 70,121,527 (+)NCBIUNSW_CanFamBas_1.0
Sdr42e1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934930,186,548 - 30,196,828 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647529,391,957 - 29,402,487 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647529,392,736 - 29,402,487 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDR42E1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl66,387,363 - 6,399,629 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.166,387,280 - 6,400,371 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SDR42E1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1567,429,130 - 67,442,768 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl567,427,810 - 67,442,054 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660478,391,898 - 8,405,773 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdr42e1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247465,494,404 - 5,506,172 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247465,494,792 - 5,504,615 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sdr42e1
77 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat

Markers in Region
BQ196592  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21945,715,476 - 45,715,693 (+)MAPPERmRatBN7.2
Rnor_6.01950,208,058 - 50,208,274NCBIRnor6.0
Rnor_5.01960,996,021 - 60,996,237UniSTSRnor5.0
RGSC_v3.41947,842,024 - 47,842,240UniSTSRGSC3.4
Celera1944,986,337 - 44,986,553UniSTS
RH 3.4 Map19616.2UniSTS
Cytogenetic Map19q12UniSTS


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 23 23 23
Low 1 38 33 18 19 18 56 35 39 11
Below cutoff 5 1 7 10 18 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079760   ⟹   ENSRNOP00000068579
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1945,715,399 - 45,727,901 (-)Ensembl
Rnor_6.0 Ensembl1950,207,980 - 50,220,455 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100801   ⟹   ENSRNOP00000087023
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1945,715,399 - 45,721,737 (-)Ensembl
RefSeq Acc Id: NM_001271269   ⟹   NP_001258198
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81962,624,130 - 62,636,652 (-)NCBI
mRatBN7.21945,715,379 - 45,727,901 (-)NCBI
Rnor_6.01950,207,960 - 50,220,455 (-)NCBI
Rnor_5.01960,995,923 - 61,008,283 (-)NCBI
Celera1944,986,239 - 44,997,699 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001258198 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92654 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000068579
  ENSRNOP00000068579.2
  ENSRNOP00000087023.1
Reference Protein Sequences
RefSeq Acc Id: NP_001258198   ⟸   NM_001271269
- UniProtKB: A0A0G2JT58 (UniProtKB/TrEMBL),   A6IZH6 (UniProtKB/TrEMBL),   A0A8I6GEP8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068579   ⟸   ENSRNOT00000079760
RefSeq Acc Id: ENSRNOP00000087023   ⟸   ENSRNOT00000100801
Protein Domains
3-beta hydroxysteroid dehydrogenase/isomerase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JT58-F1-model_v2 AlphaFold A0A0G2JT58 1-392 view protein structure

Transcriptome

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

Promoters
RGD ID:13701172
Promoter ID:EPDNEW_R11695
Type:initiation region
Name:Sdr42e1_1
Description:short chain dehydrogenase/reductase family 42E, member 1
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_6.01950,220,424 - 50,220,484EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308481 AgrOrtholog
BioCyc Gene G2FUF-5543 BioCyc
Ensembl Genes ENSRNOG00000051819 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079760 ENTREZGENE
  ENSRNOT00000079760.2 UniProtKB/TrEMBL
  ENSRNOT00000100801.1 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro 3Beta_OHSteriod_DH/Estase UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
KEGG Report rno:307897 UniProtKB/TrEMBL
NCBI Gene 307897 ENTREZGENE
PANTHER BIFUNCTIONAL POLYMYXIN RESISTANCE PROTEIN ARNA UniProtKB/TrEMBL
  EPIMERASE DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam 3Beta_HSD UniProtKB/TrEMBL
PhenoGen Sdr42e1 PhenoGen
RatGTEx ENSRNOG00000051819 RatGTEx
Superfamily-SCOP SSF51735 UniProtKB/TrEMBL
UniProt A0A0G2JT58 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GEP8 ENTREZGENE, UniProtKB/TrEMBL
  A6IZH6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-01-05 Sdr42e1  short chain dehydrogenase/reductase family 42E, member 1  Hspc105  NAD(P) dependent steroid dehydrogenase-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Hspc105  NAD(P) dependent steroid dehydrogenase-like  RGD1308481_predicted  similar to RIKEN cDNA 4632417N05 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1308481_predicted  similar to RIKEN cDNA 4632417N05 (predicted)  LOC307897_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC307897_predicted  similar to RIKEN cDNA 4632417N05 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL