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 endoplasmic reticulum 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81962,624,130 - 62,636,652 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1962,624,150 - 62,636,756 (-)EnsemblGRCr8
mRatBN7.21945,715,366 - 45,727,901 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,715,399 - 45,727,901 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1952,526,898 - 52,539,342 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01953,178,090 - 53,190,532 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01955,422,321 - 55,434,764 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01950,207,960 - 50,220,455 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1950,207,980 - 50,220,455 (-)Ensemblrn6Rnor6.0
Rnor_5.01960,995,923 - 61,008,283 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41947,828,669 - 47,841,129 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1944,986,239 - 44,997,699 (-)NCBICelera
RGSC_v3.11947,843,122 - 47,845,871 (+)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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. 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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1962,624,150 - 62,636,756 (-)EnsemblGRCr8
mRatBN7.21945,715,366 - 45,727,901 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,715,399 - 45,727,901 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1952,526,898 - 52,539,342 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01953,178,090 - 53,190,532 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01955,422,321 - 55,434,764 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01950,207,960 - 50,220,455 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1950,207,980 - 50,220,455 (-)Ensemblrn6Rnor6.0
Rnor_5.01960,995,923 - 61,008,283 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41947,828,669 - 47,841,129 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1944,986,239 - 44,997,699 (-)NCBICelera
RGSC_v3.11947,843,122 - 47,845,871 (+)NCBI
Cytogenetic Map19q12NCBI
SDR42E1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381681,988,855 - 82,011,470 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1681,988,855 - 82,011,482 (-)Ensemblhg38GRCh38
GRCh371682,022,460 - 82,045,075 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361680,588,752 - 80,602,594 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm388117,661,399 - 117,673,689 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8117,661,399 - 117,673,689 (-)Ensemblmm10GRCm38
MGSCv378120,185,299 - 120,195,415 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha570,027,914 - 70,051,811 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0570,318,528 - 70,342,536 (+)NCBIROS_Cfam_1.0ROS_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 (-)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247465,494,792 - 5,504,615 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sdr42e1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11737,316,317 - 37,328,923 (-)NCBIRrattus_CSIRO_v1


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)196124916174246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat

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

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 11 67 161 91 90 59 87 59 6 349 187 11 140 80 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000079760   ⟹   ENSRNOP00000068579
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1962,624,150 - 62,636,652 (-)Ensembl
mRatBN7.2 Ensembl1945,715,399 - 45,727,901 (-)Ensembl
Rnor_6.0 Ensembl1950,207,980 - 50,220,455 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100801   ⟹   ENSRNOP00000087023
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1962,624,150 - 62,636,756 (-)Ensembl
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
RefSeq Acc Id: NP_001258198   ⟸   NM_001271269
- UniProtKB: A0A0G2JT58 (UniProtKB/TrEMBL),   A6IZH6 (UniProtKB/TrEMBL),   A0A8I6GEP8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000068579   ⟸   ENSRNOT00000079760
Ensembl 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
  ENSRNOT00000079760.3 UniProtKB/TrEMBL
  ENSRNOT00000100801.2 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro 3Beta_OHSteriod_DH/Estase UniProtKB/TrEMBL
  Lipid_A_modif_metabolic_enz 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