Sdr39u1 (short chain dehydrogenase/reductase family 39U, member 1) - Rat Genome Database

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Gene: Sdr39u1 (short chain dehydrogenase/reductase family 39U, member 1) Rattus norvegicus
Analyze
Symbol: Sdr39u1
Name: short chain dehydrogenase/reductase family 39U, member 1
RGD ID: 1309307
Description: Orthologous to human SDR39U1 (short chain dehydrogenase/reductase family 39U member 1); INTERACTS WITH 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: epimerase family protein SDR39U1; hypothetical protein LOC361044; LOC361044; RGD1309307; similar to HCDI protein
RGD Orthologs
Human
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
GRCr81533,348,057 - 33,350,892 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1533,348,059 - 33,354,600 (-)EnsemblGRCr8
mRatBN7.21529,378,156 - 29,380,989 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,378,026 - 29,381,560 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1531,223,813 - 31,226,646 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,371,029 - 32,373,862 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,613,384 - 30,616,217 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,563,786 - 34,567,465 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,563,786 - 34,566,719 (-)Ensemblrn6Rnor6.0
Rnor_5.01538,452,084 - 38,455,763 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41534,042,416 - 34,045,349 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,951,688 - 28,954,621 (-)NCBICelera
RGSC_v3.11534,058,555 - 34,061,010 (-)NCBI
Cytogenetic Map15p13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:21630459   PMID:34800366  


Genomics

Comparative Map Data
Sdr39u1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81533,348,057 - 33,350,892 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1533,348,059 - 33,354,600 (-)EnsemblGRCr8
mRatBN7.21529,378,156 - 29,380,989 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,378,026 - 29,381,560 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1531,223,813 - 31,226,646 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,371,029 - 32,373,862 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,613,384 - 30,616,217 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,563,786 - 34,567,465 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,563,786 - 34,566,719 (-)Ensemblrn6Rnor6.0
Rnor_5.01538,452,084 - 38,455,763 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41534,042,416 - 34,045,349 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,951,688 - 28,954,621 (-)NCBICelera
RGSC_v3.11534,058,555 - 34,061,010 (-)NCBI
Cytogenetic Map15p13NCBI
SDR39U1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381424,439,766 - 24,442,843 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1424,439,766 - 24,442,905 (-)Ensemblhg38GRCh38
GRCh371424,908,972 - 24,912,049 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,978,812 - 23,981,847 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341423,978,813 - 23,981,822NCBI
Celera144,773,608 - 4,776,643 (-)NCBICelera
Cytogenetic Map14q12NCBI
HuRef145,023,627 - 5,026,664 (-)NCBIHuRef
CHM1_11424,907,545 - 24,910,582 (-)NCBICHM1_1
T2T-CHM13v2.01418,638,496 - 18,641,575 (-)NCBIT2T-CHM13v2.0
Sdr39u1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540935,867,944 - 35,870,847 (+)Ensembl
ChiLan1.0NW_00495540935,867,944 - 35,870,847 (+)NCBIChiLan1.0ChiLan1.0
SDR39U1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21525,794,733 - 25,797,882 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11425,011,225 - 25,014,299 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0145,216,102 - 5,219,234 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11423,339,388 - 23,342,525 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1423,339,388 - 23,342,423 (-)EnsemblpanPan2panpan1.1
SDR39U1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,412,944 - 4,416,013 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl84,412,951 - 4,416,013 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha84,334,649 - 4,337,674 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.084,524,596 - 4,527,621 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl84,524,598 - 4,527,557 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.184,213,926 - 4,216,949 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.084,276,615 - 4,279,640 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.084,538,820 - 4,541,845 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sdr39u1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864036,274,067 - 36,277,227 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936722111,896 - 117,820 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936722111,958 - 114,925 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDR39U1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl774,851,202 - 74,858,921 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1774,851,049 - 74,855,740 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,122,003 - 80,125,107 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SDR39U1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,422,339 - 1,425,490 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603613,108,607 - 13,111,693 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdr39u1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248208,072,577 - 8,075,673 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248208,072,477 - 8,075,664 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sdr39u1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11269,121,386 - 69,124,326 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sdr39u1
16 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:131
Count of miRNA genes:98
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000064643
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152272835342072050Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat

Markers in Region
RH143687  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,381,301 - 29,381,409 (+)MAPPERmRatBN7.2
Rnor_6.01534,567,062 - 34,567,169NCBIRnor6.0
Rnor_5.01538,455,360 - 38,455,467UniSTSRnor5.0
RGSC_v3.41534,045,692 - 34,045,799UniSTSRGSC3.4
Celera1528,954,964 - 28,955,071UniSTS
Cytogenetic Map15p13UniSTS
RH135012  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,379,252 - 29,379,435 (+)MAPPERmRatBN7.2
Rnor_6.01534,565,013 - 34,565,195NCBIRnor6.0
Rnor_5.01538,453,311 - 38,453,493UniSTSRnor5.0
RGSC_v3.41534,043,643 - 34,043,825UniSTSRGSC3.4
Celera1528,952,915 - 28,953,097UniSTS
RH 3.4 Map15260.41UniSTS
Cytogenetic Map15p13UniSTS


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 67 163 91 90 59 88 59 6 351 187 10 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000064643   ⟹   ENSRNOP00000063340
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1533,348,059 - 33,350,901 (-)Ensembl
mRatBN7.2 Ensembl1529,378,026 - 29,380,761 (-)Ensembl
Rnor_6.0 Ensembl1534,563,786 - 34,566,719 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100964   ⟹   ENSRNOP00000089306
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1533,348,059 - 33,354,600 (-)Ensembl
mRatBN7.2 Ensembl1529,378,026 - 29,381,560 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114661   ⟹   ENSRNOP00000096958
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1533,348,059 - 33,351,464 (-)Ensembl
mRatBN7.2 Ensembl1529,378,026 - 29,381,560 (-)Ensembl
RefSeq Acc Id: NM_001108378   ⟹   NP_001101848
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,348,059 - 33,350,862 (-)NCBI
mRatBN7.21529,378,156 - 29,380,959 (-)NCBI
Rnor_6.01534,563,786 - 34,566,719 (-)NCBI
Rnor_5.01538,452,084 - 38,455,763 (-)NCBI
RGSC_v3.41534,042,416 - 34,045,349 (-)RGD
Celera1528,951,688 - 28,954,621 (-)RGD
Sequence:
RefSeq Acc Id: NM_001399584   ⟹   NP_001386513
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,348,059 - 33,350,892 (-)NCBI
mRatBN7.21529,378,156 - 29,380,989 (-)NCBI
RefSeq Acc Id: XM_006251994   ⟹   XP_006252056
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,348,057 - 33,350,814 (-)NCBI
mRatBN7.21529,378,156 - 29,380,921 (-)NCBI
Rnor_6.01534,563,914 - 34,566,721 (-)NCBI
Rnor_5.01538,452,084 - 38,455,763 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001101848   ⟸   NM_001108378
- Peptide Label: isoform 2
- UniProtKB: A6KH64 (UniProtKB/TrEMBL),   A0A8I6GHZ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252056   ⟸   XM_006251994
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000063340   ⟸   ENSRNOT00000064643
Ensembl Acc Id: ENSRNOP00000096958   ⟸   ENSRNOT00000114661
Ensembl Acc Id: ENSRNOP00000089306   ⟸   ENSRNOT00000100964
RefSeq Acc Id: NP_001386513   ⟸   NM_001399584
- Peptide Label: isoform 1
- UniProtKB: A6KH63 (UniProtKB/TrEMBL),   A0A8I6GHZ4 (UniProtKB/TrEMBL)
Protein Domains
DUF1731   NAD-dependent epimerase/dehydratase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYY0-F1-model_v2 AlphaFold D3ZYY0 1-298 view protein structure

Transcriptome

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

Promoters
RGD ID:13699695
Promoter ID:EPDNEW_R10219
Type:single initiation site
Name:Sdr39u1_1
Description:short chain dehydrogenase/reductase family 39U, 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_6.01534,566,749 - 34,566,809EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309307 AgrOrtholog
BioCyc Gene G2FUF-13676 BioCyc
Ensembl Genes ENSRNOG00000020544 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064643 ENTREZGENE
  ENSRNOT00000064643.3 UniProtKB/TrEMBL
  ENSRNOT00000100964 ENTREZGENE
  ENSRNOT00000100964.2 UniProtKB/TrEMBL
  ENSRNOT00000114661.2 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro DUF1731_C UniProtKB/TrEMBL
  Epimerase_deHydtase UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
  Sugar_nucleotide_epimerase_put UniProtKB/TrEMBL
KEGG Report rno:361044 UniProtKB/TrEMBL
NCBI Gene 361044 ENTREZGENE
PANTHER EPIMERASE FAMILY PROTEIN SDR39U1 UniProtKB/TrEMBL
  SUGAR NUCLEOTIDE EPIMERASE RELATED UniProtKB/TrEMBL
Pfam DUF1731 UniProtKB/TrEMBL
  Epimerase UniProtKB/TrEMBL
PhenoGen Sdr39u1 PhenoGen
RatGTEx ENSRNOG00000020544 RatGTEx
Superfamily-SCOP SSF51735 UniProtKB/TrEMBL
UniProt A0A8I6AMY4_RAT UniProtKB/TrEMBL
  A0A8I6GHZ4 ENTREZGENE
  A6KH63 ENTREZGENE, UniProtKB/TrEMBL
  A6KH64 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYY0_RAT UniProtKB/TrEMBL
UniProt Secondary A0A8I6GHZ4 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Sdr39u1  short chain dehydrogenase/reductase family 39U, member 1  RGD1309307  similar to HCDI protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309307  similar to HCDI protein   RGD1309307_predicted  similar to HCDI protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1309307_predicted  similar to HCDI protein (predicted)  LOC361044_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361044_predicted  similar to HCDI protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL