RDH5 (retinol dehydrogenase 5) - Rat Genome Database

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Gene: RDH5 (retinol dehydrogenase 5) Canis lupus familiaris
Analyze
Symbol: RDH5
Name: retinol dehydrogenase 5
RGD ID: 12058125
Description: ENCODES a protein that exhibits all-trans-retinol dehydrogenase (NAD+) activity (inferred); androstan-3-alpha,17-beta-diol dehydrogenase (NAD+) activity (inferred); androsterone dehydrogenase [NAD(P)+] activity (inferred); INVOLVED IN retinoid metabolic process (inferred); steroid metabolic process (inferred); PARTICIPATES IN retinoid cycle metabolic pathway; ASSOCIATED WITH Congenital Abnormalities (ortholog); congenital stationary night blindness (ortholog); fundus albipunctatus (ortholog); FOUND IN cell body (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: 11-cis retinol dehydrogenase; biogenesis of lysosome-related organelles complex-1, subunit 1; retinol dehydrogenase 5 (11-cis/9-cis)
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110120,386 - 125,195 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10120,057 - 125,197 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10182,788 - 187,948 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010127,659 - 132,829 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10124,738 - 132,464 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110105,355 - 110,512 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010348,472 - 353,628 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.010472,362 - 477,524 (+)NCBIUU_Cfam_GSD_1.0
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
RDH5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110120,386 - 125,195 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl10120,057 - 125,197 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10182,788 - 187,948 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010127,659 - 132,829 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10124,738 - 132,464 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110105,355 - 110,512 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010348,472 - 353,628 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.010472,362 - 477,524 (+)NCBIUU_Cfam_GSD_1.0
RDH5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381255,720,393 - 55,724,705 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1255,720,367 - 55,724,705 (+)EnsemblGRCh38hg38GRCh38
GRCh371256,114,177 - 56,118,489 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,400,488 - 54,404,756 (+)NCBINCBI36Build 36hg18NCBI36
Build 341254,400,487 - 54,404,754NCBI
Celera1255,766,620 - 55,770,996 (+)NCBICelera
Cytogenetic Map12q13.2NCBI
HuRef1253,152,966 - 53,157,341 (+)NCBIHuRef
CHM1_11256,080,940 - 56,085,314 (+)NCBICHM1_1
T2T-CHM13v2.01255,687,027 - 55,691,339 (+)NCBIT2T-CHM13v2.0
Rdh5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,749,457 - 128,755,906 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,749,462 - 128,758,757 (-)EnsemblGRCm39 Ensembl
GRCm3810128,913,588 - 128,920,037 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,913,593 - 128,922,888 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710128,350,646 - 128,356,353 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610128,316,537 - 128,322,222 (-)NCBIMGSCv36mm8
Celera10131,306,272 - 131,311,979 (-)NCBICelera
Cytogenetic Map10D3NCBI
cM Map1077.19NCBI
Rdh5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr871,912,120 - 1,931,836 (-)NCBIGRCr8
mRatBN7.271,341,172 - 1,346,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl71,340,934 - 1,351,558 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx74,105,451 - 4,111,129 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.075,981,111 - 5,986,789 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.076,282,399 - 6,288,308 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.073,335,681 - 3,342,573 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl73,335,742 - 3,342,491 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.073,305,900 - 3,311,463 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.472,212,121 - 2,217,394 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.172,215,941 - 2,216,641 (-)NCBI
Celera71,211,351 - 1,216,834 (-)NCBICelera
Cytogenetic Map7q11NCBI
Rdh5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,352,012 - 3,365,080 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,356,324 - 3,361,701 (+)NCBIChiLan1.0ChiLan1.0
RDH5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21038,603,587 - 38,608,452 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11238,600,356 - 38,605,222 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01233,186,871 - 33,191,539 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11233,911,309 - 33,916,301 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1233,911,309 - 33,920,506 (-)Ensemblpanpan1.1panPan2
Rdh5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,674,990 - 58,678,776 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936646191,128 - 199,777 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936646191,136 - 195,279 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RDH5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,166,510 - 21,170,897 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,166,869 - 21,170,913 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2522,646,730 - 22,650,759 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RDH5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11151,667,461 - 51,672,386 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1151,668,803 - 51,672,192 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037194,322,273 - 194,327,136 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rdh5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480212,290,688 - 12,304,712 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480212,293,578 - 12,299,981 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RDH5
44 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 22 16 6 6 6 6 33 22 12 14 10

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_014117128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014117129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_014117130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038487692 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038487693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038487694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038549580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038549581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038549582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038613552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038613553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038613554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038639063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038639072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038639083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038678914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038678915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038678916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSCAFT00000000100   ⟹   ENSCAFP00000000084
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl10120,057 - 125,197 (+)Ensembl
Ensembl Acc Id: ENSCAFT00845009701   ⟹   ENSCAFP00845007585
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl10124,738 - 132,464 (+)Ensembl
RefSeq Acc Id: XM_038487692   ⟹   XP_038343620
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.110105,355 - 110,512 (+)NCBI
RefSeq Acc Id: XM_038487693   ⟹   XP_038343621
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.110105,355 - 110,512 (+)NCBI
RefSeq Acc Id: XM_038487694   ⟹   XP_038343622
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.110105,355 - 110,512 (+)NCBI
RefSeq Acc Id: XM_038549580   ⟹   XP_038405508
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.010472,362 - 477,524 (+)NCBI
RefSeq Acc Id: XM_038549581   ⟹   XP_038405509
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.010472,362 - 477,524 (+)NCBI
RefSeq Acc Id: XM_038549582   ⟹   XP_038405510
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.010472,362 - 477,524 (+)NCBI
RefSeq Acc Id: XM_038613552   ⟹   XP_038469480
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.010348,472 - 353,628 (+)NCBI
RefSeq Acc Id: XM_038613553   ⟹   XP_038469481
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.010348,472 - 353,628 (+)NCBI
RefSeq Acc Id: XM_038613554   ⟹   XP_038469482
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.010348,472 - 353,628 (+)NCBI
RefSeq Acc Id: XM_038639063   ⟹   XP_038494991
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha10182,788 - 187,948 (+)NCBI
RefSeq Acc Id: XM_038639072   ⟹   XP_038495000
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha10182,788 - 187,948 (+)NCBI
RefSeq Acc Id: XM_038639083   ⟹   XP_038495011
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha10182,788 - 187,948 (+)NCBI
RefSeq Acc Id: XM_038678914   ⟹   XP_038534842
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.010127,659 - 132,829 (+)NCBI
RefSeq Acc Id: XM_038678915   ⟹   XP_038534843
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.010127,659 - 132,829 (+)NCBI
RefSeq Acc Id: XM_038678916   ⟹   XP_038534844
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.010127,659 - 132,829 (+)NCBI
Ensembl Acc Id: ENSCAFP00000000084   ⟸   ENSCAFT00000000100
RefSeq Acc Id: XP_038343620   ⟸   XM_038487692
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038343621   ⟸   XM_038487693
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038343622   ⟸   XM_038487694
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038469480   ⟸   XM_038613552
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038469481   ⟸   XM_038613553
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038469482   ⟸   XM_038613554
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038534842   ⟸   XM_038678914
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LRK9 (UniProtKB/TrEMBL),   A0A8I3MTG2 (UniProtKB/TrEMBL),   A0A8P0N389 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038534843   ⟸   XM_038678915
- Peptide Label: isoform X2
- UniProtKB: A0A8C0QE71 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038534844   ⟸   XM_038678916
- Peptide Label: isoform X2
- UniProtKB: A0A8C0QE71 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038494991   ⟸   XM_038639063
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LRK9 (UniProtKB/TrEMBL),   A0A8I3MTG2 (UniProtKB/TrEMBL),   A0A8P0N389 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038495000   ⟸   XM_038639072
- Peptide Label: isoform X2
- UniProtKB: A0A8C0QE71 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038495011   ⟸   XM_038639083
- Peptide Label: isoform X2
- UniProtKB: A0A8C0QE71 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038405508   ⟸   XM_038549580
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LRK9 (UniProtKB/TrEMBL),   A0A8I3MTG2 (UniProtKB/TrEMBL),   A0A8P0N389 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038405509   ⟸   XM_038549581
- Peptide Label: isoform X2
- UniProtKB: A0A8C0QE71 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038405510   ⟸   XM_038549582
- Peptide Label: isoform X2
- UniProtKB: A0A8C0QE71 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSCAFP00845007585   ⟸   ENSCAFT00845009701

Promoters
RGD ID:13684858
Promoter ID:EPDNEW_C2925
Type:single initiation site
Name:RDH5_1
Description:retinol dehydrogenase 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.110121,630 - 121,690EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000000063 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030014084 UniProtKB/TrEMBL
  ENSCAFG00040003595 UniProtKB/TrEMBL
  ENSCAFG00845005441 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000000100.5 UniProtKB/TrEMBL
  ENSCAFT00030026140.1 UniProtKB/TrEMBL
  ENSCAFT00040006851.1 UniProtKB/TrEMBL
  ENSCAFT00845009701 ENTREZGENE
  ENSCAFT00845009701.1 UniProtKB/TrEMBL
Gene3D-CATH NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
InterPro NAD(P)-bd_dom_sf UniProtKB/TrEMBL
  Sc_DH/Rdtase_CS UniProtKB/TrEMBL
  SDR_fam UniProtKB/TrEMBL
NCBI Gene RDH5 ENTREZGENE
PANTHER RETINOL DEHYDROGENASE 5 UniProtKB/TrEMBL
  SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 9C UniProtKB/TrEMBL
Pfam adh_short UniProtKB/TrEMBL
PRINTS GDHRDH UniProtKB/TrEMBL
  SDRFAMILY UniProtKB/TrEMBL
PROSITE ADH_SHORT UniProtKB/TrEMBL
Superfamily-SCOP SSF51735 UniProtKB/TrEMBL
UniProt A0A8C0LRK9 ENTREZGENE
  A0A8C0QE71 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3MTG2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0N389 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:45454 ENTREZGENE