Rdh13 (retinol dehydrogenase 13) - Rat Genome Database

Name: Rdh13
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Rdh13 (retinol dehydrogenase 13) Ictidomys tridecemlineatus

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Symbol:

Rdh13

Name:

retinol dehydrogenase 13

RGD ID:

12583717

Description:

ENCODES a protein that exhibits all-trans-retinol dehydrogenase (NADP+) activity (inferred); oxidoreductase activity (inferred); INVOLVED IN eye photoreceptor cell development (ortholog); response to high light intensity (ortholog); retina layer formation (ortholog); ASSOCIATED WITH Chemical and Drug Induced Liver Injury (ortholog); Experimental Liver Cirrhosis (ortholog); Necrosis (ortholog); FOUND IN mitochondrion (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

retinol dehydrogenase 13 (all-trans/9-cis)

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409349	2,190,702 - 2,203,203 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936886	355,879 - 368,608 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936886	356,068 - 368,525 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Chemical and Drug Induced Liver Injury (ISO)

Experimental Liver Cirrhosis (ISO)

Necrosis (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

eye photoreceptor cell development (IEA,ISO)

response to high light intensity (IEA,ISO)

retina layer formation (IEA,ISO)

retinal metabolic process (IEA)

retinol metabolic process (IEA)

Cellular Component

mitochondrial inner membrane (IEA)

mitochondrion (ISO)

Molecular Function

all-trans-retinol dehydrogenase (NADP+) activity (IEA)

oxidoreductase activity (IEA)

References

Additional References at PubMed

PMID:22301074

Genomics

Comparative Map Data

Rdh13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409349	2,190,702 - 2,203,203 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936886	355,879 - 368,608 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936886	356,068 - 368,525 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RDH13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	55,039,103 - 55,069,520 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	55,039,108 - 55,071,291 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	55,555,684 - 55,580,888 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	60,247,519 - 60,272,709 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	19	60,247,522 - 60,272,709	NCBI
Celera	19	52,595,491 - 52,620,880 (-)	NCBI		Celera
Cytogenetic Map	19	q13.42	NCBI
HuRef	19	51,879,124 - 51,904,646 (-)	NCBI		HuRef
CHM1_1	19	55,549,512 - 55,574,991 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	19	58,133,057 - 58,164,455 (-)	NCBI		T2T-CHM13v2.0

Rdh13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	4,428,664 - 4,474,279 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	4,427,769 - 4,448,648 (-)	Ensembl		GRCm39 Ensembl
GRCm38	7	4,425,665 - 4,471,280 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	4,424,770 - 4,445,649 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	4,377,267 - 4,397,259 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	4,028,754 - 4,048,696 (-)	NCBI		MGSCv36	mm8
Celera	7	4,175,108 - 4,195,097 (-)	NCBI		Celera
Cytogenetic Map	7	A1	NCBI
cM Map	7	2.56	NCBI

Rdh13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	78,415,765 - 78,444,116 (+)	NCBI		GRCr8
mRatBN7.2	1	69,373,014 - 69,401,454 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	69,373,113 - 69,400,908 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	74,732,033 - 74,759,827 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	83,296,338 - 83,324,132 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	76,445,981 - 76,467,129 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	72,956,017 - 72,983,811 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	72,956,026 - 72,984,350 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	75,563,122 - 75,590,916 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	68,102,308 - 68,130,102 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	68,180,552 - 68,206,726 (+)	NCBI
Celera	1	67,727,709 - 67,754,934 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

Rdh13
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955567	1,091,636 - 1,108,732 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955567	1,091,636 - 1,108,648 (+)	NCBI	ChiLan1.0	ChiLan1.0

RDH13
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	20	61,164,188 - 61,202,316 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	62,893,564 - 62,931,725 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	52,081,674 - 52,107,781 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	60,776,108 - 60,801,313 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	60,776,114 - 60,794,267 (-)	Ensembl	panpan1.1		panPan2

RDH13
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	102,539,363 - 102,552,749 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	102,539,124 - 102,554,027 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	102,596,419 - 102,609,782 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	103,192,952 - 103,206,329 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	103,192,925 - 103,207,630 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	102,829,842 - 102,843,203 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	102,541,523 - 102,554,897 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	103,305,733 - 103,319,108 (+)	NCBI		UU_Cfam_GSD_1.0

RDH13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	59,274,387 - 59,292,765 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	59,274,383 - 59,293,139 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

RDH13
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	6	47,634,909 - 47,652,829 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	47,636,094 - 47,652,772 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	190,278 - 206,824 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rdh13
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624832	2,141,902 - 2,159,009 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624832	2,141,906 - 2,159,009 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005341561	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010004409	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000001119 ⟹ ENSSTOP00000000999

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936886	355,879 - 368,608 (-)	Ensembl

RefSeq Acc Id:

XM_005341561 ⟹ XP_005341618

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024409349	2,190,702 - 2,203,203 (+)	NCBI
SpeTri2.0	NW_004936886	356,068 - 368,525 (-)	NCBI

Sequence:

show sequence

GGGCCGCGGCCGGCGGGGCTGCACGGCCGCACGTGGGTAGCTGCGCTGCGTGCTGGTTCTCGGG
CCGCCTCGGCGGAGCCCGCTCCTCGCCGGGCATGAGCCGCTACCTGCTGCCGGCGTCGGTGCTG
GGCACCGCGGTGGGTGGCGCCGTGCTGCTCAAGGACTATGTTGCTGGTGGGACTTGTCCCAGCA
AGGCCACCATACCCGGGAAGACAGTCATCGTGACGGGAGCCAACACAGGCATCGGGAAACAAAC
TGCCTTGGAACTGGCCAGAAGAGGAGGCCACGTCATCCTGGCCTGCCGAGACATGGAGAAGTGC
GAGGCTGCGGCCAGGGACATCCGCGGGGAGACCCTCAATCACCGCGTCAGCGCCCGGCACCTGG
ACCTGGCTTCCCTCAAGTCCGTCCGGGAGTTTGCTGCGAAGGTCATTGAAGAGGAGGAGCGGGT
GGACATTCTGATCAACAACGCTGCCGTGATGCGGTGCCCGCACTGGACCACTGAGGACGGCTTC
GAGATGCAGCTTGGCGTCAACTACCTGGGTCACTTCCTCTTGACGAACCTGCTGCTGGACAAGC
TGAAAGCCTCGGCCCCTGGGCGTGTGGTTAACCTCTCGTCCCTGGCCCACGTCGCCGGGCACGT
GGACCTCGAGGACCTGAACTGGCAGAGGAGGAAGTACGACACCAAGGCCGCCTACTGCCAGAGC
AAGCTGGCCCTGGTCCTCTTCACCAAGGAGCTGAGCCGGCGGCTGCGAGGCACGGGTGTGACCG
TCAACGCGCTGCACCCTGGTGTGGCCAGGACGGAGCTGGGCAGACACACGGGCATGCACAGGTC
CACCTTCTCCAGCTTCACACTCGGGCCCATCTTCTGGCTGCTGGTCAAGAGCCCCCAGCTGGCA
GCGCAGCCCAGCACCTACCTGGCCGTGGCCGAGGAACTGGAGGACGTTTCCGGGAAGTACTTTG
ATGGATTCAAAGAGAAGGCACCAGCTCCCGAGGCTGAGGATGAGGAACTAGCCCAGAGGCTTTG
GGCTGAAAGTGCCCGCTTGGTGGGCTTGGACTTGTCTCGTGGGTCCCCTGTGAGGGGACAGTCC
CTGTCCAGGTCACCTCTGGAGCAGGTTTGAAAGCCACTTGGGTCTCCAGGATGGAGCTTCAGGA
TCCAGGATGCTGCCAGCCTTGCCTCTATCATTCTCTGGGGGACAGTGTTGGCACCATGTGAGCC
TCAAGAACGAGGGTGGAGGCTGCCATACCCTCGCCATCCTCCAGGGGGCAAATTGGACTCAGCC
TCAAGACCAAGGGCACAGGCTGCCACACCCTCGCCATCCTCCAGTACCGGCCCCATGTCCATCA
GCAGCTCACAGTGGGTTGAGCCTGCTGGGGGCTTGCAGGAACCACGAGCCCTGCTGACAGTGTG
TGAGCTGGGCCATCAGAAGCCTGCCTCTCTTTGGGAATCAAACAGCAGGGAGGAGTGGTGCTGT
GGAGAGGCACTGTGCCCTGTGTGCTCTGGGCCTGGGCACTCACCTCATGTCGCCTGGCTGAGGG
AAGGGCCAGGTGGGCGTGCCAGACCCCTCCACCAGGGTGTGCCAGACCTGGGCCCGCCACCCTG
CTCCAGGGCCCGCCTCGCTGATTCAGTCCTCTGTGGGGAGGTGCCAGTGAGCGCAGGACGACGG
CTGTGTCCTTACTCCTTTCAGGGACAGACCCTCTGCCCTCGCTGAAGCCTGGGGTTCTTGTGAG
ACGTGTCAGAAATGGGGCGGGAGGGGCTGAGGCTGGGACGCAGTGGCAGAGCGCCCGCCCAGCA
CGTGTGAGGCG

hide sequence

Protein Sequences


Protein RefSeqs	XP_005341618	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000000999.3
GenBank Protein	KAG3255643	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005341618 ⟸ XM_005341561

- UniProtKB:

I3LY02 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSRYLLPASVLGTAVGGAVLLKDYVAGGTCPSKATIPGKTVIVTGANTGIGKQTALELARRGGH
VILACRDMEKCEAAARDIRGETLNHRVSARHLDLASLKSVREFAAKVIEEEERVDILINNAAVM
RCPHWTTEDGFEMQLGVNYLGHFLLTNLLLDKLKASAPGRVVNLSSLAHVAGHVDLEDLNWQRR
KYDTKAAYCQSKLALVLFTKELSRRLRGTGVTVNALHPGVARTELGRHTGMHRSTFSSFTLGPI
FWLLVKSPQLAAQPSTYLAVAEELEDVSGKYFDGFKEKAPAPEAEDEELAQRLWAESARLVGLD
LSRGSPVRGQSLSRSPLEQV

hide sequence

Ensembl Acc Id:

ENSSTOP00000000999 ⟸ ENSSTOT00000001119

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000001121	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000001119.3	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	Rdh13	ENTREZGENE
PANTHER	PHOSPHATIDYLINOSITOL-GLYCAN BIOSYNTHESIS CLASS F PROTEIN-RELATED	UniProtKB/TrEMBL
	PHOSPHATIDYLINOSITOL-GLYCAN BIOSYNTHESIS CLASS F PROTEIN-RELATED	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	I3LY02	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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