UBD (ubiquitin D) - Rat Genome Database

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

Gene: UBD (ubiquitin D) Chlorocebus sabaeus

Analyze

Symbol:

UBD

Name:

ubiquitin D

RGD ID:

18769992

Description:

ENCODES a protein that exhibits proteasome binding (inferred); INVOLVED IN response to hypoxia (ortholog); response to ischemia (ortholog); response to organonitrogen compound (ortholog); ASSOCIATED WITH Alcoholic Fatty Liver (ortholog); Animal Hepatitis (ortholog); Breast Neoplasms (ortholog); FOUND IN aggresome (inferred); cytoplasm (inferred); fibrillar center (inferred)

Type:

protein-coding

RefSeq Status:

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	UBD (ubiquitin D)	NCBI	Ortholog
Mus musculus (house mouse):	Ubd (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Ubd (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ubd (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	UBD (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	UBD (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ubd (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	UBD (ubiquitin D)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	17	43,061,243 - 43,065,135 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	43,061,826 - 43,064,869 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666044	29,083,461 - 29,084,403 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Alcoholic Fatty Liver (ISO)

Animal Hepatitis (ISO)

Breast Neoplasms (ISO)

celiac disease (ISO)

Experimental Liver Cirrhosis (ISO)

hepatocellular carcinoma (ISO)

megacolon (ISO)

metabolic dysfunction-associated steatohepatitis (ISO)

myocardial infarction (ISO)

primary biliary cholangitis (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aggresome assembly (IEA)

myeloid dendritic cell differentiation (IEA)

positive regulation of apoptotic process (IEA)

positive regulation of canonical NF-kappaB signal transduction (IEA)

protein ubiquitination (IEA)

regulation of mitotic cell cycle phase transition (IEA)

response to hypoxia (ISO)

response to ischemia (ISO)

response to organonitrogen compound (ISO)

response to tumor necrosis factor (IEA)

response to type II interferon (IEA)

ubiquitin-dependent protein catabolic process (IEA)

Cellular Component

aggresome (IEA)

cytoplasm (IEA)

fibrillar center (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

proteasome binding (IEA)

protein binding (ISO)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

UBD
(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	17	43,061,243 - 43,065,135 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	43,061,826 - 43,064,869 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666044	29,083,461 - 29,084,403 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

UBD
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	29,555,515 - 29,559,732 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	29,555,515 - 29,559,732 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	29,523,292 - 29,527,509 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	29,631,387 - 29,635,681 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	29,631,386 - 29,635,681	NCBI
Celera	6	31,129,472 - 31,133,785 (-)	NCBI		Celera
Cytogenetic Map	6	p22.1	NCBI
HuRef	6	29,330,776 - 29,334,782 (-)	NCBI		HuRef
CHM1_1	6	29,525,538 - 29,529,852 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	29,430,199 - 29,434,416 (-)	NCBI		T2T-CHM13v2.0

Ubd
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	37,504,783 - 37,506,992 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	37,504,783 - 37,506,986 (+)	Ensembl		GRCm39 Ensembl
GRCm38	17	37,193,892 - 37,196,101 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	37,193,892 - 37,196,095 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	37,330,837 - 37,333,046 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	36,801,615 - 36,803,894 (+)	NCBI		MGSCv36	mm8
Celera	17	40,616,710 - 40,618,919 (+)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	19.16	NCBI

Ubd
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	1,390,734 - 1,392,685 (-)	NCBI		GRCr8
mRatBN7.2	20	1,385,487 - 1,387,438 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	1,385,864 - 1,408,639 (-)	Ensembl		mRatBN7.2 Ensembl
mRatBN7.2 Ensembl	20	1,383,424 - 1,389,406 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	20	1,438,896 - 1,440,847 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	1,442,376 - 1,444,327 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	1,383,905 - 1,385,856 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	1,876,175 - 1,878,126 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	1,876,173 - 1,897,814 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	3,917,777 - 3,919,728 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	1,475,944 - 1,477,895 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	20	1,475,953 - 1,477,895 (-)	NCBI
Celera	20	2,096,127 - 2,098,078 (-)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

Ubd
(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_004955583	29,438 - 31,555 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955583	29,438 - 29,873 (-)	NCBI	ChiLan1.0	ChiLan1.0

UBD
(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	5	44,174,991 - 44,179,180 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	40,138,320 - 40,142,544 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	29,359,680 - 29,364,014 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	30,018,444 - 30,022,814 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	30,018,444 - 30,022,814 (-)	Ensembl	panpan1.1		panPan2

UBD
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	35	26,426,919 - 26,436,189 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
ROS_Cfam_1.0	35	26,734,293 - 26,741,905 (+)	NCBI		ROS_Cfam_1.0
UNSW_CanFamBas_1.0	35	26,451,220 - 26,457,222 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	35	27,920,623 - 27,928,239 (+)	NCBI		UU_Cfam_GSD_1.0

Ubd
(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_024404946	32,370,418 - 32,400,704 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936723	1,218,258 - 1,221,451 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936723	1,218,621 - 1,221,070 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

UBD
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	22,501,130 - 22,503,094 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	22,501,130 - 22,502,883 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	25,330,502 - 25,332,256 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

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

	endocrine system	hemolymphoid system	nervous system
High
Medium
Low	21	12	21
Below cutoff	14	5	18

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007973301	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC242652	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACDXN010000012	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000006118 ⟹ ENSCSAP00000004330

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	17	43,061,826 - 43,064,869 (+)	Ensembl

RefSeq Acc Id:

XM_007973301 ⟹ XP_007971492

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	17	43,061,243 - 43,065,135 (+)	NCBI
Vero_WHO_p1.0	NW_023666044	29,083,461 - 29,084,403 (-)	NCBI

Sequence:

show sequence

TAGCAAGTGGCCCTCCTGGGACTCTAACTTGTGTCTCCTCTCAGTCTGAGGTTATTTCTCCTAT
GTCTTCTTAAGGCATATTTTACACCTTCTGCCAGACTAGCCATGTCAGGCTCACAGTCACAGCA
CTCCACACAATGCTGACTGCCGTATCCTGCCTGGGTGCTCTCGTTCTTAGGACGGCCCCTGAGT
AATGGGGTGCTCTTAAAGGCAGCATGAGAGGTTCAGCAAGCATTACAGGTCTTCATGCCAGTGA
GGGCCCAGGCCACAGGACGGACAGTAATAAGTCAAGACTGGGAGAGGAGAGGTGGATTTTTAAT
CAGGGAAAAGTTTTCAACACAGAAAGACCATCCCGTTTGGAATGAGGATTGCAAATAGATTGCC
TGAGGGGAGAAGTACGTAATCAGAAAGCATTCTTTGTTTATTAACTCCTGCCCAGCAAAAGTGA
AAGAAAATTCATGGGAGCATGCAAGAACAAAGGGCACAGCAAAGCTGGACAAACACAGCAATCC
AGGAGGGGATTTCCAATTCAACGCTGGTATATAAGCTGGATGCAAAATCCTTTTTCTGTCTCTG
GTTTCTGGCCCCTTGACTGCAAAGATGGCTCCCAATGCTTCCTGCCTCACTGTGCATGTTTGCT
CCGAGGAATGGGATTTAATGACCTTTGATGCCAACCCAGAGGACAGCGTGAAAAAAATCAATGA
ACACGTCCGGTCTAAGACCAAGGTTCCTGTGCAGGACCAGGTTCTTTTGCTGGGCTCCAAGATC
CTAAAGCCACGGAGAAGGCTCTCATCTTATGGCATTGACAAGGAGAAGACCATCCACCTTACCC
TGAAAGTGGTGAAGCCTAGTGATGAGGAGCTGCCCTTGTATCTTGTGGAGTCAGGTGATGAGGG
GCAGAGGCACCTCCTCCAGGTGCGAAGGTCCAGCTCAGTGGCACAAGTGAAAGCAATGATCGAG
ACCAAGACGGGTGTAACCCCTGAGACCCAGATTGTGAATTGCAATGGAAAGAGACTGGAAGATG
GGAAGATGATGGCAGATTATGGAATCAGAAAGGGCAACTTACTCTTCCTGACATCTTATTGTAT
TGCAGGGTGACCACCCTGGGGATGGGGTGTTGGCAAGGGCCAAAAAGCTTATTTCTTCTAATCT
CTTAATCAACGACCACATCCTTTGATGATTTCCCAAAATTAATGAGAATGAGATGAGTAGAGTA
AGATTTGCTTGGGATGGGTAGGATGAAGAATATTGTCCAACTCTGTTTCTTTGATTCTAACACA
ATTAATTAAGTGGCAGGATTTTTAATAATGTATTACTGAGACTAGTAAATAAAATTTTAAGGCA
AAATACAGCATTCAAAGCCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_007971492	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000004330.1

RefSeq Acc Id:	XP_007971492 ⟸ XM_007973301
- UniProtKB:	A0A0D9R6U1 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000004330 ⟸ ENSCSAT00000006118

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000008065	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000006118.1	UniProtKB/TrEMBL
InterPro	Ubiquitin-like_dom	UniProtKB/TrEMBL
	Ubiquitin-like_domsf	UniProtKB/TrEMBL
	Ubiquitin_D	UniProtKB/TrEMBL
	Ubiquitin_dom	UniProtKB/TrEMBL
KEGG Report	csab:103221875	UniProtKB/TrEMBL
NCBI Gene	UBD	ENTREZGENE
PANTHER	PTHR47731	UniProtKB/TrEMBL
	UBIQUITIN D	UniProtKB/TrEMBL
Pfam	ubiquitin	UniProtKB/TrEMBL
PRINTS	UBIQUITIN	UniProtKB/TrEMBL
PROSITE	UBIQUITIN_2	UniProtKB/TrEMBL
SMART	UBQ	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54236	UniProtKB/TrEMBL
UniProt	A0A0D9R6U1	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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Imported Disease Annotations - ClinVar

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