UBD (ubiquitin D) - Rat Genome Database

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

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Gene: UBD (ubiquitin D) Homo sapiens

Analyze

Symbol:

UBD

Name:

ubiquitin D

RGD ID:

69468

HGNC Page

HGNC:18795

Description:

Enables proteasome binding activity. Involved in several processes, including aggresome assembly; positive regulation of I-kappaB kinase/NF-kappaB signaling; and response to type II interferon. Located in aggresome; fibrillar center; and nucleoplasm.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

diubiquitin; FAT10; GABBR1; UBD-3; ubiquitin-like protein FAT10

RGD Orthologs

Mouse

Rat

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Mus musculus (house mouse):	Ubd (ubiquitin D)	HGNC	Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OrthoDB, Panther, PhylomeDB
Rattus norvegicus (Norway rat):	Ubd (ubiquitin D)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OrthoDB, Panther
Chinchilla lanigera (long-tailed chinchilla):	Ubd (ubiquitin D)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	UBD (ubiquitin D)	NCBI	Ortholog
Canis lupus familiaris (dog):	UBD (ubiquitin D)	HGNC	HomoloGene, NCBI
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ubd (ubiquitin D)	NCBI	Ortholog
Sus scrofa (pig):	UBD (ubiquitin D)	HGNC	NCBI
Chlorocebus sabaeus (green monkey):	UBD (ubiquitin D)	NCBI	Ortholog
Other homologs ²
Rattus norvegicus (Norway rat):	Prickle3 (prickle planar cell polarity protein 3)	HGNC	OMA
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Ubd (ubiquitin D)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ubd (ubiquitin D)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Related Pseudogenes:

UBDP1

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

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.p13 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

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Animal Hepatitis (EXP)

Breast Neoplasms (EXP)

celiac disease (EXP)

Experimental Liver Cirrhosis (EXP)

genetic disease (IAGP)

hepatocellular carcinoma (EXP)

megacolon (IAGP)

myocardial infarction (ISO)

primary biliary cholangitis (EXP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (ISO)

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

1,3-dinitrobenzene (ISO)

1-chloro-2,4-dinitrobenzene (ISO)

1-naphthyl isothiocyanate (ISO)

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,6-trinitrobenzenesulfonic acid (ISO)

3,4-dichloroaniline (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3,5-diethoxycarbonyl-1,4-dihydrocollidine (ISO)

3,7-dihydropurine-6-thione (ISO)

4,4'-diaminodiphenylmethane (ISO)

4-(ethoxymethylene)-2-phenyloxazol-5-one (ISO)

4-hydroxyphenyl retinamide (ISO)

7,12-dimethyltetraphene (ISO)

acrylamide (ISO)

aflatoxin B1 (EXP,ISO)

all-trans-retinoic acid (EXP)

ammonium chloride (ISO)

amphetamine (ISO)

antirheumatic drug (EXP)

arsane (EXP)

arsenic atom (EXP)

azathioprine (EXP)

benzo[a]pyrene (EXP,ISO)

benzo[a]pyrene diol epoxide I (EXP)

beta-naphthoflavone (ISO)

bisphenol A (EXP,ISO)

bromobenzene (ISO)

Butylparaben (EXP)

cadmium dichloride (ISO)

carbon nanotube (EXP,ISO)

cefaloridine (ISO)

CGP 52608 (EXP)

chlorohydrocarbon (ISO)

cholesterol (ISO)

choline (ISO)

cisplatin (ISO)

clofibrate (ISO)

copper(II) sulfate (EXP)

cyclophosphamide (ISO)

cyclosporin A (EXP)

dibenz[a,h]anthracene (EXP)

dibenzo[a,l]pyrene (ISO)

dicrotophos (EXP)

diethyl maleate (ISO)

diethylstilbestrol (ISO)

dimethylarsinic acid (ISO)

dioxygen (ISO)

endosulfan (ISO)

ethanol (EXP)

flutamide (ISO)

folic acid (ISO)

gadodiamide hydrate (EXP)

Genipin (ISO)

glycidol (ISO)

GW 4064 (ISO)

indole-3-methanol (ISO)

irinotecan (ISO)

iron(III) nitrilotriacetate (ISO)

L-methionine (ISO)

leflunomide (ISO)

lidocaine (ISO)

lipopolysaccharide (ISO)

manganese(II) chloride (ISO)

mercaptopurine (ISO)

methotrexate (EXP)

methylmercury chloride (ISO)

methylparaben (EXP)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (ISO)

N-nitrosodimethylamine (EXP)

naphthalene (ISO)

nickel sulfate (EXP)

O-methyleugenol (ISO)

ochratoxin A (ISO)

oxaliplatin (ISO)

paracetamol (EXP,ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (EXP,ISO)

phenylmercury acetate (EXP)

pirinixic acid (ISO)

potassium bromate (ISO)

progesterone (EXP)

promethazine (ISO)

propiconazole (ISO)

purine-6-thiol (ISO)

quercetin (EXP)

quinolin-8-ol (EXP)

S-adenosyl-L-methioninate (ISO)

S-adenosyl-L-methionine (ISO)

silicon dioxide (EXP,ISO)

silver atom (EXP)

silver(0) (EXP)

sodium arsenite (EXP)

sodium dichromate (ISO)

tacrolimus hydrate (ISO)

testosterone (ISO)

tetrachloroethene (ISO)

tetrachloromethane (ISO)

thioacetamide (ISO)

titanium dioxide (ISO)

topotecan (ISO)

trichloroethene (ISO)

trimellitic anhydride (ISO)

tris(2-butoxyethyl) phosphate (EXP)

urethane (EXP)

ursodeoxycholic acid (ISO)

valproic acid (EXP)

zoledronic acid (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aggresome assembly (IDA)

myeloid dendritic cell differentiation (IMP)

positive regulation of apoptotic process (IBA,IEA,IMP)

positive regulation of I-kappaB kinase/NF-kappaB signaling (IBA,IEA,IMP)

protein modification by small protein conjugation (NAS)

protein ubiquitination (IBA,IDA,IEA)

proteolysis (NAS)

regulation of mitotic cell cycle phase transition (IMP)

response to hypoxia (ISO)

response to ischemia (ISO)

response to organonitrogen compound (ISO)

response to tumor necrosis factor (IBA,IEA,IEP)

response to type II interferon (IBA,IEA,IEP)

ubiquitin-dependent protein catabolic process (IBA,IDA,IEA)

Cellular Component

aggresome (IDA)

cytoplasm (IEA,ISS)

cytosol (TAS)

fibrillar center (IDA)

nucleoplasm (IDA)

nucleus (IBA,IDA,IEA)

Molecular Function

proteasome binding (IBA,IDA,IEA)

protein binding (IPI)

Phenotype Annotations Click to see Annotation Detail View

Human Phenotype

Aganglionic megacolon (IAGP)

References

References - curated

#	Reference Title	Reference Citation
1.	Identification and analysis of a novel member of the ubiquitin family expressed in dendritic cells and mature B cells.	Bates EE, etal., Eur J Immunol 1997 Oct;27(10):2471-7.
2.	GOAs Human GO annotations	GOA_HUMAN data from the GO Consortium
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	FAT10 attenuates hypoxia-induced cardiomyocyte apoptosis by stabilizing caveolin-3.	Zhou Q, etal., J Mol Cell Cardiol. 2018 Mar;116:115-124. doi: 10.1016/j.yjmcc.2018.02.008. Epub 2018 Feb 10.

Additional References at PubMed

PMID:8662070	PMID:9525617	PMID:10200259	PMID:11087859	PMID:11087860	PMID:11112487	PMID:11991975	PMID:12477932	PMID:12610113	PMID:12730673	PMID:12883554	PMID:14574404
PMID:14757770	PMID:15489334	PMID:15761153	PMID:15831455	PMID:15994808	PMID:16344560	PMID:16495226	PMID:16495380	PMID:16707496	PMID:16712791	PMID:16775314	PMID:16808324
PMID:17067581	PMID:17889673	PMID:17971048	PMID:18574467	PMID:19028597	PMID:19033385	PMID:19185524	PMID:19303852	PMID:19437562	PMID:19726511	PMID:19808075	PMID:19851445
PMID:19959714	PMID:20587610	PMID:20975683	PMID:21090589	PMID:21121635	PMID:21351261	PMID:21396347	PMID:21631897	PMID:21757738	PMID:21873635	PMID:22025632	PMID:22072791
PMID:22164771	PMID:22281738	PMID:22292662	PMID:22347407	PMID:22349260	PMID:22402871	PMID:22412388	PMID:22427669	PMID:22434192	PMID:22569823	PMID:22797925	PMID:23036196
PMID:23333871	PMID:23416168	PMID:23602568	PMID:23812429	PMID:23862649	PMID:24325913	PMID:24440736	PMID:24492942	PMID:24518302	PMID:24528925	PMID:24893112	PMID:25056121
PMID:25422469	PMID:25429064	PMID:25768649	PMID:25814554	PMID:25983082	PMID:26401002	PMID:26733179	PMID:26996158	PMID:27044747	PMID:27279480	PMID:27312528	PMID:27354218
PMID:27393295	PMID:27569286	PMID:27655726	PMID:27725184	PMID:27806337	PMID:27926780	PMID:28234446	PMID:29208314	PMID:29458176	PMID:29531077	PMID:29620277	PMID:29749526
PMID:29790184	PMID:30127417	PMID:30336976	PMID:30361097	PMID:30395194	PMID:30718280	PMID:31433974	PMID:31575873	PMID:31601934	PMID:31729307	PMID:31877302	PMID:32296183
PMID:32586037	PMID:32814053	PMID:32817338	PMID:32946796	PMID:33238157	PMID:33253711	PMID:33730565	PMID:33961781	PMID:35614040	PMID:35728518	PMID:35883685	PMID:36361504
PMID:36660934	PMID:37057207	PMID:37188463

Genomics

Comparative Map Data

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.p13 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

Ubd
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
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_SHRSP_BbbUtx_1.0	20	1,442,376 - 1,444,327 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	20	1,383,905 - 1,385,856 (-)	NCBI	Rnor_WKY
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	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	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

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

Variants

Variants in UBD
3 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 6p22.3-21.33(chr6:18120520-30767516)x1	copy number loss	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]\|See cases [RCV000052180]	Chr6:18120520..30767516 [GRCh38] Chr6:18120751..30735293 [GRCh37] Chr6:18228730..30843272 [NCBI36] Chr6:6p22.3-21.33	pathogenic
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3	copy number gain	See cases [RCV000138956]	Chr6:3224310..30657190 [GRCh38] Chr6:3224544..30624967 [GRCh37] Chr6:3169543..30732946 [NCBI36] Chr6:6p25.2-21.33	pathogenic
GRCh38/hg38 6p22.1(chr6:28763187-29769828)x3	copy number gain	See cases [RCV000141858]	Chr6:28763187..29769828 [GRCh38] Chr6:28730964..29737605 [GRCh37] Chr6:28838943..29845584 [NCBI36] Chr6:6p22.1	uncertain significance
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3	copy number gain	See cases [RCV000143497]	Chr6:156974..46789291 [GRCh38] Chr6:156974..46757028 [GRCh37] Chr6:101974..46864987 [NCBI36] Chr6:6p25.3-12.3	pathogenic
GRCh37/hg19 6p22.1(chr6:28735761-29585573)x1	copy number loss	See cases [RCV000445803]	Chr6:28735761..29585573 [GRCh37] Chr6:6p22.1	uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3	copy number gain	See cases [RCV000512067]	Chr6:156975..170919482 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)	copy number gain	See cases [RCV000510595]	Chr6:156975..170919482 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3	copy number gain	not provided [RCV000745400]	Chr6:60107..171054786 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3	copy number gain	not provided [RCV000745403]	Chr6:108666..170980171 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3	copy number gain	not provided [RCV000745404]	Chr6:165632..170919470 [GRCh37] Chr6:6p25.3-q27	pathogenic
GRCh37/hg19 6p22.1-21.32(chr6:28130359-32108367)x3	copy number gain	not provided [RCV000745592]	Chr6:28130359..32108367 [GRCh37] Chr6:6p22.1-21.32	uncertain significance
NM_006398.4(UBD):c.445G>A (p.Gly149Ser)	single nucleotide variant	not provided [RCV000926007]	Chr6:29555933 [GRCh38] Chr6:29523710 [GRCh37] Chr6:6p22.1	likely benign
GRCh37/hg19 6p22.1-q14.1(chr6:29455465-81447367)	copy number gain	not provided [RCV000767714]	Chr6:29455465..81447367 [GRCh37] Chr6:6p22.1-q14.1	pathogenic
NC_000006.11:g.28005012_31683185del	deletion	Megacolon [RCV001290055]	Chr6:28005012..31683185 [GRCh37] Chr6:6p22.1-21.33	likely pathogenic
GRCh37/hg19 6p22.1(chr6:28735761-29585573)	copy number loss	not specified [RCV002053563]	Chr6:28735761..29585573 [GRCh37] Chr6:6p22.1	uncertain significance
GRCh37/hg19 6p22.1(chr6:29162783-30236331)x3	copy number gain	not provided [RCV002472477]	Chr6:29162783..30236331 [GRCh37] Chr6:6p22.1	uncertain significance
NM_006398.4(UBD):c.12T>A (p.Asn4Lys)	single nucleotide variant	Inborn genetic diseases [RCV002738920]	Chr6:29559690 [GRCh38] Chr6:29527467 [GRCh37] Chr6:6p22.1	uncertain significance

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	118
Count of miRNA genes:	117
Interacting mature miRNAs:	117
Transcripts:	ENST00000377050
Prediction methods:	Microtar, Miranda, Rnahybrid
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.

Markers in Region

STS-N33920

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	6	29,523,707 - 29,523,845	UniSTS	GRCh37
Build 36	6	29,631,686 - 29,631,824	RGD	NCBI36
Celera	6	31,129,790 - 31,129,928	RGD
Cytogenetic Map	6	p21.3	UniSTS
HuRef	6	29,330,787 - 29,330,925	UniSTS
GeneMap99-GB4 RH Map	6	108.84	UniSTS

RH93792

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	6	29,523,716 - 29,523,867	UniSTS	GRCh37
Build 36	6	29,631,695 - 29,631,846	RGD	NCBI36
Celera	6	31,129,799 - 31,129,950	RGD
Cytogenetic Map	6	p21.3	UniSTS
HuRef	6	29,330,796 - 29,330,947	UniSTS
GeneMap99-GB4 RH Map	6	114.82	UniSTS

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

alimentary part of gastrointestinal system

circulatory system

endocrine system

exocrine system

hemolymphoid system

hepatobiliary system

integumental system

musculoskeletal system

nervous system

renal system

reproductive system

respiratory system

sensory system

visual system

adipose tissue

appendage

entire extraembryonic component

pharyngeal arch

High

Medium

151

194

196

207

165

103

116

124

Low

1114

338

554

323

378

215

1464

414

584

226

420

769

115

613

833

Below cutoff

896

1115

534

289

1599

881

984

454

423

414

1012

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_006398	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AA878968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF123050	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK311914	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL031983	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL645936	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL662826	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC012472	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX000688	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX927223	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CB111380	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471081	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068272	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR759766	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR759770	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR788300	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CR942274	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DB181897	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KY500724	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KY500725	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KY500726	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KY500727	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KY500728	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KY500729	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	LC420317	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Y12653	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENST00000377050 ⟹ ENSP00000366249

RefSeq Status:

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p13 Ensembl	6	29,555,515 - 29,559,732 (-)	Ensembl

RefSeq Acc Id:

NM_006398 ⟹ NP_006389

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	29,555,515 - 29,559,732 (-)	NCBI
GRCh37	6	29,523,389 - 29,527,702 (-)	ENTREZGENE
Build 36	6	29,631,387 - 29,635,681 (-)	NCBI Archive
HuRef	6	29,330,776 - 29,334,782 (-)	NCBI
CHM1_1	6	29,525,538 - 29,529,852 (-)	NCBI
T2T-CHM13v2.0	6	29,430,199 - 29,434,416 (-)	NCBI

Sequence:

show sequence

GTCTCTGGTTTCTGGCCCCTTGTCTGCAGAGATGGCTCCCAATGCTTCCTGCCTCTGTGTGCAT
GTCCGTTCCGAGGAATGGGATTTAATGACCTTTGATGCCAACCCATATGACAGCGTGAAAAAAA
TCAAAGAACATGTCCGGTCTAAGACCAAGGTTCCTGTGCAGGACCAGGTTCTTTTGCTGGGCTC
CAAGATCTTAAAGCCACGGAGAAGCCTCTCATCTTATGGCATTGACAAAGAGAAGACCATCCAC
CTTACCCTGAAAGTGGTGAAGCCCAGTGATGAGGAGCTGCCCTTGTTTCTTGTGGAGTCAGGTG
ATGAGGCAAAGAGGCACCTCCTCCAGGTGCGAAGGTCCAGCTCAGTGGCACAAGTGAAAGCAAT
GATCGAGACTAAGACGGGTATAATCCCTGAGACCCAGATTGTGACTTGCAATGGAAAGAGACTG
GAAGATGGGAAGATGATGGCAGATTACGGCATCAGAAAGGGCAACTTACTCTTCCTGGCATGTT
ATTGTATTGGAGGGTGACCACCCTGGGCATGGGGTGTTGGCAGGGGTCAAAAAGCTTATTTCTT
TTAATCTCTTACTCAACGAACACATCTTCTGATGATTTCCCAAAATTAATGAGAATGAGATGAG
TAGAGTAAGATTTGGGTGGGATGGGTAGGATGAAGTATATTGCCCAACTCTATGTTTCTTTGAT
TCTAACACAATTAATTAAGTGACATGATTTTTACTAATGTATTACTGAGACTAGTAAATAAATT
TTTAAGGCAAAATAGAGCATTCAAAGCCAGCTTGGAATTTAATTCTGTCTTGATACCTTGTTAT
TTATGCAAAAACTCCTATCTCCTTTCCTTTATGACAAGAGAGTAAGTTTTAGGTTGGGATCC

hide sequence

Protein Sequences


Protein RefSeqs	NP_006389	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD52982	(Get FASTA)	NCBI Sequence Viewer
	AAH12472	(Get FASTA)	NCBI Sequence Viewer
	AQY77194	(Get FASTA)	NCBI Sequence Viewer
	AQY77195	(Get FASTA)	NCBI Sequence Viewer
	AQY77196	(Get FASTA)	NCBI Sequence Viewer
	AQY77197	(Get FASTA)	NCBI Sequence Viewer
	AQY77198	(Get FASTA)	NCBI Sequence Viewer
	AQY77199	(Get FASTA)	NCBI Sequence Viewer
	BAG34855	(Get FASTA)	NCBI Sequence Viewer
	BBG06134	(Get FASTA)	NCBI Sequence Viewer
	CAA21458	(Get FASTA)	NCBI Sequence Viewer
	CAA73200	(Get FASTA)	NCBI Sequence Viewer
	EAX03201	(Get FASTA)	NCBI Sequence Viewer
	O15205	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_006389 ⟸ NM_006398
- UniProtKB:	Q96EC7 (UniProtKB/Swiss-Prot), O15205 (UniProtKB/Swiss-Prot), A0A1U9X8S6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAPNASCLCVHVRSEEWDLMTFDANPYDSVKKIKEHVRSKTKVPVQDQVLLLGSKILKPRRSLS SYGIDKEKTIHLTLKVVKPSDEELPLFLVESGDEAKRHLLQVRRSSSVAQVKAMIETKTGIIPE TQIVTCNGKRLEDGKMMADYGIRKGNLLFLACYCIGG hide sequence

RefSeq Acc Id:

ENSP00000366249 ⟸ ENST00000377050

Protein Domains

Ubiquitin-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-O15205-F1-model_v2	AlphaFold	O15205	1-165	view protein structure

Promoters

RGD ID:

6872336

Promoter ID:

EPDNEW_H9332

Type:

multiple initiation site

Name:

UBD_1

Description:

ubiquitin D

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	29,559,732 - 29,559,792	EPDNEW

RGD ID:

6804908

Promoter ID:

HG_KWN:52744

Type:

Non-CpG

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

Lymphoblastoid

Transcripts:

OTTHUMT00000076628

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	6	29,635,176 - 29,635,676 (-)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:18795	AgrOrtholog
COSMIC	UBD	COSMIC
Ensembl Genes	ENSG00000206468	UniProtKB/Swiss-Prot
	ENSG00000206513	UniProtKB/TrEMBL
	ENSG00000213886	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
	ENSG00000224654	UniProtKB/TrEMBL
	ENSG00000226898	UniProtKB/TrEMBL
	ENSG00000228913	UniProtKB/Swiss-Prot
	ENSG00000231968	UniProtKB/Swiss-Prot
Ensembl Protein	ENSP00000366249	ENTREZGENE
	ENSP00000366249.4	UniProtKB/Swiss-Prot
	ENSP00000373039.3	UniProtKB/Swiss-Prot
	ENSP00000373137.2	UniProtKB/TrEMBL
	ENSP00000396152.2	UniProtKB/Swiss-Prot
	ENSP00000396477.2	UniProtKB/TrEMBL
	ENSP00000398539.2	UniProtKB/TrEMBL
	ENSP00000410416.2	UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000377050	ENTREZGENE
	ENST00000377050.5	UniProtKB/Swiss-Prot
	ENST00000383547.3	UniProtKB/Swiss-Prot
	ENST00000383641.2	UniProtKB/TrEMBL
	ENST00000414436.2	UniProtKB/TrEMBL
	ENST00000421519.2	UniProtKB/Swiss-Prot
	ENST00000429935.2	UniProtKB/TrEMBL
	ENST00000432676.2	UniProtKB/Swiss-Prot
GTEx	ENSG00000206468	GTEx
	ENSG00000206513	GTEx
	ENSG00000213886	GTEx
	ENSG00000224654	GTEx
	ENSG00000226898	GTEx
	ENSG00000228913	GTEx
	ENSG00000231968	GTEx
HGNC ID	HGNC:18795	ENTREZGENE
Human Proteome Map	UBD	Human Proteome Map
InterPro	Ubiquitin	UniProtKB/Swiss-Prot
	Ubiquitin-like_dom	UniProtKB/TrEMBL
	Ubiquitin-like_domsf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ubiquitin_D	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ubiquitin_dom	UniProtKB/Swiss-Prot
	Ubiquitin_dom	UniProtKB/TrEMBL
KEGG Report	hsa:10537	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene	10537	ENTREZGENE
OMIM	606050	OMIM
PANTHER	PTHR47731	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	UBIQUITIN D	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	ubiquitin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	PA38682	PharmGKB
PRINTS	UBIQUITIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	UBIQUITIN_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	UBQ	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF54236	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JH67_HUMAN	UniProtKB/TrEMBL
	A0A1U9X8S6	ENTREZGENE, UniProtKB/TrEMBL
	O15205	ENTREZGENE
	Q96EC7	ENTREZGENE
	UBD_HUMAN	UniProtKB/Swiss-Prot
UniProt Secondary	B0UZT6	UniProtKB/Swiss-Prot
	Q5STL2	UniProtKB/Swiss-Prot
	Q5SUK2	UniProtKB/Swiss-Prot
	Q96EC7	UniProtKB/Swiss-Prot

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Human Phenotype Annotations - ClinVar

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

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