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UBD Gene

protein-coding GIFtS: 54

GC06M029634

ubiquitin D
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases
Diubiquitin ^³
FAT10 ^¹, ², ³, ⁵
GABBR1 ^²
OTTHUMP00000029427 ^²
UBD-3 ^²
diubiquitin ^²

Descriptions
Ubiquitin-like protein FAT10 ^³
ubiquitin D ^²

External Ids
HGNC: 18795¹
Entrez Gene: 10537²
UniProtKB: O15205³
Ensembl: ENSG00000213886⁷

Search outside databases for aliases for UBD gene

Previous GC identifers: GC06M029580 GC06M029294 GC06M029632 GC06M029633 GC06Mc29667

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Gene Wiki entry for UBD

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the UBD gene

Entrez Gene cytogenetic band: 6p21.3 Ensembl cytogenetic band: 6p22.1 HGNC cytogenetic band: 6p21.3

UBD Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 6 GeneLoc Exon Structure

GeneLoc location for GC06M029634: (about GC identifiers)

Start:	29,631,387 bp from pter
End:	29,635,681 bp from pter
Size:	4,295 bases
Orientation:	minus strand

2 alternative locations:

Chr6-,c6_COX 29,667,268-29,671,562

Chr6-,c6_QBL 29,666,182-29,670,477

RefSeq DNA sequence:

NC_000006.10 NT_007592.14 NT_113891.1 NT_113893.1

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: UBD_HUMAN, O15205 (See protein sequence)

Recommended Name: Ubiquitin D

Size: 165 amino acids; 18457 Da

Subunit: Interacts with MAD2

Secondary accessions: B0UZT6 Q5SUK2 Q96EC7

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_006389.2

ENSEMBL proteins:

ENSP00000366249

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Millipore Purified and/or Recombinant UBD Protein
	Browse Human Recombinant Proteins at Sigma-Aldrich
	Browse R&D Systems for human recombinant proteins
	Enzo Life Sciences proteins for UBD
	Recombinant Proteins from Abcam (Diubiquitin)
	Human Recombinant Proteins from Abnova (UBD)

OriGene Purified Recombinant Human Protein: UBD

Antibodies for UBD:

	Browse Antibodies Central at Invitrogen
	Millipore Mono- and Polyclonal Antibodies for the study of UBD
	Sigma-Aldrich Antibodies for UBD
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (Diubiquitin), each with their Abpromise^SM
	Monoclonal and Polyclonal Antibodies from Abnova (UBD)
	Novus Biologicals Antibody for UBD

Assays for UBD:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

Graphical View of Domain Structure for InterPro Entry O15205

ProtoNet protein and cluster: O15205

1 Blocks protein family: IPB000626 Ubiquitin domain

UniProtKB/Swiss-Prot: UBD_HUMAN, O15205

Similarity: Contains 2 ubiquitin-like domains

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (UBD)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006398

Applied Biosystems Silencer® siRNAs for UBD

Sigma-Aldrich siRNA and siRNA Panels for UBD

Sigma-Aldrich shRNA Panels and shRNA for UBD

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for UBD
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_006398
Myc/DDK tagged cDNA clone in CMV expression vector: NM_006398
untagged cDNA clone in CMV expression vector: NM_006398

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_006398

2 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Ubd):

cellular

immune system

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

5/9 Sigma-Aldrich "Your Favorite Gene" Pathways for UBD (Your Favorite Gene powered by Ingenuity) (see all 9 )

Cell Cycle: G2/M DNA Damage Checkpoint Regulation
GABA Receptor Signaling
TGF-&beta
Hypoxia Signaling in the Cardiovascular System
Protein Ubiquitination Pathway

GeneDecks UBD for the pathways selected above

About GeneDecksing

Gene Network Central^TM Interacting Genes and Proteins Network for UBD

3 Gene Ontology (GO) biological process terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006464	protein modification process	NAS	9368598
GO:0006508	proteolysis	NAS	9368598
GO:0019941	modification-dependent protein catabolic process	IEA	--

About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for UBD

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (UBD)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006398

Sigma-Aldrich siRNA and siRNA Panels for UBD

Sigma-Aldrich shRNA Panels and shRNA for UBD

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_006398

REFSEQ mRNAs for UBD gene:

NM_006398.3

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_006398

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_006398
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_006398
                                 untagged cDNA clone in CMV expression vector: NM_006398

Additional cDNA sequence:

AF123050.1 AK311914.1 BC012472.1 Y12653.1

6 DOTS entries:

DT.100645165 DT.112373 DT.121390472 DT.95368176 DT.95359346 DT.92324520

24/255 AceView cDNA sequences (see all 255 ):

BX644916 AA583465 BM717516 AW264022 BM929866 BX431259 BG818076 BE047768

AU280038 BM661640 NM_021904 AL602784 BF476724 CF552729 AJ012185 NM_021903

Y11044 BX111922 BM702959 BC023336 NM_001470 AJ225029 BG910376 AW105586

highest scoring ESTs for UBD:

AF123050 AI133610 BC012472 BG290370 BX280913 CB985708 Y12653 AW383833 U37231 AW270961

Unigene Cluster for UBD:

Ubiquitin D

Hs.719331 [show with all ESTs]

Unigene Representative Sequence: NM_006398

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:

ENST00000377050

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

UBD expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for UBD

¹ / ² / ³

3 probe-sets matching UBD gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
39959_at²^{, 3}	U95-A	3	1.00	0.34	1.00	1.00	AL031983	0.20	0.25	0.23	1
205890_s_at²^{, 3}	U133-A	3	1.00	0.33	--	--	NM_006398	0.60	0.83	0.73	1
205890_s_at²	U133Plus2	3	1.00	0.33	--	--	--	--	--	--	--

GeneDecks UBD for binary patterns associated with the probe-sets selected above

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Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.719331
Expression variation in blood from EXPOLDB for UBD

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for UBD gene from 4 species

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
chimpanzee (Pan troglodytes)	UBD¹	--	ubiquitin D	98.59(n) 96.36(a)	471944 XM_527322.2 XP_527322.2
cow (Bos taurus)	UBD¹	--	ubiquitin D	79.75(n) 72.15(a)	504548 XM_580689.3 XP_580689.1
rat (Rattus norvegicus)	Ubd¹	--	ubiquitin D	76.67(n) 76.25(a)	29168 NM_053299.1 NP_445751.1
mouse (Mus musculus)	Ubd^{1, 5}	17⁵	ubiquitin D^{1, 5}	75.64(n)¹ 73.08(a)¹	24108¹ NM_023137.2¹ NP_075626.1¹ AF314088⁵ AK008116⁵ (see all 10)

About this table Species with no ortholog for UBD

ENSEMBL Gene Tree for UBD

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/57 NCBI SNPs in UBD are shown (see all 57 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 88)

AB	SNP ID	Valid	Chr 6 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--			--
	rs2076485^1,2	A,C,F,H,O	29631931(-)	`TGGCAC/TTGACA`	1	I/T	mis¹		14	EU EA WA MN NA	1214
	rs2076484^1,2	A,C,F,H	29631982(-)	`TCTTTT/CGCTGG`	1	S/L	mis¹		18	NS MN NA EU EA WA	1248
	rs2076487^1,2	A,C,F,H	29631838(-)	`TGAGGC/GAAAGA`	1	A/G	mis¹		13	MN NA EU EA WA	1144
	rs362513^1,2	A,C,F,H	29636297(-)	`CTCACT/CAAATA`	1	--	ng3¹		9	EU EA WA NS	1004
	rs7757931^1,2	A,C,F,H	29631649(+)	`CAATAC/AAATAA`	1	F/C	mis¹		12	MN NA EA WA EU	1016
	rs8337^1,2	A,C,F,H	29631655(-)	`GGCATC/GTTATT`	1	S/C	mis¹		21	MN EU EA WA NA	2122
	rs2076486^1,2	A,C,F,H	29631851(-)	`TGGAGT/CCAGGT`	1	P/S	mis¹		9	MN NA EU EA WA	718
	rs444013^1,2	A,C,F,H	29631625(-)	`CTGGGG/CATGGG`	1	--	ut3¹		9	MN EU EA WA NA	788
	rs2272991^1,2	A,C,F,H	29635578(-)	`CAAAGA/GGCACA`	1	--	ut5¹		5	EA EU WA	1852
	rs995185^1,2	A,C,F,H	29637116(-)	`TGGCTT/ATGGGC`	1	--	ng3¹		8	EA NA EU WA	554

About this table

HapMap Linkage Disequilibrium images for UBD (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 606050

2 Novoseek disease relationships for UBD gene

Disease	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
cancer	9.21	7	12730673 (4), 10602013 (1), 16495226 (1)
tumors	0.00	2	18280469 (1), 12730673 (1)

About this table

Human Genome Epidemiology Navigator: UBD (2 documents)

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

10/59 PubMed articles for UBD gene (see all 59 ):

Identification and analysis of a novel member of the ubiquitin family expressed in dentritic cells and mature B cells. (PubMed id 9368598)^{2, 3, 4} Bates E.E.M.... Lebecque S. (1997)
A MHC-encoded ubiquitin-like protein (FAT10) binds noncovalently to the spindle assembly checkpoint protein MAD2. (PubMed id 10200259)^{1, 3, 4} Liu Y.-C....Weissman S.M. (1999)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)^{3, 4} Mungall A.J.... Beck S. (2003)
Identification of seven new human MHC class I region genes around the HLA-F locus. (PubMed id 8662070)^{2, 3} Fan W....Weissman S.M. (1996)
Expression of the FAT10 gene is highly upregulated in hepatocellular carcinoma and other gastrointestinal and gynecological cancers. (PubMed id 12730673)^{1, 3} Lee C.G....Lee L.A. (2003)
Structural basis for recognition of diubiquitins by NEMO. (PubMed id 19185524)^{1, 3} Lo Y.C....Wu H. (2009)
FAT10 plays a role in the regulation of chromosomal stability. (PubMed id 16495226)^{1, 3} Ren J....Lee C.G. (2006)
The ubiquitin-like modifier FAT10 interacts with HDAC6 and localizes to aggresomes under proteasome inhibition. (PubMed id 19033385)^{1, 3} Kalveram B....Groettrup M. (2008)
Role of ubiquitin-like protein FAT10 in epithelial apoptosis in renal disease. (PubMed id 16495380)^{1, 3} Ross M.J....Klotman P.E. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 10537	HGNC: 18795	AceView: GABBR1andUBD	Ensembl:ENSG00000213886	euGenes: HUgn10537
ECgene: UBD	H-InvDB: UBD

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Licensable Technologies for UBD
(Available from WIS Yeda, Salk, Tufts)

About This Section

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section

Products for UBD:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for UBD-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for UBD		Antibodies for UBD
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for UBD		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

	Antibodies		Primer Pairs
	Cell Culture Products		ELISAs
	Flow Cytometry Kits		Protease Activity Assays & Reagents
	Cell Selection/Detection Kits & Reagents		ELISA/Assay Development Kits & Reagents
	Multiplex/Array Assay Kits & Reagents		ELISpot Kits & Development Modules
	Recombinant & Natural Proteins

	Recombinant Proteins (UBD)
	Antibodies (UBD)
	Search for Chimera RNAi
	Custom Service for Mouse Mab
	Custom Service for Rabbit Pab from Full-length Protein

Search for Antibodies & Assays

	Recombinant Proteins (Diubiquitin)
	Antibodies (Diubiquitin)

	Tagged/untagged cDNA clones
	Validated SYBR primer pairs
	Purified proteins from HEK293T cells
	Western blot validated antibodies
	shRNA in GFP-retroviral vector

Search Tocris compounds for UBD

	Proteins for UBD
	Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies

Antibodies for UBD

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UBD Gene

protein-coding GIFtS: 54

Aliases &
Descriptions
for UBD

Summaries
for UBD

Genomic Location
for UBD

Proteins
for UBD

Protein Domains/
Families
for UBD

Gene Function
for UBD

Pathways & Interactions
for UBD

Drugs & Compounds
for UBD

Transcripts
for UBD

Expression
for UBD

Orthologs
for UBD

Paralogs
for UBD

SNPs/Variants
for UBD

Disorders & Mutations
for UBD

Medical News
for UBD

Publications
for UBD

Search for UBD

Genome Databases showing UBD

Other Databases showing UBD

Specialized Databases showing UBD

Licensable Technologies
for UBD

Services
for UBD

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

UBD Gene

protein-coding GIFtS: 54

Aliases & Descriptionsfor UBD

Summariesfor UBD

Genomic Locationfor UBD

Proteinsfor UBD

Protein Domains/Familiesfor UBD

Gene Functionfor UBD

Pathways & Interactionsfor UBD

Drugs & Compoundsfor UBD

Transcriptsfor UBD

Expression for UBD

Orthologsfor UBD

Paralogsfor UBD

SNPs/Variantsfor UBD

Disorders & Mutationsfor UBD

Medical Newsfor UBD

Publicationsfor UBD

Search for UBD

Genome Databases showing UBD

Other Databases showing UBD

Specialized Databases showing UBD

Licensable Technologiesfor UBD

Servicesfor UBD

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for UBD

Summaries
for UBD

Genomic Location
for UBD

Proteins
for UBD

Protein Domains/
Families
for UBD

Gene Function
for UBD

Pathways & Interactions
for UBD

Drugs & Compounds
for UBD

Transcripts
for UBD

Expression
for UBD

Orthologs
for UBD

Paralogs
for UBD

SNPs/Variants
for UBD

Disorders & Mutations
for UBD

Medical News
for UBD

Publications
for UBD

Licensable Technologies
for UBD

Services
for UBD