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UBFD1 Gene

protein-coding GIFtS: 43

GC16P023476

ubiquitin family domain containing 1
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
FLJ38870 ^¹, ²
FLJ42145 ^¹, ²
OTTHUMP00000159076 ^²
UBPH ^¹, ², ³

Descriptions
Ubiquitin-binding protein homolog ^², ³
ubiquitin family domain containing 1 ^²

External Ids
HGNC: 30565¹
Entrez Gene: 56061²
UniProtKB: O14562³
Ensembl: ENSG00000103353⁷

Search outside databases for aliases for UBFD1 gene

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

(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)
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Genomic View:

UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p12 Ensembl cytogenetic band: 16p12.1 HGNC cytogenetic band: 16p12.1

UBFD1 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 16 GeneLoc Exon Structure

GeneLoc location for GC16P023476: (about GC identifiers)

Start:	23,475,893 bp from pter
End:	23,493,211 bp from pter
Size:	17,319 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000016.8 NT_010393.15

(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: UBFD1_HUMAN, O14562 (See protein sequence)

Recommended Name: Ubiquitin domain-containing protein UBFD1

Size: 533 amino acids; 56896 Da

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_061989.2

ENSEMBL proteins:

ENSP00000219638 ENSP00000379217

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Browse Purified and Recombinant Proteins at Millipore
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	Browse recombinant and purified proteins available from Enzo Life Sciences
	Browse Abcam for Recombinant Proteins
	Browse Abnova for Human Recombinant Proteins

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

Antibodies for UBFD1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Browse Antibodies at Sigma-Aldrich
	Browse R&D Systems for Antibodies
	Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for UBFD1

Assays for UBFD1:

	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)
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Graphical View of Domain Structure for InterPro Entry O14562

ProtoNet protein and cluster: O14562

1 Blocks protein family: IPB000626 Ubiquitin domain

UniProtKB/Swiss-Prot: UBFD1_HUMAN, O14562

Similarity: Contains 1 ubiquitin-like domain

(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 (UBFD1)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_019116

Applied Biosystems Silencer® siRNAs for UBFD1

Sigma-Aldrich siRNA and siRNA Panels for UBFD1

Sigma-Aldrich shRNA for UBFD1

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_019116
Myc/DDK tagged cDNA clone in CMV expression vector: NM_019116
untagged cDNA clones in CMV expression vector (see all 2): AK092696

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_019116

(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.)
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1 Gene Ontology (GO) biological process term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006464	protein modification 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 UBFD1

(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 (UBFD1)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_019116

Sigma-Aldrich siRNA and siRNA Panels for UBFD1

Sigma-Aldrich shRNA for UBFD1

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_019116

REFSEQ mRNAs for UBFD1 gene:

NM_019116.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_019116

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_019116
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_019116
                                 untagged cDNA clones in CMV expression vector (see all 2): AK092696

Additional cDNA sequence:

AJ001827.1 AK025656.1 AK092696.1 AK093029.1 AK096189.1 AK124139.1 BC001413.2 BC007880.2

BC011830.2

17 DOTS entries:

DT.100849115 DT.101981431 DT.75185424 DT.101963913 DT.101958261 DT.120690965 DT.120691042 DT.86842276

DT.120691072 DT.75102731 DT.95199993 DT.120690932 DT.91910987 DT.40195555 DT.91754170 DT.95293757

DT.97844952

24/323 AceView cDNA sequences (see all 323 ):

BU501867 AA805529 AA452679 CD244634 F09558 BM792964 BQ940963 BU675052

BQ182649 AW104069 AW471388 BQ228240 AA554228 AI635068 AI242934 BM454830

AK124139 BE301960 Z44584 CA443432 BM722190 AL705144 AL134842 AA478609

Unigene Cluster for UBFD1:

Ubiquitin family domain containing 1

Hs.3459 [show with all ESTs]

Unigene Representative Sequence: NM_019116

GeneLoc Exon Structure

5/6 Alternative Splicing Database (ASD) splice patterns (SP) for UBFD1 (see all 6 )

ExUns:	1	^	2	^	3a	·	3b	^	4	^	5a	·	5b	^	6a	·	6b	^	7a	·	7b	^	8a	·	8b	·	8c
SP1:					-				-		-								-
SP2:																			-
SP3:					-
SP4:									-		-
SP5:

About this scheme

ECgene alternative splicing isoforms for UBFD1

2 Ensembl transcripts including schematic representations:

ENST00000219638 ENST00000395878

(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 )
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UBFD1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for UBFD1

¹ / ²

6 probe-sets matching UBFD1 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
65861_at²	U95-C	1	1.00	1.00	0.94	1.44	--	--	--	--	--
39975_at²	U95-A	1	1.00	1.00	0.97	0.56	--	--	--	--	--
224878_at²	U133-B	1	1.00	1.00	--	--	--	--	--	--	--
205687_at²	U133-A	2	1.00	0.95	--	--	--	--	--	--	--
224878_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
205687_at²	U133Plus2	2	1.00	0.95	--	--	--	--	--	--	--

About this table

Data from

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

CGAP SAGE TAG: TTTCCTTGTG

SOURCE GeneReport for Unigene cluster: Hs.3459

(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)
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Orthologs for UBFD1 gene from 5/10 species (see all 10 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	UBFD1¹	--	ubiquitin family domain containing 1	94.17(n) 98.71(a)	479806 XM_536933.2 XP_536933.1
chimpanzee (Pan troglodytes)	UBFD1¹	--	ubiquitin family domain containing 1	99.14(n) 98.71(a)	746639 XM_001154407.1 XP_001154407.1
rat (Rattus norvegicus)	Ubfd1¹	--	ubiquitin family domain containing 1	91.26(n) 96.12(a)	293454 NM_001034911.1 NP_001030083.1
mouse (Mus musculus)	Ubfd1^{1, 5}	7 (59.00 cM)⁵	ubiquitin family domain containing 1^{1, 5}	91.15(n)¹ 96.76(a)¹	28018¹ NM_138589.2¹ NP_613055.2¹ AA388099⁵ AA407625⁵ (see all 20)
chicken (Gallus gallus)	UBFD1¹	--	ubiquitin family domain containing 1	79.47(n) 82.89(a)	771251 XM_001234542.1 XP_001234543.1

About this table Species with no ortholog for UBFD1

ENSEMBL Gene Tree for UBFD1

(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)
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10/69 NCBI SNPs in UBFD1 are shown (see all 69 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 54)

AB	SNP ID	Valid	Chr 16 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs1610^1,2	A,C,F,H,O	23489654(-)	`TCCATC/TGTATT`	1	--	ut3¹		10		EA MN EU WA	2514
	rs152454^1,2	C,F,H	23490612(+)	`TTTCAT/CGATTA`	1	--	ut3¹ ese³		5		EA EU WA	1920
	rs8046838^1,2	C,F,H	23491862(+)	`CTTCAT/CACATT`	1	--	ut3¹ ese³		8		EU EA WA	838
	rs9871^1,2	C,F	23492562(-)	`AAAACA/GAGCCC`	1	--	ut3¹		2		MN	372
	rs152455^1,2	A,C	23490574(+)	`GGCCAA/GTGTTA`	1	--	ut3¹ ese³		0	--	--	--	--
	rs3803720^1,2	A,C	23490341(-)	`AGAGGC/TCTTTG`	1	--	ut3¹ ese³		0	--	--	--	--
	rs152458^1,2	A,C,F,H	23484768(-)	`GGACTG/TGGTGA`	1	--	int¹		4		EU EA WA	418
	rs7199641^1,2	A,C,F,H	23478247(+)	`TTTCTG/TTCCTT`	1	--	int¹		8		EU EA WA	840
	rs7205366^1,2	A,C,F,H	23478873(+)	`TTGTGG/ACTTTC`	1	--	int¹		4		EU EA WA	418
	rs9924599^1,2	C,F,H	23480607(+)	`TTGTCG/ACCCTC`	1	--	int¹		4		EU EA WA	412

About this table

HapMap Linkage Disequilibrium images for UBFD1 (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.)
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1 Novoseek disease relationship for UBFD1 gene

Disease	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
neurodegenerative diseases	48.27	1	16820172 (1)

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(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)
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10/42 PubMed articles for UBFD1 gene (see all 42 ):

Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PubMed id 10493829)^{2, 3, 4} Loftus B.J....Adams M.D. (1999)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{3, 4} Ota T....Sugano S. (2004)
Ubiquitin-binding proteins: similar, but different. (PubMed id 16250897)¹ Andersen K.M....Hartmann-Petersen R. (2005)
Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins. (PubMed id 14570567)¹ Hicke L. and Dunn R. (2003)
Conjugation of complex polyubiquitin chains to WRNIP1. (PubMed id 18613717)¹ Bish R.A....Myers M.P. (2008)
Regulation of ubiquitin-binding proteins by monoubiquitination. (PubMed id 16429130)¹ Hoeller D....Dikic I. (2006)
IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis. (PubMed id 18931663)¹ Gyrd-Hansen M....Meier P. (2008)
E3-independent monoubiquitination of ubiquitin-binding proteins. (PubMed id 17588522)¹ Hoeller D....Dikic I. (2007)
The function of ubiquitin-binding protein complexes in endocytic downregulation of growth factor receptors. (PubMed id 17425510)¹ Bache K.G. (2006)
The Polycomb-associated protein Rybp is a ubiquitin binding protein. (PubMed id 17070805)¹ Arrigoni R....Schreiber-Agus N. (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)
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Entrez Gene: 56061	HGNC: 30565	AceView: UBPH	Ensembl:ENSG00000103353	euGenes: HUgn56061
ECgene: UBFD1	H-InvDB: UBFD1

(According to HUGE)
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(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for UBFD1
(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)
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Products for UBFD1:

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 UBFD1-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 UBFD1		Browse antibodies at Sigma-Aldrich
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
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UBFD1 Gene

protein-coding GIFtS: 43

Aliases &
Descriptions
for UBFD1

Summaries
for UBFD1

Genomic Location
for UBFD1

Proteins
for UBFD1

Protein Domains/
Families
for UBFD1

Gene Function
for UBFD1

Pathways & Interactions
for UBFD1

Drugs & Compounds
for UBFD1

Transcripts
for UBFD1

Expression
for UBFD1

Orthologs
for UBFD1

Paralogs
for UBFD1

SNPs/Variants
for UBFD1

Disorders & Mutations
for UBFD1

Medical News
for UBFD1

Publications
for UBFD1

Search for UBFD1

Genome Databases showing UBFD1

Other Databases showing UBFD1

Specialized Databases showing UBFD1

Licensable Technologies
for UBFD1

Services
for UBFD1

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

UBFD1 Gene

protein-coding GIFtS: 43

Aliases & Descriptionsfor UBFD1

Summariesfor UBFD1

Genomic Locationfor UBFD1

Proteinsfor UBFD1

Protein Domains/Familiesfor UBFD1

Gene Functionfor UBFD1

Pathways & Interactionsfor UBFD1

Drugs & Compoundsfor UBFD1

Transcriptsfor UBFD1

Expression for UBFD1

Orthologsfor UBFD1

Paralogsfor UBFD1

SNPs/Variantsfor UBFD1

Disorders & Mutationsfor UBFD1

Medical Newsfor UBFD1

Publicationsfor UBFD1

Search for UBFD1

Genome Databases showing UBFD1

Other Databases showing UBFD1

Specialized Databases showing UBFD1

Licensable Technologiesfor UBFD1

Servicesfor UBFD1

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 UBFD1

Summaries
for UBFD1

Genomic Location
for UBFD1

Proteins
for UBFD1

Protein Domains/
Families
for UBFD1

Gene Function
for UBFD1

Pathways & Interactions
for UBFD1

Drugs & Compounds
for UBFD1

Transcripts
for UBFD1

Expression
for UBFD1

Orthologs
for UBFD1

Paralogs
for UBFD1

SNPs/Variants
for UBFD1

Disorders & Mutations
for UBFD1

Medical News
for UBFD1

Publications
for UBFD1

Licensable Technologies
for UBFD1

Services
for UBFD1