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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

USB1 Gene

protein-coding   GIFtS: 41
GCID: GC16P058033

U6 snRNA biogenesis 1

(Previous name: chromosome 16 open reading frame 57 )
(Previous symbol: C16orf57)
 Explore 8 diseases affiliated with
USB1 via our new
 Human Malady Compendium 
Biological research products
for USB1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
U6 SnRNA Biogenesis 11 2     Chromosome 16 Open Reading Frame 571
C16orf571 2 3 5     HVSL Motif Containing 12
HVSL11 2     Mutated In Poikiloderma With Neutropenia Protein 12
Mpn11 2     Putative U6 SnRNA Phosphodiesterase2
HUsb11     U Six Biogenesis 12
PN2 5     UPF0406 Protein C16orf572
FLJ131541     EC 3.1.4.-3

External Ids:    HGNC: 257921   Entrez Gene: 796502   Ensembl: ENSG000001030057   OMIM: 6132765   UniProtKB: Q9BQ653   

Export aliases for USB1 gene to outside databases


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

Entrez Gene summary for USB1:
This gene encodes a protein with several conserved domains, however, its exact function is not known. Mutations in this
gene are associated with poikiloderma with neutropenia (PN), which shows phenotypic overlap with Rothmund-Thomson
syndrome (RTS) caused by mutations in the RECQL4 gene. It is believed that this gene product interacts with RECQL4
protein via SMAD4 proteins, explaining the partial clinical overlap between PN and RTS. Alternatively spliced
transcript variants encoding different isoforms have been noted for this gene. (provided by RefSeq, Mar 2011)

UniProtKB/Swiss-Prot: USB1_HUMAN, Q9BQ65
Function: Putative phosphodiesterase responsible for the U6 snRNA 3' end processing. Acts as a ribonuclease (RNase)
responsible for trimming the poly(U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the
formation of mature U6 snRNA 3' end-terminated with a 2',3'-cyclic phosphate




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.1  NT_010498.15  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for USB1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUSB1 promoter sequence
   Search SABiosciences Chromatin IP Primers for USB1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat USB1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q21   Ensembl cytogenetic band:  16q21   HGNC cytogenetic band: 16q13

USB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
USB1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P058033:  view genomic region     (about GC identifiers)

Start:
58,033,450 bp from pter      End:
58,055,522 bp from pter
Size:
22,073 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: USB1_HUMAN, Q9BQ65 (See protein sequence)
Recommended Name: Putative U6 snRNA phosphodiesterase  
Size: 265 amino acids; 30268 Da
Subcellular location: Nucleus
1 PDB 3D structure from and Proteopedia for USB1:
4H7W (3D)    
Secondary accessions: B4DWE3 B4DZW5 Q96FZ9 Q9H8X8
Alternative splicing: 3 isoforms:  Q9BQ65-1   Q9BQ65-2   Q9BQ65-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for USB1: NX_Q9BQ65

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BQ65

  • USB1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001182231.1  NP_001191840.1  NP_078874.2  

    ENSEMBL proteins: 
     ENSP00000454928   ENSP00000219281   ENSP00000446143   ENSP00000409792   ENSP00000457322  
     ENSP00000454692   ENSP00000457302  

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    Uscn Proteins for USB1

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005634nucleus IDA--


    USB1 for ontologies           About GeneDecksing



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

    USB1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR019146 UPF0406

    Graphical View of Domain Structure for InterPro Entry Q9BQ65

    ProtoNet protein and cluster: Q9BQ65

    UniProtKB/Swiss-Prot: USB1_HUMAN, Q9BQ65
    Similarity: Belongs to the USB1 family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: USB1_HUMAN, Q9BQ65
    Function: Putative phosphodiesterase responsible for the U6 snRNA 3' end processing. Acts as a ribonuclease (RNase)
    responsible for trimming the poly(U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the
    formation of mature U6 snRNA 3' end-terminated with a 2',3'-cyclic phosphate

    Enzyme Number (IUBMB): EC 3.1.4.-1

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    SwitchGear 3'UTR luciferase reporter plasmidUSB1 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0004518nuclease activity IEA--


    USB1 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for USB1:
     Downregulation of NF-kappaB pa  Downregulation of NF-kappaB pa 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for USB1

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for USB1 (Q9BQ652, 3 ENSP000002192814) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SMAD4Q134852, 3, ENSP000003415514MINT-61983 I2D: score=3 STRING: ENSP00000341551
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0008150biological_process ND--
    GO:0008380RNA splicing IMP--
    GO:0034477U6 snRNA 3'-end processing IMP--


    USB1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for USB1
    Search CenterWatch for drugs/clinical trials and news about USB1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for USB1 gene (3 alternative transcripts): 
    NM_001195302.1  NM_001204911.1  NM_024598.3  

    Unigene Cluster for USB1:

    U6 snRNA biogenesis 1
    Hs.408702  [show with all ESTs]
    Unigene Representative Sequence: NM_001204911
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000561743 ENST00000219281(uc002emz.3 uc010vib.2) ENST00000539737
    ENST00000423271 ENST00000561568 ENST00000565662 ENST00000566292 ENST00000569252(uc010vic.1)
    ENST00000562534 ENST00000568848 ENST00000563149(uc002emy.3 uc010via.2)
    ENST00000564387 ENST00000563207 ENST00000563321 ENST00000565151 ENST00000566082


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    Additional cDNA sequence: 

    AK023216.1 AK124443.1 AK293220.1 AK298473.1 AK301494.1 AK303121.1 BC004415.1 BC006291.2 
    BC007774.2 BC010099.2 BC021554.1 

    15 DOTS entries:

    DT.113937  DT.95134812  DT.95134814  DT.70101689  DT.100707681  DT.91645193  DT.100711352  DT.100797548 
    DT.92450672  DT.99981502  DT.100740697  DT.100797546  DT.75113607  DT.99971494  DT.92450665 

    24/202 AceView cDNA sequences (see all 202):

    CB153912 BI907485 AI739249 AI278903 BQ882326 BU167906 BQ069736 AI954274 
    AI656177 AW305204 BI819525 AI281175 CD368146 BX106523 BM459994 BM543924 
    CD369864 AI278657 BX474597 AI216420 BU683771 BX401638 BC010099 AW304355 

    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for USB1 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b
    SP1:                    -                 -           -     -     -     -     -                                       
    SP2:                    -                 -           -     -     -     -     -     -                                 
    SP3:                    -           -     -     -     -     -     -     -     -     -     -                           
    SP4:                    -                 -                                                                           
    SP5:                    -                 -           -                                                               


    ECgene alternative splicing isoforms for USB1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section
    See probesets specificity/sensitivity at GeneAnnot
    CGAP TAG: --

    See USB1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for USB1

    SOURCE GeneReport for Unigene cluster: Hs.408702
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for USB1 gene from 8/26 species (see all 26)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Usb15
    AA9604361
    expressed sequence AA9604361, 5 83.65(n)1
    81.13(a)1
      8 (47.12 cM)5
    1019851  NM_133954.21  NP_598715.21 
     953322925 
    chicken
    (Gallus gallus)
    Aves USB11 U6 snRNA biogenesis 1 75(n)
    70.83(a)
      415628  XM_413994.3  XP_413994.3 
    lizard
    (Anolis carolinensis)
    Reptilia C16orf576
    --
    64(a)
    1 ↔ 1
    GL344621.1(359-7410)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC529442 hypothetical protein MGC52944 74.2(n)    BC043765.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CK361000.12   -- 70.67(n)    CK361000.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG167901 CG16790 49.24(n)
    41.08(a)
      41155  NM_141654.2  NP_649911.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G511701 hypothetical protein 43.98(n)
    36.1(a)
      835191  NM_124496.3  NP_568753.1 
    rice
    (Oryza sativa)
    Liliopsida Os02g06510001 hypothetical protein 40.89(n)
    30.67(a)
      4330165  NM_001054125.1  NP_001047590.1 


    ENSEMBL Gene Tree for USB1 (if available)
    TreeFam Gene Tree for USB1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/315 NCBI SNPs in USB1 are shown (see all 315    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs37435591,2
    C,F,H,--58035429(+) GGCTCC/AGAGGA 6 /S syn1 ese319Minor allele frequency- A:0.06EA NS NA CSA EU 6871
    rs1422760221,2
    --58035806(+) ATTGCG/TATAGT 3 -- int10--------
    rs1512479771,2
    --58035952(+) TCTTAA/GATGCT 3 -- int10--------
    rs1406412401,2
    --58035966(+) CCTTAC/TCTTTG 3 -- int10--------
    rs1891798571,2
    --58035984(+) CTTTAC/TAAGCA 3 -- int10--------
    rs609342471,2
    C,--58036149(+) TGAACC/TACATT 3 -- int12Minor allele frequency- T:0.05WA 120
    rs1148019601,2
    F,--58036200(+) AGAGTT/GGGAGA 3 -- int11Minor allele frequency- G:0.02WA 118
    rs1822214941,2
    --58036296(+) CATATA/GTAAGG 3 -- int10--------
    rs37435601,2
    C,F,A,H,--58036347(+) AACAGA/GATAAA 3 -- int129Minor allele frequency- G:0.42NS EA NA WA EU 3253
    rs1871458571,2
    C,F,--58036349(+) CAGGAT/AAAATG 3 -- int11Minor allele frequency- A:0.09EU 839

    HapMap Linkage Disequilibrium report for USB1 (58033450 - 58055522 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for USB1: --

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    USB1 for disorders           About GeneDecksing

    OMIM gene information: 613276   
    OMIM disorders: 604173  
    UniProtKB/Swiss-Prot: USB1_HUMAN, Q9BQ65
  • Defects in USB1 are the cause of poikiloderma with neutropenia (PN) [MIM:604173]. PN is a genodermatosis
  • characterized by poikiloderma, pachyonychia and chronic neutropenia. The disorder starts as a papular erythematous
    rash on the limbs during the first year of life. It gradually spreads centripetally and, as the papular rash resolves,
    hypo- and hyperpigmentation result, with development of telangiectasias. Another skin manifestation is pachyonychia,
    but alopecia and leukoplakia are distinctively absent. One of the most important extracutaneous symptoms is an
    increased susceptibility to infections, mainly affecting the respiratory system, primarily due to a chronic
    neutropenia and to neutrophil functional defects. Bone marrow abnormalities account for neutropenia and may evolve
    into myelodysplasia associated with the risk of leukemic transformation. Poikiloderma with neutropenia shows
    phenotypic overlap with Rothmund-Thomson syndrome

    8 diseases for USB1:    About MalaCards
    poikiloderma with neutropenia    rothmund-thomson syndrome    neutropenia    dyskeratosis congenita
    dyskeratosis    leukoplakia    keratosis    alopecia


    Export disorders for USB1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for USB1 gene, integrated from 9 sources (see all 20):
    (articles sorted by number of sources associating them with USB1)
        Utopia: connect your pdf to the dynamic
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    1. C16orf57, a gene mutated in poikiloderma with neutrope nia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end mo dification. (PubMed id 22899009)1, 2, 3 Mroczek S....Dziembowski A. (2012)
    2. Identification of a homozygous deletion mutation in C 16orf57 in a family with Clericuzio-type poikiloderma with neutropenia. (PubMed id 20503306)1, 2, 3 Tanaka A....McGrath J. (2010)
    3. Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene. (PubMed id 20004881)1, 2, 3 Volpi L....Larizza L. (2010)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Novel C16orf57 mutations in patients with Poikiloderma with Neutropenia: bioinformatic analysis of the protein and predicted effects o f all reported mutations. (PubMed id 22269211)1 Colombo E.A....Larizza L. (2012)
    7. Systematic search for neutropenia should be part of t he first screening in patients with poikiloderma. (PubMed id 21872685)1 Piard J....Thauvin-Robinet C. (2012)
    8. Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA. (PubMed id 23022480)1 Shchepachev V....Azzalin C.M. (2012)
    9. Poikiloderma with neutropenia: report of three cases i ncluding one with calcinosis cutis. (PubMed id 21967010)1 Chantorn R. and Shwayder T. (2012)
    10. [Mutations of C16orf57 gene have been identified in t he poikiloderma-neutropenia syndrome and in a specific subset of congenital dys keratosis with normal-length telomeres]. (PubMed id 21497268)1 Dereure O. (2011)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 79650 HGNC: 25792 AceView: FLJ13154 Ensembl:ENSG00000103005 euGenes: HUgn79650
    ECgene: USB1 H-InvDB: USB1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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