Human Gene USB1 (uc002emz.3) Description and Page Index
  Description: Homo sapiens U6 snRNA biogenesis 1 (USB1), transcript variant 1, mRNA.
RefSeq Summary (NM_024598): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:58,035,277-58,055,527 Size: 20,251 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr16:58,035,388-58,054,149 Size: 18,762 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:58,035,277-58,055,527)mRNA (may differ from genome)Protein (265 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: USB1_HUMAN
DESCRIPTION: RecName: Full=Putative U6 snRNA phosphodiesterase; Short=hUsb1; EC=3.1.4.-;
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.
SUBCELLULAR LOCATION: Nucleus.
DISEASE: 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.
SIMILARITY: Belongs to the USB1 family.

-  MalaCards Disease Associations
  MalaCards Gene Search: USB1
Diseases sorted by gene-association score: poikiloderma with neutropenia* (1412), dyskeratosis congenita* (108), rothmund-thomson syndrome (34), neutropenia (20), dubowitz syndrome (7), ablepharon-macrostomia syndrome (7), calcinosis (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.29 RPKM in Whole Blood
Total median expression: 434.26 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -55.30111-0.498 Picture PostScript Text
3' UTR -384.851378-0.279 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019146 - UPF0406

Pfam Domains:
PF09749 - Uncharacterised conserved protein

ModBase Predicted Comparative 3D Structure on Q9BQ65
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000175 3'-5'-exoribonuclease activity
GO:0004518 nuclease activity
GO:0016787 hydrolase activity

Biological Process:
GO:0008380 RNA splicing
GO:0034477 U6 snRNA 3'-end processing
GO:0090305 nucleic acid phosphodiester bond hydrolysis
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic

Cellular Component:
GO:0005634 nucleus
GO:0045171 intercellular bridge


-  Descriptions from all associated GenBank mRNAs
  AK023216 - Homo sapiens cDNA FLJ13154 fis, clone NT2RP3003427.
AK293220 - Homo sapiens cDNA FLJ53705 complete cds.
AK298473 - Homo sapiens cDNA FLJ55128 complete cds.
AK303121 - Homo sapiens cDNA FLJ60009 complete cds.
BC010099 - Homo sapiens chromosome 16 open reading frame 57, mRNA (cDNA clone IMAGE:3506308), complete cds.
AK301494 - Homo sapiens cDNA FLJ59088 complete cds.
JD520703 - Sequence 501727 from Patent EP1572962.
JD396086 - Sequence 377110 from Patent EP1572962.
BC004415 - Homo sapiens chromosome 16 open reading frame 57, mRNA (cDNA clone MGC:11014 IMAGE:3641317), complete cds.
JD291815 - Sequence 272839 from Patent EP1572962.
BC007774 - Homo sapiens chromosome 16 open reading frame 57, mRNA (cDNA clone MGC:13154 IMAGE:4302289), complete cds.
BC006291 - Homo sapiens chromosome 16 open reading frame 57, mRNA (cDNA clone MGC:10683 IMAGE:4025993), complete cds.
BC021554 - Homo sapiens chromosome 16 open reading frame 57, mRNA (cDNA clone MGC:31809 IMAGE:4541229), complete cds.
JD198265 - Sequence 179289 from Patent EP1572962.
KJ903188 - Synthetic construct Homo sapiens clone ccsbBroadEn_12582 C16orf57 gene, encodes complete protein.
JF432668 - Synthetic construct Homo sapiens clone IMAGE:100073906 chromosome 16 open reading frame 57 (C16orf57) gene, encodes complete protein.
KJ894705 - Synthetic construct Homo sapiens clone ccsbBroadEn_04099 C16orf57 gene, encodes complete protein.
AK126223 - Homo sapiens cDNA FLJ44235 fis, clone THYMU3007368.
JD216746 - Sequence 197770 from Patent EP1572962.
JD216747 - Sequence 197771 from Patent EP1572962.
JD351520 - Sequence 332544 from Patent EP1572962.
JD522666 - Sequence 503690 from Patent EP1572962.
JD335009 - Sequence 316033 from Patent EP1572962.
JD354379 - Sequence 335403 from Patent EP1572962.
JD164080 - Sequence 145104 from Patent EP1572962.
JD259407 - Sequence 240431 from Patent EP1572962.
JD262797 - Sequence 243821 from Patent EP1572962.
JD418806 - Sequence 399830 from Patent EP1572962.
JD154017 - Sequence 135041 from Patent EP1572962.
JD151263 - Sequence 132287 from Patent EP1572962.
JD151264 - Sequence 132288 from Patent EP1572962.
JD161918 - Sequence 142942 from Patent EP1572962.
JD228737 - Sequence 209761 from Patent EP1572962.
JD228738 - Sequence 209762 from Patent EP1572962.
JD132834 - Sequence 113858 from Patent EP1572962.
JD418760 - Sequence 399784 from Patent EP1572962.
JD259288 - Sequence 240312 from Patent EP1572962.
JD418565 - Sequence 399589 from Patent EP1572962.
JD418564 - Sequence 399588 from Patent EP1572962.
JD151264 - Sequence 132288 from Patent EP1572962.
JD151263 - Sequence 132287 from Patent EP1572962.
JD161919 - Sequence 142943 from Patent EP1572962.
JD161918 - Sequence 142942 from Patent EP1572962.
JD391853 - Sequence 372877 from Patent EP1572962.
JD259845 - Sequence 240869 from Patent EP1572962.
JD150607 - Sequence 131631 from Patent EP1572962.
JD150606 - Sequence 131630 from Patent EP1572962.
JD525859 - Sequence 506883 from Patent EP1572962.
JD555940 - Sequence 536964 from Patent EP1572962.
JD259853 - Sequence 240877 from Patent EP1572962.
JD259830 - Sequence 240854 from Patent EP1572962.
JD150553 - Sequence 131577 from Patent EP1572962.
JD259845 - Sequence 240869 from Patent EP1572962.
JD256153 - Sequence 237177 from Patent EP1572962.
JD235055 - Sequence 216079 from Patent EP1572962.
JD489981 - Sequence 471005 from Patent EP1572962.
JD328343 - Sequence 309367 from Patent EP1572962.
JD492333 - Sequence 473357 from Patent EP1572962.
JD410413 - Sequence 391437 from Patent EP1572962.
JD360433 - Sequence 341457 from Patent EP1572962.
JD515934 - Sequence 496958 from Patent EP1572962.
JD376203 - Sequence 357227 from Patent EP1572962.
JD429865 - Sequence 410889 from Patent EP1572962.
JD124516 - Sequence 105540 from Patent EP1572962.
JD333513 - Sequence 314537 from Patent EP1572962.
JD477439 - Sequence 458463 from Patent EP1572962.
JD123613 - Sequence 104637 from Patent EP1572962.
JD195318 - Sequence 176342 from Patent EP1572962.
JD163284 - Sequence 144308 from Patent EP1572962.
JD192132 - Sequence 173156 from Patent EP1572962.
JD500750 - Sequence 481774 from Patent EP1572962.
JD290630 - Sequence 271654 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DWE3, B4DZW5, C16orf57, NM_024598, NP_078874, Q96FZ9, Q9BQ65, Q9H8X8, USB1_HUMAN
UCSC ID: uc002emz.3
RefSeq Accession: NM_024598
Protein: Q9BQ65 (aka USB1_HUMAN)
CCDS: CCDS10791.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene USB1:
poikiloderma-n (Poikiloderma with Neutropenia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024598.3
exon count: 7CDS single in 3' UTR: no RNA size: 2287
ORF size: 798CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1396.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.