Human Gene BYSL (ENST00000230340.9_5) from GENCODE V47lift37
  Description: bystin like (from RefSeq NM_004053.4)
Gencode Transcript: ENST00000230340.9_5
Gencode Gene: ENSG00000112578.11_9
Transcript (Including UTRs)
   Position: hg19 chr6:41,889,237-41,900,784 Size: 11,548 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr6:41,889,301-41,900,444 Size: 11,144 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:41,889,237-41,900,784)mRNA (may differ from genome)Protein (437 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BYST_HUMAN
DESCRIPTION: RecName: Full=Bystin;
FUNCTION: Required for processing of 20S pre-rRNA precursor and biogenesis of 40S ribosomal subunits. May be required for trophinin-dependent regulation of cell adhesion during implantation of human embryos.
SUBUNIT: Binds trophinin, tastin and cytokeratins.
INTERACTION: Q12816:TRO; NbExp=4; IntAct=EBI-358049, EBI-950001; Q12815:TROAP; NbExp=9; IntAct=EBI-358049, EBI-2349743;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus. Note=Associated with 40S ribosomal subunits.
TISSUE SPECIFICITY: Found in the placenta from the sixth week of pregnancy. Was localized in the cytoplasm of the syncytiotrophoblast in the chorionic villi and in endometrial decidual cells at the uteroplacental interface. After week 10, the level decreased and then disappeared from placental villi.
MISCELLANEOUS: HeLa cells lacking BYSL show a delay in the processing of the 18S rRNA component of the 40S ribosomal subunit. HT-H cells lacking BYSL show trophinin-independent signaling through ERBB4.
SIMILARITY: Belongs to the bystin family.
SEQUENCE CAUTION: Sequence=AAC16603.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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: 13.76 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 266.32 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 -8.9064-0.139 Picture PostScript Text
3' UTR -117.20340-0.345 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
IPR007955 - Bystin

Pfam Domains:
PF05291 - Bystin

ModBase Predicted Comparative 3D Structure on Q13895
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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 orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0001701 in utero embryonic development
GO:0001825 blastocyst formation
GO:0001829 trophectodermal cell differentiation
GO:0007155 cell adhesion
GO:0007565 female pregnancy
GO:0008283 cell proliferation
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle
GO:0045177 apical part of cell


-  Descriptions from all associated GenBank mRNAs
  BC050645 - Homo sapiens bystin-like, mRNA (cDNA clone MGC:60140 IMAGE:6011459), complete cds.
AK095253 - Homo sapiens cDNA FLJ37934 fis, clone CTONG2005265, highly similar to BYSTIN.
BC062627 - Homo sapiens bystin-like, mRNA (cDNA clone MGC:74801 IMAGE:5226210), complete cds.
AK314147 - Homo sapiens cDNA, FLJ94850.
BC007340 - Homo sapiens bystin-like, mRNA (cDNA clone MGC:1526 IMAGE:2989807), complete cds.
CU690756 - Synthetic construct Homo sapiens gateway clone IMAGE:100021403 5' read BYSL mRNA.
JD159365 - Sequence 140389 from Patent EP1572962.
JD409623 - Sequence 390647 from Patent EP1572962.
JD487654 - Sequence 468678 from Patent EP1572962.
JD336772 - Sequence 317796 from Patent EP1572962.
JD462690 - Sequence 443714 from Patent EP1572962.
JD138708 - Sequence 119732 from Patent EP1572962.
JD170458 - Sequence 151482 from Patent EP1572962.
CU675625 - Synthetic construct Homo sapiens gateway clone IMAGE:100018937 5' read BYSL mRNA.
KJ901306 - Synthetic construct Homo sapiens clone ccsbBroadEn_10700 BYSL gene, encodes complete protein.
L36720 - Homo sapiens bystin mRNA, complete cds.
DQ892914 - Synthetic construct clone IMAGE:100005544; FLH190784.01X; RZPDo839D1276D bystin-like (BYSL) gene, encodes complete protein.
DQ896163 - Synthetic construct Homo sapiens clone IMAGE:100010623; FLH190780.01L; RZPDo839D1266D bystin-like (BYSL) gene, encodes complete protein.
JD498079 - Sequence 479103 from Patent EP1572962.
JD380512 - Sequence 361536 from Patent EP1572962.
JD154940 - Sequence 135964 from Patent EP1572962.
JD357946 - Sequence 338970 from Patent EP1572962.
JD524192 - Sequence 505216 from Patent EP1572962.
JD093164 - Sequence 74188 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q13895 (Reactome details) participates in the following event(s):

R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: BYSL , BYST_HUMAN, ENP1 , ENST00000230340.1, ENST00000230340.2, ENST00000230340.3, ENST00000230340.4, ENST00000230340.5, ENST00000230340.6, ENST00000230340.7, ENST00000230340.8, NM_004053, Q13895, Q6P5W4, Q86W44, Q96IP8, uc317dsk.1, uc317dsk.2
UCSC ID: ENST00000230340.9_5
RefSeq Accession: NM_004053.4
Protein: Q13895 (aka BYST_HUMAN)

-  Gene Model Information
  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.