Human Gene TSR1 (ENST00000301364.10_6) from GENCODE V47lift37
  Description: TSR1 ribosome maturation factor (from RefSeq NM_018128.5)
Gencode Transcript: ENST00000301364.10_6
Gencode Gene: ENSG00000167721.11_9
Transcript (Including UTRs)
   Position: hg19 chr17:2,225,690-2,239,751 Size: 14,062 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr17:2,227,490-2,239,721 Size: 12,232 Coding Exon Count: 15 

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 (chr17:2,225,690-2,239,751)mRNA (may differ from genome)Protein (804 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TSR1_HUMAN
DESCRIPTION: RecName: Full=Pre-rRNA-processing protein TSR1 homolog;
FUNCTION: Required during maturation of the 40S ribosomal subunit in the nucleolus (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleolus (By similarity).
SIMILARITY: Belongs to the BMS1/TSR1 family. TSR1 subfamily.
SEQUENCE CAUTION: Sequence=BAA91667.1; Type=Erroneous initiation; Sequence=BAA92639.1; 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: 36.13 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 510.59 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 -6.0030-0.200 Picture PostScript Text
3' UTR -550.001800-0.306 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
IPR012948 - AARP2CN
IPR007034 - BMS1_TSR1_C

Pfam Domains:
PF04950 - 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
PF08142 - AARP2CN (NUC121) domain

SCOP Domains:
50447 - Translation proteins

ModBase Predicted Comparative 3D Structure on Q2NL82
FrontTopSide
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 orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0034511 U3 snoRNA binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0030688 preribosome, small subunit precursor


-  Descriptions from all associated GenBank mRNAs
  LF209189 - JP 2014500723-A/16692: Polycomb-Associated Non-Coding RNAs.
AK026565 - Homo sapiens cDNA: FLJ22912 fis, clone KAT06132.
BC019090 - Homo sapiens TSR1, 20S rRNA accumulation, homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4896567), partial cds.
BC110851 - Homo sapiens TSR1, 20S rRNA accumulation, homolog (S. cerevisiae), mRNA (cDNA clone MGC:131829 IMAGE:5786818), complete cds.
BC126110 - Homo sapiens TSR1, 20S rRNA accumulation, homolog (S. cerevisiae), mRNA (cDNA clone MGC:161388 IMAGE:8991826), complete cds.
AB037822 - Homo sapiens KIAA1401 mRNA for KIAA1401 protein.
AK001396 - Homo sapiens cDNA FLJ10534 fis, clone NT2RP2001065.
KJ902866 - Synthetic construct Homo sapiens clone ccsbBroadEn_12260 TSR1 gene, encodes complete protein.
KJ899176 - Synthetic construct Homo sapiens clone ccsbBroadEn_08570 TSR1 gene, encodes complete protein.
AB463326 - Synthetic construct DNA, clone: pF1KA1401, Homo sapiens TSR1 gene for TSR1, 20S rRNA accumulation, homolog, without stop codon, in Flexi system.
MA444766 - JP 2018138019-A/16692: Polycomb-Associated Non-Coding RNAs.
JD411795 - Sequence 392819 from Patent EP1572962.
JD139079 - Sequence 120103 from Patent EP1572962.
JD056820 - Sequence 37844 from Patent EP1572962.
JD165427 - Sequence 146451 from Patent EP1572962.
JD327276 - Sequence 308300 from Patent EP1572962.
JD042111 - Sequence 23135 from Patent EP1572962.
JD435814 - Sequence 416838 from Patent EP1572962.
JD530031 - Sequence 511055 from Patent EP1572962.
JD557614 - Sequence 538638 from Patent EP1572962.
JD430594 - Sequence 411618 from Patent EP1572962.
JD324128 - Sequence 305152 from Patent EP1572962.
JD329402 - Sequence 310426 from Patent EP1572962.
JD144565 - Sequence 125589 from Patent EP1572962.
JD119085 - Sequence 100109 from Patent EP1572962.
JD511528 - Sequence 492552 from Patent EP1572962.
JD286690 - Sequence 267714 from Patent EP1572962.
JD128015 - Sequence 109039 from Patent EP1572962.
JD561257 - Sequence 542281 from Patent EP1572962.
JD101841 - Sequence 82865 from Patent EP1572962.
JD356016 - Sequence 337040 from Patent EP1572962.
JD293831 - Sequence 274855 from Patent EP1572962.
JD565199 - Sequence 546223 from Patent EP1572962.
JD239194 - Sequence 220218 from Patent EP1572962.
JD057495 - Sequence 38519 from Patent EP1572962.
JD114734 - Sequence 95758 from Patent EP1572962.
JD451031 - Sequence 432055 from Patent EP1572962.
JD558215 - Sequence 539239 from Patent EP1572962.
JD051938 - Sequence 32962 from Patent EP1572962.
JD202698 - Sequence 183722 from Patent EP1572962.
JD205959 - Sequence 186983 from Patent EP1572962.
JD042997 - Sequence 24021 from Patent EP1572962.
JD551923 - Sequence 532947 from Patent EP1572962.
JD243787 - Sequence 224811 from Patent EP1572962.
DQ596113 - Homo sapiens piRNA piR-34179, complete sequence.
LF326718 - JP 2014500723-A/134221: Polycomb-Associated Non-Coding RNAs.
CU676378 - Synthetic construct Homo sapiens gateway clone IMAGE:100019984 5' read TSR1 mRNA.
LF326717 - JP 2014500723-A/134220: Polycomb-Associated Non-Coding RNAs.
LF326716 - JP 2014500723-A/134219: Polycomb-Associated Non-Coding RNAs.
DQ585510 - Homo sapiens piRNA piR-52622, complete sequence.
LF326714 - JP 2014500723-A/134217: Polycomb-Associated Non-Coding RNAs.
LF326713 - JP 2014500723-A/134216: Polycomb-Associated Non-Coding RNAs.
LF326712 - JP 2014500723-A/134215: Polycomb-Associated Non-Coding RNAs.
AJ276247 - Homo sapiens partial mRNA, clone c1-1c9.
LF326711 - JP 2014500723-A/134214: Polycomb-Associated Non-Coding RNAs.
JD209574 - Sequence 190598 from Patent EP1572962.
JD296938 - Sequence 277962 from Patent EP1572962.
LF326710 - JP 2014500723-A/134213: Polycomb-Associated Non-Coding RNAs.
LF326709 - JP 2014500723-A/134212: Polycomb-Associated Non-Coding RNAs.
JD270829 - Sequence 251853 from Patent EP1572962.
LF326708 - JP 2014500723-A/134211: Polycomb-Associated Non-Coding RNAs.
JD104095 - Sequence 85119 from Patent EP1572962.
JD180674 - Sequence 161698 from Patent EP1572962.
LF326706 - JP 2014500723-A/134209: Polycomb-Associated Non-Coding RNAs.
MA562295 - JP 2018138019-A/134221: Polycomb-Associated Non-Coding RNAs.
MA562294 - JP 2018138019-A/134220: Polycomb-Associated Non-Coding RNAs.
MA562293 - JP 2018138019-A/134219: Polycomb-Associated Non-Coding RNAs.
MA562291 - JP 2018138019-A/134217: Polycomb-Associated Non-Coding RNAs.
MA562290 - JP 2018138019-A/134216: Polycomb-Associated Non-Coding RNAs.
MA562289 - JP 2018138019-A/134215: Polycomb-Associated Non-Coding RNAs.
MA562288 - JP 2018138019-A/134214: Polycomb-Associated Non-Coding RNAs.
MA562287 - JP 2018138019-A/134213: Polycomb-Associated Non-Coding RNAs.
MA562286 - JP 2018138019-A/134212: Polycomb-Associated Non-Coding RNAs.
MA562285 - JP 2018138019-A/134211: Polycomb-Associated Non-Coding RNAs.
MA562283 - JP 2018138019-A/134209: Polycomb-Associated Non-Coding RNAs.

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

Protein Q2NL82 (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: ENST00000301364.1, ENST00000301364.2, ENST00000301364.3, ENST00000301364.4, ENST00000301364.5, ENST00000301364.6, ENST00000301364.7, ENST00000301364.8, ENST00000301364.9, KIAA1401, NM_018128, Q2NL82, Q8WUY5, Q9NVT0, Q9P2E6, TSR1_HUMAN, uc317mui.1, uc317mui.2
UCSC ID: ENST00000301364.10_6
RefSeq Accession: NM_018128.5
Protein: Q2NL82 (aka TSR1_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.