Human Gene FTSJ3 (ENST00000427159.7_7) from GENCODE V47lift37
  Description: FtsJ RNA 2'-O-methyltransferase 3 (from RefSeq NM_017647.4)
Gencode Transcript: ENST00000427159.7_7
Gencode Gene: ENSG00000108592.17_11
Transcript (Including UTRs)
   Position: hg19 chr17:61,896,793-61,905,023 Size: 8,231 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr17:61,897,162-61,904,262 Size: 7,101 Coding Exon Count: 20 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:61,896,793-61,905,023)mRNA (may differ from genome)Protein (847 aa)
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-  Comments and Description Text from UniProtKB
  ID: RRMJ3_HUMAN
DESCRIPTION: RecName: Full=pre-rRNA processing protein FTSJ3; EC=2.1.1.-; AltName: Full=Protein ftsJ homolog 3; AltName: Full=Putative rRNA methyltransferase 3; AltName: Full=rRNA (uridine-2'-O-)-methyltransferase 3;
FUNCTION: Probable methyltransferase involved in the processing of the 34S pre-rRNA to 18S rRNA.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + rRNA = S-adenosyl-L- homocysteine + rRNA containing 2'-O-methyluridine.
SUBUNIT: Interacts with NIP7.
INTERACTION: P19525:EIF2AK2; NbExp=2; IntAct=EBI-744088, EBI-640775; Q9Y6K5:OAS3; NbExp=2; IntAct=EBI-744088, EBI-6115729;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Belongs to the methyltransferase superfamily. RlmE family.
SEQUENCE CAUTION: Sequence=BAA90924.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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           more ... click here to view the complete list

+  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: 25.63 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 844.58 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 -235.60638-0.369 Picture PostScript Text
3' UTR -134.10369-0.363 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
IPR015507 - rRNA-MeTfrase_E
IPR012920 - rRNA_MeTfrase_Spb1_C
IPR024576 - rRNA_MeTfrase_Spb1_DUF3381
IPR002877 - rRNA_MeTrfase_FtsJ_dom

Pfam Domains:
PF01728 - FtsJ-like methyltransferase
PF07780 - Spb1 C-terminal domain
PF11861 - Domain of unknown function (DUF3381)

SCOP Domains:
53335 - S-adenosyl-L-methionine-dependent methyltransferases

ModBase Predicted Comparative 3D Structure on Q8IY81
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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
GO:0008168 methyltransferase activity
GO:0008649 rRNA methyltransferase activity
GO:0008650 rRNA (uridine-2'-O-)-methyltransferase activity
GO:0016435 rRNA (guanine) methyltransferase activity
GO:0016740 transferase activity

Biological Process:
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0001510 RNA methylation
GO:0006364 rRNA processing
GO:0031167 rRNA methylation
GO:0032259 methylation
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0030687 preribosome, large subunit precursor


-  Descriptions from all associated GenBank mRNAs
  AF147378 - Homo sapiens full length insert cDNA clone YB66G11.
AK000069 - Homo sapiens cDNA FLJ20062 fis, clone COL01508.
AL834482 - Homo sapiens mRNA; cDNA DKFZp762O0311 (from clone DKFZp762O0311).
BC000131 - Homo sapiens FtsJ homolog 3 (E. coli), mRNA (cDNA clone IMAGE:3445488), partial cds.
BC036710 - Homo sapiens FtsJ homolog 3 (E. coli), mRNA (cDNA clone MGC:23312 IMAGE:4641078), complete cds.
AF327355 - Homo sapiens hypothetical protein SB92 mRNA, complete cds.
JD186256 - Sequence 167280 from Patent EP1572962.
JD536439 - Sequence 517463 from Patent EP1572962.
JD496132 - Sequence 477156 from Patent EP1572962.
JD072634 - Sequence 53658 from Patent EP1572962.
JD228903 - Sequence 209927 from Patent EP1572962.
AK296715 - Homo sapiens cDNA FLJ53449 complete cds, highly similar to rRNA methyltransferase 3 (EC 2.1.1.-).
JD395001 - Sequence 376025 from Patent EP1572962.
JD078131 - Sequence 59155 from Patent EP1572962.
DQ892321 - Synthetic construct clone IMAGE:100004951; FLH185241.01X; RZPDo839G11146D FtsJ homolog 3 (E. coli) (FTSJ3) gene, encodes complete protein.
AK315010 - Homo sapiens cDNA, FLJ95942, Homo sapiens FtsJ homolog 3 (E. coli) (FTSJ3), mRNA.
KJ903670 - Synthetic construct Homo sapiens clone ccsbBroadEn_13064 FTSJ3 gene, encodes complete protein.
DQ895523 - Synthetic construct Homo sapiens clone IMAGE:100009983; FLH185237.01L; RZPDo839G11145D FtsJ homolog 3 (E. coli) (FTSJ3) gene, encodes complete protein.
AB590341 - Synthetic construct DNA, clone: pFN21AE1550, Homo sapiens FTSJ3 gene for FtsJ homolog 3, without stop codon, in Flexi system.
AK307398 - Homo sapiens cDNA, FLJ97346.
AK095861 - Homo sapiens cDNA FLJ38542 fis, clone HCHON2001535, weakly similar to RRNA METHYLTRANSFERASE SPB1 (EC 2.1.1.-).
CU674054 - Synthetic construct Homo sapiens gateway clone IMAGE:100017413 5' read FTSJ3 mRNA.
AK027463 - Homo sapiens cDNA FLJ14557 fis, clone NT2RM2001896.
CU691390 - Synthetic construct Homo sapiens gateway clone IMAGE:100021970 5' read FTSJ3 mRNA.
JD544855 - Sequence 525879 from Patent EP1572962.
LF328295 - JP 2014500723-A/135798: Polycomb-Associated Non-Coding RNAs.
MA563872 - JP 2018138019-A/135798: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RCA5, D3DU22, ENST00000427159.1, ENST00000427159.2, ENST00000427159.3, ENST00000427159.4, ENST00000427159.5, ENST00000427159.6, FTSJ3 , NM_017647, Q8IY81, Q8N3A3, Q8WXX1, Q9BWM4, Q9NXT6, SB92, SPB1_HUMAN, uc319wfo.1, uc319wfo.2
UCSC ID: ENST00000427159.7_7
RefSeq Accession: NM_017647.4
Protein: Q8IY81 (aka RRMJ3_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.