Human Gene MRM3 (ENST00000304478.9_4) from GENCODE V47lift37
  Description: mitochondrial rRNA methyltransferase 3, transcript variant 1 (from RefSeq NM_018146.4)
Gencode Transcript: ENST00000304478.9_4
Gencode Gene: ENSG00000171861.11_10
Transcript (Including UTRs)
   Position: hg19 chr17:685,593-695,749 Size: 10,157 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr17:685,619-695,309 Size: 9,691 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:685,593-695,749)mRNA (may differ from genome)Protein (420 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RMTL1_HUMAN
DESCRIPTION: RecName: Full=RNA methyltransferase-like protein 1; EC=2.1.1.-;
FUNCTION: Probable RNA methyltransferase (By similarity).
INTERACTION: Q13617:CUL2; NbExp=1; IntAct=EBI-1045440, EBI-456179; P78549:NTHL1; NbExp=1; IntAct=EBI-1045440, EBI-1049350; P36639:NUDT1; NbExp=1; IntAct=EBI-1045440, EBI-1048967; Q9UHX1:PUF60; NbExp=1; IntAct=EBI-1045440, EBI-1053259; O75940:SMNDC1; NbExp=1; IntAct=EBI-1045440, EBI-1052641; Q15654:TRIP6; NbExp=1; IntAct=EBI-1045440, EBI-742327;
TISSUE SPECIFICITY: Expressed at same level in normal liver and hepatocarcinoma.
SIMILARITY: Belongs to the RNA methyltransferase TrmH family.

-  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


+  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: 22.94 RPKM in Testis
Total median expression: 396.27 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 -4.7026-0.181 Picture PostScript Text
3' UTR -154.40440-0.351 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
IPR001537 - SpoU_MeTrfase
IPR013123 - SpoU_subst-bd

Pfam Domains:
PF00588 - SpoU rRNA Methylase family

SCOP Domains:
75217 - alpha/beta knot
55315 - L30e-like

ModBase Predicted Comparative 3D Structure on Q9HC36
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 orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008173 RNA methyltransferase activity
GO:0016740 transferase activity
GO:0070039 rRNA (guanosine-2'-O-)-methyltransferase activity

Biological Process:
GO:0000451 rRNA 2'-O-methylation
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0032259 methylation

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  AF177344 - Homo sapiens clone HC90 unknown mRNA.
JD289391 - Sequence 270415 from Patent EP1572962.
AK001443 - Homo sapiens cDNA FLJ10581 fis, clone NT2RP2003543, weakly similar to HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE SLR1673 (EC 2.1.1.-).
AK222900 - Homo sapiens mRNA for RNA methyltransferase like 1 variant, clone: HRC02632.
BC011550 - Homo sapiens RNA methyltransferase like 1, mRNA (cDNA clone MGC:19968 IMAGE:4620063), complete cds.
BC050614 - Homo sapiens RNA methyltransferase like 1, mRNA (cDNA clone MGC:60073 IMAGE:5248052), complete cds.
AK225128 - Homo sapiens mRNA for RNA methyltransferase like 1 variant, clone: CBL03055.
CU690740 - Synthetic construct Homo sapiens gateway clone IMAGE:100021368 5' read RNMTL1 mRNA.
CU679954 - Synthetic construct Homo sapiens gateway clone IMAGE:100017648 5' read RNMTL1 mRNA.
AB590841 - Synthetic construct DNA, clone: pFN21AE1891, Homo sapiens RNMTL1 gene for RNA methyltransferase like 1, without stop codon, in Flexi system.
HQ448718 - Synthetic construct Homo sapiens clone IMAGE:100072163; CCSB007181_01 RNA methyltransferase like 1 (RNMTL1) gene, encodes complete protein.
KJ899090 - Synthetic construct Homo sapiens clone ccsbBroadEn_08484 RNMTL1 gene, encodes complete protein.
KJ899091 - Synthetic construct Homo sapiens clone ccsbBroadEn_08485 RNMTL1 gene, encodes complete protein.
JD368104 - Sequence 349128 from Patent EP1572962.
JD060865 - Sequence 41889 from Patent EP1572962.
JD373126 - Sequence 354150 from Patent EP1572962.
JD456767 - Sequence 437791 from Patent EP1572962.
JD475160 - Sequence 456184 from Patent EP1572962.

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

Protein Q9HC36 (Reactome details) participates in the following event(s):

R-HSA-6793096 MRM3 (RNMTL1) methylates guanosine-1370 of 16S rRNA yielding 2'-O-methylguanosine-1370
R-HSA-6793080 rRNA modification in the mitochondrion
R-HSA-8868766 rRNA processing in the mitochondrion
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000304478.1, ENST00000304478.2, ENST00000304478.3, ENST00000304478.4, ENST00000304478.5, ENST00000304478.6, ENST00000304478.7, ENST00000304478.8, HC90, MRM3 , MRM3_HUMAN, NM_018146, Q53GN1, Q86VC3, Q96F76, Q9HC36, Q9NVQ5, RNMTL1 , uc317nlc.1, uc317nlc.2
UCSC ID: ENST00000304478.9_4
RefSeq Accession: NM_018146.4
Protein: Q9HC36 (aka RMTL1_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.