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NSUN4 NOP2/Sun RNA methyltransferase family member 4 [ Homo sapiens (human) ]

Gene ID: 387338, updated on 8-Jul-2018
Official Symbol
NSUN4provided by HGNC
Official Full Name
NOP2/Sun RNA methyltransferase family member 4provided by HGNC
Primary source
HGNC:HGNC:31802
See related
Ensembl:ENSG00000117481 MIM:615394; Vega:OTTHUMG00000007808
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SHTAP
Expression
Broad expression in testis (RPKM 13.3), thyroid (RPKM 4.5) and 25 other tissues See more
Orthologs
See NSUN4 in Genome Data Viewer
Location:
1p33
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (46340177..46365152)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (46805849..46830824)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RAD54 like Neighboring gene leucine rich repeat containing 41 Neighboring gene ubiquinol-cytochrome c reductase hinge protein Neighboring gene fatty acid amide hydrolase Neighboring gene fatty acid amide hydrolase pseudogene 1

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • rRNA modification in the mitochondrion, organism-specific biosystem (from REACTOME)
    rRNA modification in the mitochondrion, organism-specific biosystemFive modified nucleotides have been detected in the 12S rRNA: 5-methylcytidine-841 catalyzed by NSUN4, 6-dimethyladenosine-936 catalyzed by TFB1M, 6-dimethyladenosine-937 catalyzed by TFB1M, 5-methy...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the mitochondrion, organism-specific biosystem (from REACTOME)
    rRNA processing in the mitochondrion, organism-specific biosystemMitochondrial ribosomes contain 16S rRNA (large subunit) and 12S rRNA (small subunit) that are encoded in the mitochondrial genome and produced by processing of a long H strand transcript (reviewed i...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Potential readthrough

Included gene: FAAH

Homology

Clone Names

  • FLJ18051, MGC22960

Gene Ontology Provided by GOA

Function Evidence Code Pubs
methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
rRNA (cytosine-C5-)-methyltransferase activity EXP
Inferred from Experiment
more info
PubMed 
small ribosomal subunit rRNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
RNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mature ribosome assembly IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mitochondrial translation IEA
Inferred from Electronic Annotation
more info
 
rRNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rRNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
rRNA methylation TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
mitochondrial large ribosomal subunit IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial large ribosomal subunit IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial matrix TAS
Traceable Author Statement
more info
 
Preferred Names
5-methylcytosine rRNA methyltransferase NSUN4
Names
NOL1/NOP2/Sun domain family member 4
NOP2/Sun domain family, member 4
putative methyltransferase NSUN4
sperm head and tail associated protein

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001256127.1NP_001243056.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform b

    See identical proteins and their annotated locations for NP_001243056.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
    Source sequence(s)
    AK057420, AL122001, BM665392, DA905308
    Consensus CDS
    CCDS57996.1
    UniProtKB/Swiss-Prot
    Q96CB9
    Related
    ENSP00000437758.1, OTTHUMP00000275505, ENST00000537428.2, OTTHUMT00000021430
    Conserved Domains (1) summary
    cl25484
    Location:106333
    Methyltr_RsmF_N; N-terminal domain of 16S rRNA methyltransferase RsmF
  2. NM_001256128.1NP_001243057.1  5-methylcytosine rRNA methyltransferase NSUN4 isoform b

    See identical proteins and their annotated locations for NP_001243057.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
    Source sequence(s)
    AK292353, AL122001, BM665392, DA905308
    Consensus CDS
    CCDS57996.1
    UniProtKB/Swiss-Prot
    Q96CB9
    UniProtKB/TrEMBL
    A8K8I8
    Conserved Domains (1) summary
    cl25484
    Location:106333
    Methyltr_RsmF_N; N-terminal domain of 16S rRNA methyltransferase RsmF
  3. NM_199044.3NP_950245.2  5-methylcytosine rRNA methyltransferase NSUN4 isoform a

    See identical proteins and their annotated locations for NP_950245.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AK291741, AL122001, BG821302, BM665392, CF593490
    Consensus CDS
    CCDS534.1
    UniProtKB/Swiss-Prot
    Q96CB9
    Related
    ENSP00000419740.1, OTTHUMP00000009478, ENST00000474844.5, OTTHUMT00000021427
    Conserved Domains (1) summary
    cl17173
    Location:166325
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

RNA

  1. NR_045789.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) includes an additional exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK295003, AL122001, BG821302, BM665392, CF593490
  2. NR_045790.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL122001, BG821302, BM665392, BX648592, CF593490
    Related
    ENST00000307089.7, OTTHUMT00000021429
  3. NR_045791.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site and lacks an exon in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK291741, AL122001, BG821302, BM665392, CF593490, DA799314

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    46340177..46365152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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