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    ATPSCKMT ATP synthase c subunit lysine N-methyltransferase [ Homo sapiens (human) ]

    Gene ID: 134145, updated on 9-Dec-2024

    Summary

    Official Symbol
    ATPSCKMTprovided by HGNC
    Official Full Name
    ATP synthase c subunit lysine N-methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:27029
    See related
    Ensembl:ENSG00000150756 MIM:618568; AllianceGenome:HGNC:27029
    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
    JS-2; FAM173B; hFAM173B
    Summary
    Enables protein-lysine N-methyltransferase activity. Involved in several processes, including peptidyl-lysine trimethylation; positive regulation of proton-transporting ATP synthase activity, rotational mechanism; and positive regulation of sensory perception of pain. Located in mitochondrial crista. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in fat (RPKM 4.0), adrenal (RPKM 3.9) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See ATPSCKMT in Genome Data Viewer
    Location:
    5p15.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (10225507..10249888, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (10164829..10189201, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (10225619..10250000, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944391-9944892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944893-9945392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15911 Neighboring gene uncharacterized LOC124900939 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10101715-10102617 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10102618-10103520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:10108167-10108948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10127135-10127785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10140102-10140735 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:10157229-10157880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15916 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:10251320-10251542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22352 Neighboring gene chaperonin containing TCP1 subunit 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:10300268-10300444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10307292-10307792 Neighboring gene carboxymethylenebutenolidase homolog

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study meta-analysis of chronic widespread pain: evidence for involvement of the 5p15.2 region.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20667

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-lysine N-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein-lysine N-methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in mitochondrial crista IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    ATP synthase subunit C lysine N-methyltransferase
    Names
    family with sequence similarity 173 member B
    protein FAM173B
    protein N-lysine methyltransferase FAM173B
    NP_001245317.1
    NP_001245318.1
    NP_954584.2
    XP_011512266.1
    XP_047272669.1
    XP_054207586.1
    XP_054207587.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001258388.2NP_001245317.1  ATP synthase subunit C lysine N-methyltransferase isoform 2

      See identical proteins and their annotated locations for NP_001245317.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC034229, AK302012, DW420473
      Consensus CDS
      CCDS58942.1
      UniProtKB/TrEMBL
      B7ZAK2
      Related
      ENSP00000420876.1, ENST00000510047.5
      Conserved Domains (1) summary
      cl17173
      Location:83190
      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). ...
    2. NM_001258389.2NP_001245318.1  ATP synthase subunit C lysine N-methyltransferase isoform 3

      See identical proteins and their annotated locations for NP_001245318.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC034229, DA523490
      Conserved Domains (1) summary
      cl17173
      Location:88123
      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). ...
    3. NM_199133.4NP_954584.2  ATP synthase subunit C lysine N-methyltransferase isoform 1

      See identical proteins and their annotated locations for NP_954584.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC034229, AK300042, GD160552
      Consensus CDS
      CCDS43301.1
      UniProtKB/Swiss-Prot
      B4DT41, B4DXK2, E9PBZ4, Q6P4H8
      UniProtKB/TrEMBL
      B7ZAK2
      Related
      ENSP00000422338.1, ENST00000511437.6
      Conserved Domains (1) summary
      cl17173
      Location:83188
      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_047668.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an internal exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC034229, DA843869, DW420473
    2. NR_047669.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC034229, BG611454
    3. NR_047670.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains an alternate internal exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC034229, AK055604

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      10225507..10249888 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416713.1XP_047272669.1  ATP synthase subunit C lysine N-methyltransferase isoform X1

    2. XM_011513964.2XP_011512266.1  ATP synthase subunit C lysine N-methyltransferase isoform X2

      Conserved Domains (1) summary
      cl17173
      Location:83176
      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). ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      10164829..10189201 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351611.1XP_054207586.1  ATP synthase subunit C lysine N-methyltransferase isoform X1

    2. XM_054351612.1XP_054207587.1  ATP synthase subunit C lysine N-methyltransferase isoform X2