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    NTMT1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 [ Homo sapiens (human) ]

    Gene ID: 28989, updated on 17-Jun-2024

    Summary

    Official Symbol
    NTMT1provided by HGNC
    Official Full Name
    N-terminal Xaa-Pro-Lys N-methyltransferase 1provided by HGNC
    Primary source
    HGNC:HGNC:23373
    See related
    Ensembl:ENSG00000148335 MIM:613560; AllianceGenome:HGNC:23373
    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
    NRMT; NRMT1; NTM1A; AD-003; HOMT1A; C9orf32; METTL11A
    Summary
    The METTL11A gene encodes an N-terminal methyltransferase for the RAN (MIM 601179) guanine nucleotide exchange factor regulator of chromosome condensation 1 (RCC1; MIM 179710). METTL11A enzyme alpha-N-methylates other protein targets such as SET (MIM 600960) and RB (MIM 180200).[supplied by OMIM, Nov 2010]
    Expression
    Ubiquitous expression in testis (RPKM 16.4), adrenal (RPKM 9.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See NTMT1 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129608872..129636135)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141813472..141840743)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (132371151..132398414)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132252097-132252756 Neighboring gene extensin-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132252757-132253416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132253417-132254075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132256099-132256899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132256900-132257699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132257700-132258500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132258501-132259299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132259614-132260182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132260183-132260750 Neighboring gene long intergenic non-protein coding RNA 963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132287329-132287829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132310394-132310894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132317282-132317929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132318577-132319224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132319225-132319870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132320519-132321164 Neighboring gene HNF1 motif-containing MPRA enhancer 89 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332093-132332956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332957-132333820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132333821-132334682 Neighboring gene uncharacterized LOC105376292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132346053-132346610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132349961-132350644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132362549-132363048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132366575-132367074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132369161-132369798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373341-132373842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373843-132374342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132382842-132383492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29118 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132388415-132388953 Neighboring gene chromosome 9 open reading frame 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132393630-132394420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132402376-132402933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132402934-132403490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132409664-132410412 Neighboring gene ankyrin repeat and SOCS box containing 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132431437-132431938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132431939-132432438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132439411-132440254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132441550-132442050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132442051-132442551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132448034-132448578 Neighboring gene paired related homeobox 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132474701-132475516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132486991-132487490 Neighboring gene uncharacterized LOC124902284 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:132489030-132489223 Neighboring gene PRRX2 antisense RNA 1

    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?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables N-terminal protein N-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables N-terminal protein N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    N-terminal Xaa-Pro-Lys N-methyltransferase 1
    Names
    N-terminal RCC1 methyltransferase
    X-Pro-Lys N-terminal protein methyltransferase 1A
    alpha N-terminal protein methyltransferase 1A
    methyltransferase-like protein 11A
    NP_001273725.1
    NP_001273726.1
    NP_001273727.1
    NP_001273728.1
    NP_001273729.1
    NP_001273730.1
    NP_001273731.1
    NP_001273732.1
    NP_054783.2
    XP_047279213.1
    XP_047279214.1
    XP_047279215.1
    XP_047279216.1
    XP_047279217.1
    XP_054218776.1
    XP_054218777.1
    XP_054218778.1
    XP_054218779.1
    XP_054218780.1

    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_001286796.2NP_001273725.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_001273725.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 through 5 all encode isoform a.
      Source sequence(s)
      AK298840, AL391056, AL590369, BC001396, BG468453
      Consensus CDS
      CCDS35160.1
      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
      Related
      ENSP00000361564.1, ENST00000372486.5
      Conserved Domains (1) summary
      pfam05891
      Location:8223
      Methyltransf_PK; AdoMet dependent proline di-methyltransferase
    2. NM_001286797.2NP_001273726.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_001273726.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.
      Source sequence(s)
      AK298840, AL590369, BI083998
      Consensus CDS
      CCDS35160.1
      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
      Related
      ENSP00000478521.1, ENST00000613644.4
      Conserved Domains (1) summary
      pfam05891
      Location:8223
      Methyltransf_PK; AdoMet dependent proline di-methyltransferase
    3. NM_001286798.2NP_001273727.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_001273727.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.
      Source sequence(s)
      AK298840, AL590369, BQ636193, BQ923165, CN406947
      Consensus CDS
      CCDS35160.1
      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
      Related
      ENSP00000483489.1, ENST00000611055.4
      Conserved Domains (1) summary
      pfam05891
      Location:8223
      Methyltransf_PK; AdoMet dependent proline di-methyltransferase
    4. NM_001286799.2NP_001273728.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_001273728.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.
      Source sequence(s)
      AK298840, AL590369, BM554138
      Consensus CDS
      CCDS35160.1
      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
      Related
      ENSP00000361558.1, ENST00000372480.1
      Conserved Domains (1) summary
      pfam05891
      Location:8223
      Methyltransf_PK; AdoMet dependent proline di-methyltransferase
    5. NM_001286800.2NP_001273729.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform b

      See identical proteins and their annotated locations for NP_001273729.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, and uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a. Both variants 6 and 7 encode isoform b.
      Source sequence(s)
      AK298840, AL590369
      Consensus CDS
      CCDS69682.1
      UniProtKB/Swiss-Prot
      Q9BV86
      Related
      ENSP00000361559.3, ENST00000372481.7
      Conserved Domains (1) summary
      cl17173
      Location:8118
      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). ...
    6. NM_001286801.2NP_001273730.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform b

      See identical proteins and their annotated locations for NP_001273730.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, and uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a. Both variants 6 and 7 encode isoform b.
      Source sequence(s)
      AK298840, AL590369, BE392289, BQ636193, HY058177
      Consensus CDS
      CCDS69682.1
      UniProtKB/Swiss-Prot
      Q9BV86
      Conserved Domains (1) summary
      cl17173
      Location:8118
      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). ...
    7. NM_001286802.2NP_001273731.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform c

      See identical proteins and their annotated locations for NP_001273731.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform c.
      Source sequence(s)
      AK298840, AL590369, HY058177
      Consensus CDS
      CCDS75918.1
      UniProtKB/TrEMBL
      S4R338
      Related
      ENSP00000484447.1, ENST00000617943.4
      Conserved Domains (1) summary
      cl17173
      Location:1135
      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). ...
    8. NM_001286803.2NP_001273732.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform c

      See identical proteins and their annotated locations for NP_001273732.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform c.
      Source sequence(s)
      AK298840, AL590369, BM009113, BQ636193
      Consensus CDS
      CCDS75918.1
      UniProtKB/TrEMBL
      S4R338
      Related
      ENSP00000473900.1, ENST00000482347.1
      Conserved Domains (1) summary
      cl17173
      Location:1135
      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). ...
    9. NM_014064.4NP_054783.2  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

      See identical proteins and their annotated locations for NP_054783.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.
      Source sequence(s)
      AK298840, AL590369, BC001396, BQ636193
      Consensus CDS
      CCDS35160.1
      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
      Related
      ENSP00000361561.4, ENST00000372483.9
      Conserved Domains (1) summary
      pfam05891
      Location:8223
      Methyltransf_PK; AdoMet dependent proline di-methyltransferase

    RNA

    1. NR_104596.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) contains an alternate 5' terminal exon, and uses alternate splice sites in two internal exons, 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)
      AK298840, AK307056, AL590369

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      129608872..129636135
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423259.1XP_047279215.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2

    2. XM_047423258.1XP_047279214.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
    3. XM_047423257.1XP_047279213.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
    4. XM_047423260.1XP_047279216.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2

    5. XM_047423261.1XP_047279217.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X3

      UniProtKB/TrEMBL
      S4R338

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      141813472..141840743
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362803.1XP_054218778.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2

    2. XM_054362802.1XP_054218777.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
    3. XM_054362801.1XP_054218776.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

      UniProtKB/Swiss-Prot
      A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
    4. XM_054362804.1XP_054218779.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2

    5. XM_054362805.1XP_054218780.1  N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X3

      UniProtKB/TrEMBL
      S4R338