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THUMPD2 THUMP domain 2 tRNA and snRNA guanosine methyltransferase [ Homo sapiens (human) ]

Gene ID: 80745, updated on 8-Mar-2025

Summary

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Official Symbol
THUMPD2provided by HGNC
Official Full Name
THUMP domain 2 tRNA and snRNA guanosine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:14890
See related
Ensembl:ENSG00000138050 MIM:611751; AllianceGenome:HGNC:14890
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
C2orf8
Summary
Predicted to enable tRNA (guanine) methyltransferase activity. Predicted to be involved in tRNA methylation. [provided by Alliance of Genome Resources, Mar 2025]
Expression
Ubiquitous expression in bone marrow (RPKM 6.9), ovary (RPKM 4.8) and 25 other tissues See more
Orthologs
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Genomic context

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See THUMPD2 in Genome Data Viewer
Location:
2p22.1; 2p22-p21
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (39736060..39779276, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (39745056..39788273, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (39963200..40006416, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11387 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:39696648-39697148 Neighboring gene MAP4K3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11388 Neighboring gene Sharpr-MPRA regulatory region 10578 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:39742467-39742687 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:39742776-39743368 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:39743369-39743960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:39743961-39744553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15618 Neighboring gene transmembrane protein 178A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:39948663-39949162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:39948161-39948662 Neighboring gene uncharacterized LOC124905994 Neighboring gene NANOG hESC enhancer GRCh37_chr2:39999086-40000066 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:40016715-40017914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:40065678-40066225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15619 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:40128919-40130118 Neighboring gene uncharacterized LOC112268436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:40147641-40148300 Neighboring gene zinc finger protein 19 pseudogene Neighboring gene SLC8A1 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Localization, genomic organization, and alternative transcription of a novel human SAM-dependent methyltransferase gene on chromosome 2p22-->p21. Zhang Y, et al. Cytogenet Cell Genet, 2001. PMID 12063391
  2. THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration. Yang WQ, et al. Nucleic Acids Res, 2024 Apr 12. PMID 38165050, Free PMC Article
  3. N 2-methylguanosine modifications on human tRNAs and snRNA U6 are important for cell proliferation, protein translation and pre-mRNA splicing. Wang C, et al. Nucleic Acids Res, 2023 Aug 11. PMID 37283053, Free PMC Article
  4. Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor. Brūmele B, et al. Int J Mol Sci, 2021 Dec 18. PMID 34948388, Free PMC Article
  5. Genome-wide association scan for five major dimensions of personality. Terracciano A, et al. Mol Psychiatry, 2010 Jun. PMID 18957941, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration.
    Title: THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan for five major dimensions of personality.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC2454

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables snRNA methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA (guanine) methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in regulation of alternative mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in tRNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of tRNA methyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
THUMP domain-containing protein 2
Names
SAM-dependent methyltransferase
THUMP domain containing 2
epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

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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_001321468.1 → NP_001308397.1  THUMP domain-containing protein 2 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (2) summary
    smart00981
    Location:186 → 264
    THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
    cl17173
    Location:274 → 353
    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_001321469.1 → NP_001308398.1  THUMP domain-containing protein 2 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    UniProtKB/TrEMBL
    B4DP37
    Conserved Domains (2) summary
    smart00981
    Location:93 → 171
    THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
    cl17173
    Location:181 → 326
    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_001321470.1 → NP_001308399.1  THUMP domain-containing protein 2 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC007253, AF380577, AK226034, AK298178, DC379776
    UniProtKB/TrEMBL
    B4DP37
    Conserved Domains (2) summary
    smart00981
    Location:93 → 155
    THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
    cl17173
    Location:165 → 310
    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). ...

  4. NM_001321474.1 → NP_001308403.1  THUMP domain-containing protein 2 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (2) summary
    smart00981
    Location:186 → 264
    THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
    cl17173
    Location:274 → 323
    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). ...

  5. NM_001321475.1 → NP_001308404.1  THUMP domain-containing protein 2 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (2) summary
    smart00981
    Location:93 → 171
    THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
    cl17173
    Location:181 → 260
    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_001321477.1 → NP_001308406.1  THUMP domain-containing protein 2 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (1) summary
    cl17173
    Location:40 → 185
    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_001321478.1 → NP_001308407.1  THUMP domain-containing protein 2 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (1) summary
    cl17173
    Location:40 → 185
    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_001321479.1 → NP_001308408.1  THUMP domain-containing protein 2 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (1) summary
    cl17173
    Location:40 → 185
    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_001321480.1 → NP_001308409.1  THUMP domain-containing protein 2 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (1) summary
    cl17173
    Location:40 → 185
    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). ...

  10. NM_001321481.1 → NP_001308410.1  THUMP domain-containing protein 2 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253
    Conserved Domains (1) summary
    cl17173
    Location:40 → 185
    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). ...

  11. NM_025264.5 → NP_079540.2  THUMP domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_079540.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the functional protein (isoform 1).
    Source sequence(s)
    AF380578, AK226034, BC004163, DC379776
    Consensus CDS
    CCDS1805.2
    UniProtKB/Swiss-Prot
    A8K7I7, Q53TT8, Q53TV0, Q9BTF0
    UniProtKB/TrEMBL
    A0A384ME97
    Related
    ENSP00000423933.1, ENST00000505747.6
    Conserved Domains (2) summary
    smart00981
    Location:186 → 264
    THUMP; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs
    cl17173
    Location:274 → 419
    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_028102.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes an alternate exon in the central coding region resulting in a frameshift, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF380578, AK226034, AL832115, DC379776
    Related
    ENST00000378727.8

  2. NR_135659.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253

  3. NR_135660.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253

  4. NR_135661.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253

  5. NR_135662.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253

  6. NR_135663.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253

  7. NR_135664.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC007246, AC007253

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    39736060..39779276 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533119.3 → XP_011531421.1  THUMP domain-containing protein 2 isoform X2

    Conserved Domains (1) summary
    cl17173
    Location:66 → 211
    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. XM_017005050.3 → XP_016860539.1  THUMP domain-containing protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A384ME97

  3. XM_017005053.3 → XP_016860542.1  THUMP domain-containing protein 2 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    39745056..39788273 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054344078.1 → XP_054200053.1  THUMP domain-containing protein 2 isoform X2

  2. XM_054344077.1 → XP_054200052.1  THUMP domain-containing protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A384ME97

  3. XM_054344079.1 → XP_054200054.1  THUMP domain-containing protein 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BTF0.2 GenPept UniProtKB/Swiss-Prot:Q9BTF0

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