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    THUMPD2 THUMP domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 80745, updated on 2-Nov-2024

    Summary

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    Official Symbol
    THUMPD2provided by HGNC
    Official Full Name
    THUMP domain containing 2provided 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, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 6.9), ovary (RPKM 4.8) and 25 other tissues See more
    Orthologs
    mouse all
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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: HPA RNA-seq normal tissues 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

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    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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    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 Variation Viewer (GRCh37.p13)

    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 tRNA (guanine) methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    THUMP domain-containing protein 2
    Names
    SAM-dependent methyltransferase
    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

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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