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    MSANTD2 Myb/SANT DNA binding domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 79684, updated on 17-Sep-2024

    Summary

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    Official Symbol
    MSANTD2provided by HGNC
    Official Full Name
    Myb/SANT DNA binding domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:26266
    See related
    Ensembl:ENSG00000120458 AllianceGenome:HGNC:26266
    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
    C11orf61
    Expression
    Ubiquitous expression in thyroid (RPKM 1.6), endometrium (RPKM 1.2) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
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    Genomic context

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    See MSANTD2 in Genome Data Viewer
    Location:
    11q24.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (124766498..124800406, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (124795161..124829077, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (124636394..124670302, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124621349-124621910 Neighboring gene Sharpr-MPRA regulatory region 10895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5691 Neighboring gene V-set and immunoglobulin domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124631741-124632244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4029 Neighboring gene Sharpr-MPRA regulatory region 2909 Neighboring gene ESAM antisense RNA 1 Neighboring gene endothelial cell adhesion molecule Neighboring gene NANOG hESC enhancer GRCh37_chr11:124663166-124663667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4031 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124669881-124670488 Neighboring gene MSANTD2 antisense RNA 1 Neighboring gene E3 ubiquitin-protein ligase RNF181-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124712489-124713052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124713053-124713614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124732803-124733304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:124735644-124736320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:124738370-124738900 Neighboring gene Sharpr-MPRA regulatory region 2144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4035 Neighboring gene roundabout guidance receptor 3

    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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    Related articles in PubMed

    1. The neurodevelopmental gene MSANTD2 belongs to a gene family formed by recurrent molecular domestication of Harbinger transposons at the base of vertebrates. Etchegaray E, et al. Mol Biol Evol, 2022 Aug 17. PMID 35980103, Free PMC Article
    2. LncRNA BCLET variant confers bladder cancer susceptibility through alternative splicing of MSANTD2 exon 1. Liu H, et al. Cancer Med, 2023 Jul. PMID 37211917, Free PMC Article
    3. Conserved Mitotic Phosphorylation of a Proteasome Subunit Regulates Cell Proliferation. Duan J, et al. Cells, 2021 Nov 8. PMID 34831298, Free PMC Article
    4. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Connaughton DM, et al. Am J Hum Genet, 2020 Oct 1. PMID 32891193, Free PMC Article
    5. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Trynka G, et al. Gut, 2009 Aug. PMID 19240061

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA BCLET variant confers bladder cancer susceptibility through alternative splicing of MSANTD2 exon 1.
      Title: LncRNA BCLET variant confers bladder cancer susceptibility through alternative splicing of MSANTD2 exon 1.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    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
    Biological insights from 108 schizophrenia-associated genetic loci.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23342

    General protein information

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    Preferred Names
    myb/SANT-like DNA-binding domain-containing protein 2
    Names
    Myb/SANT-like DNA-binding domain containing 2

    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_001308027.2 → NP_001294956.1  myb/SANT-like DNA-binding domain-containing protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001294956.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) encodes the longest isoform (3).
      Source sequence(s)
      AK026995, AP000866, BC064919, DA379833, H97225
      Consensus CDS
      CCDS76491.1
      UniProtKB/Swiss-Prot
      B3KRY6, Q6P1R3, Q9H042, Q9H5K8
      UniProtKB/TrEMBL
      A0A6I8PS01
      Related
      ENSP00000364118.3, ENST00000374979.8
      Conserved Domains (1) summary
      pfam13837
      Location:104 → 195
      Myb_DNA-bind_4; Myb/SANT-like DNA-binding domain

    2. NM_001312919.2 → NP_001299848.1  myb/SANT-like DNA-binding domain-containing protein 2 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon that results in a frameshift in the 3' coding region and differences in the 3' UTR, compared to variant 3. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 3.
      Source sequence(s)
      AK026995, AK303902, AL512691, AP000866, BC064919, DA379833
      Consensus CDS
      CCDS81641.1
      UniProtKB/TrEMBL
      B4E1M0, E9PPE2
      Related
      ENSP00000431707.1, ENST00000524950.1
      Conserved Domains (1) summary
      pfam13837
      Location:104 → 170
      Myb_DNA-bind_4; Myb/SANT-like DNA-binding domain

    3. NM_001312920.2 → NP_001299849.1  myb/SANT-like DNA-binding domain-containing protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 3. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 3. Variants 5-8 all encode the same isoform (2).
      Source sequence(s)
      AK026995, AL512691, BC064919
      Consensus CDS
      CCDS73408.1
      UniProtKB/Swiss-Prot
      Q6P1R3
      Related
      ENSP00000435705.1, ENST00000526629.1

    4. NM_001312921.2 → NP_001299850.1  myb/SANT-like DNA-binding domain-containing protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in an internal exon, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 3. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 3. Variants 5-8 all encode the same isoform (2).
      Source sequence(s)
      AK026995, AL512691, AP000866, BC064919, CX781748, DA379833
      Consensus CDS
      CCDS73408.1
      UniProtKB/Swiss-Prot
      Q6P1R3

    5. NM_001352400.2 → NP_001339329.1  myb/SANT-like DNA-binding domain-containing protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7), as well as variants 5, 6, and 8, encodes isoform 2.
      Source sequence(s)
      AP000866
      Consensus CDS
      CCDS73408.1

    6. NM_001352401.2 → NP_001339330.1  myb/SANT-like DNA-binding domain-containing protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variants 5, 6, and 7, encodes isoform 2.
      Source sequence(s)
      AP000866
      Consensus CDS
      CCDS73408.1

    7. NM_024631.4 → NP_078907.2  myb/SANT-like DNA-binding domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_078907.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site in an internal exon, compared to variant 3, resulting in an isoform (1) that is shorter than isoform 3.
      Source sequence(s)
      AK026995, AL512691, AP000866, DA379833, H97225
      Consensus CDS
      CCDS8454.1
      UniProtKB/TrEMBL
      A0A6I8PS01
      Related
      ENSP00000239614.4, ENST00000239614.8
      Conserved Domains (1) summary
      pfam13837
      Location:104 → 172
      Myb_DNA-bind_4; Myb/SANT-like DNA-binding domain

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      124766498..124800406 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      124795161..124829077 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001301087.1: Suppressed sequence

      Description
      NM_001301087.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P1R3.1 GenPept UniProtKB/Swiss-Prot:Q6P1R3

    Gene LinkOut

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

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