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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
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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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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)

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

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Chemical Information
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