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    MIR9-2HG MIR9-2 host gene [ Homo sapiens (human) ]

    Gene ID: 645323, updated on 9-Dec-2024

    Summary

    Official Symbol
    MIR9-2HGprovided by HGNC
    Official Full Name
    MIR9-2 host geneprovided by HGNC
    Primary source
    HGNC:HGNC:42810
    See related
    Ensembl:ENSG00000245526 MIM:616611; AllianceGenome:HGNC:42810
    Gene type
    ncRNA
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    VISC; NDIME; ECONEXIN; EyeLinc1; LINC00461; LINC02060
    Summary
    This is an evolutionarily conserved gene that produces alternatively spliced long non-coding RNAs that may be expressed predominantly in the brain and visual cortex. These transcripts may be involved in tumorigenesis, as depletion by siRNA suppressed glioma cell division. Transcripts may also bind to and regulate the activity of miR-411-5p and argonaut 2, thereby altering the expression of genes involved in tumor growth. [provided by RefSeq, Nov 2017]
    Expression
    Restricted expression toward brain (RPKM 29.6) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See MIR9-2HG in Genome Data Viewer
    Location:
    5q14.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (88538266..88691041, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (89019338..89172172, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (87834084..87986858, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene TMEM161B divergent transcript Neighboring gene small nucleolar RNA SNORA70 Neighboring gene long intergenic non-protein coding RNA 2060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22757 Neighboring gene CRE1 CAGE-defined tissue-specific enhancer Neighboring gene NANOG hESC enhancer GRCh37_chr5:87956815-87957640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87955707-87956218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87955193-87955706 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:87959465-87960288 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:87960289-87961111 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87967483-87968095 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87968096-87968709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22758 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:87971545-87972110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87975792-87976292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87980449-87981073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87981074-87981697 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87985094-87985772 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87985773-87986452 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:87987008-87987234 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:87991751-87992730 Neighboring gene H3 histone pseudogene 23 Neighboring gene MEF2C antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22761 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:88039231-88040430 Neighboring gene microRNA 9-2 Neighboring gene glioma stem cell association long noncoding RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22764 Neighboring gene Sharpr-MPRA regulatory region 14259 Neighboring gene myocyte enhancer factor 2C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:88185154-88185690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:88185691-88186225 Neighboring gene MEF2C 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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Other Names

    • evolutionary conserved and expressed in neural tissues (ECONEXIN)
    • lincRNA 461
    • long intergenic non-protein coding RNA 2060
    • long intergenic non-protein coding RNA 461
    • neural differentiation initiation of MEF2C expression
    • visual cortex-expressed

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in miRNA-mediated post-transcriptional gene silencing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of RISC complex IEA
    Inferred from Electronic Annotation
    more info
     

    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.

    RNA

    1. NR_015436.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008526, DA495096, DA778665
    2. NR_024383.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AK055372, BC047100, BM661956, DA217450, DA493278
      Related
      ENST00000666195.1
    3. NR_024384.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is also known as ECONEXIN.
      Source sequence(s)
      AC026701, AK055372, BC047100, BM661956, DB490657, DC320345
      Related
      ENST00000505030.6
    4. NR_152232.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC026701, AK055372, BC047100, BM661956, DA807261
    5. NR_152233.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008525, AC026701, BC047100
      Related
      ENST00000663276.2
    6. NR_152234.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008525, AC026701, BC047100
      Related
      ENST00000511014.8
    7. NR_152235.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008525, AC008526, AC026701
    8. NR_152236.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008525, AC026701, BC047100
      Related
      ENST00000509265.2
    9. NR_152237.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AA082758, AC008525, AK055372, BC047100, BM661956
    10. NR_152238.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008526, DA217450, DA807977
    11. NR_152239.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008526, DA217450, DA783765
    12. NR_152240.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC026701, AK055372, AK091356, BC047100, BM661956, DC320345
    13. NR_152241.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC026701, AK055372, BC036480, BC047100, BM661956
      Related
      ENST00000500197.6
    14. NR_152242.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC008526, AC026701

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      88538266..88691041 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      89019338..89172172 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)