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LOC106783509 nonconserved acetylation island sequence 60 enhancer [ Homo sapiens (human) ]

Gene ID: 106783509, updated on 17-Sep-2024

Summary

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Gene symbol
LOC106783509
Gene description
nonconserved acetylation island sequence 60 enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region, which is poorly conserved between human and mouse at the sequence level, can function as an enhancer in human Jurkat T cells. It overlaps the HLA-T (major histocompatibility complex, class I, T) pseudogene in the major histocompatibility complex (MHC) region of chromosome 6. Several haplotypes of this region are represented in the GRCh38 reference genome assembly. The sequence shown to have enhancer activity in T cells is represented in the ALT_REF_LOCI_1, ALT_REF_LOCI_2 and ALT_REF_LOCI_3 haplotypes, whereas it is unknown if the primary chromosome 6 allele, as represented in NC_000006.12, has enhancer activity. The chromatin structure of this region represents a histone acetylation island in human T cells based on the diacetylation of histone H3 at lysines 9 and 14. [provided by RefSeq, Nov 2015]
Annotation information
Annotation category: only annotated on alternate loci in reference assembly
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Genomic context

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See LOC106783509 in Genome Data Viewer
Location:
6p21.3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 (ALT_REF_LOCI_2) NT_113891.3 (1377874..1378275)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 (ALT_REF_LOCI_1) NT_167244.2 (1156200..1156601)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 (ALT_REF_LOCI_3) NT_167245.2 (1153679..1154080)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 (ALT_REF_LOCI_5) NT_167247.2 (1153316..1153717)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 (ALT_REF_LOCI_6) NT_167248.2 (1153335..1153736)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29762380..29762781)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 (PATCHES) NW_003871063.1 (132377..132778)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 Unlocalized Scaffold (ALT_REF_LOCI_2) NT_113891.2 (1377980..1378381)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 Unlocalized Scaffold (ALT_REF_LOCI_1) NT_167244.1 (1106116..1106517)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 Unlocalized Scaffold (ALT_REF_LOCI_3) NT_167245.1 (1159264..1159665)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 Unlocalized Scaffold (ALT_REF_LOCI_5) NT_167247.1 (1158901..1159302)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 Unlocalized Scaffold (ALT_REF_LOCI_6) NT_167248.1 (1158931..1159332)

NT_167244.2Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905339 Neighboring gene HLA complex P5B Neighboring gene major histocompatibility complex, class I, H (pseudogene) Neighboring gene uncharacterized LOC124905340 Neighboring gene uncharacterized LOC124901298 Neighboring gene HLA complex group 4B Neighboring gene major histocompatibility complex, class I, K (pseudogene) Neighboring gene major histocompatibility complex, class I, A

NT_113891.3Genomic Context describing neighboring genes Neighboring gene HLA complex P5B Neighboring gene major histocompatibility complex, class I, H (pseudogene) Neighboring gene HLA complex group 4B Neighboring gene major histocompatibility complex, class I, K (pseudogene) Neighboring gene major histocompatibility complex, class I, A

NT_167245.2Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905380 Neighboring gene major histocompatibility complex, class I, H (pseudogene) Neighboring gene HLA complex group 4B Neighboring gene major histocompatibility complex, class I, K (pseudogene) Neighboring gene major histocompatibility complex, class I, A

NT_167247.2Genomic Context describing neighboring genes Neighboring gene HLA complex P5B Neighboring gene major histocompatibility complex, class I, H (pseudogene) Neighboring gene major histocompatibility complex, class I, A Neighboring gene HLA complex group 9

NT_167248.2Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905394 Neighboring gene major histocompatibility complex, class I, H (pseudogene) Neighboring gene HLA complex group 4B Neighboring gene major histocompatibility complex, class I, K (pseudogene) Neighboring gene major histocompatibility complex, class I, A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. Shiina T, et al. Proc Natl Acad Sci U S A, 1999 Nov 9. PMID 10557312, Free PMC Article
  2. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Roh TY, et al. Genome Res, 2007 Jan. PMID 17135569, Free PMC Article
  3. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Roh TY, et al. Genes Dev, 2005 Mar 1. PMID 15706033, Free PMC Article

GeneRIFs: Gene References Into Functions

Variation

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See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • non-conserved AI 60

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.

Genomic

  1. NG_046125.1 

    Range
    101..502
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    GenBank, FASTA, Sequence Viewer (Graphics)

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 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1156200..1156601
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    1377874..1378275
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    1153679..1154080
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    1153316..1153717
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    1153335..1153736
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    29762380..29762781
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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