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LINC01643 long intergenic non-protein coding RNA 1643 [ Homo sapiens (human) ]

Gene ID: 105373010, updated on 10-Oct-2023

Summary

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Official Symbol
LINC01643provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 1643provided by HGNC
Primary source
HGNC:HGNC:52430
See related
Ensembl:ENSG00000236052 AllianceGenome:HGNC:52430
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LL22NC03-86D4.1
Expression
Low expression observed in reference dataset See more
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Genomic context

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Location:
22q12.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (34017432..34218796)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (34474768..34676540)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene LARGE xylosyl- and glucuronyltransferase 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34134097-34134616 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34134617-34135136 Neighboring gene LARGE antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34175765-34176266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:34178675-34179175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13646 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:34231147-34231704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18886 Neighboring gene Sharpr-MPRA regulatory region 672 Neighboring gene Sharpr-MPRA regulatory region 8125 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:34245227-34245862 Neighboring gene H3K27ac hESC enhancers GRCh37_chr22:34249333-34249834 and GRCh37_chr22:34249835-34250334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34263445-34263944 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34265034-34265534 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:34265535-34266035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:34271643-34272142 Neighboring gene Sharpr-MPRA regulatory region 329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:34294924-34295536 Neighboring gene Sharpr-MPRA regulatory region 1840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13650 Neighboring gene LARGE1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18888 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:34411551-34412114 Neighboring gene uncharacterized LL22NC03-13G6.2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:34556235-34556992 Neighboring gene NANOG hESC enhancer GRCh37_chr22:34590594-34591168 Neighboring gene uncharacterized LOC124905108 Neighboring gene uncharacterized LOC105373012

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
  • 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

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh38)

Genotypes

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.

RNA

  1. NR_183585.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000655455.1

  2. NR_183586.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000669488.1

  3. NR_183587.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000664028.1

  4. NR_183588.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000652942.1

  5. NR_183589.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000669802.1

  6. NR_183590.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000656434.1

  7. NR_183591.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000657115.1

  8. NR_183592.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000658055.1

  9. NR_183593.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z99704
    Related
    ENST00000670329.1

  10. NR_183594.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000671554.1

  11. NR_183595.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000664743.1

  12. NR_183596.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000658589.1

  13. NR_183597.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000661903.1

  14. NR_183598.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000667570.1

  15. NR_183599.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z69707, Z82250, Z99704
    Related
    ENST00000659067.1

  16. NR_183600.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000654009.1

  17. NR_183601.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704

  18. NR_183602.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704

  19. NR_183603.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704

  20. NR_183604.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000665392.1

  21. NR_183605.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68285, Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000658699.1

  22. NR_183606.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    Z68288, Z68323, Z69707, Z82250, Z99704
    Related
    ENST00000653369.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    34017432..34218796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    34474768..34676540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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