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LINC03033 long intergenic non-protein coding RNA 3033 [ Homo sapiens (human) ]

Gene ID: 400221, updated on 10-Oct-2023

Summary

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Official Symbol
LINC03033provided by HGNC
Official Full Name
long intergenic non-protein coding RNA 3033provided by HGNC
Primary source
HGNC:HGNC:44292
See related
Ensembl:ENSG00000232774
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
LncRNA-CAF
Expression
Low expression observed in reference dataset See more
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Genomic context

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See LINC03033 in Genome Data Viewer
Location:
14q23.1-q23.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (61570540..61654713)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (55777154..55861276)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (62037258..62121431)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene protein kinase C eta Neighboring gene PRKCH antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 13098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61788641-61789185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61789186-61789729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5819 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:61822129-61823328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8492 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34674 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34691 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_34693 and experimental_34700 Neighboring gene Sharpr-MPRA regulatory region 10871 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:61932802-61933718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8495 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34726 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61972906-61973478 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8496 Neighboring gene uncharacterized LOC105370525 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:62004017-62005216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:62018627-62019137 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:62019138-62019647 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:62028305-62029504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:62034963-62035464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:62035465-62035964 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:62036356-62036548 Neighboring gene long intergenic non-protein coding RNA 1303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:62074093-62074843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:62074844-62075593 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:62076042-62076653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8499 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:62145572-62146072 Neighboring gene Sharpr-MPRA regulatory region 861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5824 Neighboring gene HIF1A antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8501 Neighboring gene HIF1A antisense RNA 3 Neighboring gene hypoxia inducible factor 1 subunit alpha Neighboring gene HIF1A antisense RNA 2

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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Related articles in PubMed

  1. A novel stromal lncRNA signature reprograms fibroblasts to promote the growth of oral squamous cell carcinoma via LncRNA-CAF/interleukin-33. Ding L, et al. Carcinogenesis, 2018 Mar 8. PMID 29346528
  2. Low expression of LncRNA-CAF attributed to the high expression of HIF1A in esophageal squamous cell carcinoma and gastric cancer patients. Bahramian S, et al. Mol Biol Rep, 2022 Feb. PMID 35040008
  3. Interaction of amyotrophic lateral sclerosis/frontotemporal lobar degeneration-associated fused-in-sarcoma with proteins involved in metabolic and protein degradation pathways. Wang T, et al. Neurobiol Aging, 2015 Jan. PMID 25192599

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Low expression of LncRNA-CAF attributed to the high expression of HIF1A in esophageal squamous cell carcinoma and gastric cancer patients.
    Title: Low expression of LncRNA-CAF attributed to the high expression of HIF1A in esophageal squamous cell carcinoma and gastric cancer patients.
  2. We uncovered an uncharacterized lncRNA, FLJ22447, which was remarkably up-regulated in stromal carcinoma-related fibroblasts
    Title: A novel stromal lncRNA signature reprograms fibroblasts to promote the growth of oral squamous cell carcinoma via LncRNA-CAF/interleukin-33.
Submit: New GeneRIF Correction

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 (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

Other Names

  • lncRNA Cancer-associated fibroblast

Clone Names

  • FLJ22447

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_039985.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL355916, BQ014089, BQ439352
    Related
    ENST00000556569.5

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    61570540..61654713
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    55777154..55861276
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Research Materials