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SLC44A3-AS1 SLC44A3 antisense RNA 1 [ Homo sapiens (human) ]

Gene ID: 101928079, updated on 16-Jan-2024

Summary

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Official Symbol
SLC44A3-AS1provided by HGNC
Official Full Name
SLC44A3 antisense RNA 1provided by HGNC
Primary source
HGNC:HGNC:49057
See related
Ensembl:ENSG00000293271 AllianceGenome:HGNC:49057
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
LINC01057; XLOC_000303
Expression
Broad expression in colon (RPKM 1.2), gall bladder (RPKM 1.0) and 21 other tissues See more
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Genomic context

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Location:
1p21.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (94616352..94820232, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94464398..94668277, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (95081908..95285788, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1097 Neighboring gene uncharacterized LOC124904223 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95018439-95018940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95018941-95019440 Neighboring gene uncharacterized LOC105378861 Neighboring gene microRNA 12133 Neighboring gene coagulation factor III, tissue factor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:95070951-95072150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95074066-95074566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95074567-95075067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95090684-95091191 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:95124863-95125381 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:95126859-95127664 Neighboring gene katanin regulatory subunit B1 like 1 pseudogene 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95133735-95134492 Neighboring gene piggyBac transposable element derived 4 pseudogene 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:95177148-95178105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95188809-95189310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95193997-95194497 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95199763-95200705 Neighboring gene Sharpr-MPRA regulatory region 2553 Neighboring gene microRNA 378g Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95248718-95249480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1100 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:95302044-95303243 Neighboring gene solute carrier family 44 member 3 Neighboring gene NANOG hESC enhancer GRCh37_chr1:95331914-95332415 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9624 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:95349823-95350709 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:95376115-95377314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95385599-95386099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1102 Neighboring gene calponin 3 Neighboring gene CNN3 divergent transcript

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. Circulating lncRNAs associated with occurrence of colorectal cancer progression. Shi J, et al. Am J Cancer Res, 2015. PMID 26328256, Free PMC Article
  2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Role of SLC44A3-AS1 Enhancer RNA in Esophageal Cancer Prognosis.
    Title: Role of SLC44A3-AS1 Enhancer RNA in Esophageal Cancer Prognosis.
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

General gene information

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Other Names

  • long intergenic non-protein coding RNA 1057

Clone Names

  • FLJ20387

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_104131.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093117, AC093429, AL391555
    Related
    ENST00000452922.5

  2. NR_160779.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093117, AC093429
    Related
    ENST00000635440.1

  3. NR_160780.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093117, AC093429, AL391555

  4. NR_160781.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093117, AC093429, AL391555

  5. NR_160782.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093117, AC093429, AL391555

  6. NR_160783.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093117, AC093429

  7. NR_160784.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093429, BM974310, BX094709

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    94616352..94820232 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    94464398..94668277 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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