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SH3PXD2A-AS1 SH3PXD2A antisense RNA 1 [ Homo sapiens (human) ]

Gene ID: 100505839, updated on 10-Oct-2023

Summary

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Official Symbol
SH3PXD2A-AS1provided by HGNC
Official Full Name
SH3PXD2A antisense RNA 1provided by HGNC
Primary source
HGNC:HGNC:45242
See related
Ensembl:ENSG00000280693 AllianceGenome:HGNC:45242
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Biased expression in esophagus (RPKM 6.9) and skin (RPKM 2.8) See more
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Genomic context

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Location:
10q24.33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (103746779..103755409)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (104634080..104642709)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (105506537..105515167)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene neuralized E3 ubiquitin protein ligase 1 Neighboring gene uncharacterized LOC124902496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2785 Neighboring gene Sharpr-MPRA regulatory region 3797 Neighboring gene Sharpr-MPRA regulatory region 15000 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105367121-105367978 Neighboring gene SH3 and PX domains 2A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105380856-105381356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105395283-105395862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105396445-105397024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105399548-105400343 Neighboring gene Sharpr-MPRA regulatory region 2777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105417537-105418038 Neighboring gene uncharacterized LOC124902495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3967 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105441739-105442519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105451952-105452918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105455468-105456214 Neighboring gene NFE2L2 motif-containing MPRA enhancer 292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105467435-105468414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105468415-105469393 Neighboring gene NANOG hESC enhancer GRCh37_chr10:105482339-105482840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105491951-105492499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105492500-105493047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105505582-105506103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105507021-105507521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105506520-105507020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105515685-105516342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105516343-105516998 Neighboring gene Sharpr-MPRA regulatory region 10495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2789 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105531100-105532070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105539219-105539718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105544793-105545294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105549545-105550545 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105560029-105560530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105563531-105564374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:105567495-105567996 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105594413-105594969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105594970-105595525 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105667461-105668062 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 10:105668179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105677593-105678238 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:105686883-105687548 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:105688215-105688880 Neighboring gene STN1 subunit of CST complex Neighboring gene uncharacterized LOC102724351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2792

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. Association of lncRNA SH3PXD2A-AS1 with preeclampsia and its function in invasion and migration of placental trophoblast cells. Chen Q, et al. Cell Death Dis, 2020 Jul 27. PMID 32719429, Free PMC Article
  2. LncRNA-CTS promotes metastasis and epithelial-to-mesenchymal transition through regulating miR-505/ZEB2 axis in cervical cancer. Feng S, et al. Cancer Lett, 2019 Nov 28. PMID 31499118
  3. Long Non-Coding RNA SH3PXD2A-AS1 Promotes Cell Progression Partly Through Epigenetic Silencing P57 and KLF2 in Colorectal Cancer. Ma Z, et al. Cell Physiol Biochem, 2018. PMID 29734178
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association of lncRNA SH3PXD2A-AS1 with preeclampsia and its function in invasion and migration of placental trophoblast cells.
    Title: Association of lncRNA SH3PXD2A-AS1 with preeclampsia and its function in invasion and migration of placental trophoblast cells.
  2. Results found that LncRNA-CTS is expressed at high levels in cervical carcinoma (CC) tissues and associated with poor outcome. These results implied that lncRNA-CTS might be useful as a novel marker of CC progression. Also, LncRNA-CTS enhances TGF-beta1-induced cell migration, invasion and EMT through mir-505 sponging.
    Title: LncRNA-CTS promotes metastasis and epithelial-to-mesenchymal transition through regulating miR-505/ZEB2 axis in cervical cancer.
  3. SH3PXD2A-AS1 was significantly upregulated in Colorectal cancer (CRC) tissues and cell lines, and overexpression of SH3PXD2A-AS1 was correlated with tumor size, TNM stage, and lymph node metastasis in patients with CRC.
    Title: Long Non-Coding RNA SH3PXD2A-AS1 Promotes Cell Progression Partly Through Epigenetic Silencing P57 and KLF2 in Colorectal Cancer.
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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Markers

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_038940.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AK056784, AL133355, DA422325
    Related
    ENST00000627886.2

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    103746779..103755409
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    104634080..104642709
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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