Aliases for LINC01546 Gene

Subcategory (RNA class) for LINC01546 Gene

lncRNA

Aliases for LINC01546 Gene

External Ids for LINC01546 Gene

Previous HGNC Symbols for LINC01546 Gene

  • CXorf28

Summaries for LINC01546 Gene

GeneCards Summary for LINC01546 Gene

LINC01546 (Long Intergenic Non-Protein Coding RNA 1546) is an RNA Gene, and is affiliated with the lncRNA class.

Additional gene information for LINC01546 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LINC01546 Gene

Genomics for LINC01546 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LINC01546 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ003270 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE CraniofacialAtlas 257.1 +0.2 188 2.5 JUND MAFK EP300 LINC01546 HSALNG0136414 piR-33863-170 DHRSX-IT1 MXRA5 ARSF
GH0XJ003285 Enhancer 0.3 ENCODE 6.2 +15.0 14975 1.8 FOS LINC01546 piR-61514-210 piR-48325-147 MXRA5 ARSF
GH0XJ003293 Enhancer 0.2 Ensembl 5.5 +21.7 21657 0.4 LINC01546 piR-61514-210 piR-48325-147 MXRA5 ARSF
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LINC01546 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for LINC01546 Gene

Latest Assembly
chrX:3,271,544-3,286,138
(GRCh38/hg38)
Size:
14,595 bases
Orientation:
Plus strand

Previous Assembly
chrX:3,189,861-3,202,694
(GRCh37/hg19 by Entrez Gene)
Size:
12,834 bases
Orientation:
Plus strand

chrX:3,189,861-3,202,694
(GRCh37/hg19 by Ensembl)
Size:
12,834 bases
Orientation:
Plus strand

Genomic View for LINC01546 Gene

Genes around LINC01546 on UCSC Golden Path with GeneCards custom track
LINC01546 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
LINC01546 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LINC01546 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LINC01546 Gene

Proteins for LINC01546 Gene

  • Protein details for LINC01546 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NGU7-CX028_HUMAN
    Recommended name:
    Putative uncharacterized protein encoded by LINC01546
    Protein Accession:
    A6NGU7

    Protein attributes for LINC01546 Gene

    Size:
    62 amino acids
    Molecular mass:
    7222 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AA662182; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for LINC01546 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LINC01546 Gene

Post-translational modifications for LINC01546 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LINC01546 Gene

Domains & Families for LINC01546 Gene

Gene Families for LINC01546 Gene

Protein Domains for LINC01546 Gene

ProtoNet:
genes like me logo Genes that share domains with LINC01546: view

No data available for Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LINC01546 Gene

Function for LINC01546 Gene

Phenotypes From GWAS Catalog for LINC01546 Gene

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LINC01546 Gene

Localization for LINC01546 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LINC01546 gene
Compartment Confidence
cytoskeleton 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for LINC01546 Gene

Pathways & Interactions for LINC01546 Gene

PathCards logo

SuperPathways for LINC01546 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LINC01546 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for LINC01546 Gene

Drugs & Compounds for LINC01546 Gene

No Compound Related Data Available

Transcripts for LINC01546 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for LINC01546 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS0000EECC08_9606 lncRNA 2458 1

Ensembl: ENST00000656741 (view in UCSC) ,

URS0000EF48A4_9606 lncRNA 2435 1

Ensembl: ENST00000457435 (view in UCSC) ,

URS0000EEDF77_9606 lncRNA 2282 1

Ensembl: ENST00000668004 (view in UCSC) ,

URS0000EF366C_9606 lncRNA 1862 1

Ensembl: ENST00000668035 (view in UCSC) ,

URS000075B7AF_9606 lncRNA 674 1

RefSeq: NR_038428,

LINC01546 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for LINC01546 Gene

5 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for LINC01546 Gene

No ASD Table

Relevant External Links for LINC01546 Gene

GeneLoc Exon Structure for
LINC01546

Expression for LINC01546 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LINC01546 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LINC01546

genes like me logo Genes that share expression patterns with LINC01546: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LINC01546 Gene

Orthologs for LINC01546 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for LINC01546 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CXorf28 31
  • 62 (a)
OneToOne
Species where no ortholog for LINC01546 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • Dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for LINC01546 Gene

ENSEMBL:
Gene Tree for LINC01546 (if available)
TreeFam:
Gene Tree for LINC01546 (if available)

Paralogs for LINC01546 Gene

No data available for Paralogs for LINC01546 Gene

Variants for LINC01546 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LINC01546 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LINC01546 Gene

Variant ID Type Subtype PubMed ID
esv2758855 CNV gain 17122850
esv33968 CNV loss 17666407

Variation tolerance for LINC01546 Gene

Gene Damage Index Score: 2.89; 48.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LINC01546 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LINC01546

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LINC01546 Gene

Disorders for LINC01546 Gene

Additional Disease Information for LINC01546

No disorders were found for LINC01546 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LINC01546 Gene

Publications for LINC01546 Gene

  1. AKT-induced lncRNA VAL promotes EMT-independent metastasis through diminishing Trim16-dependent Vimentin degradation. (PMID: 33046716) Tian H … Cai J (Nature communications 2020) 2 3
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 4

Products for LINC01546 Gene

Sources for LINC01546 Gene