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Aliases for LINC01546 Gene

Subcategory (RNA class) for LINC01546 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for LINC01546 Gene

  • Long Intergenic Non-Protein Coding RNA 1546 2 3 5
  • CXorf28 3 4
  • Chromosome X Open Reading Frame 28 2

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 non-coding RNA class.

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LINC01546 Gene

Genomics for LINC01546 Gene

Regulatory Elements for LINC01546 Gene

Enhancers for LINC01546 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XF003285 0.7 Ensembl ENCODE 6.1 +14.7 14700 1.8 ATF3 POLR2A LINC01546 GC0XM003252 MXRA5
GH0XF003270 0.5 ENCODE 7.2 -0.1 -88 2.5 JUND JUN MAFK LINC01546 DHRSX-IT1 MXRA5 PIR40674
GH0XF003268 0.5 ENCODE 0.8 -2.8 -2846 0.2 JUND BHLHE40 FOS MXRA5 LINC01546 PIR40674
GH0XF003262 0.8 Ensembl ENCODE 0.4 -8.5 -8504 1.7 JUND EGR1 ZNF26 JUN FOS SETDB1 MXRA5 LINC01546 PIR40674
GH0XF003183 1.1 FANTOM5 Ensembl ENCODE 0.2 -87.2 -87177 2.2 GATAD2A TEAD1 FOXA3 CEBPA CEBPB CEBPG PIR40674 LINC01546
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LINC01546 on UCSC Golden Path with GeneCards custom track

Promoters for LINC01546 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001915273 80 201 JUND JUN MAFK

Genomic Location for LINC01546 Gene

3,271,820 bp from pter
3,284,653 bp from pter
12,834 bases
Plus strand

Genomic View for LINC01546 Gene

Genes around LINC01546 on UCSC Golden Path with GeneCards custom track

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:
    Recommended name:
    Putative uncharacterized protein encoded by LINC01546
    Protein Accession:

    Protein attributes for LINC01546 Gene

    62 amino acids
    Molecular mass:
    7222 Da
    Quaternary structure:
    No Data Available
    • Sequence=AA662182; Type=Frameshift; Positions=4, 8, 42; Evidence={ECO:0000305};

    Alternative splice isoforms for LINC01546 Gene


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

Protein Domains for LINC01546 Gene


Graphical View of Domain Structure for InterPro Entry

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

No data available for Gene Families , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for LINC01546 Gene

Function for LINC01546 Gene

Animal Model Products

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

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
nucleus 2
cytosol 2
extracellular 1
mitochondrion 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LINC01546 Gene

Pathways & Interactions for LINC01546 Gene

SuperPathways for LINC01546 Gene

No Data Available

Interacting Proteins for LINC01546 Gene

Gene Ontology (GO) - Biological Process for LINC01546 Gene


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

Transcripts for LINC01546 Gene

mRNA/cDNA for LINC01546 Gene

(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

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

No ASD Table

Relevant External Links for LINC01546 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LINC01546 Gene

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

NURSA nuclear receptor signaling pathways regulating expression of LINC01546 Gene:

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 and mRNA Expression by UniProt/SwissProt 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
(Pan troglodytes)
Mammalia CXorf28 35
  • 62 (a)
Species where no ortholog for LINC01546 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

Gene Tree for LINC01546 (if available)
Gene Tree for LINC01546 (if available)

Paralogs for LINC01546 Gene

No data available for Paralogs for LINC01546 Gene

Variants for LINC01546 Gene

Sequence variations from dbSNP and Humsavar for LINC01546 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs111452340 -- 3,274,852(+) TTTCA(C/T)GATAT intron-variant
rs111518772 -- 3,278,026(+) TTAGC(A/C)TGATT intron-variant
rs111801344 -- 3,274,363(+) TAGGG(G/T)TTTTA intron-variant
rs112043559 -- 3,277,532(+) TTTGT(C/T)TGTTC intron-variant
rs112130042 -- 3,271,711(+) CTGCA(A/T)GTTGA upstream-variant-2KB

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)

Relevant External Links for LINC01546 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LINC01546 Gene

Disorders for LINC01546 Gene

Relevant External Links for LINC01546

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 4 64

Products for LINC01546 Gene

Sources for LINC01546 Gene

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