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Aliases for LINC01546 Gene

Subcategory (RNA class) for LINC01546 Gene

non-coding RNA

Quality Score for this RNA gene is

13

Aliases for LINC01546 Gene

  • Long Intergenic Non-Protein Coding RNA 1546 2 3 5
  • CXorf28 3 4
  • Putative Uncharacterized Protein Encoded By LINC01546 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.

Additional gene information for LINC01546 Gene

No data available for Entrez Gene Summary , CIViC 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

GeneHancer (GH) Regulatory Elements for LINC01546 Gene

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 0.9 Ensembl ENCODE 607.1 -0.1 -88 2.5 MAFK JUND JUN LINC01546 DHRSX-IT1 MXRA5 GC0XM003252 PIR40674
GH0XJ003285 Enhancer 0.3 ENCODE 6.2 +14.7 14699 1.8 FOS LINC01546 GC0XM003252 MXRA5
GH0XJ003293 Enhancer 0.2 Ensembl 5.5 +21.3 21281 0.2 LINC01546 GC0XM003252 MXRA5
GH0XJ003268 Enhancer 0.6 Ensembl ENCODE 0.7 -2.7 -2670 0.5 JUND FOS MXRA5 LINC01546 GC0XM003252 PIR40674
GH0XJ003262 Enhancer 0.7 Ensembl ENCODE 0.4 -8.4 -8419 2.8 EGR1 RUNX3 FOS ZNF26 JUND JUN ATF2 MXRA5 LINC01546 GC0XM003252 PIR40674
- 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 UCSC Golden Path with GeneCards custom track

Genomic Locations for LINC01546 Gene

Genomic Locations for LINC01546 Gene
chrX:3,271,820-3,284,653
(GRCh38/hg38)
Size:
12,834 bases
Orientation:
Plus strand
chrX:3,189,861-3,202,694
(GRCh37/hg19)
Size:
12,834 bases
Orientation:
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:
    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; Positions=4, 8, 42; 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

Protein Domains for LINC01546 Gene

ProtoNet:

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

Phenotypes From GWAS Catalog for LINC01546 Gene

Animal Model Products

CRISPR 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

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , 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

Interacting Proteins for LINC01546 Gene

Gene Ontology (GO) - Biological Process for LINC01546 Gene

None

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

Drugs & Compounds for LINC01546 Gene

No Compound Related Data Available

Transcripts for LINC01546 Gene

mRNA/cDNA for LINC01546 Gene

(5) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(2) RNA Central transcripts :

CRISPR Products

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

No ASD Table

Relevant External Links for LINC01546 Gene

GeneLoc Exon Structure for
LINC01546
ECgene alternative splicing isoforms for
LINC01546

Expression for LINC01546 Gene

NURSA nuclear receptor signaling pathways regulating expression of LINC01546 Gene:

LINC01546
No Expression Related Data Available

No data available for mRNA expression in normal human tissues , 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 35
  • 62 (a)
OneToOne
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

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

Sequence variations from dbSNP and Humsavar for LINC01546 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000156674 -- 3,270,036(+) C/T upstream_transcript_variant
rs1000378657 -- 3,277,515(+) A/G intron_variant
rs1000752526 -- 3,273,672(+) G/A intron_variant
rs1000826563 -- 3,274,145(+) A/G intron_variant
rs1001107684 -- 3,284,899(+) G/A downstream_transcript_variant

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 58
  3. 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 58

Products for LINC01546 Gene

Sources for LINC01546 Gene

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