The Histogram tab shows a graphical representation of the mutations observed in the selected gene. The Filters panel on the right hand side of the page shows the current gene and other selections. [more details]

Note: In some web browsers, the Genome Browser may display a blank white content panel when switching back from another tab. If this happens please click and drag the blank content panel. [ Full screen view ]

Loading sample Genome browser
This tab displays a table of primary tissues with histogram showing percentage of mutated samples for both point and CNV data. Mouseover the histogram to see more data. [more details]
This tab displays pie charts and graphs, which show the distribution of mutation types for the selected gene. [more details]
This tab shows publications associated with the selected gene. [more details]
Reference Title Author Year Journal Status COSMIC Pubmed
This tab shows a graphical representation of the selected gene in JBrowse and a general overview of the information available for the gene. [more details]
Gene name
RARA
This is a known cancer gene, for more information please look here
Mouse insertional mutagenesis experiments support this gene, for more information please look here
Genomic Coordinates
17:40331219..40356226  (positive strand)
Gene Id
COSG2807
Synonyms
NR1B1,RAR,CCDS11366.1,ENSG00000131759
No.of Samples
Total number of unique samples: 38121
Unique samples with mutations: 149
Alternative Transcripts
RARA_ENST00000394081
Mouse mutagenesis
Mouse insertional mutagenesis experiments support RARA as a cancer causing gene, please click
for more information.
cDNA Sequence
ENST00000254066
Protein Sequence
RARA
Transcript and Protein Aligned
ENST00000254066+RARA
Transcript
ENST00000254066
Genome Browsers
Ensembl, UCSC
Copy Number
CONAN
CCDS
CCDS11366.1
Atlas Genetic Oncology
RARAID46
HGNC
9864

This tab displays a table of mutations for the selected gene. [more details]
Position (AA) Mutation (CDS) Mutation (Amino Acid) Mutation ID (COSM) Count Mutation Type

This tab displays a table of fusions for the selected gene. [more details]
Position Mutation (CDS) Mutation (Amino Acid) Mutation ID (COSF) Count Mutation Type

This tab shows a table of gene expression and copy number variation (CNV) data for the selected gene with links to Sample, Study, CNV and (icons) to the ChromoView page (to view CNVs across the whole chromosome), the COSMIC Genome Browser and Ensembl. [more details]

Table Information

Hide

The table currently shows only high value (numeric) copy number data. Copy number segments are excluded if the total copy number and minor allele values are unknown.

Click here to include all copy number data. For more detailed information about copy number data and gain/loss definitions click here.

Sample Expression Expr Level (Z-Score)

Over Expressed; Z-Score > 2.0

Under Expressed; Z-Score < -2.0

Normal; Z-Score within the range -2.0 to 2.0

CN Type Minor Allele Copy Number CN Segment Posn. Average Ploidy

1. N/A represents cases where average ploidy value is not available( mostly ICGC samples). For some TCGA samples where minor allele information is not available the average ploidy value could not be calculated.

2. For TCGA samples, Ascat algorithm is used to calculate the average ploidy.

3. For CGP samples, Picnic algorithm is used to calculate the average ploidy.

Study CNV

This page contains the complete Methylation data for the gene and filter selection(s). Each Methylation probe links to the COSMIC Genome Browser and Ensembl. [more details]
Sample Name Sample ID Probe ID Probe Posn. Type

High (Hypermethylation); Beta-Value > 0.8 and differs from normal average by > 0.5

Low (Hypomethylated); Beta-Value < 0.2 and differs from normal average by > 0.5

Level (Beta-Value) Normal Average Study

Filters

    • Start
    • End
    • cDNA
    • Amino Acid
    • NS Adrenal gland Biliary tract Bone Breast Central nervous system Endometrium Haematopoietic and lymphoid Kidney Large intestine Liver Lung Oesophagus Ovary Pancreas Pleura Prostate Skin Soft tissue Stomach Thyroid Upper aerodigestive tract Urinary tract
    • No selection available. Please choose the above option.
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    • No selection available. Please choose the above option.
    • Note: After making your selection(s) please close this window and click 'Apply' in the filters panel.
    • Genome View
      Many probes fall outside of coding regions and are not displayed on the Histogram. To view all methylation probes within or in close proximity to RARA please use the COSMIC Genome Browser