| Class | Ensembl::Core::Transcript |
| In: |
lib/ensembl/core/transcript.rb
|
| Parent: | CoreDBConnection |
The Transcript class provides an interface to the transcript table. This table contains mappings of transcripts for a Gene to a SeqRegion.
This class uses ActiveRecord to access data in the Ensembl database. See the general documentation of the Ensembl module for more information on what this means and what methods are available.
This class includes the mixin Sliceable, which means that it is mapped to a SeqRegion object and a Slice can be created for objects of this class. See Sliceable and Slice for more information.
#TODO
| transcript_attribs | -> | attribs |
The Transcript#find_all_by_stable_id class method returns an array of transcripts with the given stable_id. If none were found, an empty array is returned.
The Transcript#find_all_by_stable_id class method returns a transcripts with the given stable_id. If none was found, nil is returned.
The Transcript#cdna2genomic method converts cDNA coordinates to genomic coordinates for this transcript.
Arguments:
| Returns: | integer |
The Transcript#cds2genomic method converts CDS coordinates to genomic coordinates for this transcript.
Arguments:
Returns::
The Transcript#cds_seq method returns the coding sequence of the transcript, i.e. the concatenated sequence of all exons minus the UTRs.
The Transcript#coding_region_cdna_end returns the stop position of the CDS in cDNA coordinates. Note that, in contrast to the Transcript#coding_region_genomic_end, the CDS start position is always at the border of the 3’UTR. So for genes on the reverse strand, the CDS start position in cDNA coordinates will be ’’right’’ of the CDS stop position.
The Transcript#coding_region_cdna_start returns the start position of the CDS in cDNA coordinates. Note that, in contrast to the Transcript#coding_region_genomic_start, the CDS start position is always at the border of the 5’UTR. So for genes on the reverse strand, the CDS start position in cDNA coordinates will be ’’right’’ of the CDS stop position.
The Transcript#coding_region_genomic_end returns the stop position of the CDS in genomic coordinates. Note that, in contrast to Transcript#coding_region_cdna_end, the CDS stop position is always ’’right’’ of the start position. So for transcripts on the reverse strand, the CDS stop position is at the border of the 5’UTR instead of the 3’UTR.
The Transcript#coding_region_genomic_start returns the start position of the CDS in genomic coordinates. Note that, in contrast to Transcript#coding_region_cdna_start, the CDS start position is always ’’left’’ of the end position. So for transcripts on the reverse strand, the CDS start position is at the border of the 3’UTR instead of the 5’UTR.
The Transcript#exon_for_position identifies the exon that covers a given position of the cDNA.
The Transcript#exon_for_position identifies the exon that covers a given genomic position. Returns the exon object, or nil if in intron.
The Transcript#exons method returns the exons for this transcript in the order of their ranks in the exon_transcript table.
| Arguments: | none |
| Returns: | sorted array of Exon objects |
The Transcript#five_prime_utr_seq method returns the sequence of the 5’UTR of the transcript.
The Transcript#genomic2cdna method converts genomic coordinates to cDNA coordinates for this transcript.
Arguments:
Returns::
The Transcript#genomic2cds method converts genomic coordinates to CDS coordinates for this transcript.
Arguments:
Returns::
The Transcript#genomic2pep method converts genomic coordinates to peptide coordinates for this transcript.
Arguments:
Returns::
The Transcript#pep2genomic method converts peptide coordinates to genomic coordinates for this transcript.
Arguments:
Returns::
The Transcript#protein_seq method returns the sequence of the protein of the transcript.
The Transcript#stable_id method returns the stable ID of the transcript.
| Arguments: | none |
| Returns: | String |
The Transcript#three_prime_utr_seq method returns the sequence of the 3’UTR of the transcript.