chr1 1046829 1047018 NM_001077977_utr3_2_0_chr1_1046830_f 0 +
chr1 1099124 1099325 NM_001077124_utr3_0_0_chr1_1099125_r 0 -
The name column contains several pieces of information separated by underscores:
NM_001077124_utr3_0_0_chr1_1099125_r. Here's a breakdown of that information:
NM_001077124 - Transcript accession
utr3 - will be cds or utr3/5
0 - exon inFrame - This indicates the offset at the beginning
of a feature (like an exon) to reach the first base of the next complete
codon.
0 - exon outFrame - This indicates the offset remaining at the end of a feature.
- chr1_1099125 - chromosome and start position of the exon
+ chr1_1099125 - start position of the exon
r - strand, "r" for reverse or "-" and "f"
for forward or "+"
-Here we're going to focus on the inFrame and outFrame specifically. The values +Here, we're going to focus on the inFrame and outFrame specifically. The values typically range from 0 to 2. These numbers are a representation of where in the frame the exon starts and ends.
| Value | Meaning |
|---|---|
| 0 | The feature starts/ends exactly at the beginning of a codon. No offset is required. |
| 1 | There is 1 "extra" nucleotide before/after the complete codons start. |
| 2 | There are 2 "extra" nucleotides before/after the complete codons start. |
In the example lines above, the exons have "0" for both inFrame and outFrame because they are UTR exons.
-Finally, it should be noted that when the amino acid output is split per exons (where a split codon is impossible to -denote), the amino acid for split codon is placed in the exon with most of the bases.
+Finally, it should be noted that when the amino acid output is split per exons +(where a split codon is impossible to denote), the amino acid for this split codon +is placed in the exon with most of the bases.