Table of Contents
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Close the track and open it again. Yes, this is the standard 'turn it off and turn it on again' solution.
The deleted gene I'm reviewing needs to stay deleted. How do I mark this in Apollo?
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What is the meaning of the lower case letters in the nucleotide sequence?
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TRACK NAME | Description of data |
Col-CC_Genomic_Annotations_Data | Result of NCBI Eukaryotic Annotation Pipeline |
AT-Col-CC-Liftoff-from-TAIR10.1 | v11 models mapped to v12 reference using Liftoff |
| TranscriptomeReconstructoR models | Method: (1) Assembled expression evidence: ONT-DRS (ERR3764345 - ERR3764351), CAGE-Seq (SRR10045003 - SRR10045005), PAT-Seq (SRR7160296, SRR7160297, SRR7160299), plaNET-Seq (SRR9117170 - SRR9117173) (2) Aligned all the datasets to Col-CC genome (3) Built TRR based annotation using alignment (bam) files Output:
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Gnomon Models | One of the outputs of the annotation pipeline. These are a superset of the final set of annotated models. "Gnomon annotation of the genomic sequence. Sequence identifiers are provided as accession.version for the genomic sequences and Gnomon identifiers for the Gnomon models:gene.XXX for genes, GNOMON.XXX.m for transcripts and GNOMON.XXX.p for proteins. These identifiers are NOT universally unique. They are unique per annotation release only." (from NCBI documentation) |
| RNAseq combined, coverage | Combined coverage track made from the read files of the 62 individual RNAseq experiments, filtered (when possible) and capped individually, and then merged |
| RNAseq capped and merged, reads | Merged reads of all the filtered,capped read files (below) and the remaining capped unfiltered 38/62 RNAseq read files. |
| RNAseq filtered capped and merged, reads | Merged capped reads of the 24/62 RNAseq experiment files that were successfully filtered for overly long (>5K bp) inserts. |
| Protein Evidence | |
| PFAM domains | Results from an INTERPROSCAN run on the proteins from the V12 prediction to get the PFAM domain information, converted to absolute position on the Col-CC assembly. |
| PFAM domains - Liftoff | Results from an INTERPROSCAN run on the proteins from the Araport11 release to get the PFAM domain information, converted to absolute position on the Col-CC assembly (using the Liftoff file that converted Araport11 coordinates to Col-CC coordinates). |
| PANTHER families | Results from an INTERPROSCAN run on the proteins from the V12 prediction to get the PANTHER family information, converted to absolute position on the Col-CC assembly. |
| PANTHER families - Liftoff | Results from an INTERPROSCAN run on the proteins from the Araport11 release to get the PANTHER family information, converted to absolute position on the Col-CC assembly (using the Liftoff file that converted Araport11 coordinates to Col-CC coordinates). |
| Protein alignments chained | Alignments of Arabidopsis thaliana and other Brassicaceae proteins, including Araport 11 annotated proteins, to the genomic sequence(s). These alignments may have been used as evidence for gene prediction by the NCBI annotation pipeline. Pieces of the same protein have been connected together for easier visualization. |
| TRR CAGE PAT plaNET | |
| CAGE forward | TranscriptomeReconstructoR models CAGE evidence, forward strand (evidence supporting the start site of transcription) |
| CAGE reverse | TranscriptomeReconstructoR models CAGE evidence, reverse strand (evidence supporting the start site of transcription) |
| PAT forward | TranscriptomeReconstructoR models PAT evidence, forward strand (evidence supporting the end site of transcription) |
| PAT reverse | TranscriptomeReconstructoR models PAT evidence, reverse strand (evidence supporting the end site of transcription) |
| plaNET forward | TranscriptomeReconstructoR models plaNET evidence, forward strand (evidence supporting transcription of mRNAs and lncRNAs) |
| plaNET reverse | TranscriptomeReconstructoR models plaNET evidence, reverse strand (evidence supporting transcription of mRNAs and lncRNAs) |
| Transcript Evidence | |
| Known Reference Sequences | "Alignments of the annotated Known RefSeq transcripts (identified with accessions prefixed with NM_ and NR_) to the genome." (from NCBI documentation) These were NOT used in generating the Col-CC annotation. They are alignments of the annotated transcripts to the genome and can provide additional insight into the predicted gene structures independent of the prediction. |
| Model Reference Sequences | "Alignments of the annotated Model RefSeq transcripts (identified with accessions prefixed with XM_ and XR_) to the genome." (from NCBI documentation) These were NOT used in generating the Col-CC annotation. They are alignments of the annotated transcripts to the genome and can provide additional insight into the predicted gene structures independent of the prediction. |
| Col-CC Same Species Combined | Alignments of same-species cDNAs, ESTs and TSAs to the genomic sequence(s). cDNAs and ESTs alignments (not TSAs) may have used as evidence for gene prediction by the NCBI annotation pipeline. The TSA alignment track is a subset of the Col-CC Same Species track. Pieces of the same transcript have been connected together for easier visualization. |
| TSA alignment | Alignments of transcripts assembled from RNA-Seq reads, and submitted to GenBank (see accessions DAHAIV01, GGJX01, GJRK01 and GKIF01). These were not used as evidence for gene prediction by the NCBI annotation pipeline. |
RNA seq tracks from various plant parts and growth stages/conditions of those parts | Name is based on the GenBank record, for example, SRR1019221. You can link to that record using this base URL for more information on the experiment: |
| Long Read alignments | Alignments of individual IsoSeq reads in SRA. These alignments may have been used as evidence for gene prediction by the NCBI annotation pipeline. Right clicking on the read itself will allow you to ‘View Details’ and see the ID of the SRA entry for the experiment. Using the id (e.g., SRR11031292), you can go to the full GenBank record for the experiment. https://www.ncbi.nlm.nih.gov/sra/?term=SRR11031292. |
What does the warning symbol mean?
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Right click on the element and select 'Create new annotation' from the menu. Pick the type of element you want to create and it will appear in the yellow track.
Where do I add my comment/rename?
- If you have already added comments at the gene level, these will apply to all mRNAs under that gene.
- In cases where there is only one mRNA/gene, the comment/renaming (DELETE) on the mRNA transitively applies to the gene.
- If there is more than one mRNA/gene and you want to record different actions for individual mRNAs, please put the specific comments (or DELETE) on the relevant mRNAs only.
- If there is more than one mRNA/gene and you want to record the same action for ALL mRNAs/the whole gene, please put the specific comments (or DELETE) on any one of the mRNAs.
The comment or status I typed in hasn't saved. How do I make sure it saves?
For saving comments and gene status, make sure you click outside of the panel where you created the comment to ‘make it stick’.
The deleted gene I'm reviewing needs to stay deleted. How do I mark this in Apollo?
- 1. create a gene model of the gene that should stay deleted by dragging into the user-created annotations
- 2. rename so that the name ends with ‘DELETE’
- 3. set status (either ‘updated, secondary review requested’ OR ‘updated, no secondary review needed’)
- (see Q10 for what to do if there are different actions for different mRNAs of the same gene)
Check the names of the genes in the user-created annotations track to maintain AGI history.
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