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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: 

  • High Confidence (HC) genes - full length mRNA picked from ONT which have both proper start site from CAGE and end site from PAT-Seq coinciding with ONT data.
  • Medium Confidence (MC) genes - full length mRNA picked from ONT with either start site from CAGE or end site from PAT-Seq not coinciding with ONT data.
  • Low Confidence (LC) genes - full length mRNA picked from ONT with both start site from CAGE and end site from PAT-Seq not coinciding with ONT data.
  • Single Method Confidence (SMC) genes - novel genes annotated only from plaNET-Seq data.

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)

Merged, Capped, and Filtered RNAseq Reads

RNAseq capped_merged_filtered readsRNAseq reads from the 62 RNAseq experiments after filtering for overly long (>5Kbp) inserts, and successive capping to try to reduce the overabundance of highly expressed genes. File was then filtered to remove overly long (>12Kbp) introns.
Coverage Tracks, RNAseq and Long ReadRNAseq combined and recapped
Combined coverage track made from the read files of the 62 individual RNAseq experiments, filtered (when possible) and capped individually, and then sequentially recapped and merged into a final bam file that then converted into bw for coverage view. Still contains the overly long (>12Kbp) introns.RNAseq capped_merged_filtered coverageCOMING: BW coverage Coverage track version of the RNAseq capped_merged_filtered reads.
Long Read Alignments coverage, plus strand
Coverage track of the long reads, plus strand ONLY.
Long Read Alignments coverage, minus strand
Coverage track of the long reads, minus strand ONLY.
Merged, Capped, and Filtered RNAseq Reads
RNAseq capped_merged_filtered readsRNAseq reads from the 62 RNAseq experiments after filtering for overly long (>5Kbp) inserts, and successive capping and merging to try to reduce the overabundance of highly expressed genes. File was then filtered to remove overly long (>12Kbp) introns.
Protein Evidence
PFAM domainsResults 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 - LiftoffResults 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 familiesResults 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 - LiftoffResults 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 chainedAlignments 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 forwardTranscriptomeReconstructoR models CAGE evidence, forward strand  (evidence supporting the start site of transcription)
CAGE reverseTranscriptomeReconstructoR models CAGE evidence, reverse strand  (evidence supporting the start site of transcription)
PAT forwardTranscriptomeReconstructoR models PAT evidence, forward strand  (evidence supporting the end site of transcription)
PAT reverseTranscriptomeReconstructoR models PAT evidence, reverse strand  (evidence supporting the end site of transcription)
plaNET forwardTranscriptomeReconstructoR models plaNET evidence, forward strand  (evidence supporting transcription of mRNAs and lncRNAs)
plaNET reverseTranscriptomeReconstructoR 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 alignmentAlignments 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:

https://www.ncbi.nlm.nih.gov/sra/SRR1019221

Long Read alignmentsAlignments 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. 

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