Traes_pan04338

Pan: Traes_pan04338 · 48 active genes

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Export data for the selected genes

Select accessions to include.

	Accession	Source	Version	Gene count
	Accession	Source	Version	A	B	D	Total

Choose reference (radio); click a selected reference again to clear it to None. Click a gene row or block to include/exclude: light green = included, white = excluded, yellow = reference. Excluding the current reference clears the reference. Switch between Table (one gene per row) and A / B / D (one accession per row; column from chromosome coordinates).

With a reference gene chosen, Select most similar per genome excludes every gene except the reference and, for each selected accession, the single pan-gene most similar to that reference (ties: lowest gene ID alphabetically).

Legend: included excluded reference

Select reference gene Copy gene ID Sequences External databases

Tissue-specific RNA-seq (CPM) and differential expression for Chinese Spring gene(s) in this pan cluster, loaded from PlantApp.

How were RNA-seq and DEG data processed?

Reads were quality-filtered and adapter-trimmed with fastp, aligned to the reference with HISAT2, and gene counts obtained with featureCounts (exon/CDS, GTF annotation). CPM values were computed with edgeR using TMM normalization; stored CPM is rounded to one decimal place. Differential expression used edgeR quasi-likelihood models (glmQLFit, robust) and glmTreat with |log₂FC| ≥ 1 and FDR ≤ 0.05.

Full processing details on PlantApp

Tissue-specific expression

Differential expression

Genes each side

Neighbors colored if Pan in ≥

All 10% 25% 50% 75% 90% 100%

of rows (count a row if that pan / type appears anywhere in the strip). Center (focal) gene always keeps its color.

Strand: Original Strand: Forward

One row per included gene that has coordinates (same selection as Alignment / Genes). Press the (−) button on a row to deselect that gene from synteny and other views (re-include on the Genes tab). Neighbors are only genes present in gene_coords (chromosome loci, not unplaced contigs). Each row shows accession, gene ID, and genomic location; the strip uses equal width per gene. Order along the chromosome is preserved; arrow size is not genomic scale. Strand: Forward applies when the focal gene is on the minus strand: the strip is mirrored (left–right order reversed) and each arrow’s direction is flipped so the focal gene is drawn as forward (tip right), matching a “view along transcription” convention. Genes on the plus strand are unchanged in this mode. Hover an arrow for details.

Open this tab to load synteny tracks.

316 pos · 48 genes

Show ref gaps

Show all residues

Color:

Secondary Structure:

Q3 (three-state): H α-helix · E β-strand · C coil

Q8 (eight-state, DSSP-style): H α-helix · G 3₁₀-helix · I π-helix · E extended strand · B β-bridge · S bend · T turn · C coil

Press the (−) button on a row to deselect that gene from alignment, tree, synteny, and other views. Re-include it on the Genes tab.

Per-position conservation (fraction of most common residue; 1 = fully conserved). Secondary-structure block uses the same Secondary Structure toggle (None / Q3 / Q8) as Alignment / Tree.

Secondary Structure:

By default the tree is FAMSA’s approximate NJ guide tree on unaligned distances (fast but not a proper tree on the alignment). Re-align restores that default. Use FastTree from MSA to redraw from the current gapped alignment (approximate ML); tip order may change. Press the (−) button on a row to deselect that gene.

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Secondary Structure:

Q3 (three-state): H α-helix · E β-strand · C coil

Q8 (eight-state, DSSP-style): H α-helix · G 3₁₀-helix · I π-helix · E extended strand · B β-bridge · S bend · T turn · C coil

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