General information for g2023.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cysteine protease ATG4C.
Parent gene
- The parent gene g2023 is located on chr_3: 14564208..14565786 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g2023 | g2023.t4 | TSS | g2023.t4 | 14562253 | 14562253 |
| chr_3 | g2023 | g2023.t4 | isoform | g2023.t4 | 14563239 | 14564208 |
| chr_3 | g2023 | g2023.t4 | exon | g2023.t4.exon1 | 14563239 | 14563828 |
| chr_3 | g2023 | g2023.t4 | cds | g2023.t4.CDS1 | 14563666 | 14563828 |
| chr_3 | g2023 | g2023.t4 | exon | g2023.t4.exon2 | 14563992 | 14564208 |
| chr_3 | g2023 | g2023.t4 | cds | g2023.t4.CDS2 | 14563992 | 14564083 |
| chr_3 | g2023 | g2023.t4 | TTS | g2023.t4 | NA | NA |
Sequences
>g2023.t4 Gene=g2023 Length=807
AATTGTGAGATGGTTTGGTGATCAAGTTTCAAAAGCAAGTCCATTTTCAATACATAAACT
TGTTGAGTTGGGCAAGAGAAATGGAAAGAAAGTAGGAGAATGGTATGGACCAGGATCAGT
TGCACATGTGTTGAAAGATGCTGTAAAACAAGCTTCTAAAGAAAACATTGACCTCGCATC
ATTGCATGTTTATGTGTCACAAGACTGTACTATTTATAATCAAGACATTTTCGATGAATG
TTATTCAAATGAGATCCAAACAGTGCCATGGAAAAATAATTTGCCCTCAACATCATCAAA
TTCTTTTACATTATCGCCATCTCGAAATCGATCAAAAGTTATCACATGGAAACAATTGAT
TCTCTTGATTCCTCTTCGCTTAGGACACGAAAAACTCAATCCAATTTACAGTGATTGTCT
TAAAGCAATGTTGAGTCTTGAATGGTGTATTGGAATAATAGGAGGTCGACCGAAACATTC
ACTCTATTTTGTCGGTTATCAAGATGATAAATTAATTCATCTTGATCCACATTATTGTCA
GGATTTAGTGGATGTCAATGCTGAAAACTTTTCGCTCACTTCCTTTCACTCACTTCCTCT
TCTTCCTGCATATCAGCACAGTCAAATATTGAAATTTATCCAACGAGTTATCCAATGTTT
GTTTTCAATCCTAGAAAATTGAATGATGAAGAAGCACGTTCACTTCGAATTCATGCTTCA
CCATTAAATTCCCTTAAACATCTTCACATCGCTAATGACACTCATCATCCTCAAAATGAT
GATGAAACTGAGGACGATTGGTTATGA
>g2023.t4 Gene=g2023 Length=84
MLSLEWCIGIIGGRPKHSLYFVGYQDDKLIHLDPHYCQDLVDVNAENFSLTSFHSLPLLP
AYQHSQILKFIQRVIQCLFSILEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g2023.t4 | PANTHER | PTHR22624:SF52 | CYSTEINE PROTEASE | 1 | 55 | 0 |
| 3 | g2023.t4 | PANTHER | PTHR22624 | CYSTEINE PROTEASE ATG4 | 1 | 55 | 0 |
| 1 | g2023.t4 | Pfam | PF03416 | Peptidase family C54 | 1 | 55 | 0 |
| 4 | g2023.t4 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 1 | 58 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
