General information for g2020.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cysteine protease ATG4D.
Parent gene
- The parent gene g2020 is located on chr_3: 14556120..14557097 (- 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 | g2020 | g2020.t1 | TTS | g2020.t1 | 14556023 | 14556023 |
| chr_3 | g2020 | g2020.t1 | isoform | g2020.t1 | 14556120 | 14557097 |
| chr_3 | g2020 | g2020.t1 | exon | g2020.t1.exon1 | 14556120 | 14556328 |
| chr_3 | g2020 | g2020.t1 | cds | g2020.t1.CDS1 | 14556120 | 14556328 |
| chr_3 | g2020 | g2020.t1 | exon | g2020.t1.exon2 | 14556572 | 14557040 |
| chr_3 | g2020 | g2020.t1 | cds | g2020.t1.CDS2 | 14556572 | 14557040 |
| chr_3 | g2020 | g2020.t1 | exon | g2020.t1.exon3 | 14557095 | 14557097 |
| chr_3 | g2020 | g2020.t1 | cds | g2020.t1.CDS3 | 14557095 | 14557097 |
| chr_3 | g2020 | g2020.t1 | TSS | g2020.t1 | 14558096 | 14558096 |
Sequences
>g2020.t1 Gene=g2020 Length=681
ATGTGTGGCAAGAGAAATGGAAAGAAAGTAGGAGAATGGTATGGACCAGGATCAGTTGCA
CATGTGTTGAAAGATGCTGTAAAACAAGCTTCTAAAGAAAACATTGACCTCGCATCATTG
CATGTTTATGTGTCACAAGACTGTACTATTTATAATCAAGACATTTTCGATGAATGTTAT
TCAAATGAGATCCAAACAGTGCCATGGAAAAATAATTTGCCCTCAACATCATCAAATTCT
TTTACATTATCGCCATCTCGAAATCGATCAAAAGTTATCACATGGAAACAATTGATTCTC
TTGATTCCTCTTCGCTTAGGACACGAAAAACTCAATCCAATTTACAGTGATTGTCTTAAA
GCAATGTTGAGTCTTGAATGGTGTATTGGAATAATAGGAGGTCGACCGAAACATTCACTC
TATTTTGTCGGTTATCAAGATGATAAATTAATTCATCTTGATCCACATTATTCACAGTCA
AATATTGAAATTTATCCAACGAGTTATCCAATGTTTGTTTTCAATCCTAGAAAATTGAAT
GATGAAGAAGCACGTTCACTTCGAATTCATGCTTCACCATTAAATTCCCTTAAACATCTT
CACATCGCTAATGACACTCATCATCCTCAAAATGATGATGAAACTGAGGACGATGGTATT
GAAGATTTTGTAATTGTTTGA
>g2020.t1 Gene=g2020 Length=226
MCGKRNGKKVGEWYGPGSVAHVLKDAVKQASKENIDLASLHVYVSQDCTIYNQDIFDECY
SNEIQTVPWKNNLPSTSSNSFTLSPSRNRSKVITWKQLILLIPLRLGHEKLNPIYSDCLK
AMLSLEWCIGIIGGRPKHSLYFVGYQDDKLIHLDPHYSQSNIEIYPTSYPMFVFNPRKLN
DEEARSLRIHASPLNSLKHLHIANDTHHPQNDDETEDDGIEDFVIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g2020.t1 | PANTHER | PTHR22624:SF52 | CYSTEINE PROTEASE | 3 | 171 | 0 |
| 3 | g2020.t1 | PANTHER | PTHR22624 | CYSTEINE PROTEASE ATG4 | 3 | 171 | 0 |
| 1 | g2020.t1 | Pfam | PF03416 | Peptidase family C54 | 3 | 177 | 0 |
| 4 | g2020.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 3 | 165 | 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.
