General information for g2023.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cysteine protease ATG4D.
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.t1 | TSS | g2023.t1 | 14562253 | 14562253 |
| chr_3 | g2023 | g2023.t1 | isoform | g2023.t1 | 14562345 | 14564208 |
| chr_3 | g2023 | g2023.t1 | exon | g2023.t1.exon1 | 14562345 | 14562417 |
| chr_3 | g2023 | g2023.t1 | cds | g2023.t1.CDS1 | 14562345 | 14562417 |
| chr_3 | g2023 | g2023.t1 | exon | g2023.t1.exon2 | 14562476 | 14564208 |
| chr_3 | g2023 | g2023.t1 | cds | g2023.t1.CDS2 | 14562476 | 14564208 |
| chr_3 | g2023 | g2023.t1 | TTS | g2023.t1 | NA | NA |
Sequences
>g2023.t1 Gene=g2023 Length=1806
ATGTCAAATAAGAGTTCTATGCTCTCAAAATTGGCAGATACTATTTCAGAATATAGTTGG
AGCGATGCATCAGATGGTGCATCAACAACGACGGCAACAGCTTCGAATGCTGTAAAAAAT
AATGAACTTCAACCGAATAATGGTGAATTTAAAGACCGTGTTGAAACAAAACTCATGTCA
CTCTGGCATAATATGAAATATGGCTGGGGTACAAAAATGAGATCAAATTTCAATAAAGAG
TCAGCAATTTGGTTTCTCGGTCGTTGCTATCATCAAAAAGTAACACCAAGTCCCTCATTA
CAATATTCAACAATTTTCGACCATAATACAATCAATCCATCATCGACTCATCATGCAGAC
AATAATTCAAGATTAATGACATCTTCATTTCATGAAGAGTTACCTACATCATATGACTCA
TATCTAAATCAATTTCCTACAAAAAAATGTCGTAGCAATATTGATGTAAATTATGATGAT
GATGATTTTAATAATCATGTAGAACCAGCCATTGAACCAGCTGAAGAAACTGGACAAGAT
GTTATCGGTGATTACGAAGAAGGACTCGATGGTTTTAAACGTGATTTCATTACAAGAATA
TGGATGACTTATAGGAAAGACTTTGCAATGATGCCAGCAGAAGTGAAAAGTAACTCACCT
AATTCTCCAAGTAGTAGTAATGGAGGATACACTTCTGATTGCGGTTGGGGTTGCATGATT
AGATCAGGACAAATGTTGCTTGCACAAGCACTAGTTATTCATTTTCTTGGTCGAAGTTGG
CGTTATGATCCTAACACACAACTCTTTTCAACAACAGAAGATCATATTCATAGAAAAATT
GTGAGATGGTTTGGTGATCAAGTTTCAAAAGCAAGTCCATTTTCAATACATAAACTTGTT
GAGTTGGGCAAGAGAAATGGAAAGAAAGTAGGAGAATGGTATGGACCAGGATCAGTTGCA
CATGTGTTGAAAGATGCTGTAAAACAAGCTTCTAAAGAAAACATTGACCTCGCATCATTG
CATGTTTATGTGTCACAAGACTGTACTATTTATAATCAAGACATTTTCGATGAATGTTAT
TCAAATGAGATCCAAACAGTGCCATGGAAAAATAATTTGCCCTCAACATCATCAAATTCT
TTTACATTATCGCCATCTCGAAATCGATCAAAAGTTATCACATGGAAACAATTGATTCTC
TTGATTCCTCTTCGCTTAGGACACGAAAAACTCAATCCAATTTACAGTGATTGTCTTAAA
GCAATGTTGAGTCTTGAATGGTGTATTGGAATAATAGGAGGTCGACCGAAACATTCACTC
TATTTTGTCGGTTATCAAGATGATAAATTAATTCATCTTGATCCACATTATTGTCAGGAT
TTAGTGGATGTCAATGCTGAAAACTTTTCGCTCACTTCCTTTCACTGTCGATCAGCAAGA
AAAATGAAAATATCGAAAATGGATCCATCTTGCTGCATAGGTTTTTATATAGCTTCACGT
GAAGAATATGATAGATTTCAAAATACCATACAACCGTATCTTCAACCCATAAAAAATTAT
GCAGAAAGACATAAAACATCTCAATTTACCACTTCCTCTTCTTCCTGCATATCAGCACAG
TCAAATATTGAAATTTATCCAACGAGTTATCCAATGTTTGTTTTCAATCCTAGAAAATTG
AATGATGAAGAAGCACGTTCACTTCGAATTCATGCTTCACCATTAAATTCCCTTAAACAT
CTTCACATCGCTAATGACACTCATCATCCTCAAAATGATGATGAAACTGAGGACGATTGG
TTATGA
>g2023.t1 Gene=g2023 Length=601
MSNKSSMLSKLADTISEYSWSDASDGASTTTATASNAVKNNELQPNNGEFKDRVETKLMS
LWHNMKYGWGTKMRSNFNKESAIWFLGRCYHQKVTPSPSLQYSTIFDHNTINPSSTHHAD
NNSRLMTSSFHEELPTSYDSYLNQFPTKKCRSNIDVNYDDDDFNNHVEPAIEPAEETGQD
VIGDYEEGLDGFKRDFITRIWMTYRKDFAMMPAEVKSNSPNSPSSSNGGYTSDCGWGCMI
RSGQMLLAQALVIHFLGRSWRYDPNTQLFSTTEDHIHRKIVRWFGDQVSKASPFSIHKLV
ELGKRNGKKVGEWYGPGSVAHVLKDAVKQASKENIDLASLHVYVSQDCTIYNQDIFDECY
SNEIQTVPWKNNLPSTSSNSFTLSPSRNRSKVITWKQLILLIPLRLGHEKLNPIYSDCLK
AMLSLEWCIGIIGGRPKHSLYFVGYQDDKLIHLDPHYCQDLVDVNAENFSLTSFHCRSAR
KMKISKMDPSCCIGFYIASREEYDRFQNTIQPYLQPIKNYAERHKTSQFTTSSSSCISAQ
SNIEIYPTSYPMFVFNPRKLNDEEARSLRIHASPLNSLKHLHIANDTHHPQNDDETEDDW
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g2023.t1 | PANTHER | PTHR22624:SF52 | CYSTEINE PROTEASE | 17 | 565 | 0 |
| 3 | g2023.t1 | PANTHER | PTHR22624 | CYSTEINE PROTEASE ATG4 | 17 | 565 | 0 |
| 1 | g2023.t1 | Pfam | PF03416 | Peptidase family C54 | 191 | 508 | 0 |
| 4 | g2023.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 62 | 520 | 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 transcript has been annotated with K08342 (cysteine protease ATG4 [EC:3.4.22.-])
Pathway
- This transcript belongs to the following pathways
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.
