General information for g15561.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cysteine protease ATG4B.
Parent gene
- The parent gene g15561 is located on chr_4: 5868927..5870140 (- 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_4 | g15561 | g15561.t1 | TTS | g15561.t1 | 5867661 | 5867661 |
| chr_4 | g15561 | g15561.t1 | isoform | g15561.t1 | 5867669 | 5868927 |
| chr_4 | g15561 | g15561.t1 | exon | g15561.t1.exon1 | 5867669 | 5868320 |
| chr_4 | g15561 | g15561.t1 | cds | g15561.t1.CDS1 | 5867669 | 5868320 |
| chr_4 | g15561 | g15561.t1 | exon | g15561.t1.exon2 | 5868411 | 5868713 |
| chr_4 | g15561 | g15561.t1 | cds | g15561.t1.CDS2 | 5868411 | 5868713 |
| chr_4 | g15561 | g15561.t1 | exon | g15561.t1.exon3 | 5868779 | 5868927 |
| chr_4 | g15561 | g15561.t1 | cds | g15561.t1.CDS3 | 5868779 | 5868927 |
| chr_4 | g15561 | g15561.t1 | TSS | g15561.t1 | 5869006 | 5869006 |
Sequences
>g15561.t1 Gene=g15561 Length=1104
ATGGATCTCTTGTTGGCAGACAACATTGGATACGATGTTTGGGAAGTTGAAGATATACCA
TCGACAGCTGATGAAATTATTGTGCTGGGAAAAACTTATAAATATGAAGATTTAGAAAAA
ATTAGAGATGACGTGCAGTCAAGATTATGGTGCACATATAGGAAAGGATTTTCACCATTA
GGTTCACCACAATACACATCAGATAAAGGTTTTGGTTGTATGATGCGATGCGGTCAAATG
TTACTGGCAGAGGCATTAACTCAATTACATATTGGTCGACATTGGCGATGGACGATTGAT
ACCAAAGATCCAATTTACCTCGAAATTGTTAATAAATTTGAAGATACAAAAAGTGCAGTT
TATGGCATTCATCAAATCGCAATTATGGGACAAGATTCAGGAAAAAAAATTTCAGAGTGG
TACAGTCCTAATGTGATAGCTCAAGTGATAAGAAAATTAGTACGATTTGATGAATTTTCA
AATCTTCAAGTACACGTAGCACTTGATCATCAATTAGCATTAGATGACATCATTGAAATC
ACAACACCATTACTACTGATTATACCACTTCGTTTAGGTCTCAATGAATTAAATCCAATT
TACATCCCAGCACTAAAGCGGTGTTTTGAAATTCCTGGTACCCTTGGTATCATTGGTGGT
CGACCAAATCAAGCTTTATATTTTGTTGGCTATGTTGGTGATGAAGCATTGTACCTTGAT
CCACATACATGTCAGAAAAGTGGCAGCATTAATAATAAAGAATTACAATGTGAAATTGAA
ATGGATGACACTTTTCATCAAAAGCATGCAGGAAGAATAAATTTTAATTCCATGGATCCA
TCAATTGCTGTTGCATTTTTATGTAAATCACAAAAAGAATTTGATGAATTAATTGAAGCA
TTAAGAAATGTTGAGAAAGAAATGACTCCACTTTTTGAAATTGTTGAACAACGAGCACAA
CCATGGATATCAACATCGATGAGTAGTAAAGATTTAGAACATGATTTGAGTATCATTAGT
GGCGGTGGTGAAGGAAATCAAGAATTTGAAAAGGTTGAAAAAGAAGAAGATGACGATGAT
GATGATTTTGAAATTATTGATTAA
>g15561.t1 Gene=g15561 Length=367
MDLLLADNIGYDVWEVEDIPSTADEIIVLGKTYKYEDLEKIRDDVQSRLWCTYRKGFSPL
GSPQYTSDKGFGCMMRCGQMLLAEALTQLHIGRHWRWTIDTKDPIYLEIVNKFEDTKSAV
YGIHQIAIMGQDSGKKISEWYSPNVIAQVIRKLVRFDEFSNLQVHVALDHQLALDDIIEI
TTPLLLIIPLRLGLNELNPIYIPALKRCFEIPGTLGIIGGRPNQALYFVGYVGDEALYLD
PHTCQKSGSINNKELQCEIEMDDTFHQKHAGRINFNSMDPSIAVAFLCKSQKEFDELIEA
LRNVEKEMTPLFEIVEQRAQPWISTSMSSKDLEHDLSIISGGGEGNQEFEKVEKEEDDDD
DDFEIID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g15561.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 338 | 367 | - |
| 5 | g15561.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 351 | 367 | - |
| 2 | g15561.t1 | PANTHER | PTHR22624 | CYSTEINE PROTEASE ATG4 | 20 | 335 | 1.2E-102 |
| 1 | g15561.t1 | Pfam | PF03416 | Peptidase family C54 | 39 | 299 | 3.5E-88 |
| 3 | g15561.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 13 | 309 | 1.32E-99 |
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.
