General information for g17676.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cathepsin L.
Parent gene
- The parent gene g17676 is located on HiC_scaffold_52: 57..863 (+ 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_52 | g17676 | g17676.t1 | isoform | g17676.t1 | 57 | 863 |
| HiC_scaffold_52 | g17676 | g17676.t1 | exon | g17676.t1.exon1 | 57 | 158 |
| HiC_scaffold_52 | g17676 | g17676.t1 | cds | g17676.t1.CDS1 | 57 | 158 |
| HiC_scaffold_52 | g17676 | g17676.t1 | exon | g17676.t1.exon2 | 215 | 545 |
| HiC_scaffold_52 | g17676 | g17676.t1 | cds | g17676.t1.CDS2 | 215 | 545 |
| HiC_scaffold_52 | g17676 | g17676.t1 | exon | g17676.t1.exon3 | 706 | 863 |
| HiC_scaffold_52 | g17676 | g17676.t1 | cds | g17676.t1.CDS3 | 706 | 863 |
| HiC_scaffold_52 | g17676 | g17676.t1 | TSS | g17676.t1 | NA | NA |
| HiC_scaffold_52 | g17676 | g17676.t1 | TTS | g17676.t1 | NA | NA |
Sequences
>g17676.t1 Gene=g17676 Length=591
ATGAATATTTTAATTTTCATTGGATTTTTTGGTTTCTTTTATTTTAAAAATGCAGAAGCT
ATTTCAGAAGATGTTGTGAAAGATCAATATTGGAAATGGAAGACCAAATACCGTGATTCA
GATCAAGAATCGGAAGTTCCTTATGTGATTTTTCGTCAAACTCTTATGAAAGTTGCTCAA
CATGAACTTCAATATTTTACAAAACGATCAAGTTATACTTATAAACTCAATGGTCGTTCA
GCTGACACTTTTAGTGAAATGGCATTATGGAATGGACTTTTGGTTGATAATTCTATAAAT
GAGGCTGCAGTTATTAGAAATAAAAGAAGTATAAACATGACAGGAGTTTATAATTTTCCA
CCAGCACCATCAAGTTGGGATTGGAGTGAGCAAGGATACGTGACTGATGTTGATGATCAA
GGATATTATTGTGGTTCTTGCTATTCTTTTGCTACTGCGTGTGCTATGGAAGGTCAATAT
ATGAAAGTCCATAAAAAATTAAGAAAATTTTCAAAACAACAAACTGTTGATTGTTCTCGT
AGTTTTGGAAATTTTGGATGTGAAGTAAGAATTTATTTTGACATTACATAA
>g17676.t1 Gene=g17676 Length=196
MNILIFIGFFGFFYFKNAEAISEDVVKDQYWKWKTKYRDSDQESEVPYVIFRQTLMKVAQ
HELQYFTKRSSYTYKLNGRSADTFSEMALWNGLLVDNSINEAAVIRNKRSINMTGVYNFP
PAPSSWDWSEQGYVTDVDDQGYYCGSCYSFATACAMEGQYMKVHKKLRKFSKQQTVDCSR
SFGNFGCEVRIYFDIT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17676.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 12 | 194 | 5.2E-29 |
| 2 | g17676.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 26 | 188 | 7.6E-21 |
| 3 | g17676.t1 | PANTHER | PTHR12411:SF734 | CATHEPSIN S, ORTHOLOG 1 | 26 | 188 | 7.6E-21 |
| 1 | g17676.t1 | Pfam | PF00112 | Papain family cysteine protease | 123 | 188 | 3.5E-17 |
| 8 | g17676.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 9 | g17676.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g17676.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 11 | g17676.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 7 | g17676.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 196 | - |
| 4 | g17676.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 30 | 188 | 7.63E-30 |
| 5 | g17676.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008234 | cysteine-type peptidase activity | MF |
| GO:0006508 | proteolysis | BP |
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. There were no conditions that were differentially expressed