General information for g16525.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cathepsin L.
Parent gene
- The parent gene g16525 is located on chr_4: 9793728..9795506 (- 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 | g16525 | g16525.t1 | isoform | g16525.t1 | 9793728 | 9795506 |
| chr_4 | g16525 | g16525.t1 | exon | g16525.t1.exon1 | 9793728 | 9793821 |
| chr_4 | g16525 | g16525.t1 | cds | g16525.t1.CDS1 | 9793728 | 9793821 |
| chr_4 | g16525 | g16525.t1 | exon | g16525.t1.exon2 | 9793886 | 9793946 |
| chr_4 | g16525 | g16525.t1 | cds | g16525.t1.CDS2 | 9793886 | 9793946 |
| chr_4 | g16525 | g16525.t1 | exon | g16525.t1.exon3 | 9794156 | 9794459 |
| chr_4 | g16525 | g16525.t1 | cds | g16525.t1.CDS3 | 9794156 | 9794459 |
| chr_4 | g16525 | g16525.t1 | exon | g16525.t1.exon4 | 9794525 | 9794655 |
| chr_4 | g16525 | g16525.t1 | cds | g16525.t1.CDS4 | 9794525 | 9794655 |
| chr_4 | g16525 | g16525.t1 | exon | g16525.t1.exon5 | 9794713 | 9795046 |
| chr_4 | g16525 | g16525.t1 | cds | g16525.t1.CDS5 | 9794713 | 9795046 |
| chr_4 | g16525 | g16525.t1 | exon | g16525.t1.exon6 | 9795384 | 9795506 |
| chr_4 | g16525 | g16525.t1 | cds | g16525.t1.CDS6 | 9795384 | 9795506 |
| chr_4 | g16525 | g16525.t1 | TSS | g16525.t1 | NA | NA |
| chr_4 | g16525 | g16525.t1 | TTS | g16525.t1 | NA | NA |
Sequences
>g16525.t1 Gene=g16525 Length=1047
ATGAAATTTTTCGTATTCACTTTTATGACAATCTTTTGTCTTCTTCCTGCTACTATTAAA
GCTCAAAATGCTCCAAATACTCCAAATGATTCAATCATTTCAAATATTTTTGAGCAATGG
AAAACAAAATACGTAAAAGGAAAAACAGCAAATATTGTCAACAGTTCAAATTCGAATGCA
GCTTTTGAACGTTTGAAGAAACTTCTTATGAGTATTTCGAAACAAAATATCAGAAACGGT
GCAAAAAAATCATTATTCAAAATGGCATTAAATATTCGTGCAACAGATGATGAAACAACA
AGACGTAAATGGAATGGATTGATTTCTACAAGTTACGGTTTGATTGATCAAGTACAAACT
AAAGCTTTACCAATGAGTTTTCCACCAGCACCAAAAAGTTGGGATTGGAGACAGCAAGGA
CTTGTGACTAATGTTGAAGATCAAGGATATTATTGTGGAAGTTGTTATGCTTTTGCATCC
AGTTGTGCATTAGAAGGTCAAGTTGCAAAAAAATATGGAATTTTGAAATCTTTATCCAAA
CAACAAATTGTCGATTGTTCGAAACCTTATGGAAACTTTGGATGTGATGGTGGTTACATT
GACAAATCATTTAACTATACATATCGAAATCCTGGTCTCTTTGCTGAAGCTGACTATCCA
TATGCAGGCATTGATCAAAATTGCAATTTAACATCGAATTTTTCTAAATCATTTCTAGTC
AACTACAATTTCATTCAAGGTGATGAAGAAAATTTAAAAAGAGCTCTTTATGCAATTGGT
CCACTTAGTGTTGGAATGATAGGAAGTTTTGAAAGTTTCTATTTCTATAGTGAAGGAATT
TATGATGATGCTACTTGTACTGGAAAAATTGATCATGCTGTTTGTCTTGTTGGTTATGGA
ACAGATAACACAACAAGTCCACCAACTGATTACTGGATTGTAAAAAATTCTTGGTCGTCA
GATTGGGGTGAAAATGGATACTTTAGAATTCTTAGAGGTTCAAATATGTGTAACATTAGC
ACTTACGTTGCTTATCCAATAATATAA
>g16525.t1 Gene=g16525 Length=348
MKFFVFTFMTIFCLLPATIKAQNAPNTPNDSIISNIFEQWKTKYVKGKTANIVNSSNSNA
AFERLKKLLMSISKQNIRNGAKKSLFKMALNIRATDDETTRRKWNGLISTSYGLIDQVQT
KALPMSFPPAPKSWDWRQQGLVTNVEDQGYYCGSCYAFASSCALEGQVAKKYGILKSLSK
QQIVDCSKPYGNFGCDGGYIDKSFNYTYRNPGLFAEADYPYAGIDQNCNLTSNFSKSFLV
NYNFIQGDEENLKRALYAIGPLSVGMIGSFESFYFYSEGIYDDATCTGKIDHAVCLVGYG
TDNTTSPPTDYWIVKNSWSSDWGENGYFRILRGSNMCNISTYVAYPII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g16525.t1 | CDD | cd02248 | Peptidase_C1A | 131 | 346 | 1.55807E-92 |
| 10 | g16525.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 28 | 348 | 3.8E-84 |
| 2 | g16525.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 29 | 343 | 6.0E-65 |
| 3 | g16525.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 29 | 343 | 6.0E-65 |
| 5 | g16525.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 149 | 164 | 3.3E-6 |
| 4 | g16525.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 292 | 302 | 3.3E-6 |
| 6 | g16525.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 311 | 317 | 3.3E-6 |
| 1 | g16525.t1 | Pfam | PF00112 | Papain family cysteine protease | 131 | 347 | 1.2E-65 |
| 12 | g16525.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 13 | g16525.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g16525.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 15 | g16525.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 21 | - |
| 11 | g16525.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 348 | - |
| 19 | g16525.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 290 | 300 | - |
| 18 | g16525.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 311 | 330 | - |
| 20 | g16525.t1 | SMART | SM00645 | pept_c1 | 130 | 347 | 7.6E-88 |
| 7 | g16525.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 35 | 347 | 2.07E-83 |
| 9 | g16525.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 17 | g16525.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 8 | g16525.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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