General information for g16527.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 g16527 is located on chr_4: 9799593..9800155 (+ 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 | g16527 | g16527.t1 | isoform | g16527.t1 | 9798465 | 9799860 |
| chr_4 | g16527 | g16527.t1 | exon | g16527.t1.exon1 | 9798465 | 9798560 |
| chr_4 | g16527 | g16527.t1 | cds | g16527.t1.CDS1 | 9798465 | 9798560 |
| chr_4 | g16527 | g16527.t1 | exon | g16527.t1.exon2 | 9798718 | 9799069 |
| chr_4 | g16527 | g16527.t1 | cds | g16527.t1.CDS2 | 9798718 | 9799069 |
| chr_4 | g16527 | g16527.t1 | exon | g16527.t1.exon3 | 9799124 | 9799233 |
| chr_4 | g16527 | g16527.t1 | cds | g16527.t1.CDS3 | 9799124 | 9799233 |
| chr_4 | g16527 | g16527.t1 | exon | g16527.t1.exon4 | 9799290 | 9799593 |
| chr_4 | g16527 | g16527.t1 | cds | g16527.t1.CDS4 | 9799290 | 9799593 |
| chr_4 | g16527 | g16527.t1 | exon | g16527.t1.exon5 | 9799650 | 9799710 |
| chr_4 | g16527 | g16527.t1 | cds | g16527.t1.CDS5 | 9799650 | 9799710 |
| chr_4 | g16527 | g16527.t1 | exon | g16527.t1.exon6 | 9799767 | 9799860 |
| chr_4 | g16527 | g16527.t1 | cds | g16527.t1.CDS6 | 9799767 | 9799860 |
| chr_4 | g16527 | g16527.t1 | TSS | g16527.t1 | NA | NA |
| chr_4 | g16527 | g16527.t1 | TTS | g16527.t1 | NA | NA |
Sequences
>g16527.t1 Gene=g16527 Length=1017
ATGAAGTGGAAAATTTGTTTAATTTTGATTTTACATGTCAAATTTATAAATTCACTGGGA
AGTGACATGGCAAAACAGGAATTTAATGATTTTGTGCTCAAATACAACAAAACTTATAGT
TCCCCAACAGAATATGATGCAGCGTTTGAAAATTTTGCTAAAGAAAAACTTGCAATTCAA
GCACAACGATTGAAATATGAATCAAATCAATCAACATTTTTAATGGGAATAAATTATCGA
TCAGATCAAACATTTGAGCAAAAGAAAACTTGGCTTGGGCTTTTACTTGAAGAAATGCCA
ACTTCTCAAGCTCGAGCTTTAACAAATGAATTTCCTTCAACTTCTTCAAATGTTCCAGCA
CCAGCACGAATTGATTTTAGAGAATTTGGTTATGTAACAAATGTTTTAGATCAAGGATAT
TTTTGTAGTTCTTGTTACAGTTTTGCAACTTTGTGCAGTGTTGAAGGTCAATTTTTGAAA
AAAAATATCAGCACAAAAGTTTTATCAACTCAAAGTATCATTGATTGTAGTTCAAATTAT
AAAAATAAAGGATGCGATGGTGGTTACATTGAAAGCTCGTTCCGATATTTAATTGACTCT
AAAGGTATTGAAGATTTTAATAGTTATCCATACGAGGGTACTGTAGGACAATGTCGATAT
AATAATAAGAAATCGGTTGGAAGTGTCAGATGTTATGATAAAGTTCAAACTGATGAAGAA
ACATTGAAACAAATACTGGCAAACACAGGACCTATGGCAATTGGCATTAAAGCTAATTTC
CCAAGTTTTTATGGTTATCAAAATGGTGTTTATGATGATGACAATTGTTATGGAATTCCT
GACCATGCCGTTTGTCTTGTTGGTTATGGCACTGATTATTCATATAATCCACCTGCTGAT
TATTGGCTTATTAAAAATTCATGGTCCGACGAATGGGGTGAAAAAGGCTTTATTCGTATG
AAACGAGGTGTCAACCTATGTTCACTTACTTCTGCTATGTTTTATGGTGAAGTTTAA
>g16527.t1 Gene=g16527 Length=338
MKWKICLILILHVKFINSLGSDMAKQEFNDFVLKYNKTYSSPTEYDAAFENFAKEKLAIQ
AQRLKYESNQSTFLMGINYRSDQTFEQKKTWLGLLLEEMPTSQARALTNEFPSTSSNVPA
PARIDFREFGYVTNVLDQGYFCSSCYSFATLCSVEGQFLKKNISTKVLSTQSIIDCSSNY
KNKGCDGGYIESSFRYLIDSKGIEDFNSYPYEGTVGQCRYNNKKSVGSVRCYDKVQTDEE
TLKQILANTGPMAIGIKANFPSFYGYQNGVYDDDNCYGIPDHAVCLVGYGTDYSYNPPAD
YWLIKNSWSDEWGEKGFIRMKRGVNLCSLTSAMFYGEV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g16527.t1 | CDD | cd02248 | Peptidase_C1A | 121 | 335 | 4.76941E-74 |
| 11 | g16527.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 20 | 337 | 9.9E-82 |
| 3 | g16527.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 25 | 332 | 3.2E-62 |
| 4 | g16527.t1 | PANTHER | PTHR12411:SF734 | CATHEPSIN S, ORTHOLOG 1 | 25 | 332 | 3.2E-62 |
| 6 | g16527.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 139 | 154 | 6.4E-5 |
| 7 | g16527.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 282 | 292 | 6.4E-5 |
| 5 | g16527.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 301 | 307 | 6.4E-5 |
| 1 | g16527.t1 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 28 | 86 | 2.2E-6 |
| 2 | g16527.t1 | Pfam | PF00112 | Papain family cysteine protease | 121 | 335 | 3.7E-57 |
| 13 | g16527.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 14 | g16527.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 15 | g16527.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 16 | - |
| 16 | g16527.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 20 | - |
| 12 | g16527.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 338 | - |
| 18 | g16527.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 301 | 320 | - |
| 20 | g16527.t1 | SMART | SM00848 | Inhibitor_I29_2 | 28 | 88 | 8.6E-7 |
| 19 | g16527.t1 | SMART | SM00645 | pept_c1 | 120 | 337 | 2.2E-58 |
| 8 | g16527.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 26 | 336 | 5.26E-80 |
| 10 | g16527.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 9 | g16527.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 24 | - |
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