General information for g16523.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cathepsin L1.
Parent gene
- The parent gene g16523 is located on chr_4: 9789504..9791088 (- 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 | g16523 | g16523.t1 | isoform | g16523.t1 | 9789504 | 9791088 |
| chr_4 | g16523 | g16523.t1 | exon | g16523.t1.exon1 | 9789504 | 9789655 |
| chr_4 | g16523 | g16523.t1 | cds | g16523.t1.CDS1 | 9789504 | 9789655 |
| chr_4 | g16523 | g16523.t1 | exon | g16523.t1.exon2 | 9789719 | 9790152 |
| chr_4 | g16523 | g16523.t1 | cds | g16523.t1.CDS2 | 9789719 | 9790152 |
| chr_4 | g16523 | g16523.t1 | exon | g16523.t1.exon3 | 9790389 | 9790930 |
| chr_4 | g16523 | g16523.t1 | cds | g16523.t1.CDS3 | 9790389 | 9790930 |
| chr_4 | g16523 | g16523.t1 | exon | g16523.t1.exon4 | 9790984 | 9791088 |
| chr_4 | g16523 | g16523.t1 | cds | g16523.t1.CDS4 | 9790984 | 9791088 |
| chr_4 | g16523 | g16523.t1 | TSS | g16523.t1 | NA | NA |
| chr_4 | g16523 | g16523.t1 | TTS | g16523.t1 | NA | NA |
Sequences
>g16523.t1 Gene=g16523 Length=1233
ATGACAAGATTTATTTTGTGGGTATTTATAATTTTTCTAATTGAATTTAAAAATGTTCAA
GCAGGATTGCTTGATAAACTTGATGTTCCTAAAATTGAACCTAAATCAATAGTAAAAAAA
GCAACAGAAACAACATCAGATTTTGACATAGATTTGGATGATATTGATATACCAAATATC
ACAAAAAAAGAACTTTTAACTTTCATTAATTTTAAAAGTACCTTCAATAAAACTTATGCA
ACAATAGAAGAAGAAAAAGTTGCAATAAAAAATTTGATTTCTATGAAAAGAGAAGTTGAT
TTGCATAATAAAAGATATGAAGATGGTGAAGAAACCTTCATGAGAGGGCTCAATATTTTG
TCTGATTTGACACCTGAAGATGTTAATAAATTAGTCAATGGATTTGTCAAACCTAAACGT
GAGAAAAGTTTTATAAAAAGTGAAGATTATGATGATGGTGAAGAAGAAAATTATGAAAAT
TTTTATGATGAAGATGAGGATGAGAATGAAGAAGAAGGAACTATTTTAGATATTTTAAAA
AGAAGAAAAAGATCAAATAAAGTTGAAGATAAAAATGAAAGTTTGAACTACACAGCAAAA
GGTTTCATTCATCCTGTAATTGCTCAAGGAAAGTGCGGAAGTTGCTGGTCTTTTGCATCA
ATTTCAGCAATTGAAGCTCAATGGTTTAAGAAAACTGGAAAGTTAGAAAAATTGTCAGAG
CAACAGTTAATCGATTGCGATCGTGATGATGAAGGTGATGGTAATTATGGTTGTGCTGGT
GGAAGCATGGATGTTGCATTTAAATTTATTAAGAAGTTTGGAAAAATTGCACCTTGTTCT
GATTATCCATATGAAGGCAATGACACATACAAATGTAAAAAATTAGATGGAATTGTCACA
GTTTTATCACATGAAAATTTGACACCTGGCGATGAAAATTTGTTGAAGAAAAAATTGTTT
GAAATTGGACCAATTCCAATTGCTGTTGATGCTTCTTTAAGTTCTTTCCAAACTTACAAA
TCTGGGGTTTATTTTGATAAACAATGCACAACAAATTCAAATCATGCAATGTTGATTGTT
GGTTTTGGATATGATGAAAAAACTGAATTGAAATATTGGTTGATTAAAAATACTTATGGA
AAATCTTGGGGTTTACAAGGATACATGAAACTTGCTAGAGATGTTGACAATCATTGTGGA
GTTGCTGAATATGCTTCTTATCCTATTGTGTAA
>g16523.t1 Gene=g16523 Length=410
MTRFILWVFIIFLIEFKNVQAGLLDKLDVPKIEPKSIVKKATETTSDFDIDLDDIDIPNI
TKKELLTFINFKSTFNKTYATIEEEKVAIKNLISMKREVDLHNKRYEDGEETFMRGLNIL
SDLTPEDVNKLVNGFVKPKREKSFIKSEDYDDGEEENYENFYDEDEDENEEEGTILDILK
RRKRSNKVEDKNESLNYTAKGFIHPVIAQGKCGSCWSFASISAIEAQWFKKTGKLEKLSE
QQLIDCDRDDEGDGNYGCAGGSMDVAFKFIKKFGKIAPCSDYPYEGNDTYKCKKLDGIVT
VLSHENLTPGDENLLKKKLFEIGPIPIAVDASLSSFQTYKSGVYFDKQCTTNSNHAMLIV
GFGYDEKTELKYWLIKNTYGKSWGLQGYMKLARDVDNHCGVAEYASYPIV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g16523.t1 | CDD | cd02248 | Peptidase_C1A | 193 | 408 | 6.47299E-88 |
| 2 | g16523.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 58 | 406 | 2.4E-65 |
| 3 | g16523.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 58 | 406 | 2.4E-65 |
| 5 | g16523.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 209 | 224 | 2.3E-8 |
| 4 | g16523.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 355 | 365 | 2.3E-8 |
| 6 | g16523.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 372 | 378 | 2.3E-8 |
| 1 | g16523.t1 | Pfam | PF00112 | Papain family cysteine protease | 194 | 409 | 5.5E-61 |
| 10 | g16523.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 11 | g16523.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 12 | g16523.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 13 | g16523.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 21 | - |
| 9 | g16523.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 410 | - |
| 16 | g16523.t1 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 209 | 220 | - |
| 15 | g16523.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 353 | 363 | - |
| 18 | g16523.t1 | SMART | SM00848 | Inhibitor_I29_2 | 68 | 128 | 5.3E-11 |
| 17 | g16523.t1 | SMART | SM00645 | pept_c1 | 191 | 409 | 1.7E-88 |
| 7 | g16523.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 63 | 410 | 6.67E-86 |
| 8 | g16523.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
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