General information for g5942.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cathepsin L.
Parent gene
- The parent gene g5942 is located on chr_2: 12947901..12949977 (- 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_2 | g5942 | g5942.t3 | isoform | g5942.t3 | 12943621 | 12946206 |
| chr_2 | g5942 | g5942.t3 | exon | g5942.t3.exon1 | 12943621 | 12943700 |
| chr_2 | g5942 | g5942.t3 | TTS | g5942.t3 | 12943666 | 12943666 |
| chr_2 | g5942 | g5942.t3 | cds | g5942.t3.CDS1 | 12943700 | 12943700 |
| chr_2 | g5942 | g5942.t3 | exon | g5942.t3.exon2 | 12943910 | 12944396 |
| chr_2 | g5942 | g5942.t3 | cds | g5942.t3.CDS2 | 12943910 | 12944396 |
| chr_2 | g5942 | g5942.t3 | exon | g5942.t3.exon3 | 12944457 | 12944805 |
| chr_2 | g5942 | g5942.t3 | cds | g5942.t3.CDS3 | 12944457 | 12944805 |
| chr_2 | g5942 | g5942.t3 | exon | g5942.t3.exon4 | 12946018 | 12946117 |
| chr_2 | g5942 | g5942.t3 | cds | g5942.t3.CDS4 | 12946018 | 12946110 |
| chr_2 | g5942 | g5942.t3 | exon | g5942.t3.exon5 | 12946187 | 12946206 |
| chr_2 | g5942 | g5942.t3 | TSS | g5942.t3 | 12946276 | 12946276 |
Sequences
>g5942.t3 Gene=g5942 Length=1036
TTTGTACTTTTTAATAGAAGCATAAACATGAAATTCTTAATCTTTTTTGCATTATTGATT
GGTGTGAGCTATGCAATTAAATTTTCTGAATTAGCTAAAGAAGAATGGGATGAATTTAAG
GCTCTTCACAAAAAAGAGTACAAAGATGAGACCGAAGAAAGATTCCGTTATAAAATCTAT
GTAGATAATCGTCATAAGATCGCTAAACACAATAAACTCTTCCATACAAATGAAAAACCA
TATAAAATGAGCCTTAACAAATATTCTGATATGTTGCATACTGAATTTGTTAAAACACTC
AATGGATTCAATCGTTCATATGTTCATAGTGTTAATTCAGTTTATAAGTCATCAAGCCCA
ATTGATGAAGGCATCACATTTATTGCAGCTGAAAACCTTAACTTACCAGTATCAATGGAT
TGGAGAACTAAGGGTGCTGTTACACCAATTAAGGATCAAGGCCATTGCGGTTCATGCTGG
GCATTTTCCACAACTGGCGCATTAGAAGGACAAACATTCCGTAAAACTGGAAAACTCATT
TCACTATCTGAACAAAATTTGGTAGATTGCTCAGGAAAATATGGCAATAACGGTTGCAAT
GGAGGACTTATGGACAACGCATTCCAATATATCAAAGAAAATGGAGGAATTGACACAGAA
AAGTCCTATCCATATGAAGGAATTGATGATACTTGTCACTTTTCGAAACAAACTATTGGT
GCAACTGACAAAGGATTCGTTGATATTCCAGAGGGAGATGAAGATGCATTGTTGAAAGCT
ATTGCTTCAGTTGGACCTGTTTCAGTCGCTATTGATGCCAGTCACGAATCATTCCAATTC
TACTCTGAAGGAGTTTACTATGAACCACAATGTGATAGTCAGCAATTAGACCATGGCGTT
TTGCTCGTTGGATATGGTACTGAAAAGGACAAGGATGGAAATGACCAAGACTATTGATTA
TTAATGTATAGCGAGAGAAAGAAATAAAAATTTCCTAATAAAATTCAAAACTAAATTTTT
CTCTTTTATTCCAGTT
>g5942.t3 Gene=g5942 Length=309
MKFLIFFALLIGVSYAIKFSELAKEEWDEFKALHKKEYKDETEERFRYKIYVDNRHKIAK
HNKLFHTNEKPYKMSLNKYSDMLHTEFVKTLNGFNRSYVHSVNSVYKSSSPIDEGITFIA
AENLNLPVSMDWRTKGAVTPIKDQGHCGSCWAFSTTGALEGQTFRKTGKLISLSEQNLVD
CSGKYGNNGCNGGLMDNAFQYIKENGGIDTEKSYPYEGIDDTCHFSKQTIGATDKGFVDI
PEGDEDALLKAIASVGPVSVAIDASHESFQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEK
DKDGNDQDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5942.t3 | CDD | cd02248 | Peptidase_C1A | 127 | 303 | 1.06526E-101 |
| 9 | g5942.t3 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 18 | 309 | 1.6E-97 |
| 3 | g5942.t3 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 13 | 301 | 4.1E-97 |
| 4 | g5942.t3 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 13 | 301 | 4.1E-97 |
| 5 | g5942.t3 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 144 | 159 | 1.4E-8 |
| 6 | g5942.t3 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 289 | 299 | 1.4E-8 |
| 1 | g5942.t3 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 27 | 87 | 2.6E-10 |
| 2 | g5942.t3 | Pfam | PF00112 | Papain family cysteine protease | 126 | 302 | 6.9E-68 |
| 11 | g5942.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 12 | g5942.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 13 | g5942.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 14 | g5942.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 10 | g5942.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 309 | - |
| 17 | g5942.t3 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 144 | 155 | - |
| 16 | g5942.t3 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 287 | 297 | - |
| 19 | g5942.t3 | SMART | SM00848 | Inhibitor_I29_2 | 27 | 87 | 4.2E-18 |
| 18 | g5942.t3 | SMART | SM00645 | pept_c1 | 126 | 305 | 1.3E-92 |
| 7 | g5942.t3 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 21 | 303 | 6.74E-98 |
| 8 | g5942.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5942/g5942.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t3.fa.iupred3.txt does not exist
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