General information for g5942.t17
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.t17 | TTS | g5942.t17 | 12943666 | 12943666 |
| chr_2 | g5942 | g5942.t17 | isoform | g5942.t17 | 12943795 | 12946276 |
| chr_2 | g5942 | g5942.t17 | exon | g5942.t17.exon1 | 12943795 | 12944396 |
| chr_2 | g5942 | g5942.t17 | cds | g5942.t17.CDS1 | 12943795 | 12944396 |
| chr_2 | g5942 | g5942.t17 | exon | g5942.t17.exon2 | 12944457 | 12944805 |
| chr_2 | g5942 | g5942.t17 | cds | g5942.t17.CDS2 | 12944457 | 12944805 |
| chr_2 | g5942 | g5942.t17 | exon | g5942.t17.exon3 | 12946018 | 12946139 |
| chr_2 | g5942 | g5942.t17 | cds | g5942.t17.CDS3 | 12946018 | 12946110 |
| chr_2 | g5942 | g5942.t17 | exon | g5942.t17.exon4 | 12946254 | 12946276 |
| chr_2 | g5942 | g5942.t17 | TSS | g5942.t17 | 12946276 | 12946276 |
Sequences
>g5942.t17 Gene=g5942 Length=1096
AGAGTAAAATTAAACTTTGAAGTTTTCTATATTTTATACAGACAGCATAAACATGAAATT
CTTAATCTTTTTTGCATTATTGATTGGTGTGAGCTATGCAATTAAATTTTCTGAATTAGC
TAAAGAAGAATGGGATGAATTTAAGGCTCTTCACAAAAAAGAGTACAAAGATGAGACCGA
AGAAAGATTCCGTTATAAAATCTATGTAGATAATCGTCATAAGATCGCTAAACACAATAA
ACTCTTCCATACAAATGAAAAACCATATAAAATGAGCCTTAACAAATATTCTGATATGTT
GCATACTGAATTTGTTAAAACACTCAATGGATTCAATCGTTCATATGTTCATAGTGTTAA
TTCAGTTTATAAGTCATCAAGCCCAATTGATGAAGGCATCACATTTATTGCAGCTGAAAA
CCTTAACTTACCAGTATCAATGGATTGGAGAACTAAGGGTGCTGTTACACCAATTAAGGA
TCAAGGCCATTGCGGTTCATGCTGGGCATTTTCCACAACTGGCGCATTAGAAGGACAAAC
ATTCCGTAAAACTGGAAAACTCATTTCACTATCTGAACAAAATTTGGTAGATTGCTCAGG
AAAATATGGCAATAACGGTTGCAATGGAGGACTTATGGACAACGCATTCCAATATATCAA
AGAAAATGGAGGAATTGACACAGAAAAGTCCTATCCATATGAAGGAATTGATGATACTTG
TCACTTTTCGAAACAAACTATTGGTGCAACTGACAAAGGATTCGTTGATATTCCAGAGGG
AGATGAAGATGCATTGTTGAAAGCTATTGCTTCAGTTGGACCTGTTTCAGTCGCTATTGA
TGCCAGTCACGAATCATTCCAATTCTACTCTGAAGGAGTTTACTATGAACCACAATGTGA
TAGTCAGCAATTAGACCATGGCGTTTTGCTCGTTGGATATGGTACTGAAAAGGACAAGGA
TGGAAATGACCAAGACTATTGGTTAGTTAAAAACAGTTGGGGCACATCTTGGGGTGATCA
AGGCTATATTAAAATGGCTCGTAATAAGGAAAATCACTGTGGAATTGCTACATCTGCAAG
CTATCCATTAGTATAA
>g5942.t17 Gene=g5942 Length=347
MKFLIFFALLIGVSYAIKFSELAKEEWDEFKALHKKEYKDETEERFRYKIYVDNRHKIAK
HNKLFHTNEKPYKMSLNKYSDMLHTEFVKTLNGFNRSYVHSVNSVYKSSSPIDEGITFIA
AENLNLPVSMDWRTKGAVTPIKDQGHCGSCWAFSTTGALEGQTFRKTGKLISLSEQNLVD
CSGKYGNNGCNGGLMDNAFQYIKENGGIDTEKSYPYEGIDDTCHFSKQTIGATDKGFVDI
PEGDEDALLKAIASVGPVSVAIDASHESFQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEK
DKDGNDQDYWLVKNSWGTSWGDQGYIKMARNKENHCGIATSASYPLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5942.t17 | CDD | cd02248 | Peptidase_C1A | 127 | 345 | 4.22335E-128 |
| 10 | g5942.t17 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 18 | 347 | 1.8E-120 |
| 3 | g5942.t17 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 13 | 343 | 2.6E-115 |
| 4 | g5942.t17 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 13 | 343 | 2.6E-115 |
| 5 | g5942.t17 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 144 | 159 | 1.9E-11 |
| 6 | g5942.t17 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 289 | 299 | 1.9E-11 |
| 7 | g5942.t17 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 309 | 315 | 1.9E-11 |
| 1 | g5942.t17 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 27 | 87 | 3.1E-10 |
| 2 | g5942.t17 | Pfam | PF00112 | Papain family cysteine protease | 126 | 345 | 5.6E-89 |
| 12 | g5942.t17 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 13 | g5942.t17 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g5942.t17 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 15 | g5942.t17 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 11 | g5942.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 347 | - |
| 19 | g5942.t17 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 144 | 155 | - |
| 18 | g5942.t17 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 287 | 297 | - |
| 17 | g5942.t17 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 309 | 328 | - |
| 21 | g5942.t17 | SMART | SM00848 | Inhibitor_I29_2 | 27 | 87 | 4.2E-18 |
| 20 | g5942.t17 | SMART | SM00645 | pept_c1 | 126 | 346 | 1.7E-136 |
| 8 | g5942.t17 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 24 | 346 | 3.87E-121 |
| 9 | g5942.t17 | 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.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t17.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 transcript has been annotated with K01365 (cathepsin L)
Pathway
- This transcript belongs to the following pathways
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.
