General information for g5942.t1
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.t1 | TTS | g5942.t1 | 12943666 | 12943666 |
| chr_2 | g5942 | g5942.t1 | isoform | g5942.t1 | 12943795 | 12947901 |
| chr_2 | g5942 | g5942.t1 | exon | g5942.t1.exon1 | 12943795 | 12944396 |
| chr_2 | g5942 | g5942.t1 | cds | g5942.t1.CDS1 | 12943795 | 12944396 |
| chr_2 | g5942 | g5942.t1 | exon | g5942.t1.exon2 | 12944457 | 12944805 |
| chr_2 | g5942 | g5942.t1 | cds | g5942.t1.CDS2 | 12944457 | 12944805 |
| chr_2 | g5942 | g5942.t1 | exon | g5942.t1.exon3 | 12946018 | 12946121 |
| chr_2 | g5942 | g5942.t1 | cds | g5942.t1.CDS3 | 12946018 | 12946121 |
| chr_2 | g5942 | g5942.t1 | exon | g5942.t1.exon4 | 12946187 | 12946206 |
| chr_2 | g5942 | g5942.t1 | cds | g5942.t1.CDS4 | 12946187 | 12946206 |
| chr_2 | g5942 | g5942.t1 | TSS | g5942.t1 | 12946276 | 12946276 |
| chr_2 | g5942 | g5942.t1 | exon | g5942.t1.exon5 | 12947837 | 12947901 |
| chr_2 | g5942 | g5942.t1 | cds | g5942.t1.CDS5 | 12947837 | 12947901 |
Sequences
>g5942.t1 Gene=g5942 Length=1140
ATGTACTTTTTTGAAATTACATTCAAACGATCATATATATTACTAAAAGCAGCTAGAACT
AAACTTTTGTACTTTTTAATAGAAGACAGCATAAACATGAAATTCTTAATCTTTTTTGCA
TTATTGATTGGTGTGAGCTATGCAATTAAATTTTCTGAATTAGCTAAAGAAGAATGGGAT
GAATTTAAGGCTCTTCACAAAAAAGAGTACAAAGATGAGACCGAAGAAAGATTCCGTTAT
AAAATCTATGTAGATAATCGTCATAAGATCGCTAAACACAATAAACTCTTCCATACAAAT
GAAAAACCATATAAAATGAGCCTTAACAAATATTCTGATATGTTGCATACTGAATTTGTT
AAAACACTCAATGGATTCAATCGTTCATATGTTCATAGTGTTAATTCAGTTTATAAGTCA
TCAAGCCCAATTGATGAAGGCATCACATTTATTGCAGCTGAAAACCTTAACTTACCAGTA
TCAATGGATTGGAGAACTAAGGGTGCTGTTACACCAATTAAGGATCAAGGCCATTGCGGT
TCATGCTGGGCATTTTCCACAACTGGCGCATTAGAAGGACAAACATTCCGTAAAACTGGA
AAACTCATTTCACTATCTGAACAAAATTTGGTAGATTGCTCAGGAAAATATGGCAATAAC
GGTTGCAATGGAGGACTTATGGACAACGCATTCCAATATATCAAAGAAAATGGAGGAATT
GACACAGAAAAGTCCTATCCATATGAAGGAATTGATGATACTTGTCACTTTTCGAAACAA
ACTATTGGTGCAACTGACAAAGGATTCGTTGATATTCCAGAGGGAGATGAAGATGCATTG
TTGAAAGCTATTGCTTCAGTTGGACCTGTTTCAGTCGCTATTGATGCCAGTCACGAATCA
TTCCAATTCTACTCTGAAGGAGTTTACTATGAACCACAATGTGATAGTCAGCAATTAGAC
CATGGCGTTTTGCTCGTTGGATATGGTACTGAAAAGGACAAGGATGGAAATGACCAAGAC
TATTGGTTAGTTAAAAACAGTTGGGGCACATCTTGGGGTGATCAAGGCTATATTAAAATG
GCTCGTAATAAGGAAAATCACTGTGGAATTGCTACATCTGCAAGCTATCCATTAGTATAA
>g5942.t1 Gene=g5942 Length=379
MYFFEITFKRSYILLKAARTKLLYFLIEDSINMKFLIFFALLIGVSYAIKFSELAKEEWD
EFKALHKKEYKDETEERFRYKIYVDNRHKIAKHNKLFHTNEKPYKMSLNKYSDMLHTEFV
KTLNGFNRSYVHSVNSVYKSSSPIDEGITFIAAENLNLPVSMDWRTKGAVTPIKDQGHCG
SCWAFSTTGALEGQTFRKTGKLISLSEQNLVDCSGKYGNNGCNGGLMDNAFQYIKENGGI
DTEKSYPYEGIDDTCHFSKQTIGATDKGFVDIPEGDEDALLKAIASVGPVSVAIDASHES
FQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEKDKDGNDQDYWLVKNSWGTSWGDQGYIKM
ARNKENHCGIATSASYPLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5942.t1 | CDD | cd02248 | Peptidase_C1A | 159 | 377 | 1.03518E-128 |
| 9 | g5942.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 50 | 379 | 2.5E-120 |
| 3 | g5942.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 44 | 375 | 3.4E-115 |
| 4 | g5942.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 44 | 375 | 3.4E-115 |
| 7 | g5942.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 176 | 191 | 2.4E-11 |
| 6 | g5942.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 321 | 331 | 2.4E-11 |
| 5 | g5942.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 341 | 347 | 2.4E-11 |
| 1 | g5942.t1 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 59 | 119 | 3.5E-10 |
| 2 | g5942.t1 | Pfam | PF00112 | Papain family cysteine protease | 158 | 377 | 7.2E-89 |
| 11 | g5942.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 30 | - |
| 12 | g5942.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 31 | 49 | - |
| 10 | g5942.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 50 | 379 | - |
| 17 | g5942.t1 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 176 | 187 | - |
| 16 | g5942.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 319 | 329 | - |
| 15 | g5942.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 341 | 360 | - |
| 19 | g5942.t1 | SMART | SM00848 | Inhibitor_I29_2 | 59 | 119 | 4.2E-18 |
| 18 | g5942.t1 | SMART | SM00645 | pept_c1 | 158 | 378 | 1.7E-136 |
| 8 | g5942.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 56 | 378 | 5.36E-121 |
| 14 | g5942.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 22 | 44 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5942/g5942.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t1.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. There were no conditions that were differentially expressed