General information for g5942.t12
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.t12 | TTS | g5942.t12 | 12943666 | 12943666 |
| chr_2 | g5942 | g5942.t12 | isoform | g5942.t12 | 12943795 | 12946247 |
| chr_2 | g5942 | g5942.t12 | exon | g5942.t12.exon1 | 12943795 | 12944250 |
| chr_2 | g5942 | g5942.t12 | cds | g5942.t12.CDS1 | 12943795 | 12944250 |
| chr_2 | g5942 | g5942.t12 | exon | g5942.t12.exon2 | 12944397 | 12944805 |
| chr_2 | g5942 | g5942.t12 | cds | g5942.t12.CDS2 | 12944397 | 12944402 |
| chr_2 | g5942 | g5942.t12 | exon | g5942.t12.exon3 | 12946018 | 12946121 |
| chr_2 | g5942 | g5942.t12 | exon | g5942.t12.exon4 | 12946187 | 12946247 |
| chr_2 | g5942 | g5942.t12 | TSS | g5942.t12 | 12946276 | 12946276 |
Sequences
>g5942.t12 Gene=g5942 Length=1030
ACTGAAAAGAATTTAAATAGCCATTTGATTTATCATTTAAGTTTGTACTTTTTAATAGAA
GACAGCATAAACATGAAATTCTTAATCTTTTTTGCATTATTGATTGGTGTGAGCTATGCA
ATTAAATTTTCTGAATTAGCTAAAGAAGAATGGGATGAATTTAAGGCTCTTCACAAAAAA
GAGTACAAAGATGAGACCGAAGAAAGATTCCGTTATAAAATCTATGTAGATAATCGTCAT
AAGATCGCTAAACACAATAAACTCTTCCATACAAATGAAAAACCATATAAAATGAGCCTT
AACAAATATTCTGATATGTTGCATACTGAATTTGTTAAAACACTCAATGGATTCAATCGT
TCATATGTTCATAGTGTTAATTCAGTTTATAAGTCATCAAGCCCAATTGATGAAGGCATC
ACATTTATTGCAGCTGAAAACCTTAACTTACCAGTATCAATGGATTGGAGAACTAAGGGT
GCTGTTACACCAATTAAGGATCAAGGCCATTGCGGTAAATACTTTAAAAATCTTTTATCT
TTTTTGTTTTTGATAAAATTTTATAATTATGCAGAACGCATTCCAATATATCAAAGAAAA
TGGAGGAATTGACACAGAAAAGTCCTATCCATATGAAGGAATTGATGATACTTGTCACTT
TTCGAAACAAACTATTGGTGCAACTGACAAAGGATTCGTTGATATTCCAGAGGGAGATGA
AGATGCATTGTTGAAAGCTATTGCTTCAGTTGGACCTGTTTCAGTCGCTATTGATGCCAG
TCACGAATCATTCCAATTCTACTCTGAAGGAGTTTACTATGAACCACAATGTGATAGTCA
GCAATTAGACCATGGCGTTTTGCTCGTTGGATATGGTACTGAAAAGGACAAGGATGGAAA
TGACCAAGACTATTGGTTAGTTAAAAACAGTTGGGGCACATCTTGGGGTGATCAAGGCTA
TATTAAAATGGCTCGTAATAAGGAAAATCACTGTGGAATTGCTACATCTGCAAGCTATCC
ATTAGTATAA
>g5942.t12 Gene=g5942 Length=153
MQNAFQYIKENGGIDTEKSYPYEGIDDTCHFSKQTIGATDKGFVDIPEGDEDALLKAIAS
VGPVSVAIDASHESFQFYSEGVYYEPQCDSQQLDHGVLLVGYGTEKDKDGNDQDYWLVKN
SWGTSWGDQGYIKMARNKENHCGIATSASYPLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5942.t12 | CDD | cd02248 | Peptidase_C1A | 1 | 151 | 8.34656E-75 |
| 8 | g5942.t12 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 1 | 153 | 9.1E-60 |
| 2 | g5942.t12 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 1 | 149 | 4.3E-56 |
| 3 | g5942.t12 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 1 | 149 | 4.3E-56 |
| 1 | g5942.t12 | Pfam | PF00112 | Papain family cysteine protease | 1 | 151 | 6.0E-53 |
| 7 | g5942.t12 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 93 | 103 | - |
| 6 | g5942.t12 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 115 | 134 | - |
| 5 | g5942.t12 | SMART | SM00645 | pept_c1 | 1 | 152 | 1.6E-41 |
| 4 | g5942.t12 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 1 | 152 | 6.44E-62 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5942/g5942.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5942.t12.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.
