General information for g2993.t42
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cathepsin B.
Parent gene
- The parent gene g2993 is located on chr_3: 21868580..21876208 (- 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_3 | g2993 | g2993.t42 | TTS | g2993.t42 | 21867629 | 21867629 |
| chr_3 | g2993 | g2993.t42 | isoform | g2993.t42 | 21867833 | 21869132 |
| chr_3 | g2993 | g2993.t42 | exon | g2993.t42.exon1 | 21867833 | 21867921 |
| chr_3 | g2993 | g2993.t42 | cds | g2993.t42.CDS1 | 21867833 | 21867921 |
| chr_3 | g2993 | g2993.t42 | exon | g2993.t42.exon2 | 21867986 | 21868479 |
| chr_3 | g2993 | g2993.t42 | cds | g2993.t42.CDS2 | 21867986 | 21868274 |
| chr_3 | g2993 | g2993.t42 | exon | g2993.t42.exon3 | 21868542 | 21868694 |
| chr_3 | g2993 | g2993.t42 | exon | g2993.t42.exon4 | 21868752 | 21869132 |
| chr_3 | g2993 | g2993.t42 | TSS | g2993.t42 | 21869220 | 21869220 |
Sequences
>g2993.t42 Gene=g2993 Length=1117
ATGAAATATTTCATATTATTTGCTGCATTGACAGCAGTTTGCTTTGGAGCTGACATTTTT
TCTGATGAAGTAAAACAATTTTTTCGTTTCTACGTCTTAATTTGATTATCACTAATTATC
AATATTTCTAATTAAAACAGTTCATCAATGAAATTAATAAAAAAGCAACAACATGGAAGG
CTGGCCATAATTTTCATCCAGATACTAATTTGAAATATATCAAGAATTTACTTGGTGTTC
ATTCCGATTCTAAGCATTTTAAACTACCTGAGTTATTGCATGACTCACGGGACATAAAAG
ATTTACCTGAAAATTTTGATGCTCGTGAACAATGGCCTGATTGTCCAACATTGAGAGAAA
TAAGAGATCAAGGAAGTTGTGGATCTTGTTGGGCTTTTGGCGCTGTTGAGGCAATGAGTG
ACAGAGTATGCATTCATAGCAACGCAACTGAACATTTCCACTTTTCTGCTGAACATTTGG
TTTCTTGCTGTCACACTTGTGGATTTGGTTGCAATGGTGGCTTTCCAGGATCAGCTTGGA
GCTATTGGGTTAGAAAAGGTATTGTTAGTGGTGGACCATACAATTCTTCAATTGGATGTC
AGGTAAAAAATTCATTGTTAAATATTTTTTATTGTTTAAAATTTTATCCTTATTGCAGCC
ATATGAAATCGCTCCTTGTGAACATCATGTCAATGGAACTCGTATGCCATGCTCTGGAGA
AGGACATACACCAAAATGCATGAATAAATGCTCGAATCCCGCTTATAAAGTTGATTTCAA
AACAGACAAACACTTTGGCAAATCAAGCTATTCAGTAAAGCGTAATGAAGATCAAATTCG
TTTGGAAATTTTCAAAAATGGTCCAGTTGAAGGTGCATTCACAGTCTATGAAGATTTCGT
TCAATATAAATCTGGAGTTTATCAACATGTTACTGGTAAAGCACTTGGTGGCCATGCTAT
TAAAATTTTCGGATGGGGAGTTGAAAATGGTGTCAAATACTGGTTGATTGCTAATAGCTG
GAATTCAGATTGGGGTGATAATGGAACCTTCAAAATATTGCGAGGAGAAGACCATGTCGG
TATTGAGAGTGAGATTAGCGCTGGTTTGCCAAAGTAA
>g2993.t42 Gene=g2993 Length=125
MNKCSNPAYKVDFKTDKHFGKSSYSVKRNEDQIRLEIFKNGPVEGAFTVYEDFVQYKSGV
YQHVTGKALGGHAIKIFGWGVENGVKYWLIANSWNSDWGDNGTFKILRGEDHVGIESEIS
AGLPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2993.t42 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 1 | 125 | 0e+00 |
| 2 | g2993.t42 | PANTHER | PTHR12411:SF737 | CATHEPSIN B | 5 | 122 | 0e+00 |
| 3 | g2993.t42 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 5 | 122 | 0e+00 |
| 1 | g2993.t42 | Pfam | PF00112 | Papain family cysteine protease | 3 | 122 | 0e+00 |
| 5 | g2993.t42 | SMART | SM00645 | pept_c1 | 1 | 123 | 3e-07 |
| 4 | g2993.t42 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 4 | 124 | 0e+00 |
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.
