General information for g2993.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t28 | TTS | g2993.t28 | 21867629 | 21867629 |
| chr_3 | g2993 | g2993.t28 | isoform | g2993.t28 | 21867833 | 21869132 |
| chr_3 | g2993 | g2993.t28 | exon | g2993.t28.exon1 | 21867833 | 21867921 |
| chr_3 | g2993 | g2993.t28 | cds | g2993.t28.CDS1 | 21867833 | 21867921 |
| chr_3 | g2993 | g2993.t28 | exon | g2993.t28.exon2 | 21867986 | 21868355 |
| chr_3 | g2993 | g2993.t28 | cds | g2993.t28.CDS2 | 21867986 | 21868355 |
| chr_3 | g2993 | g2993.t28 | exon | g2993.t28.exon3 | 21868412 | 21868479 |
| chr_3 | g2993 | g2993.t28 | cds | g2993.t28.CDS3 | 21868412 | 21868479 |
| chr_3 | g2993 | g2993.t28 | exon | g2993.t28.exon4 | 21868542 | 21868697 |
| chr_3 | g2993 | g2993.t28 | cds | g2993.t28.CDS4 | 21868542 | 21868697 |
| chr_3 | g2993 | g2993.t28 | exon | g2993.t28.exon5 | 21868752 | 21868992 |
| chr_3 | g2993 | g2993.t28 | cds | g2993.t28.CDS5 | 21868752 | 21868992 |
| chr_3 | g2993 | g2993.t28 | exon | g2993.t28.exon6 | 21869064 | 21869132 |
| chr_3 | g2993 | g2993.t28 | cds | g2993.t28.CDS6 | 21869064 | 21869132 |
| chr_3 | g2993 | g2993.t28 | TSS | g2993.t28 | 21869220 | 21869220 |
Sequences
>g2993.t28 Gene=g2993 Length=993
ATGAAATATTTCATATTATTTGCTGCATTGACAGCAGTTTGCTTTGGAGCTGACATTTTT
TCTGATGAATTCATCAATGAAATTAATAAAAAAGCAACAACATGGAAGGCTGGCCATAAT
TTTCATCCAGATACTAATTTGAAATATATCAAGAATTTACTTGGTGTTCATTCCGATTCT
AAGCATTTTAAACTACCTGAGTTATTGCATGACTCACGGGACATAAAAGATTTACCTGAA
AATTTTGATGCTCGTGAACAATGGCCTGATTGTCCAACATTGAGAGAAATAAGAGATCAA
GGAAGTTGTGAAGGATCTTGTTGGGCTTTTGGCGCTGTTGAGGCAATGAGTGACAGAGTA
TGCATTCATAGCAACGCAACTGAACATTTCCACTTTTCTGCTGAACATTTGGTTTCTTGC
TGTCACACTTGTGGATTTGGTTGCAATGGTGGCTTTCCAGGATCAGCTTGGAGCTATTGG
GTTAGAAAAGGTATTGTTAGTGGTGGACCATACAATTCTTCAATTGGATGTCAGCCATAT
GAAATCGCTCCTTGTGAACATCATGTCAATGGAACTCGTATGCCATGCTCTGGAGAAGGA
CATACACCAAAATGCATGAATAAATGCTCGAATCCCGCTTATAAAGTTGATTTCAAAACA
GACAAACACTTTGGCAAATCAAGCTATTCAGTAAAGCGTAATGAAGATCAAATTCGTTTG
GAAATTTTCAAAAATGGTCCAGTTGAAGGTGCATTCACAGTCTATGAAGATTTCGTTCAA
TATAAATCTGGAGTTTATCAACATGTTACTGGTAAAGCACTTGGTGGCCATGCTATTAAA
ATTTTCGGATGGGGAGTTGAAAATGGTGTCAAATACTGGTTGATTGCTAATAGCTGGAAT
TCAGATTGGGGTGATAATGGAACCTTCAAAATATTGCGAGGAGAAGACCATGTCGGTATT
GAGAGTGAGATTAGCGCTGGTTTGCCAAAGTAA
>g2993.t28 Gene=g2993 Length=330
MKYFILFAALTAVCFGADIFSDEFINEINKKATTWKAGHNFHPDTNLKYIKNLLGVHSDS
KHFKLPELLHDSRDIKDLPENFDAREQWPDCPTLREIRDQGSCEGSCWAFGAVEAMSDRV
CIHSNATEHFHFSAEHLVSCCHTCGFGCNGGFPGSAWSYWVRKGIVSGGPYNSSIGCQPY
EIAPCEHHVNGTRMPCSGEGHTPKCMNKCSNPAYKVDFKTDKHFGKSSYSVKRNEDQIRL
EIFKNGPVEGAFTVYEDFVQYKSGVYQHVTGKALGGHAIKIFGWGVENGVKYWLIANSWN
SDWGDNGTFKILRGEDHVGIESEISAGLPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2993.t28 | CDD | cd02620 | Peptidase_C1A_CathepsinB | 79 | 327 | 7.33339E-148 |
| 7 | g2993.t28 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 16 | 330 | 1.5E-112 |
| 3 | g2993.t28 | PANTHER | PTHR12411:SF737 | CATHEPSIN B | 13 | 327 | 3.4E-102 |
| 4 | g2993.t28 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 13 | 327 | 3.4E-102 |
| 1 | g2993.t28 | Pfam | PF08127 | Peptidase family C1 propeptide | 20 | 59 | 9.2E-19 |
| 2 | g2993.t28 | Pfam | PF00112 | Papain family cysteine protease | 78 | 327 | 2.9E-62 |
| 9 | g2993.t28 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 10 | g2993.t28 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 11 | g2993.t28 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 12 | g2993.t28 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 8 | g2993.t28 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 330 | - |
| 14 | g2993.t28 | SMART | SM00645 | pept_c1 | 78 | 328 | 2.4E-90 |
| 5 | g2993.t28 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 21 | 329 | 3.73E-100 |
| 6 | g2993.t28 | 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.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008234 | cysteine-type peptidase activity | MF |
| GO:0006508 | proteolysis | BP |
| GO:0004197 | cysteine-type endopeptidase activity | MF |
| GO:0050790 | regulation of catalytic activity | BP |
KEGG
Orthology
- This transcript has been annotated with K01363 (cathepsin B)
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.
