General information for g2993.t38
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.t38 | TTS | g2993.t38 | 21867629 | 21867629 |
| chr_3 | g2993 | g2993.t38 | isoform | g2993.t38 | 21867833 | 21869132 |
| chr_3 | g2993 | g2993.t38 | exon | g2993.t38.exon1 | 21867833 | 21867921 |
| chr_3 | g2993 | g2993.t38 | cds | g2993.t38.CDS1 | 21867833 | 21867921 |
| chr_3 | g2993 | g2993.t38 | exon | g2993.t38.exon2 | 21867986 | 21868411 |
| chr_3 | g2993 | g2993.t38 | cds | g2993.t38.CDS2 | 21867986 | 21868411 |
| chr_3 | g2993 | g2993.t38 | exon | g2993.t38.exon3 | 21868542 | 21868694 |
| chr_3 | g2993 | g2993.t38 | cds | g2993.t38.CDS3 | 21868542 | 21868694 |
| chr_3 | g2993 | g2993.t38 | exon | g2993.t38.exon4 | 21868752 | 21868992 |
| chr_3 | g2993 | g2993.t38 | cds | g2993.t38.CDS4 | 21868752 | 21868992 |
| chr_3 | g2993 | g2993.t38 | exon | g2993.t38.exon5 | 21869064 | 21869132 |
| chr_3 | g2993 | g2993.t38 | cds | g2993.t38.CDS5 | 21869064 | 21869132 |
| chr_3 | g2993 | g2993.t38 | TSS | g2993.t38 | 21869220 | 21869220 |
Sequences
>g2993.t38 Gene=g2993 Length=978
ATGAAATATTTCATATTATTTGCTGCATTGACAGCAGTTTGCTTTGGAGCTGACATTTTT
TCTGATGAATTCATCAATGAAATTAATAAAAAAGCAACAACATGGAAGGCTGGCCATAAT
TTTCATCCAGATACTAATTTGAAATATATCAAGAATTTACTTGGTGTTCATTCCGATTCT
AAGCATTTTAAACTACCTGAGTTATTGCATGACTCACGGGACATAAAAGATTTACCTGAA
AATTTTGATGCTCGTGAACAATGGCCTGATTGTCCAACATTGAGAGAAATAAGAGATCAA
GGAAGTTGTGGATCTTGTTGGGCTTTTGGCGCTGTTGAGGCAATGAGTGACAGAGTATGC
ATTCATAGCAACGCAACTGAACATTTCCACTTTTCTGCTGAACATTTGGTTTCTTGCTGT
CACACTTGTGGATTTGGTTGCAATGGTGGCTTTCCAGGATCAGGTAAAAAATTCATTGTT
AAATATTTTTTATTGTTTAAAATTTTATCCTTATTGCAGCCATATGAAATCGCTCCTTGT
GAACATCATGTCAATGGAACTCGTATGCCATGCTCTGGAGAAGGACATACACCAAAATGC
ATGAATAAATGCTCGAATCCCGCTTATAAAGTTGATTTCAAAACAGACAAACACTTTGGC
AAATCAAGCTATTCAGTAAAGCGTAATGAAGATCAAATTCGTTTGGAAATTTTCAAAAAT
GGTCCAGTTGAAGGTGCATTCACAGTCTATGAAGATTTCGTTCAATATAAATCTGGAGTT
TATCAACATGTTACTGGTAAAGCACTTGGTGGCCATGCTATTAAAATTTTCGGATGGGGA
GTTGAAAATGGTGTCAAATACTGGTTGATTGCTAATAGCTGGAATTCAGATTGGGGTGAT
AATGGAACCTTCAAAATATTGCGAGGAGAAGACCATGTCGGTATTGAGAGTGAGATTAGC
GCTGGTTTGCCAAAGTAA
>g2993.t38 Gene=g2993 Length=325
MKYFILFAALTAVCFGADIFSDEFINEINKKATTWKAGHNFHPDTNLKYIKNLLGVHSDS
KHFKLPELLHDSRDIKDLPENFDAREQWPDCPTLREIRDQGSCGSCWAFGAVEAMSDRVC
IHSNATEHFHFSAEHLVSCCHTCGFGCNGGFPGSGKKFIVKYFLLFKILSLLQPYEIAPC
EHHVNGTRMPCSGEGHTPKCMNKCSNPAYKVDFKTDKHFGKSSYSVKRNEDQIRLEIFKN
GPVEGAFTVYEDFVQYKSGVYQHVTGKALGGHAIKIFGWGVENGVKYWLIANSWNSDWGD
NGTFKILRGEDHVGIESEISAGLPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g2993.t38 | CDD | cd02620 | Peptidase_C1A_CathepsinB | 79 | 322 | 8.47284E-140 |
| 10 | g2993.t38 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 16 | 325 | 1.2E-104 |
| 3 | g2993.t38 | PANTHER | PTHR12411:SF737 | CATHEPSIN B | 13 | 322 | 2.0E-90 |
| 4 | g2993.t38 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 13 | 322 | 2.0E-90 |
| 5 | g2993.t38 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 100 | 115 | 2.6E-8 |
| 7 | g2993.t38 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 272 | 282 | 2.6E-8 |
| 6 | g2993.t38 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 287 | 293 | 2.6E-8 |
| 1 | g2993.t38 | Pfam | PF08127 | Peptidase family C1 propeptide | 20 | 59 | 9.0E-19 |
| 2 | g2993.t38 | Pfam | PF00112 | Papain family cysteine protease | 78 | 322 | 2.8E-59 |
| 12 | g2993.t38 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 13 | g2993.t38 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g2993.t38 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 15 | g2993.t38 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 11 | g2993.t38 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 325 | - |
| 17 | g2993.t38 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 100 | 111 | - |
| 18 | g2993.t38 | SMART | SM00645 | pept_c1 | 78 | 323 | 6.8E-88 |
| 8 | g2993.t38 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 21 | 324 | 1.22E-94 |
| 9 | g2993.t38 | 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 K01275 (cathepsin C)
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