General information for g15800.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Fruit bromelain.
Parent gene
- The parent gene g15800 is located on chr_4: 6805508..6806890 (- 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_4 | g15800 | g15800.t1 | isoform | g15800.t1 | 6805508 | 6806890 |
| chr_4 | g15800 | g15800.t1 | exon | g15800.t1.exon1 | 6805508 | 6805605 |
| chr_4 | g15800 | g15800.t1 | cds | g15800.t1.CDS1 | 6805508 | 6805605 |
| chr_4 | g15800 | g15800.t1 | exon | g15800.t1.exon2 | 6805733 | 6806631 |
| chr_4 | g15800 | g15800.t1 | cds | g15800.t1.CDS2 | 6805733 | 6806631 |
| chr_4 | g15800 | g15800.t1 | exon | g15800.t1.exon3 | 6806883 | 6806890 |
| chr_4 | g15800 | g15800.t1 | cds | g15800.t1.CDS3 | 6806883 | 6806890 |
| chr_4 | g15800 | g15800.t1 | TSS | g15800.t1 | NA | NA |
| chr_4 | g15800 | g15800.t1 | TTS | g15800.t1 | NA | NA |
Sequences
>g15800.t1 Gene=g15800 Length=1005
ATGTTGAAATACACTCTAATTTTCATAATAGCTGCACTATCAGCAGTCTTATGTCAACAA
GACCAAAAAACTCTCATTGAAGAGGAGAAAATTTTCAATGCATGGCTCAAACGTCATGGT
ATTGATGTCCCAGCTGATGCTGATTTTAACAAATGGAAAGCTAATGTAATTGCCAAATTT
CGTGAGCATGAAAAACACAATGAAAAATATCGTAAAGGTGAAGAACTTTTTATGCGTGGA
ATCAATCATTTATCACATCTTTCAAATGAGGAACTTAAAGCTACTGTTCTTGGATTTTCT
GCACCAACTGCTGATGACACATTACCTGTTGTTTCTAAAGATGCATTAAAAGATTTACCT
GACTATTTTAACTGGCATGATAAAGGAATCGTTCAACCACCACAAGATCAAAAACAATGC
GGAAGTTGCTATATTTTCAGTACCATTGGTGCTATTGAAGCTCATTCATGTTATTACAAT
CATCAATGTGAAAAACTTTCAGAGCAAGAAGCTCTTGAATGCTCAGATGGTCGTGGTTGT
AATGGTGGTTGGTCACAACTTATTTACAAATACACACAATCTAAAAATGGTGCAACTGCC
TTAAAAAATTATGGCTATCAAGCTAAAGTTGTTAATAAATGTGAAGATGCAGGATCAAGA
CCTCGAGTTAATGGAACAACTGTTGTTGGATGGAAAACTTTACCAAAACATGCTGACACA
ATAAAATTTTACTTATACTCCAATGGACCAATGTTTGTGGGCTTCGATGTTTATCAAAAT
TTTGTTGATTACAAAAGTGGAATTTATCACAATATCAGTGGTGATAAACTTGGAGGTCAT
GCTGTACTTTTGATTGGTTATGGAACTGAGAATGGTGTTGACTATTGGATTTTGAAAAAT
AGTTGGACAACCAACTGGGGTGAAAGTGGTTTCTTCCGTTTCAAACGTGGAGTTGATCTT
TGTGGAATCGAATCTGGTGGACCAACTTATCCAATCATGTCTTAA
>g15800.t1 Gene=g15800 Length=334
MLKYTLIFIIAALSAVLCQQDQKTLIEEEKIFNAWLKRHGIDVPADADFNKWKANVIAKF
REHEKHNEKYRKGEELFMRGINHLSHLSNEELKATVLGFSAPTADDTLPVVSKDALKDLP
DYFNWHDKGIVQPPQDQKQCGSCYIFSTIGAIEAHSCYYNHQCEKLSEQEALECSDGRGC
NGGWSQLIYKYTQSKNGATALKNYGYQAKVVNKCEDAGSRPRVNGTTVVGWKTLPKHADT
IKFYLYSNGPMFVGFDVYQNFVDYKSGIYHNISGDKLGGHAVLLIGYGTENGVDYWILKN
SWTTNWGESGFFRFKRGVDLCGIESGGPTYPIMS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g15800.t1 | CDD | cd02248 | Peptidase_C1A | 120 | 331 | 2.03768E-71 |
| 9 | g15800.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 26 | 332 | 1.6E-79 |
| 2 | g15800.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 24 | 324 | 9.9E-49 |
| 3 | g15800.t1 | PANTHER | PTHR12411:SF586 | CATHEPSIN L,-LIKE-RELATED | 24 | 324 | 9.9E-49 |
| 6 | g15800.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 137 | 152 | 1.2E-8 |
| 5 | g15800.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 280 | 290 | 1.2E-8 |
| 4 | g15800.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 295 | 301 | 1.2E-8 |
| 1 | g15800.t1 | Pfam | PF00112 | Papain family cysteine protease | 119 | 325 | 6.0E-57 |
| 11 | g15800.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 12 | g15800.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 13 | g15800.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 13 | - |
| 14 | g15800.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 10 | g15800.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 334 | - |
| 18 | g15800.t1 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 137 | 148 | - |
| 17 | g15800.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 278 | 288 | - |
| 16 | g15800.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 295 | 314 | - |
| 19 | g15800.t1 | SMART | SM00645 | pept_c1 | 119 | 332 | 2.1E-58 |
| 7 | g15800.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 30 | 330 | 7.72E-76 |
| 8 | g15800.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
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 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