General information for g17229.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cysteine proteinase 3.
Parent gene
- The parent gene g17229 is located on chr_4: 12885678..12887768 (+ 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 | g17229 | g17229.t1 | TSS | g17229.t1 | 12885072 | 12885072 |
| chr_4 | g17229 | g17229.t1 | isoform | g17229.t1 | 12885103 | 12886759 |
| chr_4 | g17229 | g17229.t1 | exon | g17229.t1.exon1 | 12885103 | 12885430 |
| chr_4 | g17229 | g17229.t1 | cds | g17229.t1.CDS1 | 12885103 | 12885430 |
| chr_4 | g17229 | g17229.t1 | exon | g17229.t1.exon2 | 12885550 | 12885678 |
| chr_4 | g17229 | g17229.t1 | cds | g17229.t1.CDS2 | 12885550 | 12885678 |
| chr_4 | g17229 | g17229.t1 | exon | g17229.t1.exon3 | 12885947 | 12886068 |
| chr_4 | g17229 | g17229.t1 | cds | g17229.t1.CDS3 | 12885947 | 12886068 |
| chr_4 | g17229 | g17229.t1 | exon | g17229.t1.exon4 | 12886267 | 12886624 |
| chr_4 | g17229 | g17229.t1 | cds | g17229.t1.CDS4 | 12886267 | 12886624 |
| chr_4 | g17229 | g17229.t1 | exon | g17229.t1.exon5 | 12886683 | 12886759 |
| chr_4 | g17229 | g17229.t1 | cds | g17229.t1.CDS5 | 12886683 | 12886759 |
| chr_4 | g17229 | g17229.t1 | TTS | g17229.t1 | 12886793 | 12886793 |
Sequences
>g17229.t1 Gene=g17229 Length=1014
ATGGATTTTAAAATTTTCTTAATTTTTCTTGGAATTTTTTGTGAAATTTTTGCTAAAATT
GAATTAAGTAAAGAAGATGAAGAAAGAATTTTTGAAGAATATGCAGCAAGATATAATTTG
AGAAGAGGAAGAACAAATGAAGTTGATGAAATGAAGAAAAATGTGCTGAGAAGGTATAAA
AATATTTTACAGCACAATGAACTTTATGGAAAAGGTGCAAGCAGTTTTTTGGAGACTTTG
AATGAATTTTCTTACAAAAGTAATGAAGAATTGAAAAAAACTTCTTTAGGATTTAAAGGA
AATGCAAGTTCAAATTTTAATGATGGAGGGATAAAAGTTCCAATATTAGAAAGAAATGCT
CGAAGTTCTCTACCATCATATTTTAATTGGGCTGATCATGGCATTGTGAGACCTGTTCAA
AATCAACATTCTTGTAATGCTTGCTATGCTTTTGCTGCAATAGGAGCAATTGAAGGAGCT
GCATGTAAAAATCTTGGTCAATGTTCAAAATTGTCTGAACAAGAAGCAATGGAGTGCACA
AATGGATGTGATTCTGGATGGGATTATGAAGTTTATCAGTATTCAACTCTAAATTATGGC
TGCACATCAGCTGCCTACCCATATTATGCAAGAAACATGGCACATTGTACTGCAGCAAGA
TCACGAAAGCGTGTTGCAAATACACGAGTGACAGGATGGCATAATTTGCCACCAGATGCT
GAAACAATTCGTTATCATTTATTCCATTCAGGTCCAATTTCCATGTCTTTTTATGTTTAT
GAAAATTTCTTCAGTTATTATTCTGGAATTTATTCATCAACTGAAGGAAGTGACTTAATG
GGTGGTCATGCTGTATTACTGACTGGTTATGGAACTGAAAATGGAATTGATTATTGGATT
TTAAGAAATTCATGGGGCGACGACTGGGGCGAAAAAGGTTATTTTAGAATTAGAAGGGGA
ATAAATTTATGTAATTGTGAAAGCTGGAAAGTTTCTTATCCTATTGTTGCTTAA
>g17229.t1 Gene=g17229 Length=337
MDFKIFLIFLGIFCEIFAKIELSKEDEERIFEEYAARYNLRRGRTNEVDEMKKNVLRRYK
NILQHNELYGKGASSFLETLNEFSYKSNEELKKTSLGFKGNASSNFNDGGIKVPILERNA
RSSLPSYFNWADHGIVRPVQNQHSCNACYAFAAIGAIEGAACKNLGQCSKLSEQEAMECT
NGCDSGWDYEVYQYSTLNYGCTSAAYPYYARNMAHCTAARSRKRVANTRVTGWHNLPPDA
ETIRYHLFHSGPISMSFYVYENFFSYYSGIYSSTEGSDLMGGHAVLLTGYGTENGIDYWI
LRNSWGDDWGEKGYFRIRRGINLCNCESWKVSYPIVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g17229.t1 | CDD | cd02248 | Peptidase_C1A | 125 | 334 | 6.63134E-64 |
| 9 | g17229.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 28 | 337 | 5.4E-77 |
| 2 | g17229.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 17 | 325 | 6.7E-47 |
| 3 | g17229.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 17 | 325 | 6.7E-47 |
| 6 | g17229.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 142 | 157 | 5.7E-7 |
| 5 | g17229.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 283 | 293 | 5.7E-7 |
| 4 | g17229.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 298 | 304 | 5.7E-7 |
| 1 | g17229.t1 | Pfam | PF00112 | Papain family cysteine protease | 124 | 329 | 4.8E-55 |
| 11 | g17229.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 12 | g17229.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 13 | g17229.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 13 | - |
| 14 | g17229.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 10 | g17229.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 337 | - |
| 17 | g17229.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 281 | 291 | - |
| 16 | g17229.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 298 | 317 | - |
| 18 | g17229.t1 | SMART | SM00645 | pept_c1 | 124 | 335 | 3.8E-64 |
| 7 | g17229.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 26 | 330 | 2.46E-73 |
| 8 | g17229.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