General information for g12896.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Digestive cysteine proteinase 3.
Parent gene
- The parent gene g12896 is located on chr_1: 26772028..26773326 (- 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_1 | g12896 | g12896.t1 | isoform | g12896.t1 | 26772028 | 26773326 |
| chr_1 | g12896 | g12896.t1 | exon | g12896.t1.exon1 | 26772028 | 26772138 |
| chr_1 | g12896 | g12896.t1 | cds | g12896.t1.CDS1 | 26772028 | 26772138 |
| chr_1 | g12896 | g12896.t1 | exon | g12896.t1.exon2 | 26772217 | 26772299 |
| chr_1 | g12896 | g12896.t1 | cds | g12896.t1.CDS2 | 26772217 | 26772299 |
| chr_1 | g12896 | g12896.t1 | exon | g12896.t1.exon3 | 26772350 | 26772559 |
| chr_1 | g12896 | g12896.t1 | cds | g12896.t1.CDS3 | 26772350 | 26772559 |
| chr_1 | g12896 | g12896.t1 | exon | g12896.t1.exon4 | 26772612 | 26772749 |
| chr_1 | g12896 | g12896.t1 | cds | g12896.t1.CDS4 | 26772612 | 26772749 |
| chr_1 | g12896 | g12896.t1 | exon | g12896.t1.exon5 | 26772812 | 26773094 |
| chr_1 | g12896 | g12896.t1 | cds | g12896.t1.CDS5 | 26772812 | 26773094 |
| chr_1 | g12896 | g12896.t1 | exon | g12896.t1.exon6 | 26773153 | 26773326 |
| chr_1 | g12896 | g12896.t1 | cds | g12896.t1.CDS6 | 26773153 | 26773326 |
| chr_1 | g12896 | g12896.t1 | TSS | g12896.t1 | NA | NA |
| chr_1 | g12896 | g12896.t1 | TTS | g12896.t1 | NA | NA |
Sequences
>g12896.t1 Gene=g12896 Length=999
ATGAAAAATTTAAATTTTCTTTCCTTATTTCTTATTTCATTTCAATTAATTGAAGCTGCA
TCAAAAAATGGAGTGAGAGCAACAACAAATTCTGTAAAAAGTTATAAAAATGATTCACAT
GCAAACGTTAAATTAAAAGGTTTAAATGACCTAATGGATTTTGACACTTGGGCTAAAAAG
TATAGGAAAAATTATAAAAATTATGTCAAATCGAAAAAAGATGCAGAAAAAGCTTTTAAA
CAAAATGCAGCAAGCATTAAAGCACATAACAGTCGTAAAACTGAAACTTATGAAAGAAAA
CTTCAAGCTCATTCTGATTTGACTTATGAAGAACAAAAAATATATCGAATGGGTTTTATT
GATGTTAGTGAAAGTGAAAATTCAACAATTCCTGACTTTAGTTCAAAAAAAACTTACACT
AAAGTCAATTATACAAAATTGTTTCCGCCAGCTAAAGATCAAGGATTATGCGGTTGCTGT
TTTATTTTTGCTACAGTTTCAATTCTTGAATATATATCAAGAATAAATGGTGACAATGAT
ATTTATTCAGAACAAGATTTACTTGATTGTGATACTTTAGACACTGGTTGTGATGGTGGT
TGGTTAGGAAATGCATTTCGTTATGTAAGAGATAAAGGAATTTCAAATGGATTAGTTTAT
CCTTATGAAGGATGGAATAACACGTGCAGAAAATATTTATATCCCTCAATCTTCAGTATT
GGTGAAGTGTGTACATATAGCTTAAATGGAAATGAAATTCTTTTGCAGGCACTTATTGAT
CAAGGACCTGTTGCTGGTGCAATTGCATTAACTGATGGGTTTACAAGTTATAGTAGTGGC
GTATTTTATGATAAAAATTGTTCTTCAACTGTTTTGGATCATGCAATTACAATTGTAGGC
TATGGAACTGACCTAAAGGGAGGAGACTTTTGGTTAATAAGAAATTCATGGGGGACTGAC
TGGGGTTTGAATGGTGATCTTAAAAAAAGTTTCCAGTAA
>g12896.t1 Gene=g12896 Length=332
MKNLNFLSLFLISFQLIEAASKNGVRATTNSVKSYKNDSHANVKLKGLNDLMDFDTWAKK
YRKNYKNYVKSKKDAEKAFKQNAASIKAHNSRKTETYERKLQAHSDLTYEEQKIYRMGFI
DVSESENSTIPDFSSKKTYTKVNYTKLFPPAKDQGLCGCCFIFATVSILEYISRINGDND
IYSEQDLLDCDTLDTGCDGGWLGNAFRYVRDKGISNGLVYPYEGWNNTCRKYLYPSIFSI
GEVCTYSLNGNEILLQALIDQGPVAGAIALTDGFTSYSSGVFYDKNCSSTVLDHAITIVG
YGTDLKGGDFWLIRNSWGTDWGLNGDLKKSFQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g12896.t1 | CDD | cd02248 | Peptidase_C1A | 150 | 325 | 2.79438E-66 |
| 12 | g12896.t1 | Coils | Coil | Coil | 58 | 78 | - |
| 11 | g12896.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 51 | 332 | 1.1E-67 |
| 3 | g12896.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 46 | 327 | 8.5E-46 |
| 4 | g12896.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 46 | 327 | 8.5E-46 |
| 5 | g12896.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 154 | 169 | 1.3E-6 |
| 7 | g12896.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 294 | 304 | 1.3E-6 |
| 6 | g12896.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 310 | 316 | 1.3E-6 |
| 1 | g12896.t1 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 54 | 111 | 1.9E-6 |
| 2 | g12896.t1 | Pfam | PF00112 | Papain family cysteine protease | 148 | 325 | 3.4E-47 |
| 14 | g12896.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 15 | g12896.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 16 | g12896.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 14 | - |
| 17 | g12896.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 13 | g12896.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 332 | - |
| 20 | g12896.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 292 | 302 | - |
| 19 | g12896.t1 | SMART | SM00645 | pept_c1 | 138 | 331 | 2.0E-41 |
| 8 | g12896.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 49 | 325 | 7.12E-69 |
| 10 | g12896.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 9 | g12896.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
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. There were no conditions that were differentially expressed