General information for g17225.t19
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Trypsin-4.
Parent gene
- The parent gene g17225 is located on chr_4: 12874617..12876909 (- 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 | g17225 | g17225.t19 | TTS | g17225.t19 | 12873922 | 12873922 |
| chr_4 | g17225 | g17225.t19 | isoform | g17225.t19 | 12874617 | 12876909 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon1 | 12874617 | 12874699 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS1 | 12874672 | 12874699 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon2 | 12874821 | 12874862 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS2 | 12874821 | 12874862 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon3 | 12874924 | 12874941 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS3 | 12874924 | 12874941 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon4 | 12875005 | 12875164 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS4 | 12875005 | 12875164 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon5 | 12875221 | 12875466 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS5 | 12875221 | 12875466 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon6 | 12875681 | 12875773 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS6 | 12875681 | 12875773 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon7 | 12875828 | 12875905 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS7 | 12875828 | 12875905 |
| chr_4 | g17225 | g17225.t19 | exon | g17225.t19.exon8 | 12876855 | 12876909 |
| chr_4 | g17225 | g17225.t19 | cds | g17225.t19.CDS8 | 12876855 | 12876909 |
| chr_4 | g17225 | g17225.t19 | TSS | g17225.t19 | 12876927 | 12876927 |
Sequences
>g17225.t19 Gene=g17225 Length=775
ATGTTTCAAGTCACTGTTGCCTGTTTAACTTTGATTTTATTAGCAAGTGGAGCTAATGTT
CCTGATGCAACGACAAATGATGAATTCCAAATGTGGGAAGGAAGAATTGTTGGTGGATCA
CAAGCTCAATTAGGTCAATTTCCATATCAAGTCTCGTTGAGAACAATTCAAAATAGTCAT
TTTTGTGGTGGATTCATTCTTAGTAATCGTTGGATTGGATCAGCTGCACATTGCACAACA
CCTCGATCAACATCAAACACACGTGCAGTTGTTGGCACAATTCATCGTTCAACAGGCGGA
AACATTCACAATCTTGCTCGTTTTGTTAATCATCCAGGTTATCAATCAACAACCCTTGCC
AATGATATTTCACTTATTCAAACTGTCAATACAATTACTTTTAACAACATGGTGCAACCT
GTTGGTGTATCATCGACTTTTATTAATGGTGGTGTTAATGCTGTTGCTACAGGTTGGGGA
CAAACCAGCAGGACAGGACCAACTTCAAATGTTCTTCTTTGGGTGACTTTAAGGACATTA
AATAACAATGAATGCAGAGAAAAATTCACAAAATCAAATGCTGCAAGAATTACTGATCAA
ACAATTTGTACATTTACAAGAGTTGGTCAAGGAACTTGCATGGGTGATAGCGGTGGTCCT
TTAGTAGCTGGTGGTAATGTCATTGGAGGTAAGAATTCCATGTGCTTCCGGATCACCTGA
TGTTTATGTCAGAATTGCATCATATCGATCATGGATTATGAATACCATCGGATAA
>g17225.t19 Gene=g17225 Length=239
MFQVTVACLTLILLASGANVPDATTNDEFQMWEGRIVGGSQAQLGQFPYQVSLRTIQNSH
FCGGFILSNRWIGSAAHCTTPRSTSNTRAVVGTIHRSTGGNIHNLARFVNHPGYQSTTLA
NDISLIQTVNTITFNNMVQPVGVSSTFINGGVNAVATGWGQTSRTGPTSNVLLWVTLRTL
NNNECREKFTKSNAARITDQTICTFTRVGQGTCMGDSGGPLVAGGNVIGGKNSMCFRIT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g17225.t19 | CDD | cd00190 | Tryp_SPc | 36 | 229 | 9.23075E-60 |
| 10 | g17225.t19 | Gene3D | G3DSA:2.40.10.10 | - | 37 | 229 | 2.1E-49 |
| 11 | g17225.t19 | Gene3D | G3DSA:2.40.10.10 | - | 48 | 140 | 2.1E-49 |
| 2 | g17225.t19 | PANTHER | PTHR24276 | POLYSERASE-RELATED | 28 | 229 | 9.7E-47 |
| 3 | g17225.t19 | PANTHER | PTHR24276:SF83 | GH13245P2-RELATED | 28 | 229 | 9.7E-47 |
| 6 | g17225.t19 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 63 | 78 | 1.5E-11 |
| 5 | g17225.t19 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 118 | 132 | 1.5E-11 |
| 4 | g17225.t19 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 210 | 222 | 1.5E-11 |
| 1 | g17225.t19 | Pfam | PF00089 | Trypsin | 36 | 229 | 2.0E-43 |
| 13 | g17225.t19 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 14 | g17225.t19 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 15 | g17225.t19 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 16 | g17225.t19 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 17 | - |
| 12 | g17225.t19 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 239 | - |
| 20 | g17225.t19 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 211 | 222 | - |
| 21 | g17225.t19 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 36 | 239 | 23.675 |
| 19 | g17225.t19 | SMART | SM00020 | trypsin_2 | 35 | 238 | 2.2E-40 |
| 7 | g17225.t19 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 3 | 225 | 1.05E-55 |
| 9 | g17225.t19 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 18 | g17225.t19 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 8 | g17225.t19 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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:0004252 | serine-type endopeptidase 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