General information for g13559.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Trypsin-1.
Parent gene
- The parent gene g13559 is located on chr_1: 30920004..30920841 (- 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 | g13559 | g13559.t1 | isoform | g13559.t1 | 30920004 | 30920841 |
| chr_1 | g13559 | g13559.t1 | exon | g13559.t1.exon1 | 30920004 | 30920161 |
| chr_1 | g13559 | g13559.t1 | cds | g13559.t1.CDS1 | 30920004 | 30920161 |
| chr_1 | g13559 | g13559.t1 | exon | g13559.t1.exon2 | 30920226 | 30920841 |
| chr_1 | g13559 | g13559.t1 | cds | g13559.t1.CDS2 | 30920226 | 30920841 |
| chr_1 | g13559 | g13559.t1 | TSS | g13559.t1 | NA | NA |
| chr_1 | g13559 | g13559.t1 | TTS | g13559.t1 | NA | NA |
Sequences
>g13559.t1 Gene=g13559 Length=774
ATGAAGTTTTTATTAATTATTTTTTTCTCAATCATCTTTGTAAATGTTGAAGCGCAAAGA
AGAATTATCAATGGAACAACAATTAAACCAAGTGATGCACCTTATCAAGCAGTTTTATTA
TATCCTAATGTATCAGTAGCTTGGTGTGGTGGATCATTTCTATCAGAAAAATTTGTCATT
AGTGCTGCTCATTGTACGTTTGGAAGAGAACATAGCAAGTTTAAAATATCTGGTGGTGGC
TATTGGTTTGAGCCGTACTCAACAAAGTTTAATGTTGAAAAAATTGTCAATCATGAAAAA
TACAATGATTCAATGACCTATAATGACATTACTATTTTTATTTTAAAAACCATTAAAAAT
TTCCCTGAGAGAATTACTTTTGTGAAACTAGTAAAGAAAAATTATGAGCCAAAGAATGGT
GAATTAATGATGATAACTGGCTATGGAAAAACTGAAAAACTCTTAGATAATAATAAAGTG
CTAAAACGAGCGTTTGTTCCAATTTATAATCACCAAAAATGTGTTAAAGATTATAATCGT
ATTCTTATAGCTGGTGAAGTTACAAAAAATATGATTTGTGCTGGTTATGAAAAAGGTGAA
ATTGATTCATGTTTCGGTGACAGTGGTGGACCTTTATTACATGCCGACACAAAAGAATTA
GTTGGAATCACAAGCTGGGGTGGGATATGTGGAGGAAGATATCAACCAGGAGTTTATACA
AAAGTTTCTAAATATATTAATTGGATTGAAGATGTTATGACTAAAACGTTTTAA
>g13559.t1 Gene=g13559 Length=257
MKFLLIIFFSIIFVNVEAQRRIINGTTIKPSDAPYQAVLLYPNVSVAWCGGSFLSEKFVI
SAAHCTFGREHSKFKISGGGYWFEPYSTKFNVEKIVNHEKYNDSMTYNDITIFILKTIKN
FPERITFVKLVKKNYEPKNGELMMITGYGKTEKLLDNNKVLKRAFVPIYNHQKCVKDYNR
ILIAGEVTKNMICAGYEKGEIDSCFGDSGGPLLHADTKELVGITSWGGICGGRYQPGVYT
KVSKYINWIEDVMTKTF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13559.t1 | CDD | cd00190 | Tryp_SPc | 22 | 252 | 7.28259E-75 |
| 7 | g13559.t1 | Gene3D | G3DSA:2.40.10.10 | - | 14 | 255 | 4.3E-60 |
| 2 | g13559.t1 | PANTHER | PTHR24264 | TRYPSIN-RELATED | 16 | 254 | 2.3E-57 |
| 3 | g13559.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 50 | 65 | 3.1E-8 |
| 4 | g13559.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 201 | 213 | 3.1E-8 |
| 1 | g13559.t1 | Pfam | PF00089 | Trypsin | 22 | 249 | 6.8E-51 |
| 9 | g13559.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 10 | g13559.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 11 | g13559.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 12 | g13559.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 8 | g13559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 257 | - |
| 15 | g13559.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 60 | 65 | - |
| 16 | g13559.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 202 | 213 | - |
| 17 | g13559.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 22 | 254 | 29.027 |
| 14 | g13559.t1 | SMART | SM00020 | trypsin_2 | 21 | 249 | 8.1E-65 |
| 5 | g13559.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 15 | 254 | 2.6E-65 |
| 6 | g13559.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: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