General information for g4559.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 g4559 is located on chr_2: 3237898..3240235 (+ 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_2 | g4559 | g4559.t1 | TSS | g4559.t1 | 3236817 | 3236817 |
| chr_2 | g4559 | g4559.t1 | isoform | g4559.t1 | 3236844 | 3237898 |
| chr_2 | g4559 | g4559.t1 | exon | g4559.t1.exon1 | 3236844 | 3237048 |
| chr_2 | g4559 | g4559.t1 | cds | g4559.t1.CDS1 | 3236844 | 3237048 |
| chr_2 | g4559 | g4559.t1 | exon | g4559.t1.exon2 | 3237108 | 3237140 |
| chr_2 | g4559 | g4559.t1 | cds | g4559.t1.CDS2 | 3237108 | 3237140 |
| chr_2 | g4559 | g4559.t1 | exon | g4559.t1.exon3 | 3237202 | 3237539 |
| chr_2 | g4559 | g4559.t1 | cds | g4559.t1.CDS3 | 3237202 | 3237539 |
| chr_2 | g4559 | g4559.t1 | exon | g4559.t1.exon4 | 3237596 | 3237635 |
| chr_2 | g4559 | g4559.t1 | cds | g4559.t1.CDS4 | 3237596 | 3237635 |
| chr_2 | g4559 | g4559.t1 | exon | g4559.t1.exon5 | 3237687 | 3237782 |
| chr_2 | g4559 | g4559.t1 | cds | g4559.t1.CDS5 | 3237687 | 3237782 |
| chr_2 | g4559 | g4559.t1 | exon | g4559.t1.exon6 | 3237840 | 3237898 |
| chr_2 | g4559 | g4559.t1 | cds | g4559.t1.CDS6 | 3237840 | 3237898 |
| chr_2 | g4559 | g4559.t1 | TTS | g4559.t1 | 3238027 | 3238027 |
Sequences
>g4559.t1 Gene=g4559 Length=771
ATGAAATTTTTCAAGCTTTTAATTTTAATTTTATCAGTTTTTAAATTTAGTAAAGCTAGA
GAAAGATCGACTGATGGTAGAATTGTAGGTGGAAAAGAAATTGATATTGAAACAGCTCCT
TTTCAAGTCGGATTATTATTATATGGAGGACATATATGTGGTGGAAGTATTTTGTCGTGT
AAATATGTTTTGACTGCTTCACATTGCATTGAAACTTATACACCATCAATATATAGTGTT
CGTGCAGGTTCTTCAATGAGAGAATCAGGTGGTTCAATACATGATGTCAGTAGAATTGAC
ATTCATCCACTTTGGAATCCAAATTTATATGATTATGATGCTGCTATTTTGACATTAAGA
AATCTTATTAGATATGATGCATCACGACAAGCAATTCAATTACCTTTTTTGAATGAAGTA
ATTTTTGTTGGTACTGATGTTGCTACATCTGGCTGGGGACTGACACAGAATGATAATGAA
TCCAGAGATAATTTGCGAATGGTTGAATTGAAAGTTGTAAATCAAATTTTATGCAATAAT
GCTCATTTAAAAGATGGTGGTGTAACATTGAGAATGGTTTGTGCTGCTGCTGATAATAAA
GATAGCTGCAATGGAGATAGCGGCGGACCTCTATGGAACATAAGAACAAGAAGACTTATC
GGAATCGTTTCATTTGGTCAAGATACTGGATGCGCTATAAACGGAATCCCAGGTGTTTAC
ACAAGAGTTGCTGCAATAAGACCTTGGATAAGAACGATTGTGGGTTTTTAA
>g4559.t1 Gene=g4559 Length=256
MKFFKLLILILSVFKFSKARERSTDGRIVGGKEIDIETAPFQVGLLLYGGHICGGSILSC
KYVLTASHCIETYTPSIYSVRAGSSMRESGGSIHDVSRIDIHPLWNPNLYDYDAAILTLR
NLIRYDASRQAIQLPFLNEVIFVGTDVATSGWGLTQNDNESRDNLRMVELKVVNQILCNN
AHLKDGGVTLRMVCAAADNKDSCNGDSGGPLWNIRTRRLIGIVSFGQDTGCAINGIPGVY
TRVAAIRPWIRTIVGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g4559.t1 | CDD | cd00190 | Tryp_SPc | 28 | 253 | 1.27956E-74 |
| 9 | g4559.t1 | Gene3D | G3DSA:2.40.10.10 | - | 21 | 254 | 1.1E-58 |
| 2 | g4559.t1 | PANTHER | PTHR24276 | POLYSERASE-RELATED | 16 | 252 | 1.6E-69 |
| 3 | g4559.t1 | PANTHER | PTHR24276:SF83 | GH13245P2-RELATED | 16 | 252 | 1.6E-69 |
| 6 | g4559.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 54 | 69 | 9.9E-11 |
| 5 | g4559.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 109 | 123 | 9.9E-11 |
| 4 | g4559.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 200 | 212 | 9.9E-11 |
| 1 | g4559.t1 | Pfam | PF00089 | Trypsin | 28 | 250 | 6.9E-52 |
| 11 | g4559.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 12 | g4559.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 13 | g4559.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 14 | - |
| 14 | g4559.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 10 | g4559.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 256 | - |
| 17 | g4559.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 64 | 69 | - |
| 18 | g4559.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 28 | 255 | 29.211 |
| 16 | g4559.t1 | SMART | SM00020 | trypsin_2 | 27 | 250 | 7.5E-63 |
| 7 | g4559.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 9 | 255 | 8.07E-68 |
| 8 | g4559.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
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