General information for g4558.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Trypsin-3.
Parent gene
- The parent gene g4558 is located on chr_2: 3235587..3236652 (+ 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 | g4558 | g4558.t1 | TSS | g4558.t1 | 3235559 | 3235559 |
| chr_2 | g4558 | g4558.t1 | isoform | g4558.t1 | 3235587 | 3236652 |
| chr_2 | g4558 | g4558.t1 | exon | g4558.t1.exon1 | 3235587 | 3235800 |
| chr_2 | g4558 | g4558.t1 | cds | g4558.t1.CDS1 | 3235587 | 3235800 |
| chr_2 | g4558 | g4558.t1 | exon | g4558.t1.exon2 | 3235855 | 3235890 |
| chr_2 | g4558 | g4558.t1 | cds | g4558.t1.CDS2 | 3235855 | 3235890 |
| chr_2 | g4558 | g4558.t1 | exon | g4558.t1.exon3 | 3235942 | 3236279 |
| chr_2 | g4558 | g4558.t1 | cds | g4558.t1.CDS3 | 3235942 | 3236279 |
| chr_2 | g4558 | g4558.t1 | exon | g4558.t1.exon4 | 3236338 | 3236377 |
| chr_2 | g4558 | g4558.t1 | cds | g4558.t1.CDS4 | 3236338 | 3236377 |
| chr_2 | g4558 | g4558.t1 | exon | g4558.t1.exon5 | 3236438 | 3236533 |
| chr_2 | g4558 | g4558.t1 | cds | g4558.t1.CDS5 | 3236438 | 3236533 |
| chr_2 | g4558 | g4558.t1 | exon | g4558.t1.exon6 | 3236594 | 3236652 |
| chr_2 | g4558 | g4558.t1 | cds | g4558.t1.CDS6 | 3236594 | 3236652 |
| chr_2 | g4558 | g4558.t1 | TTS | g4558.t1 | 3236809 | 3236809 |
Sequences
>g4558.t1 Gene=g4558 Length=783
ATGAGATCGCTTTGGTTGATCTTGATTTTTGTACTTTCTGCGTTGATCTCAAAATGTAAT
AGTAGAGAAGCAAGAGCAATTAGTGGTAGAATTGTTGGAGGTGTTGAAGTCGATATTGAA
AAAATTCCTTATCAAGTTTCTTTACTATATTACGATTCTTTAGCATGTGGTGCAAGCATT
TTAAGTTGCAAATTTGTTTTAACAGCTGCTCATTGTTTTCGTGGAGTACTTATTGTTTCA
TCATATACTGTTCGTGCAGGATCTTCCACTTTTTTTGAGGGTGGTTCTATACATGATGTC
AGTAAAATTGATATCCATCCACAATATAATAGAACACTTTTAGATTATGATGCTGCAATT
TTGACTTTAAGAAATCTCATCAAATATGATGCTACAAGACAAGCAATTCAATTACCTTTT
TTGAATGAAGTAATTCCTGAAGGGACAGCTGTTATAACTTCTGGTTGGGGACTAACACAA
AATTTTAATGAATCAAGTTATGTTTTACGAATGGTTGAACTTAAAGTAACAAATCAAGCA
CAATGTAATATTATATTTTTAGGAGATGGTGGAATTACAACTCGTATGCTTTGTGCTGGT
GCTGATGGAAAAGACAGTTGTGAAGGAGATAGTGGTGGACCGCTTCAACATGCTGTTTCA
AAAAAACTTGTTGGAATAGTCTCATTTGGGCAATCAGGTGGTTGTGCTCAAAAAGGAATA
CCAGGTGTTTACACAAGAGTTGCAGCAATAAGAACTTGGATACGCGAAATTGTCGAAATT
TAA
>g4558.t1 Gene=g4558 Length=260
MRSLWLILIFVLSALISKCNSREARAISGRIVGGVEVDIEKIPYQVSLLYYDSLACGASI
LSCKFVLTAAHCFRGVLIVSSYTVRAGSSTFFEGGSIHDVSKIDIHPQYNRTLLDYDAAI
LTLRNLIKYDATRQAIQLPFLNEVIPEGTAVITSGWGLTQNFNESSYVLRMVELKVTNQA
QCNIIFLGDGGITTRMLCAGADGKDSCEGDSGGPLQHAVSKKLVGIVSFGQSGGCAQKGI
PGVYTRVAAIRTWIREIVEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g4558.t1 | CDD | cd00190 | Tryp_SPc | 31 | 257 | 1.29843E-78 |
| 9 | g4558.t1 | Gene3D | G3DSA:2.40.10.10 | - | 23 | 259 | 3.6E-63 |
| 2 | g4558.t1 | PANTHER | PTHR24276 | POLYSERASE-RELATED | 20 | 258 | 5.4E-74 |
| 3 | g4558.t1 | PANTHER | PTHR24276:SF83 | GH13245P2-RELATED | 20 | 258 | 5.4E-74 |
| 6 | g4558.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 57 | 72 | 2.1E-10 |
| 5 | g4558.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 113 | 127 | 2.1E-10 |
| 4 | g4558.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 204 | 216 | 2.1E-10 |
| 1 | g4558.t1 | Pfam | PF00089 | Trypsin | 31 | 254 | 5.5E-54 |
| 11 | g4558.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 12 | g4558.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 13 | g4558.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 16 | - |
| 14 | g4558.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 10 | g4558.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 260 | - |
| 17 | g4558.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 67 | 72 | - |
| 18 | g4558.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 205 | 216 | - |
| 19 | g4558.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 31 | 259 | 30.515 |
| 16 | g4558.t1 | SMART | SM00020 | trypsin_2 | 30 | 254 | 1.6E-76 |
| 7 | g4558.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 14 | 259 | 1.3E-72 |
| 8 | g4558.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
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 transcript has been annotated with K09635 (transmembrane protease serine 4 [EC:3.4.21.-])
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.
