General information for g16398.t39
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Brachyurin.
Parent gene
- The parent gene g16398 is located on chr_4: 9341613..9346552 (+ 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 | g16398 | g16398.t39 | TSS | g16398.t39 | 9340829 | 9340829 |
| chr_4 | g16398 | g16398.t39 | isoform | g16398.t39 | 9340865 | 9342001 |
| chr_4 | g16398 | g16398.t39 | exon | g16398.t39.exon1 | 9340865 | 9341153 |
| chr_4 | g16398 | g16398.t39 | exon | g16398.t39.exon2 | 9341214 | 9341364 |
| chr_4 | g16398 | g16398.t39 | exon | g16398.t39.exon3 | 9341430 | 9341528 |
| chr_4 | g16398 | g16398.t39 | cds | g16398.t39.CDS1 | 9341478 | 9341528 |
| chr_4 | g16398 | g16398.t39 | exon | g16398.t39.exon4 | 9341613 | 9341767 |
| chr_4 | g16398 | g16398.t39 | cds | g16398.t39.CDS2 | 9341613 | 9341767 |
| chr_4 | g16398 | g16398.t39 | exon | g16398.t39.exon5 | 9341830 | 9342001 |
| chr_4 | g16398 | g16398.t39 | cds | g16398.t39.CDS3 | 9341830 | 9342001 |
| chr_4 | g16398 | g16398.t39 | TTS | g16398.t39 | 9342130 | 9342130 |
Sequences
>g16398.t39 Gene=g16398 Length=866
ATGAAACTCTTGCTTCTCGCACTTTTCGCTGCTGTGGCACTTGCCCAGGAAAACTATGAT
GGACCAGAATACGCTCCATTTGATGCCTCAGAAATCATCCCAGTTGAAGATTTCCCAGGT
TTCTGGACAATCGTGAATTCCCAAAAGAAGTTTTCACACCAAATCCACGTGCCTCAAGAA
TTGTCGGTGGTGTTGAAGTTGTTCCACACAGCCATCCATACCAAGTTGCCCTTCACATGC
AATTCGGTACTGGCACTGGTCTCTGCCGGTGGTTCAGTTTCTTTTGACCGCTGCTCATTG
TCCAATTGGTTCAAGCTCAACCTTGGTCATTGCTGGTGCTCACAACAGAAATGTCGTTGA
ACCAAATCAACAACGTCGTACTGTTCCATCATCAGGCTACCGCATCCACGCCAACTACAA
CCCATCAAACTTGAACAATGATATCGCTATCCTCATCACACCAACACCAAACTTTGCCTT
CGGTGCACATGTTCAAGCCGCTCGTATGCCAACTGCTTTTGCTAGTGAACTTTTCGTCGG
GAAGAACAACTAACACTGGTGCAACCTCAGCTGTCCTTCGTAAGGCTTACAATCCAGTCA
TTACTAATGCTGCTTGCTCAGCTGTCTATGGTGGATCAGTTGTAATTGCTTCAGTCATTT
GCATTGCTACAAGCGGTGTCAACCAAGGAACATGCAACGGTGACTCAGGCGGTGTCCTTT
CAGTTCCAAGAGCTGGAGATACTCGTCCAATCCAAATTGGTGTTACATCATTCGTCGCTG
CAGCTGGTTGCGTTGCTGGATTCCCATCAGGCTTCGCAAGAGTTACATCATTCCTTACCT
GGATTAACAACAACCAAAATCCATAA
>g16398.t39 Gene=g16398 Length=125
MFKPLVCQLLLLVNFSSGRTTNTGATSAVLRKAYNPVITNAACSAVYGGSVVIASVICIA
TSGVNQGTCNGDSGGVLSVPRAGDTRPIQIGVTSFVAAAGCVAGFPSGFARVTSFLTWIN
NNQNP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g16398.t39 | Gene3D | G3DSA:2.40.10.10 | - | 11 | 115 | 6.8E-22 |
| 2 | g16398.t39 | PANTHER | PTHR24250:SF56 | SERINE PROTEASE P96 | 18 | 122 | 9.6E-29 |
| 3 | g16398.t39 | PANTHER | PTHR24250 | CHYMOTRYPSIN-RELATED | 18 | 122 | 9.6E-29 |
| 1 | g16398.t39 | Pfam | PF00089 | Trypsin | 17 | 119 | 4.6E-14 |
| 9 | g16398.t39 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 10 | g16398.t39 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 11 | g16398.t39 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 13 | - |
| 12 | g16398.t39 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 8 | g16398.t39 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 125 | - |
| 13 | g16398.t39 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 67 | 78 | - |
| 14 | g16398.t39 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 18 | 124 | 10.813 |
| 4 | g16398.t39 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 18 | 123 | 2.16E-23 |
| 6 | g16398.t39 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 18 | - |
| 5 | g16398.t39 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 25 | - |
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