General information for g16397.t58
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Brachyurin.
Parent gene
- The parent gene g16397 is located on chr_4: 9336657..9342138 (- 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 | g16397 | g16397.t58 | TTS | g16397.t58 | 9336138 | 9336138 |
| chr_4 | g16397 | g16397.t58 | isoform | g16397.t58 | 9336209 | 9337367 |
| chr_4 | g16397 | g16397.t58 | exon | g16397.t58.exon1 | 9336209 | 9336380 |
| chr_4 | g16397 | g16397.t58 | cds | g16397.t58.CDS1 | 9336209 | 9336380 |
| chr_4 | g16397 | g16397.t58 | exon | g16397.t58.exon2 | 9336435 | 9336589 |
| chr_4 | g16397 | g16397.t58 | cds | g16397.t58.CDS2 | 9336435 | 9336589 |
| chr_4 | g16397 | g16397.t58 | exon | g16397.t58.exon3 | 9336649 | 9336776 |
| chr_4 | g16397 | g16397.t58 | cds | g16397.t58.CDS3 | 9336649 | 9336776 |
| chr_4 | g16397 | g16397.t58 | exon | g16397.t58.exon4 | 9336840 | 9336990 |
| chr_4 | g16397 | g16397.t58 | cds | g16397.t58.CDS4 | 9336840 | 9336990 |
| chr_4 | g16397 | g16397.t58 | exon | g16397.t58.exon5 | 9337115 | 9337367 |
| chr_4 | g16397 | g16397.t58 | cds | g16397.t58.CDS5 | 9337115 | 9337198 |
| chr_4 | g16397 | g16397.t58 | TSS | g16397.t58 | 9337406 | 9337406 |
Sequences
>g16397.t58 Gene=g16397 Length=859
ATGAAACTTTTCCTTCTCGCGATCCTCGCCGTTGGCGCTCTTGCCCAGGAGAACTATGAG
GGCCCAGAGTACGCTCCAATTGATCCATCATCAATCATTCCTGTTCAGGAAATGCCCGGT
TTCTGGGATGACAAGACCGAATTCCCAGCATGGATGAAGTCACCAGTCAATGTCCGTGAT
CGTCGTATTGTCGGTGGTGTTGAAGTTGTTCCACACAGCCATCCATACCAAGTTGCCCTT
CACATTCAATTCGGCTGCTCATTGTCCAATTGGTTCAAGCTCAACCTTGGTCATTGCTGG
TGCTCACAACAGAAATGTCGTTGAAGCCAATCAACAACGTCGTACTGTTCCATCATCAGG
CTACCGCATCCACGCCAACTACAATCCATCAAACTTGAACAATGATATTGCTGTTCTCAT
CACACCAACACCAAACTTTGCATGGACCACAGCTGTTCAACCAACACGTCGTCCAACTGG
TGCTCAACTTAGCGATCTTTTCGTTGGAGATAGATCACGTGCAACTGGCTGGGGTCGTGT
TACCAACACTGGTGCAACATCAGCTGTCCTCCGTAAGGCTTACAATACAATCATCACTAA
TGCTGCTTGCGCTCAAGTTTATGGAACAAGCGTCGTAAATGCTGGAGTTATTTGCAAGGA
AACAGCTCAATCAAATCAAGGAACATGCAACGGAGATTCAGGCGGTGTGCTTTCAGTTGA
ACGTCCTGGACACGCTCAATGGGTCCAAGTTGGTGTTACCTCATTTGGTGCTGCTGCTGG
TTGTGTTGCTGGATTCCCATCAGGCTTCGCTCGTATGACTCATTTCGATGCATGGATTAA
TGCCAACCAAAATCCATAA
>g16397.t58 Gene=g16397 Length=229
MSVIVVLSVVLKLFHTAIHTKLPFTFNSAAHCPIGSSSTLVIAGAHNRNVVEANQQRRTV
PSSGYRIHANYNPSNLNNDIAVLITPTPNFAWTTAVQPTRRPTGAQLSDLFVGDRSRATG
WGRVTNTGATSAVLRKAYNTIITNAACAQVYGTSVVNAGVICKETAQSNQGTCNGDSGGV
LSVERPGHAQWVQVGVTSFGAAAGCVAGFPSGFARMTHFDAWINANQNP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g16397.t58 | CDD | cd00190 | Tryp_SPc | 28 | 226 | 3.02435E-44 |
| 7 | g16397.t58 | Gene3D | G3DSA:2.40.10.10 | - | 28 | 224 | 9.0E-39 |
| 8 | g16397.t58 | Gene3D | G3DSA:2.40.10.10 | - | 100 | 219 | 9.0E-39 |
| 2 | g16397.t58 | PANTHER | PTHR24250:SF56 | SERINE PROTEASE P96 | 28 | 225 | 1.9E-47 |
| 3 | g16397.t58 | PANTHER | PTHR24250 | CHYMOTRYPSIN-RELATED | 28 | 225 | 1.9E-47 |
| 1 | g16397.t58 | Pfam | PF00089 | Trypsin | 28 | 223 | 3.6E-31 |
| 10 | g16397.t58 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 11 | g16397.t58 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 12 | g16397.t58 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 13 | g16397.t58 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 9 | g16397.t58 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 229 | - |
| 15 | g16397.t58 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 171 | 182 | - |
| 17 | g16397.t58 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 28 | 228 | 18.975 |
| 16 | g16397.t58 | SMART | SM00020 | trypsin_2 | 3 | 223 | 3.3E-22 |
| 4 | g16397.t58 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 28 | 226 | 1.21E-41 |
| 6 | g16397.t58 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 5 | g16397.t58 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 22 | - |
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