General information for g16397.t65
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Collagenase.
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.t65 | TTS | g16397.t65 | 9336138 | 9336138 |
| chr_4 | g16397 | g16397.t65 | isoform | g16397.t65 | 9336209 | 9337367 |
| chr_4 | g16397 | g16397.t65 | exon | g16397.t65.exon1 | 9336209 | 9336380 |
| chr_4 | g16397 | g16397.t65 | cds | g16397.t65.CDS1 | 9336209 | 9336380 |
| chr_4 | g16397 | g16397.t65 | exon | g16397.t65.exon2 | 9336435 | 9336589 |
| chr_4 | g16397 | g16397.t65 | cds | g16397.t65.CDS2 | 9336435 | 9336589 |
| chr_4 | g16397 | g16397.t65 | exon | g16397.t65.exon3 | 9336649 | 9336756 |
| chr_4 | g16397 | g16397.t65 | cds | g16397.t65.CDS3 | 9336649 | 9336756 |
| chr_4 | g16397 | g16397.t65 | exon | g16397.t65.exon4 | 9336840 | 9336990 |
| chr_4 | g16397 | g16397.t65 | cds | g16397.t65.CDS4 | 9336840 | 9336842 |
| chr_4 | g16397 | g16397.t65 | exon | g16397.t65.exon5 | 9337059 | 9337367 |
| chr_4 | g16397 | g16397.t65 | TSS | g16397.t65 | 9337406 | 9337406 |
Sequences
>g16397.t65 Gene=g16397 Length=895
ATGAAACTTTTCCTTCTCGCGATCCTCGCCGTTGGCGCTCTTGCCCAGGAGAACTATGAG
GGCCCAGAGTACGCTCCAATTGATCCATCATCAATCATTCCTGTTCAGGAAATGCCCGGT
TTCTGGGATGACAAGACCGAATTCCCAGCATGGATGAAGTCACCAGTCAATGTCCGTGAT
CGTCGTATTGTCGGTGGTGTTGAAGTTGTTCCACACAGCCATCCATACCAAGTTGCCCTT
CACATTCAATTCGGTGGTGGTACTGGTCTCTGCGGTGGTTCAGTTTTGACAATCCGTTCA
GTTTTGACTGCTGCTCATTGTCCAATTGGTTCAAGCTCAACCTTGGTCATTGCTGGTGCT
CACAACAGAAATGTCGTTGAAGCCAATCAACAACGTCGTACTGTTCCATCATCAGGCTAC
CGCATCCACGCCAACTACAATCCATCAAACTTGAACAATGCCAACACCAAACTTTGCATG
GACCACAGCTGTTCAACCAACACGTCGTCCAACTGGTGCTCAACTTAGCGATCTTTTCGT
TGGAGATAGATCACGTGCAACTGGCTGGGGTCGTGTTACCAACACTGGTGCAACATCAGC
TGTCCTCCGTAAGGCTTACAATACAATCATCACTAATGCTGCTTGCGCTCAAGTTTATGG
AACAAGCGTCGTAAATGCTGGAGTTATTTGCAAGGAAACAGCTCAATCAAATCAAGGAAC
ATGCAACGGAGATTCAGGCGGTGTGCTTTCAGTTGAACGTCCTGGACACGCTCAATGGGT
CCAAGTTGGTGTTACCTCATTTGGTGCTGCTGCTGGTTGTGTTGCTGGATTCCCATCAGG
CTTCGCTCGTATGACTCATTTCGATGCATGGATTAATGCCAACCAAAATCCATAA
>g16397.t65 Gene=g16397 Length=145
MPTPNFAWTTAVQPTRRPTGAQLSDLFVGDRSRATGWGRVTNTGATSAVLRKAYNTIITN
AACAQVYGTSVVNAGVICKETAQSNQGTCNGDSGGVLSVERPGHAQWVQVGVTSFGAAAG
CVAGFPSGFARMTHFDAWINANQNP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g16397.t65 | Gene3D | G3DSA:2.40.10.10 | - | 4 | 135 | 2.5E-27 |
| 2 | g16397.t65 | PANTHER | PTHR24250:SF56 | SERINE PROTEASE P96 | 8 | 141 | 1.5E-29 |
| 3 | g16397.t65 | PANTHER | PTHR24250 | CHYMOTRYPSIN-RELATED | 8 | 141 | 1.5E-29 |
| 1 | g16397.t65 | Pfam | PF00089 | Trypsin | 9 | 139 | 1.5E-18 |
| 6 | g16397.t65 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 87 | 98 | - |
| 8 | g16397.t65 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 1 | 144 | 14.074 |
| 5 | g16397.t65 | SMART | SM00020 | trypsin_2 | 2 | 139 | 4.7E-4 |
| 4 | g16397.t65 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 6 | 142 | 3.01E-28 |
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