General information for g13907.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine protease snake.
Parent gene
- The parent gene g13907 is located on chr_1: 33256459..33257071 (+ 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_1 | g13907 | g13907.t1 | TSS | g13907.t1 | 33254844 | 33254844 |
| chr_1 | g13907 | g13907.t1 | isoform | g13907.t1 | 33254871 | 33257071 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon1 | 33254871 | 33254940 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS1 | 33254871 | 33254940 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon2 | 33255198 | 33255374 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS2 | 33255198 | 33255374 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon3 | 33255851 | 33255967 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS3 | 33255851 | 33255967 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon4 | 33256023 | 33256049 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS4 | 33256023 | 33256049 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon5 | 33256100 | 33256388 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS5 | 33256100 | 33256388 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon6 | 33256450 | 33256709 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS6 | 33256450 | 33256709 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon7 | 33256782 | 33256793 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS7 | 33256782 | 33256793 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon8 | 33256851 | 33256965 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS8 | 33256851 | 33256965 |
| chr_1 | g13907 | g13907.t1 | exon | g13907.t1.exon9 | 33257026 | 33257071 |
| chr_1 | g13907 | g13907.t1 | cds | g13907.t1.CDS9 | 33257026 | 33257071 |
| chr_1 | g13907 | g13907.t1 | TTS | g13907.t1 | 33257197 | 33257197 |
Sequences
>g13907.t1 Gene=g13907 Length=1113
ATGATCATTAGAAATCGAGTTTGTATTTTACTTCAAATTCTCTGCTGTGCATTTGTAAAT
TCTCAACTCGTGGGAGAAGAGTGTATCAGAGATTACGACAATGCACGAGGTATTTGTGTT
TCGCATAGAGAATGCAAAAGAGCGAGAGAAGAACATGCATTGGGAATTCCGTTGACTTAT
TGTTCGTTTTTGGATGGCGTGACGAACATTTGTTGTCCGCAATTTGAAAAAAGAAAAAGT
GCATCAAAATGTGAAGAATATGGGGATCTAACAAAGAAGAAAGATTGTGTGTGGACGAGT
TTAATTCAGAATCATGAACCGCAATGTTTTGAAACTTTCACATGCAATCCAAGCACACCA
CTGATTTATGGTGGTGATATTGCAAAAGGAGGTGAATTTCCTCATATGGTTGCAATTGGA
TGGCAAAAATTGAATACAATTTCATTTGATTGTGGTGGAAGTTTGATTTCTGAACGTTAT
GTTCTAACAGCAGCGCATTGTGAAAAATCTGACAATATAAGGCCATCATTTGTAAGACTT
GGCGATCAAAATGTGAAAACACGTGATGATGGAATGATAGAAATTGACATTGCTATAGAA
GATTTTATTGTTCACCAAGATTATTCATCAATAACTCATAAAAATGATATTGCCCTCATT
AGAATGGCACAAGAAGTAAAATTCTCAGAATCCATTAGACCCGCTTGTTTGTGGCAGACA
AGCAGTGTCAATTTCACGAAGTTGATCGCTTGTGGCTGGGGTGCTCTTGAGTATGCTTCT
CAGACGAGTGATGAGTTGAGAAAAGTTGAACTTGACGTTGTCAATAATACTTTATGTAAT
CAACTGTTAAGGGAATCATTGGCTCTTTCTAATAATAAATTGATTGGTGACTCACAGTTA
TGTGCTGGATTACTTAAGGGCGGTAAAGATACGTGTCAAGGTGATTCAGGAGGACCACTT
CATGTTTCAATTCGTGATGGAAATCCTTGCCAATTTCATATAGTTGGTATAACAAGTTAT
GGATCAATTCTCTGTGGAACTCCAAATACTCCTGCTGTTTATACTAGAGTTTCTGCTTAT
TTGGATTGGATTGAAAGCATCGTATGGCGATAG
>g13907.t1 Gene=g13907 Length=370
MIIRNRVCILLQILCCAFVNSQLVGEECIRDYDNARGICVSHRECKRAREEHALGIPLTY
CSFLDGVTNICCPQFEKRKSASKCEEYGDLTKKKDCVWTSLIQNHEPQCFETFTCNPSTP
LIYGGDIAKGGEFPHMVAIGWQKLNTISFDCGGSLISERYVLTAAHCEKSDNIRPSFVRL
GDQNVKTRDDGMIEIDIAIEDFIVHQDYSSITHKNDIALIRMAQEVKFSESIRPACLWQT
SSVNFTKLIACGWGALEYASQTSDELRKVELDVVNNTLCNQLLRESLALSNNKLIGDSQL
CAGLLKGGKDTCQGDSGGPLHVSIRDGNPCQFHIVGITSYGSILCGTPNTPAVYTRVSAY
LDWIESIVWR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g13907.t1 | CDD | cd00190 | Tryp_SPc | 122 | 367 | 7.88894E-84 |
| 10 | g13907.t1 | Gene3D | G3DSA:2.40.10.10 | - | 122 | 357 | 7.3E-73 |
| 9 | g13907.t1 | Gene3D | G3DSA:2.40.10.10 | - | 134 | 365 | 7.3E-73 |
| 2 | g13907.t1 | PANTHER | PTHR24260:SF107 | EG:BACR7A4.3 PROTEIN-RELATED | 6 | 370 | 7.2E-81 |
| 3 | g13907.t1 | PANTHER | PTHR24260 | - | 6 | 370 | 7.2E-81 |
| 4 | g13907.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 152 | 167 | 7.7E-16 |
| 6 | g13907.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 212 | 226 | 7.7E-16 |
| 5 | g13907.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 309 | 321 | 7.7E-16 |
| 1 | g13907.t1 | Pfam | PF00089 | Trypsin | 122 | 364 | 1.0E-55 |
| 12 | g13907.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 13 | g13907.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 14 | g13907.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 15 | g13907.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 25 | - |
| 11 | g13907.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 370 | - |
| 18 | g13907.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 162 | 167 | - |
| 19 | g13907.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 310 | 321 | - |
| 21 | g13907.t1 | ProSiteProfiles | PS51888 | Clip domain profile. | 27 | 72 | 6.65 |
| 20 | g13907.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 122 | 369 | 31.126 |
| 17 | g13907.t1 | SMART | SM00020 | trypsin_2 | 121 | 364 | 3.7E-81 |
| 7 | g13907.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 114 | 369 | 2.33E-79 |
| 8 | g13907.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.
## Warning: Removed 1 row(s) containing missing values (geom_path).
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