General information for g17539.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Brachyurin.
Parent gene
- The parent gene g17539 is located on chr_4: 13820904..13822033 (- 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 | g17539 | g17539.t11 | TTS | g17539.t11 | 13820876 | 13820876 |
| chr_4 | g17539 | g17539.t11 | isoform | g17539.t11 | 13820904 | 13821421 |
| chr_4 | g17539 | g17539.t11 | exon | g17539.t11.exon1 | 13820904 | 13821124 |
| chr_4 | g17539 | g17539.t11 | cds | g17539.t11.CDS1 | 13820904 | 13821124 |
| chr_4 | g17539 | g17539.t11 | exon | g17539.t11.exon2 | 13821181 | 13821361 |
| chr_4 | g17539 | g17539.t11 | cds | g17539.t11.CDS2 | 13821181 | 13821307 |
| chr_4 | g17539 | g17539.t11 | exon | g17539.t11.exon3 | 13821416 | 13821421 |
| chr_4 | g17539 | g17539.t11 | TSS | g17539.t11 | 13822059 | 13822059 |
Sequences
>g17539.t11 Gene=g17539 Length=408
TCTACAGTTAGTGGATTTGGAGCAACTTTTAATGCACCTAATAATTCACCATCAGATGTG
ATGAGATTTGTGTCAGTTCCAATTATGTCTAATATGCAATGTCGTCAAAGTTTTGGTCAA
TTTATTCTTGATTCAAACATTTGTGTAGACACAACTGGTGGAAGATCTCCTTGCAGTGGT
GATTCAGGAGGACCACTTACAGTTGAAATAGAACAAGGTCGATCAGTTTTAATAGGTGTT
GTTAGCTTTGGACGTATTGAAGGTTGTGGTTTAGGGTATCCAGCAGTTTTTGCAAGAACC
ACTTCGTTTCTTGATTGGATTGAGCAAGTTACTTCAAATGGTTACAAAATGACATTGAAA
TTTATTTATTTTTTCATAATTTTTATTATTATCTTTGAAATAATTTAA
>g17539.t11 Gene=g17539 Length=115
MRFVSVPIMSNMQCRQSFGQFILDSNICVDTTGGRSPCSGDSGGPLTVEIEQGRSVLIGV
VSFGRIEGCGLGYPAVFARTTSFLDWIEQVTSNGYKMTLKFIYFFIIFIIIFEII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g17539.t11 | Gene3D | G3DSA:2.40.10.10 | - | 1 | 94 | 7.3E-26 |
| 2 | g17539.t11 | PANTHER | PTHR24250:SF56 | SERINE PROTEASE P96 | 1 | 93 | 2.8E-32 |
| 3 | g17539.t11 | PANTHER | PTHR24250 | CHYMOTRYPSIN-RELATED | 1 | 93 | 2.8E-32 |
| 1 | g17539.t11 | Pfam | PF00089 | Trypsin | 3 | 87 | 1.3E-18 |
| 6 | g17539.t11 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 96 | - |
| 8 | g17539.t11 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 114 | - |
| 7 | g17539.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 115 | 115 | - |
| 10 | g17539.t11 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 36 | 47 | - |
| 11 | g17539.t11 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 1 | 92 | 13.999 |
| 4 | g17539.t11 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 2 | 93 | 1.79E-28 |
| 9 | g17539.t11 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 114 | - |
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.
