General information for g4087.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vacuolar protein sorting-associated protein 45.
Parent gene
- The parent gene g4087 is located on chr_3: 30512401..30513633 (+ 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_3 | g4087 | g4087.t18 | isoform | g4087.t18 | 30512084 | 30513164 |
| chr_3 | g4087 | g4087.t18 | exon | g4087.t18.exon1 | 30512084 | 30512604 |
| chr_3 | g4087 | g4087.t18 | cds | g4087.t18.CDS1 | 30512084 | 30512401 |
| chr_3 | g4087 | g4087.t18 | exon | g4087.t18.exon2 | 30512684 | 30513164 |
| chr_3 | g4087 | g4087.t18 | TSS | g4087.t18 | NA | NA |
| chr_3 | g4087 | g4087.t18 | TTS | g4087.t18 | NA | NA |
Sequences
>g4087.t18 Gene=g4087 Length=1002
GTTTGTGTATTGAAAGAGTTGCTTGAAGAAATTTTTAAAGGTCGACCAATTGATCAACAA
TATCCATTTATTAATTCATCAGAAGTTCCTTATAGGCGACCACCGACAGAAATTATTGTT
TTTATAGTTGGTGGTGCCACATATGAAGAAGCTTTGGCAGTTCATCAACTTAATCAATTG
GGTTATCGTGTTATATTAGGAGGCACAACTATTCATAATTCTGAAACTTTCCTAGAAGAA
GTTATTGCAGCAACAAATGGAGCACCTTTTAAACATTCCCGATCACTGCAAGCTTTTCAT
AATGCATCAAATGCCTAAAATTTGATATCACATTACTTTCATAATATATTATTCAATTAT
ATTATTGTATTCACAATTATTAATTTATTATAATAAAATATATAACCAAAACTATAAATG
AATTGATGTATTCACTACTCATCGTCATTATCTGTGTAGTCATTAAAATCACTGAATGAT
GTCTCGGGTTCATTCAGTCTCAATTTTTCAGCTATAACAATATTAAATATTCCACTAAAA
TATCCATATCCAAACATTGCAATTGAAGCAATTAAACCTGACATGATGTATCTTTTTCTA
ATTTCTGACGGTGGATCTTCATCTTCTTGCCCAGTAAAAACTTTTTGTTCTTTCTTTAGA
TTTTGTGCCTTTACTTTTTCACTCTCAAAGCACTCATTTTCATTAAAGAACTTTTTCTTT
AAATTATCCACATAACGTGATAGATTTTTACATTGATTAGCATGTGATTGAAGTTGATTA
TTTGGTAATTGAAATTTAAGTATAATTGCTAAATAAGCAAAAATAGTTGCATCAACTTCA
TTTTGTGATCCATTAATGAAGAATTCTTTATTTCCCAGTCGTTCGCTTATCCAATTAAGA
CATTTTTTTGCATCCACTTCCATTTTCGTTGTATCATGTGCAGTAACTGGGTCTTCTAGT
GAAAAATTAGCTACATTTTGACATACTTGTTCACATTTCCGC
>g4087.t18 Gene=g4087 Length=105
VCVLKELLEEIFKGRPIDQQYPFINSSEVPYRRPPTEIIVFIVGGATYEEALAVHQLNQL
GYRVILGGTTIHNSETFLEEVIAATNGAPFKHSRSLQAFHNASNA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4087.t18 | Gene3D | G3DSA:3.40.50.1910 | - | 2 | 88 | 0 |
| 2 | g4087.t18 | PANTHER | PTHR11679:SF3 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 45 | 2 | 82 | 0 |
| 3 | g4087.t18 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 2 | 82 | 0 |
| 1 | g4087.t18 | Pfam | PF00995 | Sec1 family | 4 | 80 | 0 |
| 4 | g4087.t18 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 3 | 86 | 0 |
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:0016192 | vesicle-mediated transport | 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.
