General information for g3620.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar-sorting protein SNF8.
Parent gene
- The parent gene g3620 is located on chr_3: 26791752..26792561 (- 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 | g3620 | g3620.t1 | TTS | g3620.t1 | 26791727 | 26791727 |
| chr_3 | g3620 | g3620.t1 | isoform | g3620.t1 | 26791752 | 26792561 |
| chr_3 | g3620 | g3620.t1 | exon | g3620.t1.exon1 | 26791752 | 26792283 |
| chr_3 | g3620 | g3620.t1 | cds | g3620.t1.CDS1 | 26791752 | 26792283 |
| chr_3 | g3620 | g3620.t1 | exon | g3620.t1.exon2 | 26792338 | 26792561 |
| chr_3 | g3620 | g3620.t1 | cds | g3620.t1.CDS2 | 26792338 | 26792561 |
| chr_3 | g3620 | g3620.t1 | TSS | g3620.t1 | 26792619 | 26792619 |
Sequences
>g3620.t1 Gene=g3620 Length=756
ATGAGAAGACGTGCAGGAGTTGGTGCTATTCAAAAACAGAAGTTAGAAGCTGATAAGTTT
CGTGATAAAGGAACACAATTACAAGAAAACCAATTTGAGCAAATGACAAAGCAAGTTCAA
GTTTTAAAAGACAATTTAGAAGAGTTTGCTGATAAATACAAATCAGAAATTAAAAAGAAT
CCTACATTTAGGAAGCAATTTACTGAAATGTGTGCTGCAATTGGTGTTGATCCTTTATCT
TCATCGAAGGGAGTTTGGAGTATATTAGGAATGGGTGATTTTTATTTTGAATTGAGCATT
CAAATTGTGGAAATTTGTTTAGCTCTAGCAGAATCAACAGGTGGAATGCTTGAAATTAGT
GAATTAAAAGAGCGTCTCATGAAATCTCGAAGACAAAAGAAACAACAGGAAATTTCAACA
GAAGATATACTGCTTGCAACAAAGAAACTAAAAATTTTTGGCACTAGTTTTCAAGTGCAC
TCACTAGGAAAGAATCGCTTCATAATTCAATCAATTCCTGGTGAATTAAGCTTGCAAGAA
ACAAAAGCTATGACAGTTGCTGCTAATCAAGATAATGGAGCTATAACTAAATCATTGCTT
ATGAAAGAATTAGGATGGAATGAATTTCGAACGCAACAAGCAATAAACAAACTCATAAGT
GAGGGTCTTGTTTGGATCGATGAACAAAATGAAGGAGAACCAAATTACTTTTTTCCAAGT
TTATTTCCTGATAGAAAACTCAATATTGATTCATAA
>g3620.t1 Gene=g3620 Length=251
MRRRAGVGAIQKQKLEADKFRDKGTQLQENQFEQMTKQVQVLKDNLEEFADKYKSEIKKN
PTFRKQFTEMCAAIGVDPLSSSKGVWSILGMGDFYFELSIQIVEICLALAESTGGMLEIS
ELKERLMKSRRQKKQQEISTEDILLATKKLKIFGTSFQVHSLGKNRFIIQSIPGELSLQE
TKAMTVAANQDNGAITKSLLMKELGWNEFRTQQAINKLISEGLVWIDEQNEGEPNYFFPS
LFPDRKLNIDS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3620.t1 | Coils | Coil | Coil | 10 | 59 | - |
| 7 | g3620.t1 | Coils | Coil | Coil | 119 | 139 | - |
| 6 | g3620.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 90 | 172 | 1.7E-25 |
| 5 | g3620.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 173 | 250 | 8.9E-22 |
| 2 | g3620.t1 | PANTHER | PTHR12806 | EAP30 SUBUNIT OF ELL COMPLEX | 1 | 245 | 4.6E-86 |
| 9 | g3620.t1 | PIRSF | PIRSF017215 | ESCRT2_Vps22 | 1 | 248 | 6.8E-90 |
| 1 | g3620.t1 | Pfam | PF04157 | EAP30/Vps36 family | 5 | 228 | 1.7E-62 |
| 3 | g3620.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 23 | 175 | 4.35E-45 |
| 4 | g3620.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 176 | 242 | 1.02E-13 |
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:0071985 | multivesicular body sorting pathway | BP |
| GO:0000814 | ESCRT II complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12188 (ESCRT-II complex subunit VPS22)
Pathway
- This transcript belongs to the following pathways
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.
