General information for g8593.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 28-like protein.
Parent gene
- The parent gene g8593 is located on chr_2: 31630303..31632319 (- 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_2 | g8593 | g8593.t1 | TTS | g8593.t1 | 31630193 | 31630193 |
| chr_2 | g8593 | g8593.t1 | isoform | g8593.t1 | 31630303 | 31632103 |
| chr_2 | g8593 | g8593.t1 | exon | g8593.t1.exon1 | 31630303 | 31630940 |
| chr_2 | g8593 | g8593.t1 | cds | g8593.t1.CDS1 | 31630303 | 31630940 |
| chr_2 | g8593 | g8593.t1 | exon | g8593.t1.exon2 | 31631012 | 31631019 |
| chr_2 | g8593 | g8593.t1 | cds | g8593.t1.CDS2 | 31631012 | 31631019 |
| chr_2 | g8593 | g8593.t1 | TSS | g8593.t1 | 31631109 | 31631109 |
| chr_2 | g8593 | g8593.t1 | exon | g8593.t1.exon3 | 31632087 | 31632103 |
| chr_2 | g8593 | g8593.t1 | cds | g8593.t1.CDS3 | 31632087 | 31632103 |
Sequences
>g8593.t1 Gene=g8593 Length=663
ATGCGTCGCACGATCGATCAAGCAGATTTTAAAATAATAATGCAACCAGAATTGTATGAA
GAAGTTAAATTATTTAGACATGCAAGAGAAAGAGAGAAGTACGATAACATGGCAGATTTA
TTTGCTCTCATTTCGACATTACAGAATTTAGAGAAGGCATATATCCGCGATTGTGTTACT
CCTCAAGAATATACAGCAGCATGTTCAAAATTACTCGTTCAATACAAGGTAGCTTTTAAA
TTGGTGCAAGGAGATGAATTTCCGACAATTGATTCATTTGTTAAAAAATATCGACTCGAT
TGTCCTGCAGCATTAGAGAGAATTCGTGAAGATAGACCGATTACAATTAAAGATGACAAA
GGAAATACAAGTAAATGCATTGCAGACATTGTTTCACTCTTCATCACGATTATGGATAAA
TTGAGATTGGGAATTAAAGCAATGGATGAATTACACCCTGAATTGCGTGATTTAGTCGAC
ACAATGAGTCGTCTTTCAATAATTCCCGAGAACTTTGAAGGAAAGGAAAAAGTCAAGACA
TGGCTTGACACGTTAAATTCAATGCAAGCGTCCGATGAATTGTCCGATGACCAAGTAAGG
CAATTTCTATTCGATTTAGAATCGGCATATTCTGCATTCAATAATCTTTTACATCACACA
TAA
>g8593.t1 Gene=g8593 Length=220
MRRTIDQADFKIIMQPELYEEVKLFRHAREREKYDNMADLFALISTLQNLEKAYIRDCVT
PQEYTAACSKLLVQYKVAFKLVQGDEFPTIDSFVKKYRLDCPAALERIREDRPITIKDDK
GNTSKCIADIVSLFITIMDKLRLGIKAMDELHPELRDLVDTMSRLSIIPENFEGKEKVKT
WLDTLNSMQASDELSDDQVRQFLFDLESAYSAFNNLLHHT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8593.t1 | Gene3D | G3DSA:1.20.1440.200 | - | 4 | 111 | 0.000 |
| 6 | g8593.t1 | Gene3D | G3DSA:1.20.120.1130 | - | 118 | 219 | 0.000 |
| 2 | g8593.t1 | PANTHER | PTHR12937 | VACUOLAR PROTEIN SORTING 28, ISOFORM 2 VPS28 | 12 | 218 | 0.000 |
| 3 | g8593.t1 | PANTHER | PTHR12937:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 HOMOLOG | 12 | 218 | 0.000 |
| 10 | g8593.t1 | PIRSF | PIRSF017535 | ESCRT1_Vps28 | 10 | 218 | 0.000 |
| 1 | g8593.t1 | Pfam | PF03997 | VPS28 protein | 37 | 217 | 0.000 |
| 9 | g8593.t1 | ProSiteProfiles | PS51313 | VPS28 N-terminal domain profile. | 11 | 118 | 32.663 |
| 8 | g8593.t1 | ProSiteProfiles | PS51310 | VPS28 C-terminal domain profile. | 122 | 218 | 41.578 |
| 4 | g8593.t1 | SUPERFAMILY | SSF140111 | Endosomal sorting complex assembly domain | 15 | 110 | 0.000 |
| 5 | g8593.t1 | SUPERFAMILY | SSF140427 | VPS28 C-terminal domain-like | 123 | 217 | 0.000 |
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:0032509 | endosome transport via multivesicular body sorting pathway | BP |
| GO:0000813 | ESCRT I complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12184 (ESCRT-I complex subunit VPS28)
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.
