General information for g8593.t7
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.t7 | TTS | g8593.t7 | 31630193 | 31630193 |
| chr_2 | g8593 | g8593.t7 | isoform | g8593.t7 | 31630303 | 31632319 |
| chr_2 | g8593 | g8593.t7 | exon | g8593.t7.exon1 | 31630303 | 31630916 |
| chr_2 | g8593 | g8593.t7 | cds | g8593.t7.CDS1 | 31630303 | 31630857 |
| chr_2 | g8593 | g8593.t7 | TSS | g8593.t7 | 31631109 | 31631109 |
| chr_2 | g8593 | g8593.t7 | exon | g8593.t7.exon2 | 31632302 | 31632319 |
Sequences
>g8593.t7 Gene=g8593 Length=632
TTTAAAATAATAAAGAATAATTGTATGAAGAAGTTAAATTATTTAGACATGCAAGAGAAA
GAGAGAAGTACGATAACATGGCAGATTTATTTGCTCTCATTTCGACATTACAGAATTTAG
AGAAGGCATATATCCGCGATTGTGTTACTCCTCAAGAATATACAGCAGCATGTTCAAAAT
TACTCGTTCAATACAAGGTAGCTTTTAAATTGGTGCAAGGAGATGAATTTCCGACAATTG
ATTCATTTGTTAAAAAATATCGACTCGATTGTCCTGCAGCATTAGAGAGAATTCGTGAAG
ATAGACCGATTACAATTAAAGATGACAAAGGAAATACAAGTAAATGCATTGCAGACATTG
TTTCACTCTTCATCACGATTATGGATAAATTGAGATTGGGAATTAAAGCAATGGATGAAT
TACACCCTGAATTGCGTGATTTAGTCGACACAATGAGTCGTCTTTCAATAATTCCCGAGA
ACTTTGAAGGAAAGGAAAAAGTCAAGACATGGCTTGACACGTTAAATTCAATGCAAGCGT
CCGATGAATTGTCCGATGACCAAGTAAGGCAATTTCTATTCGATTTAGAATCGGCATATT
CTGCATTCAATAATCTTTTACATCACACATAA
>g8593.t7 Gene=g8593 Length=184
MADLFALISTLQNLEKAYIRDCVTPQEYTAACSKLLVQYKVAFKLVQGDEFPTIDSFVKK
YRLDCPAALERIREDRPITIKDDKGNTSKCIADIVSLFITIMDKLRLGIKAMDELHPELR
DLVDTMSRLSIIPENFEGKEKVKTWLDTLNSMQASDELSDDQVRQFLFDLESAYSAFNNL
LHHT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8593.t7 | Gene3D | G3DSA:1.20.1440.200 | - | 1 | 75 | 0.000 |
| 6 | g8593.t7 | Gene3D | G3DSA:1.20.120.1130 | - | 82 | 183 | 0.000 |
| 2 | g8593.t7 | PANTHER | PTHR12937 | VACUOLAR PROTEIN SORTING 28, ISOFORM 2 VPS28 | 1 | 182 | 0.000 |
| 3 | g8593.t7 | PANTHER | PTHR12937:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 HOMOLOG | 1 | 182 | 0.000 |
| 10 | g8593.t7 | PIRSF | PIRSF017535 | ESCRT1_Vps28 | 1 | 182 | 0.000 |
| 1 | g8593.t7 | Pfam | PF03997 | VPS28 protein | 1 | 181 | 0.000 |
| 9 | g8593.t7 | ProSiteProfiles | PS51313 | VPS28 N-terminal domain profile. | 1 | 82 | 32.625 |
| 8 | g8593.t7 | ProSiteProfiles | PS51310 | VPS28 C-terminal domain profile. | 86 | 182 | 41.578 |
| 4 | g8593.t7 | SUPERFAMILY | SSF140111 | Endosomal sorting complex assembly domain | 1 | 80 | 0.000 |
| 5 | g8593.t7 | SUPERFAMILY | SSF140427 | VPS28 C-terminal domain-like | 87 | 181 | 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 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.
