General information for g8593.t3
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.t3 | TTS | g8593.t3 | 31627858 | 31627858 |
| chr_2 | g8593 | g8593.t3 | isoform | g8593.t3 | 31628775 | 31631019 |
| chr_2 | g8593 | g8593.t3 | exon | g8593.t3.exon1 | 31628775 | 31629109 |
| chr_2 | g8593 | g8593.t3 | exon | g8593.t3.exon2 | 31629177 | 31629223 |
| chr_2 | g8593 | g8593.t3 | cds | g8593.t3.CDS1 | 31629200 | 31629223 |
| chr_2 | g8593 | g8593.t3 | exon | g8593.t3.exon3 | 31630372 | 31630940 |
| chr_2 | g8593 | g8593.t3 | cds | g8593.t3.CDS2 | 31630372 | 31630926 |
| chr_2 | g8593 | g8593.t3 | exon | g8593.t3.exon4 | 31631012 | 31631019 |
| chr_2 | g8593 | g8593.t3 | TSS | g8593.t3 | 31631109 | 31631109 |
Sequences
>g8593.t3 Gene=g8593 Length=959
TCAAGCAGATTTTAAAATAATAATGCAACCAGAATTGTATGAAGAAGTTAAATTATTTAG
ACATGCAAGAGAAAGAGAGAAGTACGATAACATGGCAGATTTATTTGCTCTCATTTCGAC
ATTACAGAATTTAGAGAAGGCATATATCCGCGATTGTGTTACTCCTCAAGAATATACAGC
AGCATGTTCAAAATTACTCGTTCAATACAAGGTAGCTTTTAAATTGGTGCAAGGAGATGA
ATTTCCGACAATTGATTCATTTGTTAAAAAATATCGACTCGATTGTCCTGCAGCATTAGA
GAGAATTCGTGAAGATAGACCGATTACAATTAAAGATGACAAAGGAAATACAAGTAAATG
CATTGCAGACATTGTTTCACTCTTCATCACGATTATGGATAAATTGAGATTGGGAATTAA
AGCAATGGATGAATTACACCCTGAATTGCGTGATTTAGTCGACACAATGAGTCGTCTTTC
AATAATTCCCGAGAACTTTGAAGGAAAGGAAAAAGTCAAGACATGGCTTGACACGTTAAA
TTCAATGCAAGCGTCCGATGAATTGTCCGATGACCAAATTATTATTGTGGTCGTAATATG
AAGCCATAGATAGCAAGCGAGCAGCCCTTGAGAAATGTCATTGACGTCACTTTAGCCACT
GTTGCTTTATAATTACTCTTTGATGTGCATGTGTAAATGCCCTGAATAAGCCACTCTTAA
TTTGGGACTAATCTCCTCTCACTCACTCACTCTACTTCTTTTTCTTATTTCTTTTCAATG
TTGCATAAATGAACGATAATTTAATTTTGTAATTGACGTCAATATCGTTCGATGCGGTAC
CAATTAGGTAAGTATGTCCTTAGTTATGGAAAGAATAAACAATAAAAGGTGTTACATATG
AAGTAAGAACGAAGTCTGACTAATGGTTTGCGATTGTGTCATCATTTATGTTTTAGGTC
>g8593.t3 Gene=g8593 Length=192
MQPELYEEVKLFRHAREREKYDNMADLFALISTLQNLEKAYIRDCVTPQEYTAACSKLLV
QYKVAFKLVQGDEFPTIDSFVKKYRLDCPAALERIREDRPITIKDDKGNTSKCIADIVSL
FITIMDKLRLGIKAMDELHPELRDLVDTMSRLSIIPENFEGKEKVKTWLDTLNSMQASDE
LSDDQIIIVVVI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8593.t3 | Gene3D | G3DSA:1.20.1440.200 | - | 1 | 98 | 0.000 |
| 6 | g8593.t3 | Gene3D | G3DSA:1.20.120.1130 | - | 105 | 187 | 0.000 |
| 2 | g8593.t3 | PANTHER | PTHR12937 | VACUOLAR PROTEIN SORTING 28, ISOFORM 2 VPS28 | 3 | 186 | 0.000 |
| 3 | g8593.t3 | PANTHER | PTHR12937:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 HOMOLOG | 3 | 186 | 0.000 |
| 10 | g8593.t3 | PIRSF | PIRSF017535 | ESCRT1_Vps28 | 1 | 189 | 0.000 |
| 1 | g8593.t3 | Pfam | PF03997 | VPS28 protein | 24 | 186 | 0.000 |
| 9 | g8593.t3 | ProSiteProfiles | PS51313 | VPS28 N-terminal domain profile. | 1 | 105 | 34.246 |
| 8 | g8593.t3 | ProSiteProfiles | PS51310 | VPS28 C-terminal domain profile. | 109 | 192 | 29.571 |
| 4 | g8593.t3 | SUPERFAMILY | SSF140111 | Endosomal sorting complex assembly domain | 7 | 103 | 0.000 |
| 5 | g8593.t3 | SUPERFAMILY | SSF140427 | VPS28 C-terminal domain-like | 110 | 186 | 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.
