General information for g6270.t2
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 g6270 is located on chr_2: 15754398..15755021 (+ 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 | g6270 | g6270.t2 | isoform | g6270.t2 | 15754174 | 15755021 |
| chr_2 | g6270 | g6270.t2 | exon | g6270.t2.exon1 | 15754174 | 15754308 |
| chr_2 | g6270 | g6270.t2 | TSS | g6270.t2 | 15754213 | 15754213 |
| chr_2 | g6270 | g6270.t2 | exon | g6270.t2.exon2 | 15754380 | 15755021 |
| chr_2 | g6270 | g6270.t2 | cds | g6270.t2.CDS1 | 15754398 | 15755021 |
| chr_2 | g6270 | g6270.t2 | TTS | g6270.t2 | 15755165 | 15755165 |
Sequences
>g6270.t2 Gene=g6270 Length=777
AAATATTGCGCCATTTGAAACAAAAACAACAAACAATTTTGTTTTTTTGCATGATTGTGC
AATTGTCAGAAAAAAAAATTAAAATTTAATTTTCATTGAGTTCTAAACAATAGAATTTAT
TTCAAAGTCAAGCAGAATTTAAAATAATTAATAATGCAGCCAGAATTGTATGAAGAAGTC
AAATTATTTAGAGATGCAAGAGAAAGAGAGAAGTACGATAACATGGCAGATTTATTTGCT
CTCATCTCGACACTACAGAATTTAGAGAAGGCATACATCCGCGATTGTGTTACTCCTCAA
GAATATACAGCAGCATGTTCAAAATTACTCGCTCAATACAAGGTAGCTTTTAAATTAGTA
CAAGGAGATGAATTTCCTACAATTGATTCATTTGTCGAGAAATATCGACTCGATTGTCCT
GCAGCATTAGAGAGAATTCGTGAAGATAGACCGATTACAATTAAAGATGACAAAGGAAAT
ACAAATAAATGCATTTCAGACATTGTTTCACTCTTCATCACGATCATGGATAAATTGAGA
TTGGGGATTAAAGCAATGGATGAATTACACCCTGATTTACGTGATTTAATCGACACAATG
AGTCGTCTTTCAATAATTCCTGAGAACTTTGAAGGAAAGGAAAAAGTCAAGACATGGCTT
GACACATTAAATTCAATGCAAGCGTCCGATGAATTGTCTGATGACCAAATAAGGCAATTT
CTATTCGATTTAGAATCGGCACTTTCTACATTCAATAATCTTTTACAACACACATAA
>g6270.t2 Gene=g6270 Length=207
MQPELYEEVKLFRDAREREKYDNMADLFALISTLQNLEKAYIRDCVTPQEYTAACSKLLA
QYKVAFKLVQGDEFPTIDSFVEKYRLDCPAALERIREDRPITIKDDKGNTNKCISDIVSL
FITIMDKLRLGIKAMDELHPDLRDLIDTMSRLSIIPENFEGKEKVKTWLDTLNSMQASDE
LSDDQIRQFLFDLESALSTFNNLLQHT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6270.t2 | Gene3D | G3DSA:1.20.1440.200 | - | 1 | 98 | 0.000 |
| 6 | g6270.t2 | Gene3D | G3DSA:1.20.120.1130 | - | 105 | 206 | 0.000 |
| 2 | g6270.t2 | PANTHER | PTHR12937 | VACUOLAR PROTEIN SORTING 28, ISOFORM 2 VPS28 | 3 | 205 | 0.000 |
| 3 | g6270.t2 | PANTHER | PTHR12937:SF0 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28 HOMOLOG | 3 | 205 | 0.000 |
| 10 | g6270.t2 | PIRSF | PIRSF017535 | ESCRT1_Vps28 | 1 | 205 | 0.000 |
| 1 | g6270.t2 | Pfam | PF03997 | VPS28 protein | 24 | 204 | 0.000 |
| 9 | g6270.t2 | ProSiteProfiles | PS51313 | VPS28 N-terminal domain profile. | 1 | 105 | 34.623 |
| 8 | g6270.t2 | ProSiteProfiles | PS51310 | VPS28 C-terminal domain profile. | 109 | 205 | 38.203 |
| 4 | g6270.t2 | SUPERFAMILY | SSF140111 | Endosomal sorting complex assembly domain | 3 | 97 | 0.000 |
| 5 | g6270.t2 | SUPERFAMILY | SSF140427 | VPS28 C-terminal domain-like | 110 | 204 | 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.
