General information for g16323.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 18-like protein.
Parent gene
- The parent gene g16323 is located on chr_4: 9078380..9081702 (+ 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_4 | g16323 | g16323.t3 | TSS | g16323.t3 | 9078315 | 9078315 |
| chr_4 | g16323 | g16323.t3 | isoform | g16323.t3 | 9078380 | 9081702 |
| chr_4 | g16323 | g16323.t3 | exon | g16323.t3.exon1 | 9078380 | 9078811 |
| chr_4 | g16323 | g16323.t3 | exon | g16323.t3.exon2 | 9079016 | 9079133 |
| chr_4 | g16323 | g16323.t3 | exon | g16323.t3.exon3 | 9079229 | 9079861 |
| chr_4 | g16323 | g16323.t3 | cds | g16323.t3.CDS1 | 9079472 | 9079861 |
| chr_4 | g16323 | g16323.t3 | exon | g16323.t3.exon4 | 9079936 | 9081403 |
| chr_4 | g16323 | g16323.t3 | cds | g16323.t3.CDS2 | 9079936 | 9081403 |
| chr_4 | g16323 | g16323.t3 | exon | g16323.t3.exon5 | 9081470 | 9081702 |
| chr_4 | g16323 | g16323.t3 | cds | g16323.t3.CDS3 | 9081470 | 9081702 |
| chr_4 | g16323 | g16323.t3 | TTS | g16323.t3 | 9081795 | 9081795 |
Sequences
>g16323.t3 Gene=g16323 Length=2884
ATGGCATTCAATTTTGAGCAATTTAACAGTAATTCTTTAGCACAACGTGAATCAAATTCT
CGAGCAACAGAAGAAACTCAAATTGTGCCATCAGGCTATGTTCAAATCAAGAAAAATGAC
GAAAAACAAATTTTTCAAAAATCAAAAATGAATTTGAATCTGCCTGCAAATATAAATTTC
TTAAGTGTTGCAAATGATTGGCTTGTTGTGATAATGTCAAATCAAATTTTATTCAGATTA
AATTTAAAGCAACCAGACAAGCAGTATGAAGTTTTTCTTGAGAAATTCACAACTGGACAA
AGAATTTCTAAAATGTTTATTGATCCAACTGGAAGTCATCTTTTGATATCACTTGTTCCT
AAATCATCTGGTTATACTTGTGAATTGATGTATTTGAATAAAAATAGTAATAAACCAAAG
ATTCTTTCTAAGTTCCGAGATCATGAAATAACAGCAGTTGGATTTAATTATGAAAACACA
TCAGACATCAGTACTGGAAATATTCTCTTAGGAACTTCAAAAGGGCTTGTTTTTGAAGCT
GATATTGGATGTCTTTGACATAGGACGTGGAGAAAATGGACCAATAACTGGAATTGGAGT
TTTTAAAGCTCACGGCACTAACAATTTCATTGTTCTTATCTCAACAATCGATCGTCTCTA
CAAATTTCATGAAGTTCTTCGAGTTTTTGATGACAAATTTCAATCACTACAAAACATTTT
CACTCATTATTTGCATGTTCCAGAAGAAGCAAGAGATTATGAGCAACAATCGAGTAAATT
GACTTACTCACAAATGGATTTTATTTTGGAAAATAAATATCCAAAAGGCTTTGGTTGGTT
GACTGAGGCTGGAATTTTTTATGGTGAATTAAACCAAATTGCTGATAATCCAAACTTTAT
CATTAGTAAAAAAACTTTGGCATTTCCTGAGCAAGACAATGATTTTAAAACTGCAAGTTA
TATTTCAAAGAATCAAAATCAAGCACCAATTTCTTTTGTCTTGACTGATTTTCATCTTTT
GCTTCAATATTCTGATCATATTACTGGAATTTCTTTGATTAATCATGAAGTCATTTATGA
TGAATATTTCGCTGATCAATATGGAAAACTTTTGGCTGTTGTTAAGGACATTAAAAATGG
AAATGTTTATACATTCAGTAATAAGACGATTTTTAGATATCGAATAAACAACGAACAACG
CAATGTCTGGCGAATGTATTTAGATAAAAATGAATTTGAGTTAGCAAAGAAATACAGTCG
TGATAATCCAGCACATTATGACATTGTTCTCTCTAGAATTGCTGATGATTTTTATGAGAA
AAAACAGTTTATGGAAGCAGCAAAAATTTATGCTCAAACAAAGAAAAGTTTTGAGGAAGT
TACATTAAAATTCATGCAAGTTGATGAAAATTTATCATTGATTTATTATTTAAAAAGTCG
ACTTAATGAATTAAACCCAATGGTTGAACAGACTCAAATAACAATGTTGATAGTTTGGCT
TGTTGATCTTTATTTGACTGAAATAAATCGATCTTCAATTAATTCACTTGAAAGACAGAA
AGAATTTGATGAATTTATGCGACATCCGTTGTTCCAAAGTTGTTTAAAGGAAAATCGAAA
AGTAATTTACAATATTATGGCATCACATGGTGATAATGATAATTTAACAACATTAACAAC
AATTAATGAAGATTATGAAGATGTTTTAAATCATTACATACAACAAAATGAATACCGTGA
TTCACTTGACACTTTAAAAATTCAAAAACGTACTGATTTAATTTATTCATTTGCACCAAT
TGTCATGGAAGAATTACCAAAGGAAACAATTCAAATGTTTATGGAACGTGGACGAAATTT
AAATGCAGTAAAACTTTTGCCTGCTTTACTTTGTCTTAAAAGTGACAAACATCGAATTGA
AATTGTGAAATATTTGGAATTTGCCATTCATTCTTTGAGTGTTCGTGATCAATCAATTCA
TAATTATTTGATTCAACTTTATGCAAAATATAAAGAAAGTGAAAAATTAATGAGTTATTT
TGAGACACAAGGAAAAGATTTATCAATGGTTCATTATGATGTTCATTATGCTCTAAGAAT
TTGCAAAGAATTTGAAGTCAAAGAAGCTTGTGTTTTTCTACTTTGCATTCTTGAATTTTG
GCAACAAGCTGTTGAACTTGCACTGACATTTAATTCAAAATTGGCACAACAAACTGCATC
GCAACCACAAGATCGTGAATTAAAGAGAAAACTTTGGTTGACAATTGCTGAAAAGGAAAT
TAAAGGAAAAGAAAACATTCAAGAAGCACTGGAATTGCTGAAAATTTGTGACTTGCTTAA
AATTGAAGATTTACTGCCATTTTTTCCTGATTTTCAAAAAATTGATCATTTTAAAGAAGC
AATTTGTAACTCATTGAAAGAATATAATCAAAAAATTCAGGAGCAAAGAAAAGAAATGGA
AGAATCAGCAGAAGCAGCTGAAAATGTTCGAAAATCAATTCAGGCTTTTAAGTATCGATC
TGTCACAGTTTGTGGTCAAGACAAATGTTCTGGATGTGGAACTTTCTTGCTTTTAAAGCC
TTTCTTCCTTTTTCCATGCAGTCACAAATTTCATGCTGATTGTTTGGAAGCAAAACTTAT
GGAATTATTAACACCAGATGAATCACTTAAATTAATGAAATTAAAACAAAAGCTTAACAT
TTTGACCCATCAAATTGAAACAGCAAAAAATCAAAATAATAACATTCCTGAACAAACGAT
TACGGCTCGTGACCAACTTAGACAAGATATTGAAAATATTTTAGCTGCTGAATGCACCAT
GTGTGGAAGTTTAATGATTCAACAAATTGATAAAAATTTTCCCAATTCTAATGAAGAATG
GTAA
>g16323.t3 Gene=g16323 Length=696
MDFILENKYPKGFGWLTEAGIFYGELNQIADNPNFIISKKTLAFPEQDNDFKTASYISKN
QNQAPISFVLTDFHLLLQYSDHITGISLINHEVIYDEYFADQYGKLLAVVKDIKNGNVYT
FSNKTIFRYRINNEQRNVWRMYLDKNEFELAKKYSRDNPAHYDIVLSRIADDFYEKKQFM
EAAKIYAQTKKSFEEVTLKFMQVDENLSLIYYLKSRLNELNPMVEQTQITMLIVWLVDLY
LTEINRSSINSLERQKEFDEFMRHPLFQSCLKENRKVIYNIMASHGDNDNLTTLTTINED
YEDVLNHYIQQNEYRDSLDTLKIQKRTDLIYSFAPIVMEELPKETIQMFMERGRNLNAVK
LLPALLCLKSDKHRIEIVKYLEFAIHSLSVRDQSIHNYLIQLYAKYKESEKLMSYFETQG
KDLSMVHYDVHYALRICKEFEVKEACVFLLCILEFWQQAVELALTFNSKLAQQTASQPQD
RELKRKLWLTIAEKEIKGKENIQEALELLKICDLLKIEDLLPFFPDFQKIDHFKEAICNS
LKEYNQKIQEQRKEMEESAEAAENVRKSIQAFKYRSVTVCGQDKCSGCGTFLLLKPFFLF
PCSHKFHADCLEAKLMELLTPDESLKLMKLKQKLNILTHQIETAKNQNNNIPEQTITARD
QLRQDIENILAAECTMCGSLMIQQIDKNFPNSNEEW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16323.t3 | Coils | Coil | Coil | 534 | 568 | - |
| 6 | g16323.t3 | Coils | Coil | Coil | 627 | 647 | - |
| 3 | g16323.t3 | PANTHER | PTHR23323:SF26 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 18 HOMOLOG | 8 | 696 | 6.2E-155 |
| 4 | g16323.t3 | PANTHER | PTHR23323 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN | 8 | 696 | 6.2E-155 |
| 2 | g16323.t3 | Pfam | PF05131 | Pep3/Vps18/deep orange family | 20 | 174 | 1.2E-37 |
| 1 | g16323.t3 | Pfam | PF00637 | Region in Clathrin and VPS | 371 | 483 | 5.6E-9 |
| 7 | g16323.t3 | ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 353 | 504 | 20.736 |
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:0006886 | intracellular protein transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K20181 (vacuolar protein sorting-associated protein 18)
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.
