General information for g16323.t1
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.t1 | TSS | g16323.t1 | 9078315 | 9078315 |
| chr_4 | g16323 | g16323.t1 | isoform | g16323.t1 | 9078380 | 9081702 |
| chr_4 | g16323 | g16323.t1 | exon | g16323.t1.exon1 | 9078380 | 9078811 |
| chr_4 | g16323 | g16323.t1 | cds | g16323.t1.CDS1 | 9078380 | 9078811 |
| chr_4 | g16323 | g16323.t1 | exon | g16323.t1.exon2 | 9079016 | 9079171 |
| chr_4 | g16323 | g16323.t1 | cds | g16323.t1.CDS2 | 9079016 | 9079171 |
| chr_4 | g16323 | g16323.t1 | exon | g16323.t1.exon3 | 9079229 | 9079861 |
| chr_4 | g16323 | g16323.t1 | cds | g16323.t1.CDS3 | 9079229 | 9079861 |
| chr_4 | g16323 | g16323.t1 | exon | g16323.t1.exon4 | 9079936 | 9081403 |
| chr_4 | g16323 | g16323.t1 | cds | g16323.t1.CDS4 | 9079936 | 9081403 |
| chr_4 | g16323 | g16323.t1 | exon | g16323.t1.exon5 | 9081470 | 9081702 |
| chr_4 | g16323 | g16323.t1 | cds | g16323.t1.CDS5 | 9081470 | 9081702 |
| chr_4 | g16323 | g16323.t1 | TTS | g16323.t1 | 9081795 | 9081795 |
Sequences
>g16323.t1 Gene=g16323 Length=2922
ATGGCATTCAATTTTGAGCAATTTAACAGTAATTCTTTAGCACAACGTGAATCAAATTCT
CGAGCAACAGAAGAAACTCAAATTGTGCCATCAGGCTATGTTCAAATCAAGAAAAATGAC
GAAAAACAAATTTTTCAAAAATCAAAAATGAATTTGAATCTGCCTGCAAATATAAATTTC
TTAAGTGTTGCAAATGATTGGCTTGTTGTGATAATGTCAAATCAAATTTTATTCAGATTA
AATTTAAAGCAACCAGACAAGCAGTATGAAGTTTTTCTTGAGAAATTCACAACTGGACAA
AGAATTTCTAAAATGTTTATTGATCCAACTGGAAGTCATCTTTTGATATCACTTGTTCCT
AAATCATCTGGTTATACTTGTGAATTGATGTATTTGAATAAAAATAGTAATAAACCAAAG
ATTCTTTCTAAGTTCCGAGATCATGAAATAACAGCAGTTGGATTTAATTATGAAAACACA
TCAGACATCAGTACTGGAAATATTCTCTTAGGAACTTCAAAAGGGCTTGTTTTTGAAGCT
GATATTGGATGTGATGGTGATAGATTAATTCAGAATAATTGGAAGCAGGTCTTTGACATA
GGACGTGGAGAAAATGGACCAATAACTGGAATTGGAGTTTTTAAAGCTCACGGCACTAAC
AATTTCATTGTTCTTATCTCAACAATCGATCGTCTCTACAAATTTCATGAAGTTCTTCGA
GTTTTTGATGACAAATTTCAATCACTACAAAACATTTTCACTCATTATTTGCATGTTCCA
GAAGAAGCAAGAGATTATGAGCAACAATCGAGTAAATTGACTTACTCACAAATGGATTTT
ATTTTGGAAAATAAATATCCAAAAGGCTTTGGTTGGTTGACTGAGGCTGGAATTTTTTAT
GGTGAATTAAACCAAATTGCTGATAATCCAAACTTTATCATTAGTAAAAAAACTTTGGCA
TTTCCTGAGCAAGACAATGATTTTAAAACTGCAAGTTATATTTCAAAGAATCAAAATCAA
GCACCAATTTCTTTTGTCTTGACTGATTTTCATCTTTTGCTTCAATATTCTGATCATATT
ACTGGAATTTCTTTGATTAATCATGAAGTCATTTATGATGAATATTTCGCTGATCAATAT
GGAAAACTTTTGGCTGTTGTTAAGGACATTAAAAATGGAAATGTTTATACATTCAGTAAT
AAGACGATTTTTAGATATCGAATAAACAACGAACAACGCAATGTCTGGCGAATGTATTTA
GATAAAAATGAATTTGAGTTAGCAAAGAAATACAGTCGTGATAATCCAGCACATTATGAC
ATTGTTCTCTCTAGAATTGCTGATGATTTTTATGAGAAAAAACAGTTTATGGAAGCAGCA
AAAATTTATGCTCAAACAAAGAAAAGTTTTGAGGAAGTTACATTAAAATTCATGCAAGTT
GATGAAAATTTATCATTGATTTATTATTTAAAAAGTCGACTTAATGAATTAAACCCAATG
GTTGAACAGACTCAAATAACAATGTTGATAGTTTGGCTTGTTGATCTTTATTTGACTGAA
ATAAATCGATCTTCAATTAATTCACTTGAAAGACAGAAAGAATTTGATGAATTTATGCGA
CATCCGTTGTTCCAAAGTTGTTTAAAGGAAAATCGAAAAGTAATTTACAATATTATGGCA
TCACATGGTGATAATGATAATTTAACAACATTAACAACAATTAATGAAGATTATGAAGAT
GTTTTAAATCATTACATACAACAAAATGAATACCGTGATTCACTTGACACTTTAAAAATT
CAAAAACGTACTGATTTAATTTATTCATTTGCACCAATTGTCATGGAAGAATTACCAAAG
GAAACAATTCAAATGTTTATGGAACGTGGACGAAATTTAAATGCAGTAAAACTTTTGCCT
GCTTTACTTTGTCTTAAAAGTGACAAACATCGAATTGAAATTGTGAAATATTTGGAATTT
GCCATTCATTCTTTGAGTGTTCGTGATCAATCAATTCATAATTATTTGATTCAACTTTAT
GCAAAATATAAAGAAAGTGAAAAATTAATGAGTTATTTTGAGACACAAGGAAAAGATTTA
TCAATGGTTCATTATGATGTTCATTATGCTCTAAGAATTTGCAAAGAATTTGAAGTCAAA
GAAGCTTGTGTTTTTCTACTTTGCATTCTTGAATTTTGGCAACAAGCTGTTGAACTTGCA
CTGACATTTAATTCAAAATTGGCACAACAAACTGCATCGCAACCACAAGATCGTGAATTA
AAGAGAAAACTTTGGTTGACAATTGCTGAAAAGGAAATTAAAGGAAAAGAAAACATTCAA
GAAGCACTGGAATTGCTGAAAATTTGTGACTTGCTTAAAATTGAAGATTTACTGCCATTT
TTTCCTGATTTTCAAAAAATTGATCATTTTAAAGAAGCAATTTGTAACTCATTGAAAGAA
TATAATCAAAAAATTCAGGAGCAAAGAAAAGAAATGGAAGAATCAGCAGAAGCAGCTGAA
AATGTTCGAAAATCAATTCAGGCTTTTAAGTATCGATCTGTCACAGTTTGTGGTCAAGAC
AAATGTTCTGGATGTGGAACTTTCTTGCTTTTAAAGCCTTTCTTCCTTTTTCCATGCAGT
CACAAATTTCATGCTGATTGTTTGGAAGCAAAACTTATGGAATTATTAACACCAGATGAA
TCACTTAAATTAATGAAATTAAAACAAAAGCTTAACATTTTGACCCATCAAATTGAAACA
GCAAAAAATCAAAATAATAACATTCCTGAACAAACGATTACGGCTCGTGACCAACTTAGA
CAAGATATTGAAAATATTTTAGCTGCTGAATGCACCATGTGTGGAAGTTTAATGATTCAA
CAAATTGATAAAAATTTTCCCAATTCTAATGAAGAATGGTAA
>g16323.t1 Gene=g16323 Length=973
MAFNFEQFNSNSLAQRESNSRATEETQIVPSGYVQIKKNDEKQIFQKSKMNLNLPANINF
LSVANDWLVVIMSNQILFRLNLKQPDKQYEVFLEKFTTGQRISKMFIDPTGSHLLISLVP
KSSGYTCELMYLNKNSNKPKILSKFRDHEITAVGFNYENTSDISTGNILLGTSKGLVFEA
DIGCDGDRLIQNNWKQVFDIGRGENGPITGIGVFKAHGTNNFIVLISTIDRLYKFHEVLR
VFDDKFQSLQNIFTHYLHVPEEARDYEQQSSKLTYSQMDFILENKYPKGFGWLTEAGIFY
GELNQIADNPNFIISKKTLAFPEQDNDFKTASYISKNQNQAPISFVLTDFHLLLQYSDHI
TGISLINHEVIYDEYFADQYGKLLAVVKDIKNGNVYTFSNKTIFRYRINNEQRNVWRMYL
DKNEFELAKKYSRDNPAHYDIVLSRIADDFYEKKQFMEAAKIYAQTKKSFEEVTLKFMQV
DENLSLIYYLKSRLNELNPMVEQTQITMLIVWLVDLYLTEINRSSINSLERQKEFDEFMR
HPLFQSCLKENRKVIYNIMASHGDNDNLTTLTTINEDYEDVLNHYIQQNEYRDSLDTLKI
QKRTDLIYSFAPIVMEELPKETIQMFMERGRNLNAVKLLPALLCLKSDKHRIEIVKYLEF
AIHSLSVRDQSIHNYLIQLYAKYKESEKLMSYFETQGKDLSMVHYDVHYALRICKEFEVK
EACVFLLCILEFWQQAVELALTFNSKLAQQTASQPQDRELKRKLWLTIAEKEIKGKENIQ
EALELLKICDLLKIEDLLPFFPDFQKIDHFKEAICNSLKEYNQKIQEQRKEMEESAEAAE
NVRKSIQAFKYRSVTVCGQDKCSGCGTFLLLKPFFLFPCSHKFHADCLEAKLMELLTPDE
SLKLMKLKQKLNILTHQIETAKNQNNNIPEQTITARDQLRQDIENILAAECTMCGSLMIQ
QIDKNFPNSNEEW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g16323.t1 | Coils | Coil | Coil | 811 | 845 | - |
| 5 | g16323.t1 | Coils | Coil | Coil | 904 | 924 | - |
| 3 | g16323.t1 | PANTHER | PTHR23323:SF26 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 18 HOMOLOG | 17 | 973 | 2.0E-175 |
| 4 | g16323.t1 | PANTHER | PTHR23323 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN | 17 | 973 | 2.0E-175 |
| 2 | g16323.t1 | Pfam | PF05131 | Pep3/Vps18/deep orange family | 297 | 451 | 2.1E-37 |
| 1 | g16323.t1 | Pfam | PF00637 | Region in Clathrin and VPS | 648 | 760 | 8.8E-9 |
| 7 | g16323.t1 | ProSiteProfiles | PS50236 | Clathrin heavy-chain (CHCR) repeat profile. | 630 | 781 | 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.
