General information for g9268.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 16-like protein.
Parent gene
- The parent gene g9268 is located on chr_1: 1377092..1379546 (- 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_1 | g9268 | g9268.t2 | TTS | g9268.t2 | 1376734 | 1376734 |
| chr_1 | g9268 | g9268.t2 | isoform | g9268.t2 | 1377092 | 1379186 |
| chr_1 | g9268 | g9268.t2 | exon | g9268.t2.exon1 | 1377092 | 1379186 |
| chr_1 | g9268 | g9268.t2 | cds | g9268.t2.CDS1 | 1377093 | 1379162 |
| chr_1 | g9268 | g9268.t2 | TSS | g9268.t2 | 1379620 | 1379620 |
Sequences
>g9268.t2 Gene=g9268 Length=2095
TGGAACTCTGGAGTGCTCTTAACAATGGGTTGGTCTGATTCTGAAGAACTGTTGTGCATA
CAAGAGAATGGAATAGTACTAATTTATAACATTTTTGGACAATATCAGCATAAATTCAGT
ATGGGACAAGAGGCTACTGACACACAAATTGTTGATGGAAGAATATATCCGAGCTCACAA
GGCACAGGGATTGCTGTAATGACAACACATTTTAGAATTTTCATCGCAAACAATTATCAA
GATCCAAAAGTAAGATTTCTTCCTGAAATACCGAAATCTGTTCTCGATCCTACAAGTTGG
ACAGTATTAATCGAAGATAGAAAAACAACTTGTCTTATTGCACGTGATCAAGAGTTGTTT
AAGGTGAAACAAGATGATAACATATGTACAGCTGTTTGTATTTCATTTGATTTCGAATTT
AAAGCTATTCGATTTATGTCTGTTTCATATAATAATCGTCATATTGCGATTTATACAAAT
ACTGGAATTTTGTGGCTAGGAACAAGTGATTTGAGAACAAAATATTGTGAATTTAATTGT
GGACGAACAGAAATGCCAAAACAAATTGAATGGTGTTGTGATATTGAAGATCCAATGAAA
GCTGATGCTGTTGTTATTACCTATCCATCTATTTTACTCATAGTTGGTATAAATGGTGAT
TCTAATATATACACATACGATCCTGCAATATTTCTCATCCCTGAAAGTGATGGTGTTCGT
GTACTGACTAACAATTATCATGAATTGATACAAAAAGTTCCTAAATGTGTCACTAGCATT
TTTGGGATTAATATTTCAGAACCATCGAGTTTTTTATTTGAGAGCTATAGAAAATTTTGT
GAAAGAAGTCATCAGTCAGATGAATATTTGTGTCTCATAATGGACAAGATTGAAATTGCT
GTGGATGAATGCATAAAAGCCGCTGGCTATGAATTTGATACTGAAACGCAAAAGAGTCTT
ATCAGTGCTGCTCATTTTGGAAAAGGTTTTATTCATGGACACAATCCTGACGATTATATA
AGAATGTGTAAAATTTTACGTGTGCTTAATGCTGTAAGAAAAGAAGATATTGGAATTCCT
TTAACTATCAATCAATTTTTACATCTTACACCTGCTGTAATAATTGATAGATTAGTTTTT
AGAAAACATTACAGTTTAGCGATTCAAATATCGAAACATTTAAATTTATCAGAGTCACGA
ATTATGGAGCATTGGGCATATCACAAAATTATGTATGATAATAATGATAATGAAATTGTT
CAGAAAATATCCGAAAAATTCAAAGATCCCTTAAAACTTGGAATTTCTTTTTGTACTATT
GCAAAGAGAGCAGAAGAAGTAGGAAAAACAAAATTAGCAATCAAGTTATTAGAACTAGAA
CCAAATCAAAGTCTTCAAGTTCCTTTACTATTGAAATTAGGTGAAAATAAAAAGGCACTT
CTTGCTGCCACACAATCTGGAGATACAGATTTAATTTATATGGTGCTTATGCAGTTGAAA
GATCAAACACCACTTTCTAAATTTCAAATGATTATAAGAGAATTTCCCTTAGCTCAAAAT
CTCTATAAAAAATATTGCTCTCTCAATAACATTACTGCATTAAAAGACATTTATTTGCAA
GAAGACGATTTTTTGGCACAAGCAGAAATGTCTCTTGAAGAAGCACTAGATAGTCATATC
AAATTAGATTCATCACTTCTTGACATTTCAAGCAATTATAAAAGAGCGCATAAAGATATT
GAAGCTGAAATTTGCGATGATCATAGAAAGTTAATGAAACAACAAAAAACATTGGAAGAA
AAATACGCTAGAGCATTTCATGGTCTTTCACTTCATGATACAGTTAGAGAATTATTAGTG
TTGGGTGATTTGAAAATGGTTGAAAAAGTAAAGAATGATCATAAAATGTCAGATAAACAC
TATTGGCATTTGAAAGTTGAAATTTTGAGTGGAAATTATCAGTGGGAAGAGTTGGAAAAA
TTCTCTAAATCGAAAAAGTCTCCGATCGGATATGAACATTTCGTAGACGCTTGTTTAAAA
GCACGGAACATTAATGAAGCCAAAAAATACATTATTAAATGTAGAGAAGATAAGA
>g9268.t2 Gene=g9268 Length=690
MGWSDSEELLCIQENGIVLIYNIFGQYQHKFSMGQEATDTQIVDGRIYPSSQGTGIAVMT
THFRIFIANNYQDPKVRFLPEIPKSVLDPTSWTVLIEDRKTTCLIARDQELFKVKQDDNI
CTAVCISFDFEFKAIRFMSVSYNNRHIAIYTNTGILWLGTSDLRTKYCEFNCGRTEMPKQ
IEWCCDIEDPMKADAVVITYPSILLIVGINGDSNIYTYDPAIFLIPESDGVRVLTNNYHE
LIQKVPKCVTSIFGINISEPSSFLFESYRKFCERSHQSDEYLCLIMDKIEIAVDECIKAA
GYEFDTETQKSLISAAHFGKGFIHGHNPDDYIRMCKILRVLNAVRKEDIGIPLTINQFLH
LTPAVIIDRLVFRKHYSLAIQISKHLNLSESRIMEHWAYHKIMYDNNDNEIVQKISEKFK
DPLKLGISFCTIAKRAEEVGKTKLAIKLLELEPNQSLQVPLLLKLGENKKALLAATQSGD
TDLIYMVLMQLKDQTPLSKFQMIIREFPLAQNLYKKYCSLNNITALKDIYLQEDDFLAQA
EMSLEEALDSHIKLDSSLLDISSNYKRAHKDIEAEICDDHRKLMKQQKTLEEKYARAFHG
LSLHDTVRELLVLGDLKMVEKVKNDHKMSDKHYWHLKVEILSGNYQWEELEKFSKSKKSP
IGYEHFVDACLKARNINEAKKYIIKCREDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g9268.t2 | Gene3D | G3DSA:1.10.150.780 | - | 443 | 690 | 0 |
| 3 | g9268.t2 | PANTHER | PTHR12811 | VACUOLAR PROTEIN SORTING VPS16 | 1 | 688 | 0 |
| 5 | g9268.t2 | PIRSF | PIRSF007949 | Vps16 | 1 | 690 | 0 |
| 1 | g9268.t2 | Pfam | PF04841 | Vps16, N-terminal region | 1 | 333 | 0 |
| 2 | g9268.t2 | Pfam | PF04840 | Vps16, C-terminal region | 427 | 686 | 0 |
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:0007033 | vacuole organization | BP |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K20180 (vacuolar protein sorting-associated protein 16)
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.
