General information for g9268.t1
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.t1 | TTS | g9268.t1 | 1376734 | 1376734 |
| chr_1 | g9268 | g9268.t1 | isoform | g9268.t1 | 1376861 | 1379546 |
| chr_1 | g9268 | g9268.t1 | exon | g9268.t1.exon1 | 1376861 | 1377008 |
| chr_1 | g9268 | g9268.t1 | cds | g9268.t1.CDS1 | 1376861 | 1377008 |
| chr_1 | g9268 | g9268.t1 | exon | g9268.t1.exon2 | 1377067 | 1379186 |
| chr_1 | g9268 | g9268.t1 | cds | g9268.t1.CDS2 | 1377067 | 1379186 |
| chr_1 | g9268 | g9268.t1 | exon | g9268.t1.exon3 | 1379242 | 1379431 |
| chr_1 | g9268 | g9268.t1 | cds | g9268.t1.CDS3 | 1379242 | 1379431 |
| chr_1 | g9268 | g9268.t1 | exon | g9268.t1.exon4 | 1379488 | 1379546 |
| chr_1 | g9268 | g9268.t1 | cds | g9268.t1.CDS4 | 1379488 | 1379546 |
| chr_1 | g9268 | g9268.t1 | TSS | g9268.t1 | 1379620 | 1379620 |
Sequences
>g9268.t1 Gene=g9268 Length=2517
ATGAGTCTTTTATACAATATTGGTGACTGGTTCACTTTAGGAACAGGAAATACATATAGA
AAAATCGAATTATATTCGATGGATTTTAGTGATGAAGTCGATTTGAATCATATGAAAATA
TTTGGTTCACCGTTTGGAGGACCAATTGCAATAACAAAGAATTTGAATGAGCCTAAAAAA
GTTGGTGTAAACACAAAACCAGTCATTTACATATTTTCCTCATCTGGAAAATTAATTTCT
AAAATCAATTGGAACTCTGGAGTGCTCTTAACAATGGGTTGGTCTGATTCTGAAGAACTG
TTGTGCATACAAGAGAATGGAATAGTACTAATTTATAACATTTTTGGACAATATCAGCAT
AAATTCAGTATGGGACAAGAGGCTACTGACACACAAATTGTTGATGGAAGAATATATCCG
AGCTCACAAGGCACAGGGATTGCTGTAATGACAACACATTTTAGAATTTTCATCGCAAAC
AATTATCAAGATCCAAAAGTAAGATTTCTTCCTGAAATACCGAAATCTGTTCTCGATCCT
ACAAGTTGGACAGTATTAATCGAAGATAGAAAAACAACTTGTCTTATTGCACGTGATCAA
GAGTTGTTTAAGGTGAAACAAGATGATAACATATGTACAGCTGTTTGTATTTCATTTGAT
TTCGAATTTAAAGCTATTCGATTTATGTCTGTTTCATATAATAATCGTCATATTGCGATT
TATACAAATACTGGAATTTTGTGGCTAGGAACAAGTGATTTGAGAACAAAATATTGTGAA
TTTAATTGTGGACGAACAGAAATGCCAAAACAAATTGAATGGTGTTGTGATATTGAAGAT
CCAATGAAAGCTGATGCTGTTGTTATTACCTATCCATCTATTTTACTCATAGTTGGTATA
AATGGTGATTCTAATATATACACATACGATCCTGCAATATTTCTCATCCCTGAAAGTGAT
GGTGTTCGTGTACTGACTAACAATTATCATGAATTGATACAAAAAGTTCCTAAATGTGTC
ACTAGCATTTTTGGGATTAATATTTCAGAACCATCGAGTTTTTTATTTGAGAGCTATAGA
AAATTTTGTGAAAGAAGTCATCAGTCAGATGAATATTTGTGTCTCATAATGGACAAGATT
GAAATTGCTGTGGATGAATGCATAAAAGCCGCTGGCTATGAATTTGATACTGAAACGCAA
AAGAGTCTTATCAGTGCTGCTCATTTTGGAAAAGGTTTTATTCATGGACACAATCCTGAC
GATTATATAAGAATGTGTAAAATTTTACGTGTGCTTAATGCTGTAAGAAAAGAAGATATT
GGAATTCCTTTAACTATCAATCAATTTTTACATCTTACACCTGCTGTAATAATTGATAGA
TTAGTTTTTAGAAAACATTACAGTTTAGCGATTCAAATATCGAAACATTTAAATTTATCA
GAGTCACGAATTATGGAGCATTGGGCATATCACAAAATTATGTATGATAATAATGATAAT
GAAATTGTTCAGAAAATATCCGAAAAATTCAAAGATCCCTTAAAACTTGGAATTTCTTTT
TGTACTATTGCAAAGAGAGCAGAAGAAGTAGGAAAAACAAAATTAGCAATCAAGTTATTA
GAACTAGAACCAAATCAAAGTCTTCAAGTTCCTTTACTATTGAAATTAGGTGAAAATAAA
AAGGCACTTCTTGCTGCCACACAATCTGGAGATACAGATTTAATTTATATGGTGCTTATG
CAGTTGAAAGATCAAACACCACTTTCTAAATTTCAAATGATTATAAGAGAATTTCCCTTA
GCTCAAAATCTCTATAAAAAATATTGCTCTCTCAATAACATTACTGCATTAAAAGACATT
TATTTGCAAGAAGACGATTTTTTGGCACAAGCAGAAATGTCTCTTGAAGAAGCACTAGAT
AGTCATATCAAATTAGATTCATCACTTCTTGACATTTCAAGCAATTATAAAAGAGCGCAT
AAAGATATTGAAGCTGAAATTTGCGATGATCATAGAAAGTTAATGAAACAACAAAAAACA
TTGGAAGAAAAATACGCTAGAGCATTTCATGGTCTTTCACTTCATGATACAGTTAGAGAA
TTATTAGTGTTGGGTGATTTGAAAATGGTTGAAAAAGTAAAGAATGATCATAAAATGTCA
GATAAACACTATTGGCATTTGAAAGTTGAAATTTTGAGTGGAAATTATCAGTGGGAAGAG
TTGGAAAAATTCTCTAAATCGAAAAAGTCTCCGATCGGATATGAACATTTCGTAGACGCT
TGTTTAAAAGCACGGAACATTAATGAAGCCAAAAAATACATTATTAAATGTAGAGAAGAT
AAGAGAATAATTTTGTACAACAGGGCTGGTCTCTATGAAGATTCTGCTAAACTTGCTTTC
GAACTACGTGATACTCAATCGTTGATTAATATCCATAACATTGTCTCTTTAACAAATGAA
AATAATTTGATTTCAAAAATTGAGAGTTTAATCGCCTCAGTATCATCAAAAAAGTGA
>g9268.t1 Gene=g9268 Length=838
MSLLYNIGDWFTLGTGNTYRKIELYSMDFSDEVDLNHMKIFGSPFGGPIAITKNLNEPKK
VGVNTKPVIYIFSSSGKLISKINWNSGVLLTMGWSDSEELLCIQENGIVLIYNIFGQYQH
KFSMGQEATDTQIVDGRIYPSSQGTGIAVMTTHFRIFIANNYQDPKVRFLPEIPKSVLDP
TSWTVLIEDRKTTCLIARDQELFKVKQDDNICTAVCISFDFEFKAIRFMSVSYNNRHIAI
YTNTGILWLGTSDLRTKYCEFNCGRTEMPKQIEWCCDIEDPMKADAVVITYPSILLIVGI
NGDSNIYTYDPAIFLIPESDGVRVLTNNYHELIQKVPKCVTSIFGINISEPSSFLFESYR
KFCERSHQSDEYLCLIMDKIEIAVDECIKAAGYEFDTETQKSLISAAHFGKGFIHGHNPD
DYIRMCKILRVLNAVRKEDIGIPLTINQFLHLTPAVIIDRLVFRKHYSLAIQISKHLNLS
ESRIMEHWAYHKIMYDNNDNEIVQKISEKFKDPLKLGISFCTIAKRAEEVGKTKLAIKLL
ELEPNQSLQVPLLLKLGENKKALLAATQSGDTDLIYMVLMQLKDQTPLSKFQMIIREFPL
AQNLYKKYCSLNNITALKDIYLQEDDFLAQAEMSLEEALDSHIKLDSSLLDISSNYKRAH
KDIEAEICDDHRKLMKQQKTLEEKYARAFHGLSLHDTVRELLVLGDLKMVEKVKNDHKMS
DKHYWHLKVEILSGNYQWEELEKFSKSKKSPIGYEHFVDACLKARNINEAKKYIIKCRED
KRIILYNRAGLYEDSAKLAFELRDTQSLINIHNIVSLTNENNLISKIESLIASVSSKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g9268.t1 | Gene3D | G3DSA:1.10.150.780 | - | 534 | 791 | 0 |
| 3 | g9268.t1 | PANTHER | PTHR12811 | VACUOLAR PROTEIN SORTING VPS16 | 9 | 829 | 0 |
| 5 | g9268.t1 | PIRSF | PIRSF007949 | Vps16 | 2 | 835 | 0 |
| 1 | g9268.t1 | Pfam | PF04841 | Vps16, N-terminal region | 7 | 424 | 0 |
| 2 | g9268.t1 | Pfam | PF04840 | Vps16, C-terminal region | 518 | 831 | 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.
