General information for g2820.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuolar protein sorting-associated protein 33A.
Parent gene
- The parent gene g2820 is located on chr_3: 20435633..20436547 (- 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_3 | g2820 | g2820.t1 | TTS | g2820.t1 | 20434588 | 20434588 |
| chr_3 | g2820 | g2820.t1 | isoform | g2820.t1 | 20434652 | 20436547 |
| chr_3 | g2820 | g2820.t1 | exon | g2820.t1.exon1 | 20434652 | 20436373 |
| chr_3 | g2820 | g2820.t1 | cds | g2820.t1.CDS1 | 20434652 | 20436373 |
| chr_3 | g2820 | g2820.t1 | exon | g2820.t1.exon2 | 20436440 | 20436547 |
| chr_3 | g2820 | g2820.t1 | cds | g2820.t1.CDS2 | 20436440 | 20436547 |
| chr_3 | g2820 | g2820.t1 | TSS | g2820.t1 | NA | NA |
Sequences
>g2820.t1 Gene=g2820 Length=1830
ATGGGTGATTTTTCGCATTTAATTACTCAGAAAGTTAATCTAGCGCTTGTACAAGAGCTA
GCTTTAAACGAATTAATAGAAATCTTAGATAAATGTGAAGGAACAAAGGTTTTGATGTGG
GATGAAACTCTTACTGGGCCTATTTCATTGATAGCAAAGCCAGAAATTCTCAAAGATCGT
AATGTTGTAAAAATGTTTCCAATAAAGGCAGGAGATTTACCAAATGTTGATGTTCGAAAT
TTTATCTTCATTACTCGTCCTAATTTACAATTAATGAATGCCATAGCATCAAATATACAT
AGTGATGAACGCAAAAATAGAGTTTATAGGAAGAATTTCTATCTCTTTTTTCTTCCTAAA
CGATCACTTTTATGTGAAAATCAACTAAAATCAAAAGGCGTTTATGGAAATTTTCAAGTA
ATTGATGATTTCAAGTGTCAGTTATTTCCATTTGATAGTGATGTTATTTCAATGGAATAT
CCTGATGCTTATAAAGAAATATACATTGAAGGAGACTATACTTGTTTACATCATTCAGCT
ACTGCTCTTTGCACCATTCAAAAACTTTATGGTCGAATTCCAAAAATTGTTGGTAAAGGA
AAATTTGCAGAAAAAGTTAAAGAGTTAGCTAAAACTATGATTCTCAATGAAGATATTTCA
ATTGAAAGAGGAAGTATTGATCAACTGATTATTTTAGATCGTTCTATTGACATAATGAGT
GCACTTGCAACACAATTGACTTATGAAGGACTTATCGATGAATTTTACGGTATTAATAAT
ACCATAGTCAATTTTCCTGCCAGTAAATTCAATTCACAAGGAGAGGAGGCCAGTTTCAAT
CGAATGACATCTACTACAGAGAAGAAACAAATTATTCTTAACTCTAAAGAAGAATTATAT
GTGGAATTACGTGATAAAAACTTTAATGCTGTTGGGCCAGTACTATCACGACTTGCAAAA
ACACTTACTGATGCAGCCAACGAACGACATGGTGAAAAAACAATAAAAGAATTGAAAGAA
ATTGTCGAAAAATTACCAAAATTAAAAGCAAATGAATTATCATTTGCAAATCACACTACA
ATAGCAAGTTTAATAAAAGAACATATTTCACAATATGACTTTCTTGATGAATTGTCATGT
GAACAAGACTTTATGATGTGTGTAGATCTTGATAAATCAAATGAATATATTGAAGGAATG
ATATGTAAGCAAAAACCATTGGAAAATATTTTACGACTAATCTGTATGCAAAGTGCAGCA
GGAAATGGCTTGAAGCAAAAAGTTTTTGATGGATATAAAAAAGAAATTGCTCATTCATAT
GGTCTTGATGCATTGCTTAAATTAGGTAAATTAGAAAAGGTGGGTATGATTCGAGTACAA
TCAGGTGCTCGATCATATAATATCCTACGCAAAACTCTCAATTTGACTGTGGAAGATTTT
ATGGAAGTAGCACCAAAAGATATAAGCTATGTTCATAGCTTTTATGCTCCAATGTTAGTA
AGAATTGTTGAACATTCTCTCAAACCTCTCGGATGGAATGGTTTAAATGACATTTTATCT
TGCATACCAGAGCCATCATTTGAAGATTATCAATTACCATTAGTAAATGGTTCAAGTAGT
ACTACAGGGAGAAGAGATTCACTAACTAGTGAAATGTCTCAATCTGACATTCCTCGTGTG
ATTTTAGTATTTTTTGCTGGAGGATGCACATTTGCTGAAATTTCTGCCCTAAGATTTCTT
TCTCAACAAGACGATAATAATGTTGAATTTGTAATTGCTACAACAAAAATTATTAACAAA
CACACATTTCTTTCAAGCATAATAAATTAA
>g2820.t1 Gene=g2820 Length=609
MGDFSHLITQKVNLALVQELALNELIEILDKCEGTKVLMWDETLTGPISLIAKPEILKDR
NVVKMFPIKAGDLPNVDVRNFIFITRPNLQLMNAIASNIHSDERKNRVYRKNFYLFFLPK
RSLLCENQLKSKGVYGNFQVIDDFKCQLFPFDSDVISMEYPDAYKEIYIEGDYTCLHHSA
TALCTIQKLYGRIPKIVGKGKFAEKVKELAKTMILNEDISIERGSIDQLIILDRSIDIMS
ALATQLTYEGLIDEFYGINNTIVNFPASKFNSQGEEASFNRMTSTTEKKQIILNSKEELY
VELRDKNFNAVGPVLSRLAKTLTDAANERHGEKTIKELKEIVEKLPKLKANELSFANHTT
IASLIKEHISQYDFLDELSCEQDFMMCVDLDKSNEYIEGMICKQKPLENILRLICMQSAA
GNGLKQKVFDGYKKEIAHSYGLDALLKLGKLEKVGMIRVQSGARSYNILRKTLNLTVEDF
MEVAPKDISYVHSFYAPMLVRIVEHSLKPLGWNGLNDILSCIPEPSFEDYQLPLVNGSSS
TTGRRDSLTSEMSQSDIPRVILVFFAGGCTFAEISALRFLSQQDDNNVEFVIATTKIINK
HTFLSSIIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2820.t1 | Gene3D | G3DSA:3.40.50.2060 | - | 4 | 147 | 0 |
| 5 | g2820.t1 | Gene3D | G3DSA:3.40.50.1910 | - | 150 | 604 | 0 |
| 8 | g2820.t1 | Gene3D | G3DSA:3.90.830.10 | Syntaxin Binding Protein 1; Chain A | 245 | 371 | 0 |
| 7 | g2820.t1 | Gene3D | G3DSA:1.25.40.850 | - | 372 | 462 | 0 |
| 2 | g2820.t1 | PANTHER | PTHR11679:SF1 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A | 24 | 608 | 0 |
| 3 | g2820.t1 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 24 | 608 | 0 |
| 9 | g2820.t1 | PIRSF | PIRSF005715 | VPS45_Sec1 | 16 | 609 | 0 |
| 1 | g2820.t1 | Pfam | PF00995 | Sec1 family | 36 | 605 | 0 |
| 4 | g2820.t1 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 15 | 609 | 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:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K20182 (vacuolar protein sorting-associated protein 33A)
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.
