General information for g2820.t2
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.t2 | TTS | g2820.t2 | 20434588 | 20434588 |
| chr_3 | g2820 | g2820.t2 | isoform | g2820.t2 | 20434652 | 20435633 |
| chr_3 | g2820 | g2820.t2 | exon | g2820.t2.exon1 | 20434652 | 20435633 |
| chr_3 | g2820 | g2820.t2 | cds | g2820.t2.CDS1 | 20434652 | 20435329 |
| chr_3 | g2820 | g2820.t2 | TSS | g2820.t2 | NA | NA |
Sequences
>g2820.t2 Gene=g2820 Length=982
ATCTACTACAGAGAAGAAACAAATTATTCTTAACTCTAAAGAAGAATTATATGTGGAATT
ACGTGATAAAAACTTTAATGCTGTTGGGCCAGTACTATCACGACTTGCAAAAACACTTAC
TGATGCAGCCAACGAACGACATGGTGAAAAAACAATAAAAGAATTGAAAGAAATTGTCGA
AAAATTACCAAAATTAAAAGCAAATGAATTATCATTTGCAAATCACACTACAATAGCAAG
TTTAATAAAAGAACATATTTCACAATATGACTTTCTTGATGAATTGTCATGTGAACAAGA
CTTTATGATGTGTGTAGATCTTGATAAATCAAATGAATATATTGAAGGAATGATATGTAA
GCAAAAACCATTGGAAAATATTTTACGACTAATCTGTATGCAAAGTGCAGCAGGAAATGG
CTTGAAGCAAAAAGTTTTTGATGGATATAAAAAAGAAATTGCTCATTCATATGGTCTTGA
TGCATTGCTTAAATTAGGTAAATTAGAAAAGGTGGGTATGATTCGAGTACAATCAGGTGC
TCGATCATATAATATCCTACGCAAAACTCTCAATTTGACTGTGGAAGATTTTATGGAAGT
AGCACCAAAAGATATAAGCTATGTTCATAGCTTTTATGCTCCAATGTTAGTAAGAATTGT
TGAACATTCTCTCAAACCTCTCGGATGGAATGGTTTAAATGACATTTTATCTTGCATACC
AGAGCCATCATTTGAAGATTATCAATTACCATTAGTAAATGGTTCAAGTAGTACTACAGG
GAGAAGAGATTCACTAACTAGTGAAATGTCTCAATCTGACATTCCTCGTGTGATTTTAGT
ATTTTTTGCTGGAGGATGCACATTTGCTGAAATTTCTGCCCTAAGATTTCTTTCTCAACA
AGACGATAATAATGTTGAATTTGTAATTGCTACAACAAAAATTATTAACAAACACACATT
TCTTTCAAGCATAATAAATTAA
>g2820.t2 Gene=g2820 Length=225
MMCVDLDKSNEYIEGMICKQKPLENILRLICMQSAAGNGLKQKVFDGYKKEIAHSYGLDA
LLKLGKLEKVGMIRVQSGARSYNILRKTLNLTVEDFMEVAPKDISYVHSFYAPMLVRIVE
HSLKPLGWNGLNDILSCIPEPSFEDYQLPLVNGSSSTTGRRDSLTSEMSQSDIPRVILVF
FAGGCTFAEISALRFLSQQDDNNVEFVIATTKIINKHTFLSSIIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2820.t2 | Gene3D | G3DSA:1.25.40.850 | - | 1 | 76 | 0 |
| 5 | g2820.t2 | Gene3D | G3DSA:3.40.50.1910 | - | 77 | 124 | 0 |
| 6 | g2820.t2 | Gene3D | G3DSA:3.40.50.1910 | - | 125 | 225 | 0 |
| 2 | g2820.t2 | PANTHER | PTHR11679:SF1 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A | 5 | 224 | 0 |
| 3 | g2820.t2 | PANTHER | PTHR11679 | VESICLE PROTEIN SORTING-ASSOCIATED | 5 | 224 | 0 |
| 1 | g2820.t2 | Pfam | PF00995 | Sec1 family | 3 | 221 | 0 |
| 4 | g2820.t2 | SUPERFAMILY | SSF56815 | Sec1/munc18-like (SM) proteins | 5 | 225 | 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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
