General information for g2882.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g2882 is located on chr_3: 20871838..20873228 (- 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 | g2882 | g2882.t2 | TTS | g2882.t2 | 20871784 | 20871784 |
| chr_3 | g2882 | g2882.t2 | isoform | g2882.t2 | 20871838 | 20872681 |
| chr_3 | g2882 | g2882.t2 | exon | g2882.t2.exon1 | 20871838 | 20872681 |
| chr_3 | g2882 | g2882.t2 | cds | g2882.t2.CDS1 | 20871838 | 20872479 |
| chr_3 | g2882 | g2882.t2 | TSS | g2882.t2 | 20872895 | 20872895 |
Sequences
>g2882.t2 Gene=g2882 Length=844
ATATCAAATTAAATTTAAATCTGGAAAATCTAGAAAAATAACTTTAGTTATAGAATTGGA
TCAAGATTTTCCATATACACCCCCAAAATTGTCAACTATACCTTCGATAATAAATCATCC
ATGGATTGAGAATAAAGTTATAAAATCACCTGGAGTTTTGAATGTATGTATGCATTTAAT
TTTTCTTAACTCATGAATCAAAATGATTTGGTTTTACTGTCAGTTTACAATTAATTCTGA
TTTGGGAAGAGTCTGTCAAGCTGTGATTCGAGAATTTGAAAAAAATCCCCCAGAAGTGGC
AGATGATAATCAACCGAAACCTCAGCAAATTTATTCATCAATAAAAGAGATTGAAGAATT
AGATGTAGATCAACTATATGCACTTCTTAATGATGATCAATATTTAGAGGATTTTATTGA
AGAATTACAACCTATTAAAACATTAAATCAAGAATTAGATACATTAATAGAATCTAATGA
GAAATTAGCGATTGAAAATCTTGAAAAAGAGGCAATTTTAAAGGAGAGACAATCAGCTTT
AAATTTGCTTTCACAACAATTCATTGATATGGGAAACAAATACGGAGAAAAGAATATGTG
CTATAATGATAAATGCAAAGATTATTTACCAGAAAACATCAGACAGTTACTTGAAATAGC
TGTTTCAAATGCAGAGTCACAATGTGAGGAGTATGTGAATGCTTTTTTAACAAATCAATC
AACTAATGGAAATCAATCTATGAATGAATTTTTGGAGAATTTTATGAAGATTAAAAAATT
AATTGCTATACGAAAATTCAAAGAAGAAAGATTGAATTTTCAATTAAATCAACTTAAACT
CTAA
>g2882.t2 Gene=g2882 Length=213
MIWFYCQFTINSDLGRVCQAVIREFEKNPPEVADDNQPKPQQIYSSIKEIEELDVDQLYA
LLNDDQYLEDFIEELQPIKTLNQELDTLIESNEKLAIENLEKEAILKERQSALNLLSQQF
IDMGNKYGEKNMCYNDKCKDYLPENIRQLLEIAVSNAESQCEEYVNAFLTNQSTNGNQSM
NEFLENFMKIKKLIAIRKFKEERLNFQLNQLKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2882.t2 | Coils | Coil | Coil | 78 | 98 | - |
| 4 | g2882.t2 | Coils | Coil | Coil | 147 | 167 | - |
| 2 | g2882.t2 | PANTHER | PTHR13678:SF2 | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 37A | 33 | 205 | 7.4E-22 |
| 3 | g2882.t2 | PANTHER | PTHR13678 | WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN-RELATED | 33 | 205 | 7.4E-22 |
| 1 | g2882.t2 | Pfam | PF07200 | Modifier of rudimentary (Mod(r)) protein | 53 | 201 | 8.5E-23 |
| 6 | g2882.t2 | ProSiteProfiles | PS51314 | VPS37 C-terminal domain profile. | 124 | 213 | 16.924 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12185 (ESCRT-I complex subunit VPS37)
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.
