General information for g2882.t1
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.t1 | TTS | g2882.t1 | 20871784 | 20871784 |
| chr_3 | g2882 | g2882.t1 | isoform | g2882.t1 | 20871838 | 20872830 |
| chr_3 | g2882 | g2882.t1 | exon | g2882.t1.exon1 | 20871838 | 20872458 |
| chr_3 | g2882 | g2882.t1 | cds | g2882.t1.CDS1 | 20871838 | 20872458 |
| chr_3 | g2882 | g2882.t1 | exon | g2882.t1.exon2 | 20872519 | 20872708 |
| chr_3 | g2882 | g2882.t1 | cds | g2882.t1.CDS2 | 20872519 | 20872708 |
| chr_3 | g2882 | g2882.t1 | exon | g2882.t1.exon3 | 20872769 | 20872830 |
| chr_3 | g2882 | g2882.t1 | cds | g2882.t1.CDS3 | 20872769 | 20872830 |
| chr_3 | g2882 | g2882.t1 | TSS | g2882.t1 | 20872895 | 20872895 |
Sequences
>g2882.t1 Gene=g2882 Length=873
ATGTTTAATGCAAAAGAACAGCGAAAAAGACAAATAGATACATTAAAAGTCTTTAATCAC
AATGTTTCAGAAATAATCGAAGACAAAGAATATCAAATTAAATTTAAATCTGGAAAATCT
AGAAAAATAACTTTAGTTATAGAATTGGATCAAGATTTTCCATATACACCCCCAAAATTG
TCAACTATACCTTCGATAATAAATCATCCATGGATTGAGAATAAAGTTATAAAATCACCT
GGAGTTTTGAATTTTACAATTAATTCTGATTTGGGAAGAGTCTGTCAAGCTGTGATTCGA
GAATTTGAAAAAAATCCCCCAGAAGTGGCAGATGATAATCAACCGAAACCTCAGCAAATT
TATTCATCAATAAAAGAGATTGAAGAATTAGATGTAGATCAACTATATGCACTTCTTAAT
GATGATCAATATTTAGAGGATTTTATTGAAGAATTACAACCTATTAAAACATTAAATCAA
GAATTAGATACATTAATAGAATCTAATGAGAAATTAGCGATTGAAAATCTTGAAAAAGAG
GCAATTTTAAAGGAGAGACAATCAGCTTTAAATTTGCTTTCACAACAATTCATTGATATG
GGAAACAAATACGGAGAAAAGAATATGTGCTATAATGATAAATGCAAAGATTATTTACCA
GAAAACATCAGACAGTTACTTGAAATAGCTGTTTCAAATGCAGAGTCACAATGTGAGGAG
TATGTGAATGCTTTTTTAACAAATCAATCAACTAATGGAAATCAATCTATGAATGAATTT
TTGGAGAATTTTATGAAGATTAAAAAATTAATTGCTATACGAAAATTCAAAGAAGAAAGA
TTGAATTTTCAATTAAATCAACTTAAACTCTAA
>g2882.t1 Gene=g2882 Length=290
MFNAKEQRKRQIDTLKVFNHNVSEIIEDKEYQIKFKSGKSRKITLVIELDQDFPYTPPKL
STIPSIINHPWIENKVIKSPGVLNFTINSDLGRVCQAVIREFEKNPPEVADDNQPKPQQI
YSSIKEIEELDVDQLYALLNDDQYLEDFIEELQPIKTLNQELDTLIESNEKLAIENLEKE
AILKERQSALNLLSQQFIDMGNKYGEKNMCYNDKCKDYLPENIRQLLEIAVSNAESQCEE
YVNAFLTNQSTNGNQSMNEFLENFMKIKKLIAIRKFKEERLNFQLNQLKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g2882.t1 | Coils | Coil | Coil | 155 | 175 | - |
| 4 | g2882.t1 | Coils | Coil | Coil | 224 | 244 | - |
| 2 | g2882.t1 | PANTHER | PTHR13678 | WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN-RELATED | 110 | 282 | 2.9E-22 |
| 1 | g2882.t1 | Pfam | PF07200 | Modifier of rudimentary (Mod(r)) protein | 130 | 278 | 9.2E-23 |
| 5 | g2882.t1 | ProSiteProfiles | PS51314 | VPS37 C-terminal domain profile. | 201 | 290 | 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.
