General information for g3780.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable ATP-dependent RNA helicase DDX20.
Parent gene
- The parent gene g3780 is located on chr_3: 27948918..27952260 (+ 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 | g3780 | g3780.t2 | TSS | g3780.t2 | 27946756 | 27946756 |
| chr_3 | g3780 | g3780.t2 | isoform | g3780.t2 | 27946872 | 27947654 |
| chr_3 | g3780 | g3780.t2 | exon | g3780.t2.exon1 | 27946872 | 27947316 |
| chr_3 | g3780 | g3780.t2 | cds | g3780.t2.CDS1 | 27946872 | 27947316 |
| chr_3 | g3780 | g3780.t2 | exon | g3780.t2.exon2 | 27947381 | 27947654 |
| chr_3 | g3780 | g3780.t2 | cds | g3780.t2.CDS2 | 27947381 | 27947382 |
| chr_3 | g3780 | g3780.t2 | TTS | g3780.t2 | NA | NA |
Sequences
>g3780.t2 Gene=g3780 Length=719
ATGGTGGATGAAGAAGAAAAGAAATTTCATACCGCTGATGTGCTCGTTTCGCAAAATTAT
CTATTTTCAAATTTCTTGCTTTCGGAAAAACTTTTAAAATCTCTCCATGAAATGAAATAC
ATTAAACCGTCACCTATTCAAGTTAAAACTATTCCTCTAGCAAGAAGTCGATTAGATATG
ATAATACAATCAAAATCCGGCACAGGAAAGACATTGAGTTTTGCAATTTGTTTACTTGAA
ACATACGATGAAGATATTAAGTTTCCTCAAGCTTTAATTGTTGTACCAACAAGAGAGATT
GCTGTACAAATCACAAATAATCTTGAAAGTTTAGGTATACACATGAAGTATTTTAAAGCT
TGTGAATTTATTGGAGGAACTGATATGAAAAATGATCGTAAACGAATTCAAACCGCCAAA
ATTGTTATTGGTAAGTTAATTTTATGACGAATATTGCATTTAATTAATAATGCAATTTTC
AATACAACATGTATAAAGACAATTGTACTTGATGAAGCTGATAAATTACTCGAAAGCGGT
CAAATGGCTAAAGATGTACAATCAATATTAAAAAAAGTCAGAGAGAATAATGATTTGCAA
ATTATTGCTGCAACTGCAACTGTTTCAACTCAATTTGAAGAACATATTAAGCGATTTATG
AAAAATCCTATAGGCATTACTCCAAAACATGAAGCTCCAATTTTACTTGGAATCAAACA
>g3780.t2 Gene=g3780 Length=148
MVDEEEKKFHTADVLVSQNYLFSNFLLSEKLLKSLHEMKYIKPSPIQVKTIPLARSRLDM
IIQSKSGTGKTLSFAICLLETYDEDIKFPQALIVVPTREIAVQITNNLESLGIHMKYFKA
CEFIGGTDMKNDRKRIQTAKIVIGKLIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3780.t2 | Gene3D | G3DSA:3.40.50.300 | - | 21 | 146 | 0.000 |
| 2 | g3780.t2 | PANTHER | PTHR47960 | DEAD-BOX ATP-DEPENDENT RNA HELICASE 50 | 5 | 144 | 0.000 |
| 3 | g3780.t2 | PANTHER | PTHR47960:SF17 | ATP-DEPENDENT RNA HELICASE DDX6-RELATED | 5 | 144 | 0.000 |
| 1 | g3780.t2 | Pfam | PF00270 | DEAD/DEAH box helicase | 45 | 144 | 0.000 |
| 6 | g3780.t2 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 20 | 48 | 9.554 |
| 7 | g3780.t2 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 51 | 148 | 12.446 |
| 4 | g3780.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 13 | 143 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
## Warning: Removed 1 row(s) containing missing values (geom_path).
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0004386 | helicase activity | MF |
| GO:0003676 | nucleic acid binding | MF |
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. There were no conditions that were differentially expressed