General information for g5186.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable ATP-dependent RNA helicase DDX23.
Parent gene
- The parent gene g5186 is located on chr_2: 7567919..7568299 (+ 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_2 | g5186 | g5186.t1 | TTS | g5186.t1 | 7556668 | 7556668 |
| chr_2 | g5186 | g5186.t1 | isoform | g5186.t1 | 7567919 | 7568299 |
| chr_2 | g5186 | g5186.t1 | exon | g5186.t1.exon1 | 7567919 | 7568299 |
| chr_2 | g5186 | g5186.t1 | cds | g5186.t1.CDS1 | 7567919 | 7568299 |
| chr_2 | g5186 | g5186.t1 | TSS | g5186.t1 | NA | NA |
Sequences
>g5186.t1 Gene=g5186 Length=381
ATGGTGGTAAAGGCCAAGAACAGAGAGAATAACGCCCTTGCTTCTCTTAAAAATGGATCA
AAAGATATTTTGGTCGCAACAGATGTGGCAGGTCGTAGGATCGATATTAAAGATGTATCA
ATGGTTATTAATTATGATATGGCCAAGACAATTGAAGATTACACACACAGAATTGGTAGA
ACTGGTCGCGCTGGAAAAACTGGAAAAGCTATCACGTTCATTACTAAAGATGACAGCACT
ATTCTACGATTTGAAACAACTTATTATGAGCAGTCCATTTCAAATTGTCCACCAGAGCTA
ATGAATCATCCTGATGCACAGCATAAACCTGGAACTGTTATAACTAAAAAGCGAAGAGAG
GAGAAAAATTTGCTGAGATAA
>g5186.t1 Gene=g5186 Length=126
MVVKAKNRENNALASLKNGSKDILVATDVAGRRIDIKDVSMVINYDMAKTIEDYTHRIGR
TGRAGKTGKAITFITKDDSTILRFETTYYEQSISNCPPELMNHPDAQHKPGTVITKKRRE
EKNLLR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5186.t1 | CDD | cd18787 | SF2_C_DEAD | 10 | 74 | 3.70069E-35 |
| 5 | g5186.t1 | Gene3D | G3DSA:3.40.50.300 | - | 4 | 125 | 4.1E-33 |
| 9 | g5186.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 126 | - |
| 8 | g5186.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 110 | 126 | - |
| 2 | g5186.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 7 | 119 | 2.1E-53 |
| 3 | g5186.t1 | PANTHER | PTHR47958:SF96 | ATP-DEPENDENT RNA HELICASE DDX23-RELATED | 7 | 119 | 2.1E-53 |
| 1 | g5186.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 6 | 65 | 2.8E-18 |
| 10 | g5186.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 1 | 104 | 15.717 |
| 7 | g5186.t1 | SMART | SM00490 | helicmild6 | 1 | 65 | 2.5E-11 |
| 4 | g5186.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 8 | 89 | 7.15E-27 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5186/g5186.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5186.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
