General information for g5179.t4
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 g5179 is located on chr_2: 7556564..7557774 (+ 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 | g5179 | g5179.t4 | isoform | g5179.t4 | 7553785 | 7554647 |
| chr_2 | g5179 | g5179.t4 | exon | g5179.t4.exon1 | 7553785 | 7554647 |
| chr_2 | g5179 | g5179.t4 | cds | g5179.t4.CDS1 | 7553852 | 7554646 |
| chr_2 | g5179 | g5179.t4 | TTS | g5179.t4 | 7554050 | 7554050 |
| chr_2 | g5179 | g5179.t4 | TSS | g5179.t4 | NA | NA |
Sequences
>g5179.t4 Gene=g5179 Length=863
ATAATAAACTCTTATTAATAATACAAAATAGAGAGTAAACTAAAAGATAGACTAAACGTT
TAGAAAAATGGGTAAAGAAAAATCATCAAGGACTGACAAAGATAGAGATAAAGACCGTAG
TAGTAGAAGATCAAGGTCTAGATCGAGAGACCGTAGTGATCGAAAATCAGATCGTAGATA
TGAGGATGATCGCAAACCTCGAGAAGCAAGAGATGAGAAATTGAAAACTGAAGTTAAAGA
AGAGCTCGAAGATGAGCCAATGCCAGAGAAAAAAGAAAAGAAAGAACCACTGTCACTTGA
GGAGCTAATTGCAAAGAAAAAAGCAGAGGAAGAACAGAAAAGTAAACCAGTTTTTATTTC
AAAAGAGCAGAGAGCACAAGAAGCAATTAAAAGAAGGCAAGAGCAAGTGGCTGCAATGAG
AGCTGCTGCAGCAGCTGTGCCTAAGTTTGGGGATGTTCCAGTTACAGAGCTTCTTCGTAA
AGAAAAAGATCAACAGCGATCACTTGATAGAGATAGAGATCGTGATCGAAGAGATAGAGA
CAGAGACGATAGAAGATACGATGACAGACGAGATAGAGATCGTGACAGAGATAGACCAGG
AACTTCACGTGATGACAAATTTTCAGATGACATTGCTTCATTAAAAGATAAAGAAAAAGA
ATCTGAAGCTATTCGTGAAAGATATTTGGGCATGATGAAGAAAAAACGCCGTGTGAGAAG
ATTAAATGATAGAAAATTCGTATTTGACTGGGACGCGAATGAAGACACTTCAAATGATTA
TAATTTACTATATAAAGATCGTCATTATGTTCAATTCTTTGGTAGAGGAAATATTGCTGG
CATTGATATCAAAGAACAAAAAA
>g5179.t4 Gene=g5179 Length=265
MGKEKSSRTDKDRDKDRSSRRSRSRSRDRSDRKSDRRYEDDRKPREARDEKLKTEVKEEL
EDEPMPEKKEKKEPLSLEELIAKKKAEEEQKSKPVFISKEQRAQEAIKRRQEQVAAMRAA
AAAVPKFGDVPVTELLRKEKDQQRSLDRDRDRDRRDRDRDDRRYDDRRDRDRDRDRPGTS
RDDKFSDDIASLKDKEKESEAIRERYLGMMKKKRRVRRLNDRKFVFDWDANEDTSNDYNL
LYKDRHYVQFFGRGNIAGIDIKEQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value |
|---|---|---|---|---|---|---|
| g5179.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 197 | - |
| g5179.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 112 | - |
| g5179.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 132 | 197 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5179/g5179.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5179.t4.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.
