General information for g5179.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t2 | isoform | g5179.t2 | 7553367 | 7555710 |
| chr_2 | g5179 | g5179.t2 | exon | g5179.t2.exon1 | 7553367 | 7553719 |
| chr_2 | g5179 | g5179.t2 | exon | g5179.t2.exon2 | 7553785 | 7555373 |
| chr_2 | g5179 | g5179.t2 | cds | g5179.t2.CDS1 | 7553852 | 7555373 |
| chr_2 | g5179 | g5179.t2 | TTS | g5179.t2 | 7554050 | 7554050 |
| chr_2 | g5179 | g5179.t2 | exon | g5179.t2.exon3 | 7555433 | 7555710 |
| chr_2 | g5179 | g5179.t2 | cds | g5179.t2.CDS2 | 7555433 | 7555710 |
| chr_2 | g5179 | g5179.t2 | TSS | g5179.t2 | NA | NA |
Sequences
>g5179.t2 Gene=g5179 Length=2220
AACTTTTGAAAATTTGTATTTTTTTCCAGACATTCGTTTTCTTTTGTGAAGCAAGTTTTA
AAAGTTGGGCTGTGCGGGTGATTCAATTGTCTTCAAAATAATATTTTATTTACTTACATA
CTATATTAATAGATATGATCTGACCTAATTTCACCAAATAATCAACGAAAGAATCAAAAT
AAAATTTCTAAAGACTCCTATGATTGGCTAAAATAAATATTTATCTTTTTTTCAACTGTC
AGTTTGAAATTTAAAAAAAAAGAGCGGGGTGAGAAATTTGTGACAAAATATTGATAAACA
AACCATTTGTCGCTATTGTAAAATTCGCAAAAAATAATTATTTTTCACTGCAAATAATAA
ACTCTTATTAATAATACAAAATAGAGAGTAAACTAAAAGATAGACTAAACGTTTAGAAAA
ATGGGTAAAGAAAAATCATCAAGGACTGACAAAGATAGAGATAAAGACCGTAGTAGTAGA
AGATCAAGGTCTAGATCGAGAGACCGTAGTGATCGAAAATCAGATCGTAGATATGAGGAT
GATCGCAAACCTCGAGAAGCAAGAGATGAGAAATTGAAAACTGAAGTTAAAGAAGAGCTC
GAAGATGAGCCAATGCCAGAGAAAAAAGAAAAGAAAGAACCACTGTCACTTGAGGAGCTA
ATTGCAAAGAAAAAAGCAGAGGAAGAACAGAAAAGTAAACCAGTTTTTATTTCAAAAGAG
CAGAGAGCACAAGAAGCAATTAAAAGAAGGCAAGAGCAAGTGGCTGCAATGAGAGCTGCT
GCAGCAGCTGTGCCTAAGTTTGGGGATGTTCCAGTTACAGAGCTTCTTCGTAAAGAAAAA
GATCAACAGCGATCACTTGATAGAGATAGAGATCGTGATCGAAGAGATAGAGACAGAGAC
GATAGAAGATACGATGACAGACGAGATAGAGATCGTGACAGAGATAGACCAGGAACTTCA
CGTGATGACAAATTTTCAGATGACATTGCTTCATTAAAAGATAAAGAAAAAGAATCTGAA
GCTATTCGTGAAAGATATTTGGGCATGATGAAGAAAAAACGCCGTGTGAGAAGATTAAAT
GATAGAAAATTCGTATTTGACTGGGACGCGAATGAAGACACTTCAAATGATTATAATTTA
CTATATAAAGATCGTCATTATGTTCAATTCTTTGGTAGAGGAAATATTGCTGGCATTGAT
ATCAAAGAACAAAAAAGAAAGCAGAGTAAATTTTATGGAGATTTATTAGAAAAACGTCGA
ACAGAAGCTGAGAAAGAACAAGAGAAGGTTCGCTTGAAGAAAGTTAAAAAGAAGGAAGAC
AAACAAAAATGGGATGATCGTCATTGGACTGAAAAAGAATTTGATGAAATGACTGAACGT
GATTGGCGTATTTTTCGTGAAGATTACAATATCACAATCAAAGGTGGAAAAATACCAAAT
CCAATCAGAAAATGGCCAGAAGCAAGCTTATCGAAAGAAATATTGGATATTATTGATAAA
GTTGGTTATAAAGATCCAACTCCTATTCAGAGACAAGCTATACCAATTGGTTTACAAAAT
CGTGACATTATCGGTATTGCCGAAACAGGTTCTGGAAAAACTCTTGCTTTTCTCATTCCT
CTACTTACATGGATTCAATCGCTGCCAAAGCAAGAACGTCAGGAGAATATCGATCAAGGA
CCATATGCTATTATTTTAGCACCAACAAGAGAACTTGCTCAACAAATTGAGGAAGAAACA
AGAAAATTCGGAACGCCTTTGGGTATTCGCACAGTTGTCGTTGTGGGAGGTTTATCTCGA
GAAGAGCAAGGTTTTCAACTACGATTGGGCTGCGAAATTGTAATCGCGACTCCTGGTCGT
TTAATTGATGTTTTAGAGAATCGTTATTTAGTTTTGAATCAATGCACATATGTAGTCATG
GATGAAGCTGACAGAATGATTGATATGGGTTTTGAACCAGACGTACAAAAGATTCTCGAA
TATATGCCAGTATCAAATTTAAAACCAGATACAGAAGAAGCAGAAGATGCAACCAAACTC
ATGGAAAATTTCAATACACGCAAAAAGTATAGACAAACTGTCATGTTTACAGCAACTATG
CCTCCAGCTGTTGAGCGTTTAGCTCGTACATATTTGCGACGTCCAGCAACAGTTTATATT
GGATCTGTTGGTAAACCGACAGAGCGAACTGAGCAAGTAGTAATTATGACAACTGAAACA
>g5179.t2 Gene=g5179 Length=600
MGKEKSSRTDKDRDKDRSSRRSRSRSRDRSDRKSDRRYEDDRKPREARDEKLKTEVKEEL
EDEPMPEKKEKKEPLSLEELIAKKKAEEEQKSKPVFISKEQRAQEAIKRRQEQVAAMRAA
AAAVPKFGDVPVTELLRKEKDQQRSLDRDRDRDRRDRDRDDRRYDDRRDRDRDRDRPGTS
RDDKFSDDIASLKDKEKESEAIRERYLGMMKKKRRVRRLNDRKFVFDWDANEDTSNDYNL
LYKDRHYVQFFGRGNIAGIDIKEQKRKQSKFYGDLLEKRRTEAEKEQEKVRLKKVKKKED
KQKWDDRHWTEKEFDEMTERDWRIFREDYNITIKGGKIPNPIRKWPEASLSKEILDIIDK
VGYKDPTPIQRQAIPIGLQNRDIIGIAETGSGKTLAFLIPLLTWIQSLPKQERQENIDQG
PYAIILAPTRELAQQIEEETRKFGTPLGIRTVVVVGGLSREEQGFQLRLGCEIVIATPGR
LIDVLENRYLVLNQCTYVVMDEADRMIDMGFEPDVQKILEYMPVSNLKPDTEEAEDATKL
MENFNTRKKYRQTVMFTATMPPAVERLARTYLRRPATVYIGSVGKPTERTEQVVIMTTET
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5179.t2 | CDD | cd17945 | DEADc_DDX23 | 354 | 579 | 2.53861E-146 |
| 6 | g5179.t2 | Coils | Coil | Coil | 278 | 298 | - |
| 5 | g5179.t2 | Gene3D | G3DSA:3.40.50.300 | - | 304 | 582 | 1.6E-94 |
| 11 | g5179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 192 | - |
| 12 | g5179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 112 | - |
| 10 | g5179.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 132 | 192 | - |
| 2 | g5179.t2 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 83 | 599 | 6.1E-171 |
| 3 | g5179.t2 | PANTHER | PTHR47958:SF96 | ATP-DEPENDENT RNA HELICASE DDX23-RELATED | 83 | 599 | 6.1E-171 |
| 1 | g5179.t2 | Pfam | PF00270 | DEAD/DEAH box helicase | 367 | 567 | 2.4E-50 |
| 9 | g5179.t2 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 499 | 507 | - |
| 13 | g5179.t2 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 343 | 371 | 10.041 |
| 14 | g5179.t2 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 374 | 578 | 30.717 |
| 8 | g5179.t2 | SMART | SM00487 | ultradead3 | 362 | 593 | 5.5E-63 |
| 4 | g5179.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 325 | 580 | 2.08E-71 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5179/g5179.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5179.t2.fa.iupred3.txt does not exist
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 transcript has been annotated with K12858 (ATP-dependent RNA helicase DDX23/PRP28)
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.
