General information for g5179.t1
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.t1 | isoform | g5179.t1 | 7553852 | 7556572 |
| chr_2 | g5179 | g5179.t1 | exon | g5179.t1.exon1 | 7553852 | 7555373 |
| chr_2 | g5179 | g5179.t1 | cds | g5179.t1.CDS1 | 7553852 | 7555373 |
| chr_2 | g5179 | g5179.t1 | exon | g5179.t1.exon2 | 7555433 | 7556222 |
| chr_2 | g5179 | g5179.t1 | cds | g5179.t1.CDS2 | 7555433 | 7556222 |
| chr_2 | g5179 | g5179.t1 | exon | g5179.t1.exon3 | 7556566 | 7556572 |
| chr_2 | g5179 | g5179.t1 | cds | g5179.t1.CDS3 | 7556566 | 7556572 |
| chr_2 | g5179 | g5179.t1 | TTS | g5179.t1 | 7556668 | 7556668 |
| chr_2 | g5179 | g5179.t1 | TSS | g5179.t1 | NA | NA |
Sequences
>g5179.t1 Gene=g5179 Length=2319
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
GAGAAAAGGAAGAAGCTTATGGAATTATTGGCACGTGGACTCGAGCCACCAGTCATTATT
TTCGTCAATCAAAAGAAAGGTGCCGATGTATTGGCTAAAGGACTTGAGAAATTCGGCTTT
AACGCATGTACATTGCATGGTGGTAAAGGCCAAGAACAGAGAGAATACGCCCTTGCTTCT
CTTAAAAATGGATCAAAAGATATTTTGGTCGCAACAGATGTGGCAGGTCGTGGTATCGAT
ATTAAAGATGTATCAATGGTTATTAATTATGATATGGCCAAGACAATTGAAGATTACACA
CACAGAATTGGTAGAACTGGTCGCGCTGGAAAAACTGGAAAAGCTATCACGTTCATTACT
AAAGATGACAGTTCACTATTCTACGATTTGAAACAACTTATTATGAGCAGTCCCATTTCA
AATTGTCCACCTGAGTTAATGAATCATCCTGATGCACAGCATAAACCTGGAACTGTTATA
ACTAAAAAGCGAAGAGAGGAGAAAATATTTGCGGATTAA
>g5179.t1 Gene=g5179 Length=772
MGKEKSSRTDKDRDKDRSSRRSRSRSRDRSDRKSDRRYEDDRKPREARDEKLKTEVKEEL
EDEPMPEKKEKKEPLSLEELIAKKKAEEEQKSKPVFISKEQRAQEAIKRRQEQVAAMRAA
AAAVPKFGDVPVTELLRKEKDQQRSLDRDRDRDRRDRDRDDRRYDDRRDRDRDRDRPGTS
RDDKFSDDIASLKDKEKESEAIRERYLGMMKKKRRVRRLNDRKFVFDWDANEDTSNDYNL
LYKDRHYVQFFGRGNIAGIDIKEQKRKQSKFYGDLLEKRRTEAEKEQEKVRLKKVKKKED
KQKWDDRHWTEKEFDEMTERDWRIFREDYNITIKGGKIPNPIRKWPEASLSKEILDIIDK
VGYKDPTPIQRQAIPIGLQNRDIIGIAETGSGKTLAFLIPLLTWIQSLPKQERQENIDQG
PYAIILAPTRELAQQIEEETRKFGTPLGIRTVVVVGGLSREEQGFQLRLGCEIVIATPGR
LIDVLENRYLVLNQCTYVVMDEADRMIDMGFEPDVQKILEYMPVSNLKPDTEEAEDATKL
MENFNTRKKYRQTVMFTATMPPAVERLARTYLRRPATVYIGSVGKPTERTEQVVIMTTET
EKRKKLMELLARGLEPPVIIFVNQKKGADVLAKGLEKFGFNACTLHGGKGQEQREYALAS
LKNGSKDILVATDVAGRGIDIKDVSMVINYDMAKTIEDYTHRIGRTGRAGKTGKAITFIT
KDDSSLFYDLKQLIMSSPISNCPPELMNHPDAQHKPGTVITKKRREEKIFAD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5179.t1 | CDD | cd17945 | DEADc_DDX23 | 354 | 579 | 4.08332E-145 |
| 9 | g5179.t1 | CDD | cd18787 | SF2_C_DEAD | 591 | 719 | 4.30847E-56 |
| 8 | g5179.t1 | Coils | Coil | Coil | 278 | 298 | - |
| 7 | g5179.t1 | Gene3D | G3DSA:3.40.50.300 | - | 304 | 582 | 2.7E-94 |
| 6 | g5179.t1 | Gene3D | G3DSA:3.40.50.300 | - | 584 | 771 | 3.6E-58 |
| 15 | g5179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 192 | - |
| 16 | g5179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 112 | - |
| 14 | g5179.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 132 | 192 | - |
| 3 | g5179.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 84 | 770 | 5.4E-286 |
| 4 | g5179.t1 | PANTHER | PTHR47958:SF96 | ATP-DEPENDENT RNA HELICASE DDX23-RELATED | 84 | 770 | 5.4E-286 |
| 1 | g5179.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 367 | 567 | 3.9E-50 |
| 2 | g5179.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 602 | 710 | 6.5E-30 |
| 13 | g5179.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 499 | 507 | - |
| 17 | g5179.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 343 | 371 | 10.041 |
| 19 | g5179.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 374 | 578 | 30.717 |
| 18 | g5179.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 605 | 750 | 22.903 |
| 12 | g5179.t1 | SMART | SM00487 | ultradead3 | 362 | 593 | 5.5E-63 |
| 11 | g5179.t1 | SMART | SM00490 | helicmild6 | 629 | 710 | 8.3E-34 |
| 5 | g5179.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 420 | 731 | 3.4E-74 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5179/g5179.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5179.t1.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.
