General information for g5185.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 g5185 is located on chr_2: 7565921..7567785 (+ 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 | g5185 | g5185.t1 | isoform | g5185.t1 | 7565921 | 7567785 |
| chr_2 | g5185 | g5185.t1 | exon | g5185.t1.exon1 | 7565921 | 7566142 |
| chr_2 | g5185 | g5185.t1 | cds | g5185.t1.CDS1 | 7565921 | 7566142 |
| chr_2 | g5185 | g5185.t1 | exon | g5185.t1.exon2 | 7566717 | 7567446 |
| chr_2 | g5185 | g5185.t1 | cds | g5185.t1.CDS2 | 7566717 | 7567446 |
| chr_2 | g5185 | g5185.t1 | exon | g5185.t1.exon3 | 7567505 | 7567785 |
| chr_2 | g5185 | g5185.t1 | cds | g5185.t1.CDS3 | 7567505 | 7567785 |
| chr_2 | g5185 | g5185.t1 | TTS | g5185.t1 | 7568725 | 7568725 |
| chr_2 | g5185 | g5185.t1 | TSS | g5185.t1 | NA | NA |
Sequences
>g5185.t1 Gene=g5185 Length=1233
ATGGGTAAAGAAAAATCATCAAGGACTGACAAAGATAGAGATAAAGACCGTAGTAGTAGA
AGATCAAGGTCTAGATCGAGAGACCGTAGTGATCGAAAATCAGATCGTAGATATGAGGAT
GATCGCAAACCTCGAGAAGCAAGAGATGAGAAATTGAAAACTGAAGTTAAAGAAGAGCTC
GAAAGAGCCAATGCCAGAGAAAAAAGAAAAGAAAGAACCACTAAAGCAGAGAAATTTTAT
GGAGATTTATTAGAAAAACGTCGACAGAAGCTGAGAAAGAACAAGAGAAGGTTCGCTTTG
AAGAAAGTTAAAAAGAAGGAAGAAACAAACAAAAAATGGGATGATCGTCATTGGACTGAA
AAAGAATTTGATGAAATGACTGAACGTGATTGGCGTATTTTCCGTGAAAGATTACAATAT
CACAATCAAAGGTGGAAAAATACCAAATCCAATCAGAAAATGGCCAAGAAGCAAGCTTAT
CGAAAGAAATATTGGATATTATTGATAAAGTTGGTTATAAAGATCCAACTCCTATTCAGA
GACAAGCTATACCAATTGGTTTACAAAATCGTGACATTATCGGTATTGCCGAAACAAGTT
CTGGAAAAACTCTTGCTTTTTCTCATTCCTCTACTTACATGGATTTCAATCGCTGCCAAA
AGCAAGAACGTCAGAGAATATCGATCAAGGAACCATATGCTATTATTTAGCACCAACAAG
AAAACTTGCCTCAACAAATTGAGGAAGAAACAAGAAAATTCGGAACGCCTTGGGTATTCG
CCACGTTGTCGTTGTGGGAGGTTTATCTCGAGAAGAGCAAGTTTTCAACTACGATTGGGC
TGCGAAATTGTAATCGCGACTCCTGGTCGTTTAATTGATGTTTTAGAGAATCGTTATTTA
GTTTTGAATCAATGCACATATGTAGTCATGGATGAAGCTGACAGAATGATTGATATGGGT
TTTGAACCAGACGTACAAAAGATTCTCGAATATATGCCAGTATCAAATTTAAACCAGATA
CAGAAGAAGCAGAAGATGCAACCCAACATCATGGAAAATTCAATACACGCAAAAAGTATA
GACAAACTGTCATGTTTACAGCAACTATGCCTCCAGCTGTTGAGCGTTAGCTCGTACATA
TTTGCGACGTCCAGCAACAGTTTATATTGGATCTTTGGTAAACCGACAGAGCGAACTGAG
CAAGTAGTAATTATGACAACTGAAACAGATTAA
>g5185.t1 Gene=g5185 Length=410
MGKEKSSRTDKDRDKDRSSRRSRSRSRDRSDRKSDRRYEDDRKPREARDEKLKTEVKEEL
ERANAREKRKERTTKAEKFYGDLLEKRRQKLRKNKRRFALKKVKKKEETNKKWDDRHWTE
KEFDEMTERDWRIFRERLQYHNQRWKNTKSNQKMAKKQAYRKKYWILLIKLVIKIQLLFR
DKLYQLVYKIVTLSVLPKQVLEKLLLFLIPLLTWISIAAKSKNVREYRSRNHMLLFSTNK
KTCLNKLRKKQENSERLGYSPRCRCGRFISRRASFQLRLGCEIVIATPGRLIDVLENRYL
VLNQCTYVVMDEADRMIDMGFEPDVQKILEYMPVSNLNQIQKKQKMQPNIMENSIHAKSI
DKLSCLQQLCLQLLSVSSYIFATSSNSLYWIFGKPTERTEQVVIMTTETD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5185.t1 | Coils | Coil | Coil | 46 | 77 | - |
| 5 | g5185.t1 | Gene3D | G3DSA:3.40.50.300 | - | 201 | 378 | 4.4E-25 |
| 13 | g5185.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 73 | - |
| 2 | g5185.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 206 | 342 | 7.5E-43 |
| 3 | g5185.t1 | PANTHER | PTHR47958:SF96 | ATP-DEPENDENT RNA HELICASE DDX23-RELATED | 206 | 342 | 7.5E-43 |
| 1 | g5185.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 206 | 338 | 2.2E-16 |
| 8 | g5185.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 163 | - |
| 10 | g5185.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 164 | 180 | - |
| 9 | g5185.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 181 | 199 | - |
| 11 | g5185.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 219 | - |
| 7 | g5185.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 220 | 410 | - |
| 12 | g5185.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 309 | 317 | - |
| 14 | g5185.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 276 | 329 | 10.377 |
| 4 | g5185.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 205 | 335 | 1.73E-19 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5185/g5185.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5185.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | 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