General information for g6095.t25
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Spliceosome RNA helicase DDX39B.
Parent gene
- The parent gene g6095 is located on chr_2: 14095466..14096224 (+ 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 | g6095 | g6095.t25 | TSS | g6095.t25 | 14093204 | 14093204 |
| chr_2 | g6095 | g6095.t25 | isoform | g6095.t25 | 14093246 | 14095797 |
| chr_2 | g6095 | g6095.t25 | exon | g6095.t25.exon1 | 14093246 | 14093442 |
| chr_2 | g6095 | g6095.t25 | exon | g6095.t25.exon2 | 14093632 | 14093931 |
| chr_2 | g6095 | g6095.t25 | cds | g6095.t25.CDS1 | 14093697 | 14093931 |
| chr_2 | g6095 | g6095.t25 | exon | g6095.t25.exon3 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t25 | cds | g6095.t25.CDS2 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t25 | exon | g6095.t25.exon4 | 14094284 | 14094402 |
| chr_2 | g6095 | g6095.t25 | cds | g6095.t25.CDS3 | 14094284 | 14094402 |
| chr_2 | g6095 | g6095.t25 | exon | g6095.t25.exon5 | 14095120 | 14095398 |
| chr_2 | g6095 | g6095.t25 | cds | g6095.t25.CDS4 | 14095120 | 14095398 |
| chr_2 | g6095 | g6095.t25 | exon | g6095.t25.exon6 | 14095468 | 14095797 |
| chr_2 | g6095 | g6095.t25 | cds | g6095.t25.CDS5 | 14095468 | 14095746 |
| chr_2 | g6095 | g6095.t25 | TTS | g6095.t25 | 14096130 | 14096130 |
Sequences
>g6095.t25 Gene=g6095 Length=1330
ATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCGTT
GTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTGGT
TTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCGAA
CATCCTTCGGCCGGTATTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGACAT
TCTGTGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTACA
GCAACTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAACT
AGCTTTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAAGT
CGGAGTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACAAC
ACCACACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAATTT
AAATTTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAGTT
AGATATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTCAT
GATGTTCTCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTATGCAAGA
TCCTATGGAAGTATATGTGGACGATGAAACGAAATTGACTTTACACGGATTGCAACAACA
CTATGTCAAATTGAAGGAAAATGAAAAGAATAAGAAGCTTTTTGAATTACTTGATGTATT
GGAATTCAATCAAGTGGTCATCTTTGTGAAATCAGTTCAAAGATGTGAAGCTTTAGCCAC
TCTTTTGACAGATCAGAATTTTCCAGCAATTGCAATTCATCGTGGTATGGCACAAGATGA
GCGTTTGGCTAAATATCAGCAATTTAAAGATTTTCAAAAGCGTATTTTGGTGGCAACAAA
CTTATTTGGACGTGGAATGGATATTGAACGTGTTAATATCGTTTTCAACTATGATATGCC
TGAAGATTCTGATACTTATCTTCATCGAGTCGCTCGTGCTGGTCGTTTTGGTACAAAAGG
TCTCGCCATCACTTTTGTTTCTGATGAAAATGATGCAAAGATTTTGAATAATGTTCAGGA
TCGCTTCGATGTCAACATAACAGAGTTGCCCGACGAAATAGATCTCAGTTCATACAGTAA
GTCTTATATTCATTATTAATTTGAATCGTTTACTAATACTTGTTTTCTTTTATTAGTTGA
AGGACGATAA
>g6095.t25 Gene=g6095 Length=338
MGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELAFQISKEYERFSKYMSGVKVGVFFGGM
PIQKDEATLKTTTPHIVVGTPGRILALIRGKNLNLKHLKHFILDECDKMLEQLDMRKDVQ
EIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDPMEVYVDDETKLTLHGLQQHYVKLKEN
EKNKKLFELLDVLEFNQVVIFVKSVQRCEALATLLTDQNFPAIAIHRGMAQDERLAKYQQ
FKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVS
DENDAKILNNVQDRFDVNITELPDEIDLSSYSKSYIHY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6095.t25 | CDD | cd18787 | SF2_C_DEAD | 170 | 299 | 9.39937E-48 |
| 7 | g6095.t25 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 159 | 6.1E-49 |
| 6 | g6095.t25 | Gene3D | G3DSA:3.40.50.300 | - | 171 | 335 | 3.5E-53 |
| 3 | g6095.t25 | PANTHER | PTHR47958:SF10 | ATP-DEPENDENT RNA HELICASE DDX39A | 1 | 329 | 3.1E-191 |
| 4 | g6095.t25 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 329 | 3.1E-191 |
| 1 | g6095.t25 | Pfam | PF00270 | DEAD/DEAH box helicase | 1 | 143 | 5.6E-31 |
| 2 | g6095.t25 | Pfam | PF00271 | Helicase conserved C-terminal domain | 182 | 290 | 1.3E-24 |
| 9 | g6095.t25 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 10 | g6095.t25 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 11 | g6095.t25 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 12 | g6095.t25 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 8 | g6095.t25 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 338 | - |
| 17 | g6095.t25 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 157 | 24.272 |
| 16 | g6095.t25 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 169 | 330 | 21.713 |
| 15 | g6095.t25 | SMART | SM00487 | ultradead3 | 1 | 173 | 2.5E-28 |
| 14 | g6095.t25 | SMART | SM00490 | helicmild6 | 209 | 290 | 5.5E-25 |
| 5 | g6095.t25 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 21 | 305 | 1.61E-65 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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