General information for g6095.t16
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.t16 | TSS | g6095.t16 | 14092094 | 14092094 |
| chr_2 | g6095 | g6095.t16 | isoform | g6095.t16 | 14092958 | 14095125 |
| chr_2 | g6095 | g6095.t16 | exon | g6095.t16.exon1 | 14092958 | 14092978 |
| chr_2 | g6095 | g6095.t16 | exon | g6095.t16.exon2 | 14093205 | 14093442 |
| chr_2 | g6095 | g6095.t16 | exon | g6095.t16.exon3 | 14093632 | 14093931 |
| chr_2 | g6095 | g6095.t16 | cds | g6095.t16.CDS1 | 14093697 | 14093931 |
| chr_2 | g6095 | g6095.t16 | exon | g6095.t16.exon4 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t16 | cds | g6095.t16.CDS2 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t16 | exon | g6095.t16.exon5 | 14094284 | 14094402 |
| chr_2 | g6095 | g6095.t16 | cds | g6095.t16.CDS3 | 14094284 | 14094402 |
| chr_2 | g6095 | g6095.t16 | exon | g6095.t16.exon6 | 14095120 | 14095125 |
| chr_2 | g6095 | g6095.t16 | cds | g6095.t16.CDS4 | 14095120 | 14095125 |
| chr_2 | g6095 | g6095.t16 | TTS | g6095.t16 | 14096130 | 14096130 |
Sequences
>g6095.t16 Gene=g6095 Length=789
TTTTTCTTTGGATTTTATTAATTCAAGTATTACAAGAGCATTAAATAAATAATTGCAACA
ATATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCG
TTGTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTG
GTTTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCG
AACATCCTTCGGCCGGTATTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGAC
ATTCTGTGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTA
CAGCAACTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAA
CTAGCTTTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAA
GTCGGAGTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACA
ACACCACACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAAT
TTAAATTTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAG
TTAGATATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTC
ATGATGTTCTCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTATGCAA
GATCCTATG
>g6095.t16 Gene=g6095 Length=155
MGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELAFQISKEYERFSKYMSGVKVGVFFGGM
PIQKDEATLKTTTPHIVVGTPGRILALIRGKNLNLKHLKHFILDECDKMLEQLDMRKDVQ
EIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDPM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6095.t16 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 155 | 3.6E-49 |
| 2 | g6095.t16 | PANTHER | PTHR47958:SF10 | ATP-DEPENDENT RNA HELICASE DDX39A | 1 | 154 | 1.2E-84 |
| 3 | g6095.t16 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 154 | 1.2E-84 |
| 1 | g6095.t16 | Pfam | PF00270 | DEAD/DEAH box helicase | 1 | 143 | 5.5E-32 |
| 9 | g6095.t16 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 10 | g6095.t16 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 11 | g6095.t16 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 12 | g6095.t16 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 8 | g6095.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 155 | - |
| 7 | g6095.t16 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 155 | 24.109 |
| 5 | g6095.t16 | SMART | SM00487 | ultradead3 | 1 | 154 | 1.6E-17 |
| 4 | g6095.t16 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 154 | 1.87E-41 |
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.
