General information for g6095.t23
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.t23 | TSS | g6095.t23 | 14093204 | 14093204 |
| chr_2 | g6095 | g6095.t23 | isoform | g6095.t23 | 14093246 | 14094353 |
| chr_2 | g6095 | g6095.t23 | exon | g6095.t23.exon1 | 14093246 | 14093438 |
| chr_2 | g6095 | g6095.t23 | cds | g6095.t23.CDS1 | 14093246 | 14093438 |
| chr_2 | g6095 | g6095.t23 | exon | g6095.t23.exon2 | 14093632 | 14093931 |
| chr_2 | g6095 | g6095.t23 | cds | g6095.t23.CDS2 | 14093632 | 14093931 |
| chr_2 | g6095 | g6095.t23 | exon | g6095.t23.exon3 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t23 | cds | g6095.t23.CDS3 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t23 | exon | g6095.t23.exon4 | 14094284 | 14094353 |
| chr_2 | g6095 | g6095.t23 | cds | g6095.t23.CDS4 | 14094284 | 14094351 |
| chr_2 | g6095 | g6095.t23 | TTS | g6095.t23 | NA | NA |
Sequences
>g6095.t23 Gene=g6095 Length=668
ATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCGTT
GTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTGGT
TTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCGAA
CATCCTTCGGCCGTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGACATTCTG
TGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTACAGCAA
CTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAACTAGCT
TTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAAGTCGGA
GTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACAACACCA
CACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAATTTAAAT
TTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAGTTAGAT
ATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTCATGATG
TTCTCAGC
>g6095.t23 Gene=g6095 Length=222
MADNDDLLDYEDEEQNEQAVVDAGEKKDVKGTYVSIHSSGFRDFLLKPEILRAIVDCGFE
HPSAVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELA
FQISKEYERFSKYMSGVKVGVFFGGMPIQKDEATLKTTTPHIVVGTPGRILALIRGKNLN
LKHLKHFILDECDKMLEQLDMRKDVQEIFRNTPHGKQVMMFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g6095.t23 | CDD | cd17950 | DEADc_DDX39 | 38 | 222 | 0.000 |
| 6 | g6095.t23 | Gene3D | G3DSA:3.40.50.300 | - | 27 | 222 | 0.000 |
| 2 | g6095.t23 | PANTHER | PTHR47958:SF10 | ATP-DEPENDENT RNA HELICASE DDX39A | 22 | 222 | 0.000 |
| 3 | g6095.t23 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 22 | 222 | 0.000 |
| 1 | g6095.t23 | Pfam | PF00270 | DEAD/DEAH box helicase | 64 | 222 | 0.000 |
| 7 | g6095.t23 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 39 | 67 | 9.298 |
| 8 | g6095.t23 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 70 | 222 | 22.128 |
| 5 | g6095.t23 | SMART | SM00487 | ultradead3 | 58 | 218 | 0.000 |
| 4 | g6095.t23 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 27 | 222 | 0.000 |
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:0004386 | helicase activity | 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.
