General information for g6095.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent RNA helicase WM6.
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.t1 | TSS | g6095.t1 | 14093204 | 14093204 |
| chr_2 | g6095 | g6095.t1 | isoform | g6095.t1 | 14093246 | 14095797 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon1 | 14093246 | 14093438 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS1 | 14093246 | 14093438 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon2 | 14093632 | 14093931 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS2 | 14093632 | 14093931 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon3 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS3 | 14093994 | 14094098 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon4 | 14094284 | 14094402 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS4 | 14094284 | 14094402 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon5 | 14095120 | 14095398 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS5 | 14095120 | 14095398 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon6 | 14095468 | 14095723 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS6 | 14095468 | 14095723 |
| chr_2 | g6095 | g6095.t1 | exon | g6095.t1.exon7 | 14095784 | 14095797 |
| chr_2 | g6095 | g6095.t1 | cds | g6095.t1.CDS7 | 14095784 | 14095797 |
| chr_2 | g6095 | g6095.t1 | TTS | g6095.t1 | 14096130 | 14096130 |
Sequences
>g6095.t1 Gene=g6095 Length=1266
ATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCGTT
GTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTGGT
TTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCGAA
CATCCTTCGGCCGTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGACATTCTG
TGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTACAGCAA
CTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAACTAGCT
TTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAAGTCGGA
GTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACAACACCA
CACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAATTTAAAT
TTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAGTTAGAT
ATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTCATGATG
TTCTCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTATGCAAGATCCT
ATGGAAGTATATGTGGACGATGAAACGAAATTGACTTTACACGGATTGCAACAACACTAT
GTCAAATTGAAGGAAAATGAAAAGAATAAGAAGCTTTTTGAATTACTTGATGTATTGGAA
TTCAATCAAGTGGTCATCTTTGTGAAATCAGTTCAAAGATGTGAAGCTTTAGCCACTCTT
TTGACAGATCAGAATTTTCCAGCAATTGCAATTCATCGTGGTATGGCACAAGATGAGCGT
TTGGCTAAATATCAGCAATTTAAAGATTTTCAAAAGCGTATTTTGGTGGCAACAAACTTA
TTTGGACGTGGAATGGATATTGAACGTGTTAATATCGTTTTCAACTATGATATGCCTGAA
GATTCTGATACTTATCTTCATCGAGTCGCTCGTGCTGGTCGTTTTGGTACAAAAGGTCTC
GCCATCACTTTTGTTTCTGATGAAAATGATGCAAAGATTTTGAATAATGTTCAGGATCGC
TTCGATGTCAACATAACAGAGTTGCCCGACGAAATAGATCTCAGTTCATACATTGAAGGA
CGATAA
>g6095.t1 Gene=g6095 Length=421
MADNDDLLDYEDEEQNEQAVVDAGEKKDVKGTYVSIHSSGFRDFLLKPEILRAIVDCGFE
HPSAVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELA
FQISKEYERFSKYMSGVKVGVFFGGMPIQKDEATLKTTTPHIVVGTPGRILALIRGKNLN
LKHLKHFILDECDKMLEQLDMRKDVQEIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDP
MEVYVDDETKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVQRCEALATL
LTDQNFPAIAIHRGMAQDERLAKYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPE
DSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNNVQDRFDVNITELPDEIDLSSYIEG
R
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6095.t1 | CDD | cd17950 | DEADc_DDX39 | 38 | 245 | 0.000 |
| 14 | g6095.t1 | CDD | cd18787 | SF2_C_DEAD | 256 | 385 | 0.000 |
| 9 | g6095.t1 | Gene3D | G3DSA:3.40.50.300 | - | 27 | 245 | 0.000 |
| 8 | g6095.t1 | Gene3D | G3DSA:3.40.50.300 | - | 257 | 421 | 0.000 |
| 3 | g6095.t1 | PANTHER | PTHR47958:SF10 | ATP-DEPENDENT RNA HELICASE DDX39A | 23 | 415 | 0.000 |
| 4 | g6095.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 23 | 415 | 0.000 |
| 1 | g6095.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 64 | 229 | 0.000 |
| 2 | g6095.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 268 | 376 | 0.000 |
| 10 | g6095.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 39 | 67 | 9.298 |
| 12 | g6095.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 70 | 243 | 26.592 |
| 11 | g6095.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 255 | 416 | 21.713 |
| 7 | g6095.t1 | SMART | SM00487 | ultradead3 | 58 | 259 | 0.000 |
| 6 | g6095.t1 | SMART | SM00490 | helicmild6 | 295 | 376 | 0.000 |
| 5 | g6095.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 107 | 391 | 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 transcript has been annotated with K12812 (ATP-dependent RNA helicase UAP56/SUB2)
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.
