General information for g16603.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent RNA helicase DHX8.
Parent gene
- The parent gene g16603 is located on chr_4: 10172107..10174064 (+ 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_4 | g16603 | g16603.t1 | TSS | g16603.t1 | 10171303 | 10171303 |
| chr_4 | g16603 | g16603.t1 | isoform | g16603.t1 | 10171358 | 10174064 |
| chr_4 | g16603 | g16603.t1 | exon | g16603.t1.exon1 | 10171358 | 10173816 |
| chr_4 | g16603 | g16603.t1 | cds | g16603.t1.CDS1 | 10171358 | 10173816 |
| chr_4 | g16603 | g16603.t1 | exon | g16603.t1.exon2 | 10173875 | 10174064 |
| chr_4 | g16603 | g16603.t1 | cds | g16603.t1.CDS2 | 10173875 | 10174064 |
| chr_4 | g16603 | g16603.t1 | TTS | g16603.t1 | 10174414 | 10174414 |
Sequences
>g16603.t1 Gene=g16603 Length=2649
ATGAACAATAAAAATAAACAAAGTTGGAAACCTGAAGTAGATAAAATCTATACAGGTGAA
GTTATTGATGTCCTAAATCATGGAGCAATGGTTCGATTAAAAGGCTTTGGTGGTGGACGA
GGACGTCGAGAATTCAAAGGGCTTTTGCACAACAAAGACTCACCGATTGTTGAAAAATTG
ATCGATGGACATAAAGTTAAAGTTCGTGTCATTGCATTTATGCCTGATGGTTTTATTTCA
ATTACAACCAAAGACATTGAGCAGCCAGAAAATGAAACTGTAAATGTTTTTGATGAAGCT
TATGAGAAACAAAGACAAAAAATTCGTGTAATGAGTCCAGAGAGAAGAGATGTCAATCAA
TTTACAACTCCAAAGTCTGTAAGCATCGAAGTGATCACAACTGAGCCAGATTTTCTAAAA
AATGTCAATTTAAGAATTCCTTCGAGAATTCCAACAAAAATTTCGATTTACAAAAATGAA
AACAGTTTTATGGCAGAAGTTGCAAAAGAAAAGAGCAAAAATAATCAAGATTTAAAGTTT
CAGCGTGGAAGTTTCGATTCTAAATGGATTGATCCAGTTCGAATGAATTCACAAGCAACT
GAAAGTTTTGAAAATTCAACTCAGCCAGAACCGATGAAGAATCGAAATTTAATGTCAATT
ACAGAACAACGTGAATCACTTCCAATTTTTAAATTTCGTAATGAAATTATTCGATCAGTT
GTTGAAAATCAATTTTTAATCATTCAAGGCGAGACAGGATCTGGCAAGACAACCCAAGTT
GCACAGTATTTATTTGAAGGTGGATTAAATTTGAAAGGAAAAATTGCTTGCACTCAACCA
CGACGTGTTGCTGCTGTAACTGTTGCAAAACGTGTCGCAGAAGAATATGGATGCATTTTA
GGTCAAGAAGTTGGCTATAAAATTCGATTTGTTGATATGACTTCACCAAATACTGTCATT
AAATACATGACTGATGGAATTTTACTTCGTGAATGTTTATCAGATGCAAACCTTGACAAT
TATTCAGTTATAATTCTCGATGAAGCTCATGAAAGATCAATTTATACTGATGTTTTATTT
GGTGTTCTTAAAAAAGCTGCTAAAAGACGACCAAAATTAAGAGTTGTCATTTCCTCAGCA
ACTTTGAATACTGACCAATTTTCTAAATTTTTCAACAATGCAAAAGTTTTAAAAATTCCT
GGCAAAATGTTTCCAGTTGAAATCAAATATCAAGCAAATCCAGTACGTGATTATTTTAAT
GCTGCTGTCAATACAGTTTTGAATATTCACTTGCAAGAACCTGAAGGTGATATTTTATGT
TTTCTAACTGGACAAGATGAAATTGATTATGCATGTGAAATAATTGATGAAATTGCTGAA
GCTGATGATGAAAACTTTGGCAATCTTTATGCTTATGCTCTCTATTCAGCATTACCATTT
GAGGAACAATTTGAAATTTTCTCACAAATAGCCGAAGGTAATAGAAAAGTAATTTTTGCA
ACAAATATTGCTGAAACAAGTATGACAATTGATGGTGTAGTTTATGTTGTTGATCCTGGA
TATGTTAAGCAAAAAGTTTATGATGCCAAGACTGGGTTTGAGTCACTAATTGTTGTTCCA
ATTTCAAAAGCATCAGCTGATCAACGTTGTGGTCGAGCTGGAAGAGTTATGCCAGGAAAA
TGCTTTCGAATTTATACAGAATCAGCATATGAAAATGAAATGCTTGAGGTCAATGTTCCT
GACATTCAAAGATCAAATTTATCAAATGTTGTTTTGCATTTAAAGTCAATTGGTGTCAGA
GATATTTTGAATTTTGATTTTATGGATCCACCATCTCGTGACTTTTTAATTGCTGCTCTT
AAAGAACTTTATTTGTTAGAAGCATTGGACAGTGATGAAAAAGTAACACCAATGGGCCGT
CGTATGAATCAATTTCCAGTTGAACCAAATTATGCTAAAATGCTGCTCGTCTCTGATCAT
ATAAAATGCACAGATGAAATTGTAACAATTATTGCAATGTTGAGTGTTCAAAATATTTTT
TATTCACCAAAAAAGAACAAGCATCTTGCAAATGAAAAAAAAGATTCATTCAATCATCCT
GTTGGTGATCATTTGAGACTTTGGAATGTTTACAAAAAATGGGAAATGAATTACAAAAAG
AATCCCAGATGGTGCAAAAATCATTTTGTTAATGAGAAAAAACTTCATGAAGCTTATGAA
GTTCGTAAAAATTTACTTGAAATTCTTCAATCAAGAAATTTTGACATTTATTCAGCTGGA
AAAAATATTGAAAGAATTCAATTGGCGATTTGTGTTGGATTTTTTAAAAATATTGCGCAC
AAAGCTCCGTCATCAATATTCAGAAATAAAAATGATAAAAGTTACAGAACTTTGGAAGAA
AATCCTGAAATTGTTTATATCAATCGTTCGAGTTGTCTTTTTTATCAACTTCCTGAATGG
GTTGTTTACAACAACATACGTGAAACATCAAAGAAGTTTTTTCAAGAAATTACCGTCATT
AATCCTAATTGGTTGCCTTATATTGCTAAAGGAATGTATCGAAGAAAGGACAATGATGAT
AAAGATAATGAAGAAAAACTTATTAAAGCTTTTGTTGAAGCACAAAGTGCTAAAGAATAT
AAATTTTAA
>g16603.t1 Gene=g16603 Length=882
MNNKNKQSWKPEVDKIYTGEVIDVLNHGAMVRLKGFGGGRGRREFKGLLHNKDSPIVEKL
IDGHKVKVRVIAFMPDGFISITTKDIEQPENETVNVFDEAYEKQRQKIRVMSPERRDVNQ
FTTPKSVSIEVITTEPDFLKNVNLRIPSRIPTKISIYKNENSFMAEVAKEKSKNNQDLKF
QRGSFDSKWIDPVRMNSQATESFENSTQPEPMKNRNLMSITEQRESLPIFKFRNEIIRSV
VENQFLIIQGETGSGKTTQVAQYLFEGGLNLKGKIACTQPRRVAAVTVAKRVAEEYGCIL
GQEVGYKIRFVDMTSPNTVIKYMTDGILLRECLSDANLDNYSVIILDEAHERSIYTDVLF
GVLKKAAKRRPKLRVVISSATLNTDQFSKFFNNAKVLKIPGKMFPVEIKYQANPVRDYFN
AAVNTVLNIHLQEPEGDILCFLTGQDEIDYACEIIDEIAEADDENFGNLYAYALYSALPF
EEQFEIFSQIAEGNRKVIFATNIAETSMTIDGVVYVVDPGYVKQKVYDAKTGFESLIVVP
ISKASADQRCGRAGRVMPGKCFRIYTESAYENEMLEVNVPDIQRSNLSNVVLHLKSIGVR
DILNFDFMDPPSRDFLIAALKELYLLEALDSDEKVTPMGRRMNQFPVEPNYAKMLLVSDH
IKCTDEIVTIIAMLSVQNIFYSPKKNKHLANEKKDSFNHPVGDHLRLWNVYKKWEMNYKK
NPRWCKNHFVNEKKLHEAYEVRKNLLEILQSRNFDIYSAGKNIERIQLAICVGFFKNIAH
KAPSSIFRNKNDKSYRTLEENPEIVYINRSSCLFYQLPEWVVYNNIRETSKKFFQEITVI
NPNWLPYIAKGMYRRKDNDDKDNEEKLIKAFVEAQSAKEYKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16603.t1 | CDD | cd18791 | SF2_C_RHA | 404 | 565 | 2.19118E-75 |
| 8 | g16603.t1 | Gene3D | G3DSA:3.40.50.300 | - | 185 | 402 | 5.1E-85 |
| 9 | g16603.t1 | Gene3D | G3DSA:3.40.50.300 | - | 403 | 578 | 5.7E-66 |
| 10 | g16603.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 600 | 699 | 1.0E-26 |
| 5 | g16603.t1 | PANTHER | PTHR18934:SF120 | OS06G0343100 PROTEIN | 206 | 858 | 3.1E-252 |
| 6 | g16603.t1 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 206 | 858 | 3.1E-252 |
| 2 | g16603.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 234 | 386 | 1.0E-8 |
| 3 | g16603.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 425 | 556 | 4.1E-13 |
| 4 | g16603.t1 | Pfam | PF04408 | Helicase associated domain (HA2) | 619 | 710 | 3.9E-24 |
| 1 | g16603.t1 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 766 | 849 | 2.4E-14 |
| 12 | g16603.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 342 | 351 | - |
| 19 | g16603.t1 | ProSiteProfiles | PS50126 | S1 domain profile. | 14 | 84 | 9.267 |
| 18 | g16603.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 237 | 400 | 20.651 |
| 17 | g16603.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 422 | 598 | 15.488 |
| 13 | g16603.t1 | SMART | SM00316 | S1_6 | 12 | 84 | 3.5E-6 |
| 15 | g16603.t1 | SMART | SM00487 | ultradead3 | 225 | 409 | 6.4E-30 |
| 14 | g16603.t1 | SMART | SM00490 | helicmild6 | 456 | 557 | 1.8E-16 |
| 16 | g16603.t1 | SMART | SM00847 | ha2_5 | 618 | 708 | 7.4E-27 |
| 7 | g16603.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 220 | 729 | 1.09E-117 |
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.
