General information for g664.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 g664 is located on chr_3: 5054088..5056781 (+ 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_3 | g664 | g664.t1 | TSS | g664.t1 | 5054035 | 5054035 |
| chr_3 | g664 | g664.t1 | isoform | g664.t1 | 5054088 | 5056781 |
| chr_3 | g664 | g664.t1 | exon | g664.t1.exon1 | 5054088 | 5056546 |
| chr_3 | g664 | g664.t1 | cds | g664.t1.CDS1 | 5054088 | 5056546 |
| chr_3 | g664 | g664.t1 | exon | g664.t1.exon2 | 5056604 | 5056781 |
| chr_3 | g664 | g664.t1 | cds | g664.t1.CDS2 | 5056604 | 5056781 |
| chr_3 | g664 | g664.t1 | TTS | g664.t1 | 5057007 | 5057007 |
Sequences
>g664.t1 Gene=g664 Length=2637
ATGGCGAGTAATAATCGAAACTGGATGCCGAAAGTCGATGAAATTTATACTGGTGAAGTG
ATTGATGTAAATAAACATGGAGTTGTTGTTCAATTGAAAGGCTTTGGTAGTAGACGAGGA
CGTAAAGATCTCACAGGCATTCTTCATAAGACAGATTCACCGATCGTTAACAATTTGATT
GAAGGGAATAAAGTAAAAGTTCGTGTAATTTCGTGTTCATCTGATGGCTTCATTTCTATC
ACAGCAAAAGATATAGAACAACCGATAAATAAGAATGAAGCAAAGAAAAATGTTTTGGAT
GCAGATTATGAAAAGCAAAAACGTAAAATTCGTGTAGTTAGTCCAGAAAGAAATGTTATA
AAACAATGTACTACACCTTCTGCAATTGGTATTGAAGTTATAACAACCGAGCCAAATTTT
TTGAAGAATATTGATTATCGTATGTCTTCAAAAATTCCAACAAATATTCCCATTTTTAAG
AATGAATACAGTACTATGGCACTGGTTGCAAAGCAAAAGAACAAAAATATTCAACCAGGT
CAAGTTTCTTTTCAACAGTCAAGTTTTAGTTATGAGTGGGTCAATCCGAAAATTGTTACT
TCAAAACAATCTAATGCAAATTTGAATCAAAAACAGCAGTTACCAATGATTCAAAGAAAC
AAAATGACAATCACAGAACAACGTCAATCTTTGCCTATATTCAGTTATCGTGAAGATATT
ATAAGAGCTGTAACTAACAATCAATTTTTAATTGTTCAAGCAGAAACTGGTTCAGGAAAG
ACTACACAATTGCCACAATATTTGATTGAAGGTGGATTCATTATTAAAGGAAAAGTTGCA
TGCACTCAGCCTCGCCGTGTTGCAGCTGTTAGTGTTGCGAAGCGTGTTGCAGATGAATAT
GGTTGCATTATTGGTCAAGAAGTGGGATATAAGATTAGATATGATGATGTTACATCATCA
AGCACTATAATCAAATATATGACTGATGGAATTTTATTACGTGAATGTTTATCTGATAAA
ACATTAGATTCTTATTCAGTTATTATCCTCGATGAAGCTCATGAGCGAACCATCTATACT
GATGTATTATTTGGTATTTTAAAAGAAGCTGCCAAAAAACGACCAAGTTTACGAGTTGTC
ATTTCTTCTGCAACATTAAATGCACAAAAGTTTTCAAAGTATTTCAATGATGCAAAAATT
TTGACAATTCCTGGTTCCATGTTTCCTGTTGAAATCAAATTTCGAGCAAGTCCTGAGCAT
GATTATTTTAATGCTGCCATTAACACTGTTTTAAATATTCACTTGCGTGAACCAGCTGGT
GACATCCTTTGCTTTTTGACTGGTCAAGATGAAATTGAACGTGCATATGACATTATTGAA
GAAAAGGCATGTTCAAATGAATTTTCTAATTTATTTGCTTTTCCTATCTATTCTGCTATG
CCTTTTGAAGAACAATCAGAAATTTTCACACCAACGCAACGTGGTCAAAGAAAAGTAATT
TTTGCTACAAATATTGCAGAAACAAGCATGACAATTGATGGAATTGTGTATGTGGTTGAT
CCGGGCTTTGTTAAACAAAAGATCTATGATGCAAAAACAGGAATTGAATCACTTATGATT
ATACCAATCTCAAAAGCTTCTGCTGACCAACGTTCTGGTAGAGCTGGTCGAATTTCACCA
GGAAAATGCTATCGCATTTACACAGAACAAGCATATCTGACAGAAATGCTCGATTCAACT
GTTCCTGAAATTCAGCGTTCGAATTTGTCAAATGTTATCTTGCATTTAAAATCAATTGGT
GTCGGAGATATTTTAAATTTTGATTTTTTGGATCCACCACCTCGTTCATCTTTAGTTTCT
GCACTCAAAGAACTTTATTTGTTGGATGCACTTGATGAAGATGGAAAAATTACTACTATC
GGACAAAAAATGAATCGATTTCCAATTGATCCAAATTATGCTAAAATGCTTCTTCTTTCC
GAAGACATGAAATGCTCAGATGAAATTATTACAATAATTGCGATGTTGAGCGTTCCAAAT
ATTTTTTATCGTCCGAAAAAACAGCAAGCACTTGCTGATGAAAGAAAGAACATTTTCAAT
CATGCAGTTGGAGATCATTTGCGACTCTTGAATGTTTATAACAAATGGGAAATGAATTAC
ACTAATCCAAATTGGTGTAAAAATCATTATTTAAATGAAAACAAACTCTATGAAGCATAT
GAAGTTCGCAAAAATTTGCTTTCGATTCTAGAATCACGTGGTGTTGAAATATTTTCAGCA
GGCAAAAATATTTCAAGAATTCAAATGGCAATTTGTGCTGGTTTTTTCAAAAATATTGCT
CGAAAAGATTCTGAAACGATCTTTAGTCGTGGAACGGTAAAAAGCTACAAAACTTTGGAC
AAAAATCCCGAAACAGTATTCATTCACCCTTCGAGCTGCCTTTTTCAATTGCCAAAATGG
GTTGTTTTCAATAACATACGTGAAACATCAAAAAAGTTTCTGCAGGACATTACTGTCATC
GATCCACAATGGCTTCCTATAGTTGCTAAAAGAATGTACCGATCGACTGGTGTAGAGAGA
AATGATTGTGATGATTTATTGGCACTACTCAACACTATTCAAAGATTGAATTTATAA
>g664.t1 Gene=g664 Length=878
MASNNRNWMPKVDEIYTGEVIDVNKHGVVVQLKGFGSRRGRKDLTGILHKTDSPIVNNLI
EGNKVKVRVISCSSDGFISITAKDIEQPINKNEAKKNVLDADYEKQKRKIRVVSPERNVI
KQCTTPSAIGIEVITTEPNFLKNIDYRMSSKIPTNIPIFKNEYSTMALVAKQKNKNIQPG
QVSFQQSSFSYEWVNPKIVTSKQSNANLNQKQQLPMIQRNKMTITEQRQSLPIFSYREDI
IRAVTNNQFLIVQAETGSGKTTQLPQYLIEGGFIIKGKVACTQPRRVAAVSVAKRVADEY
GCIIGQEVGYKIRYDDVTSSSTIIKYMTDGILLRECLSDKTLDSYSVIILDEAHERTIYT
DVLFGILKEAAKKRPSLRVVISSATLNAQKFSKYFNDAKILTIPGSMFPVEIKFRASPEH
DYFNAAINTVLNIHLREPAGDILCFLTGQDEIERAYDIIEEKACSNEFSNLFAFPIYSAM
PFEEQSEIFTPTQRGQRKVIFATNIAETSMTIDGIVYVVDPGFVKQKIYDAKTGIESLMI
IPISKASADQRSGRAGRISPGKCYRIYTEQAYLTEMLDSTVPEIQRSNLSNVILHLKSIG
VGDILNFDFLDPPPRSSLVSALKELYLLDALDEDGKITTIGQKMNRFPIDPNYAKMLLLS
EDMKCSDEIITIIAMLSVPNIFYRPKKQQALADERKNIFNHAVGDHLRLLNVYNKWEMNY
TNPNWCKNHYLNENKLYEAYEVRKNLLSILESRGVEIFSAGKNISRIQMAICAGFFKNIA
RKDSETIFSRGTVKSYKTLDKNPETVFIHPSSCLFQLPKWVVFNNIRETSKKFLQDITVI
DPQWLPIVAKRMYRSTGVERNDCDDLLALLNTIQRLNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g664.t1 | CDD | cd18791 | SF2_C_RHA | 408 | 567 | 8.11137E-77 |
| 13 | g664.t1 | Coils | Coil | Coil | 89 | 109 | - |
| 12 | g664.t1 | Gene3D | G3DSA:2.40.50.140 | - | 11 | 90 | 3.1E-6 |
| 10 | g664.t1 | Gene3D | G3DSA:3.40.50.300 | - | 189 | 406 | 1.3E-85 |
| 9 | g664.t1 | Gene3D | G3DSA:3.40.50.300 | - | 407 | 580 | 1.4E-65 |
| 11 | g664.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 604 | 711 | 1.1E-29 |
| 5 | g664.t1 | PANTHER | PTHR18934:SF120 | OS06G0343100 PROTEIN | 210 | 856 | 1.6E-257 |
| 6 | g664.t1 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 210 | 856 | 1.6E-257 |
| 2 | g664.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 238 | 391 | 9.9E-9 |
| 3 | g664.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 428 | 558 | 1.9E-13 |
| 4 | g664.t1 | Pfam | PF04408 | Helicase associated domain (HA2) | 621 | 696 | 7.4E-24 |
| 1 | g664.t1 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 767 | 849 | 3.5E-19 |
| 15 | g664.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 346 | 355 | - |
| 22 | g664.t1 | ProSiteProfiles | PS50126 | S1 domain profile. | 13 | 83 | 10.752 |
| 21 | g664.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 241 | 404 | 19.355 |
| 20 | g664.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 426 | 600 | 16.28 |
| 16 | g664.t1 | SMART | SM00316 | S1_6 | 11 | 83 | 5.1E-8 |
| 18 | g664.t1 | SMART | SM00487 | ultradead3 | 229 | 413 | 1.0E-30 |
| 17 | g664.t1 | SMART | SM00490 | helicmild6 | 462 | 559 | 9.2E-16 |
| 19 | g664.t1 | SMART | SM00847 | ha2_5 | 620 | 710 | 8.0E-32 |
| 8 | g664.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 9 | 87 | 6.94E-7 |
| 7 | g664.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 221 | 733 | 9.96E-122 |
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.
