General information for g664.t3
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.t3 | TSS | g664.t3 | 5053469 | 5053469 |
| chr_3 | g664 | g664.t3 | isoform | g664.t3 | 5053896 | 5055456 |
| chr_3 | g664 | g664.t3 | exon | g664.t3.exon1 | 5053896 | 5053932 |
| chr_3 | g664 | g664.t3 | exon | g664.t3.exon2 | 5054036 | 5055456 |
| chr_3 | g664 | g664.t3 | cds | g664.t3.CDS1 | 5054088 | 5055455 |
| chr_3 | g664 | g664.t3 | TTS | g664.t3 | NA | NA |
Sequences
>g664.t3 Gene=g664 Length=1458
ATATAGAACGAACAGAATTTCATAATTTTCTTTCGCGTTGGAGAATTGAAAAATCAAATC
GAATTTAAAAGAAAATAAACATTAATAAAATGGCGAGTAATAATCGAAACTGGATGCCGA
AAGTCGATGAAATTTATACTGGTGAAGTGATTGATGTAAATAAACATGGAGTTGTTGTTC
AATTGAAAGGCTTTGGTAGTAGACGAGGACGTAAAGATCTCACAGGCATTCTTCATAAGA
CAGATTCACCGATCGTTAACAATTTGATTGAAGGGAATAAAGTAAAAGTTCGTGTAATTT
CGTGTTCATCTGATGGCTTCATTTCTATCACAGCAAAAGATATAGAACAACCGATAAATA
AGAATGAAGCAAAGAAAAATGTTTTGGATGCAGATTATGAAAAGCAAAAACGTAAAATTC
GTGTAGTTAGTCCAGAAAGAAATGTTATAAAACAATGTACTACACCTTCTGCAATTGGTA
TTGAAGTTATAACAACCGAGCCAAATTTTTTGAAGAATATTGATTATCGTATGTCTTCAA
AAATTCCAACAAATATTCCCATTTTTAAGAATGAATACAGTACTATGGCACTGGTTGCAA
AGCAAAAGAACAAAAATATTCAACCAGGTCAAGTTTCTTTTCAACAGTCAAGTTTTAGTT
ATGAGTGGGTCAATCCGAAAATTGTTACTTCAAAACAATCTAATGCAAATTTGAATCAAA
AACAGCAGTTACCAATGATTCAAAGAAACAAAATGACAATCACAGAACAACGTCAATCTT
TGCCTATATTCAGTTATCGTGAAGATATTATAAGAGCTGTAACTAACAATCAATTTTTAA
TTGTTCAAGCAGAAACTGGTTCAGGAAAGACTACACAATTGCCACAATATTTGATTGAAG
GTGGATTCATTATTAAAGGAAAAGTTGCATGCACTCAGCCTCGCCGTGTTGCAGCTGTTA
GTGTTGCGAAGCGTGTTGCAGATGAATATGGTTGCATTATTGGTCAAGAAGTGGGATATA
AGATTAGATATGATGATGTTACATCATCAAGCACTATAATCAAATATATGACTGATGGAA
TTTTATTACGTGAATGTTTATCTGATAAAACATTAGATTCTTATTCAGTTATTATCCTCG
ATGAAGCTCATGAGCGAACCATCTATACTGATGTATTATTTGGTATTTTAAAAGAAGCTG
CCAAAAAACGACCAAGTTTACGAGTTGTCATTTCTTCTGCAACATTAAATGCACAAAAGT
TTTCAAAGTATTTCAATGATGCAAAAATTTTGACAATTCCTGGTTCCATGTTTCCTGTTG
AAATCAAATTTCGAGCAAGTCCTGAGCATGATTATTTTAATGCTGCCATTAACACTGTTT
TAAATATTCACTTGCGTGAACCAGCTGGTGACATCCTTTGCTTTTTGACTGGTCAAGATG
AAATTGAACGTGCATATG
>g664.t3 Gene=g664 Length=456
MASNNRNWMPKVDEIYTGEVIDVNKHGVVVQLKGFGSRRGRKDLTGILHKTDSPIVNNLI
EGNKVKVRVISCSSDGFISITAKDIEQPINKNEAKKNVLDADYEKQKRKIRVVSPERNVI
KQCTTPSAIGIEVITTEPNFLKNIDYRMSSKIPTNIPIFKNEYSTMALVAKQKNKNIQPG
QVSFQQSSFSYEWVNPKIVTSKQSNANLNQKQQLPMIQRNKMTITEQRQSLPIFSYREDI
IRAVTNNQFLIVQAETGSGKTTQLPQYLIEGGFIIKGKVACTQPRRVAAVSVAKRVADEY
GCIIGQEVGYKIRYDDVTSSSTIIKYMTDGILLRECLSDKTLDSYSVIILDEAHERTIYT
DVLFGILKEAAKKRPSLRVVISSATLNAQKFSKYFNDAKILTIPGSMFPVEIKFRASPEH
DYFNAAINTVLNIHLREPAGDILCFLTGQDEIERAY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g664.t3 | Coils | Coil | Coil | 89 | 109 | - |
| 8 | g664.t3 | Gene3D | G3DSA:2.40.50.140 | - | 11 | 91 | 1.3E-6 |
| 7 | g664.t3 | Gene3D | G3DSA:3.40.50.300 | - | 188 | 406 | 3.4E-86 |
| 6 | g664.t3 | Gene3D | G3DSA:3.40.50.300 | - | 407 | 456 | 3.3E-12 |
| 2 | g664.t3 | PANTHER | PTHR18934:SF120 | OS06G0343100 PROTEIN | 210 | 455 | 4.4E-106 |
| 3 | g664.t3 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 210 | 455 | 4.4E-106 |
| 1 | g664.t3 | Pfam | PF00270 | DEAD/DEAH box helicase | 238 | 391 | 3.0E-9 |
| 10 | g664.t3 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 346 | 355 | - |
| 14 | g664.t3 | ProSiteProfiles | PS50126 | S1 domain profile. | 13 | 83 | 10.752 |
| 13 | g664.t3 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 241 | 404 | 19.355 |
| 11 | g664.t3 | SMART | SM00316 | S1_6 | 11 | 83 | 5.1E-8 |
| 12 | g664.t3 | SMART | SM00487 | ultradead3 | 229 | 413 | 1.0E-30 |
| 5 | g664.t3 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 9 | 87 | 2.01E-7 |
| 4 | g664.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 221 | 454 | 7.05E-52 |
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.
