General information for g664.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t4 | TSS | g664.t4 | 5054035 | 5054035 |
| chr_3 | g664 | g664.t4 | isoform | g664.t4 | 5054088 | 5054973 |
| chr_3 | g664 | g664.t4 | exon | g664.t4.exon1 | 5054088 | 5054973 |
| chr_3 | g664 | g664.t4 | cds | g664.t4.CDS1 | 5054088 | 5054972 |
| chr_3 | g664 | g664.t4 | TTS | g664.t4 | NA | NA |
Sequences
>g664.t4 Gene=g664 Length=886
ATGGCGAGTAATAATCGAAACTGGATGCCGAAAGTCGATGAAATTTATACTGGTGAAGTG
ATTGATGTAAATAAACATGGAGTTGTTGTTCAATTGAAAGGCTTTGGTAGTAGACGAGGA
CGTAAAGATCTCACAGGCATTCTTCATAAGACAGATTCACCGATCGTTAACAATTTGATT
GAAGGGAATAAAGTAAAAGTTCGTGTAATTTCGTGTTCATCTGATGGCTTCATTTCTATC
ACAGCAAAAGATATAGAACAACCGATAAATAAGAATGAAGCAAAGAAAAATGTTTTGGAT
GCAGATTATGAAAAGCAAAAACGTAAAATTCGTGTAGTTAGTCCAGAAAGAAATGTTATA
AAACAATGTACTACACCTTCTGCAATTGGTATTGAAGTTATAACAACCGAGCCAAATTTT
TTGAAGAATATTGATTATCGTATGTCTTCAAAAATTCCAACAAATATTCCCATTTTTAAG
AATGAATACAGTACTATGGCACTGGTTGCAAAGCAAAAGAACAAAAATATTCAACCAGGT
CAAGTTTCTTTTCAACAGTCAAGTTTTAGTTATGAGTGGGTCAATCCGAAAATTGTTACT
TCAAAACAATCTAATGCAAATTTGAATCAAAAACAGCAGTTACCAATGATTCAAAGAAAC
AAAATGACAATCACAGAACAACGTCAATCTTTGCCTATATTCAGTTATCGTGAAGATATT
ATAAGAGCTGTAACTAACAATCAATTTTTAATTGTTCAAGCAGAAACTGGTTCAGGAAAG
ACTACACAATTGCCACAATATTTGATTGAAGGTGGATTCATTATTAAAGGAAAAGTTGCA
TGCACTCAGCCTCGCCGTGTTGCAGCTGTTAGTGTTGCGAAGCGTG
>g664.t4 Gene=g664 Length=295
MASNNRNWMPKVDEIYTGEVIDVNKHGVVVQLKGFGSRRGRKDLTGILHKTDSPIVNNLI
EGNKVKVRVISCSSDGFISITAKDIEQPINKNEAKKNVLDADYEKQKRKIRVVSPERNVI
KQCTTPSAIGIEVITTEPNFLKNIDYRMSSKIPTNIPIFKNEYSTMALVAKQKNKNIQPG
QVSFQQSSFSYEWVNPKIVTSKQSNANLNQKQQLPMIQRNKMTITEQRQSLPIFSYREDI
IRAVTNNQFLIVQAETGSGKTTQLPQYLIEGGFIIKGKVACTQPRRVAAVSVAKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g664.t4 | Coils | Coil | Coil | 89 | 109 | - |
| 7 | g664.t4 | Gene3D | G3DSA:2.40.50.140 | - | 11 | 91 | 6.3E-7 |
| 6 | g664.t4 | Gene3D | G3DSA:3.40.50.300 | - | 186 | 295 | 1.4E-29 |
| 1 | g664.t4 | PANTHER | PTHR18934:SF120 | OS06G0343100 PROTEIN | 210 | 295 | 3.8E-24 |
| 2 | g664.t4 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 210 | 295 | 3.8E-24 |
| 9 | g664.t4 | ProSiteProfiles | PS50126 | S1 domain profile. | 13 | 83 | 10.752 |
| 5 | g664.t4 | SMART | SM00316 | S1_6 | 11 | 83 | 5.1E-8 |
| 4 | g664.t4 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 9 | 87 | 7.86E-8 |
| 3 | g664.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 83 | 295 | 9.74E-13 |
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: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.
