General information for g2699.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 g2699 is located on chr_3: 19771563..19772689 (- 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 | g2699 | g2699.t3 | isoform | g2699.t3 | 19769808 | 19771409 |
| chr_3 | g2699 | g2699.t3 | exon | g2699.t3.exon1 | 19769808 | 19771409 |
| chr_3 | g2699 | g2699.t3 | cds | g2699.t3.CDS1 | 19769809 | 19771284 |
| chr_3 | g2699 | g2699.t3 | TSS | g2699.t3 | NA | NA |
| chr_3 | g2699 | g2699.t3 | TTS | g2699.t3 | NA | NA |
Sequences
>g2699.t3 Gene=g2699 Length=1602
CTGAATTTATAATTCATCTTGCCGAGCAAAATCCTAATTTAGATGACTTTAGAAAGGCAC
TTGCACAAAATGGTGCAGAATTTAGTGATTCATTTACTTCAAATCTTTTGCGTATTATAT
GTCTGATGAAACCATCAGTAAAAAAGAAGTCGAATCAAACAATCACAATAGAAGGCGACT
CATCAAAAAGTGCTCTTGCACTTAAATTTCCAGGACTAGCTATTCCAAATAAGAAAATAG
ACGATGATAGTGATGAGGACAATGATAAAAAGAAAACATCCGATAATATTGTTGATGATA
TGATGGCAGAATTAGAAGCAATGGCTGCACCTCCATCGTCAAGTAAAACAATTGACGAAA
AAAAAGAAAGAAAACGAAGCCGTTCTCGTGAAATAAAAGAGAGAAAAAGGAGTCGTTCAA
GAGAAAAGAGAAGAAGATCACGTTCAAGAAGTCGTGATAGAAAAAAACGTTCAAGAAGCC
GTGATAGAGCTAAAAAGAGCAGAAGAAGTCGCTCAAGAAGTCATAGCAGAAAAGATAGAA
GACATCGTTCTAAATCAAGAGATCGAGATCGATATCACAATCGTCGGAGTCGTTCGCGTG
AAGAAAGAAAGAAAATTGAAATCAAAGATGATCCAGAACCAGGAAAAATTTATGATGGAA
AAGTTGCAAACATTGTGAATTTCGGATGTTTTGTGCAGCTTTTTGGTTTGAGAAAGAAAT
GGGAAGGTTTAGTACACATTTCACAATTGAGATCAGAGGGACGAGTGTCAGACGTTAGTG
AAGTCGTGTCACGGGGAAGTTCAGTAAAAGTCAAAGTAATTTCAATTACAGGACAAAAGG
TATCGCTTTCAATGAAAGAAGTTGATCAATTGACTGGAAAAGATTTAAATCCGTTGTCAC
ATAAAGCAGCCGATGATGATATGGGTCCAAGAAATCCAGATAGACCAATTGATAGAATTT
CAATGTTAGCTCTTCCCGGTAATGTTGATGACGATGTTGTGGAAACTGGTAAACGCGTCA
CAAGAATCTCAAGTCCAGAGCGATGGGAAATTCAGCAAATGATTTCATCAGGTGTAATTG
ATCGAAGTGAAATGCCAGATTATGATGAAGAGACTGGATTATTACAAAAAGATGAAGAGG
ACGAAGAAGATATTGAAATTGAAATTGTTGAAGACGAACCACCATTTTTACAAGGTCATG
GAAGAGCACTACATGATTTATCACCAGTTAGAATCATTAAAAATCCTGATGGCTCTTTAG
CACAAGCTGCCATGATGCAATCAGCATTGCAAAAAGAAAGACGTGAACAGAAAATGTTGC
AGCGTGAACAAGAAATGGATTCAAAACCATCAACTTTTGGTAAAGACTGGATGGATCCAT
TAAGAGAAGATGAAGACCGTAATGATGGTTCAAAAAGTTTCAATGCAGCACTTCAAGATA
TGCCTGAATGGAAGAAACATATTATAGGTGGTAAAAAAACATCTTATGGACGAAAAACAG
ATATGACAATGATTGAACAACGTCAATCACTACCAATATATAAGTTAAAAGATGATTTGA
TAAAAGCAGTCACAGATAATCAAATTTTAATTGTTGTTGGTG
>g2699.t3 Gene=g2699 Length=492
MKPSVKKKSNQTITIEGDSSKSALALKFPGLAIPNKKIDDDSDEDNDKKKTSDNIVDDMM
AELEAMAAPPSSSKTIDEKKERKRSRSREIKERKRSRSREKRRRSRSRSRDRKKRSRSRD
RAKKSRRSRSRSHSRKDRRHRSKSRDRDRYHNRRSRSREERKKIEIKDDPEPGKIYDGKV
ANIVNFGCFVQLFGLRKKWEGLVHISQLRSEGRVSDVSEVVSRGSSVKVKVISITGQKVS
LSMKEVDQLTGKDLNPLSHKAADDDMGPRNPDRPIDRISMLALPGNVDDDVVETGKRVTR
ISSPERWEIQQMISSGVIDRSEMPDYDEETGLLQKDEEDEEDIEIEIVEDEPPFLQGHGR
ALHDLSPVRIIKNPDGSLAQAAMMQSALQKERREQKMLQREQEMDSKPSTFGKDWMDPLR
EDEDRNDGSKSFNAALQDMPEWKKHIIGGKKTSYGRKTDMTMIEQRQSLPIYKLKDDLIK
AVTDNQILIVVG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2699.t3 | CDD | cd05684 | S1_DHX8_helicase | 173 | 251 | 4.60417E-41 |
| 6 | g2699.t3 | Coils | Coil | Coil | 381 | 401 | - |
| 5 | g2699.t3 | Gene3D | G3DSA:2.40.50.140 | - | 167 | 255 | 1.1E-30 |
| 9 | g2699.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 11 | g2699.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 19 | - |
| 13 | g2699.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 30 | 166 | - |
| 10 | g2699.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 34 | 57 | - |
| 12 | g2699.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 86 | 151 | - |
| 14 | g2699.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 152 | 166 | - |
| 2 | g2699.t3 | PANTHER | PTHR18934:SF120 | OS06G0343100 PROTEIN | 233 | 492 | 6.9E-47 |
| 3 | g2699.t3 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 233 | 492 | 6.9E-47 |
| 1 | g2699.t3 | Pfam | PF00575 | S1 RNA binding domain | 170 | 242 | 2.9E-12 |
| 15 | g2699.t3 | ProSiteProfiles | PS50126 | S1 domain profile. | 173 | 244 | 17.884 |
| 8 | g2699.t3 | SMART | SM00316 | S1_6 | 171 | 244 | 4.0E-18 |
| 4 | g2699.t3 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 161 | 246 | 1.27E-16 |
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.
