General information for g6648.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent RNA helicase DHX33.
Parent gene
- The parent gene g6648 is located on chr_2: 17939781..17940216 (+ 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_2 | g6648 | g6648.t1 | TSS | g6648.t1 | 17937678 | 17937678 |
| chr_2 | g6648 | g6648.t1 | isoform | g6648.t1 | 17937852 | 17940216 |
| chr_2 | g6648 | g6648.t1 | exon | g6648.t1.exon1 | 17937852 | 17937919 |
| chr_2 | g6648 | g6648.t1 | cds | g6648.t1.CDS1 | 17937852 | 17937919 |
| chr_2 | g6648 | g6648.t1 | exon | g6648.t1.exon2 | 17937977 | 17938035 |
| chr_2 | g6648 | g6648.t1 | cds | g6648.t1.CDS2 | 17937977 | 17938035 |
| chr_2 | g6648 | g6648.t1 | exon | g6648.t1.exon3 | 17938104 | 17938254 |
| chr_2 | g6648 | g6648.t1 | cds | g6648.t1.CDS3 | 17938104 | 17938254 |
| chr_2 | g6648 | g6648.t1 | exon | g6648.t1.exon4 | 17938316 | 17939597 |
| chr_2 | g6648 | g6648.t1 | cds | g6648.t1.CDS4 | 17938316 | 17939597 |
| chr_2 | g6648 | g6648.t1 | exon | g6648.t1.exon5 | 17939661 | 17939789 |
| chr_2 | g6648 | g6648.t1 | cds | g6648.t1.CDS5 | 17939661 | 17939789 |
| chr_2 | g6648 | g6648.t1 | exon | g6648.t1.exon6 | 17939854 | 17940216 |
| chr_2 | g6648 | g6648.t1 | cds | g6648.t1.CDS6 | 17939854 | 17940216 |
| chr_2 | g6648 | g6648.t1 | TTS | g6648.t1 | 17941018 | 17941018 |
Sequences
>g6648.t1 Gene=g6648 Length=2052
ATGATGGAGAAGGCATTTACTTTAGATGAGCAAAGAAGAAAGCTTCCAGTTTTTCAATAT
AGACAGCACATAATTAATTGTATACAACAACACGCTACTTTAATTTTATTAGCTGAAACA
GGATCAGGAAAAAGTACGCAAATATGTCAATACATTTATGAGAGCAATCTTTTAAAAAAT
GGAATGATAGCTATAACACAACCCCGAAGAGTAGCTGCAGTCACATTAGCTCAGAGAGTT
ACAAGAGAAAAGAATAGGCATTTGGGTGAATTAGTAAGCTACGCAATTCGATTTGAAGAT
ACTACAACGGGAACTACGAAAATAAAGTTTATGACCGAAGGAATACTTTTAAGAGAGGCC
ATCAATGACAAATATCTAAAAAAATATGATTTCATAATACTGGATGAAGCACATGAACGT
ACAATCAATACCGACGTTCTATTTGGTCTTGTTAAAACGGTTCAACGTGATAGAAAATTC
GTCAATCTTCCCGAACTAAAAATCATCATAATGTCAGCAACCATGGATGTTGATCACTTT
TCAAAATATTTCAACAACTGTAATGTTTTATATTTACCAGGACGAACTCATAATGTAACA
GTCAAACATACTAAAATTAAACAAGATGATTATATGTTCGCTGCACTTGCAACACTATTT
GATATTCATTTAAAAGCACCACCACAAGAGGATGTATTAATATTTCTCACAGGAAAGGAT
GAAATTGAATCGATGGCACAACAAATTAGAACAATTGTAAAGTCTCCTGATTTAGAAGGC
AAAATTCCACTTAAAGTGTTTCCTCTTCATGCATCTCTTCCACAAAAGAAGCAAATGGAT
GCATTTGTAAGGTCATCTGAAAATCAAAGACGTGTAGTTATAGCAACGAACATTGCAGAA
ACTTCTCTTACATTACCAGGTATCAAGTATGTGATTGACACTGGTGTTGTTAAATTTAAG
AGTTATGATCCAAAAACGGGCCTTGAAAGTTTAAAAATTCATAAAATTTCACAAGCACAA
GCTTGGCAAAGAAGCGGAAGGGCTGGTAGAGAATCTGATGGAGTTTGCTATAGAACTTAT
ACAAAAGCTGAAATGGATAGTTGGGAAAAAATGACAATACCAGAAATCTTGAGGTGTAAT
TTAGCTTCAACTATGCTAAACCTTCTCGCCATTAATCTTAACGTAGAGAAATTTGATTTT
ATAGATAAACCACCTAAAAATGCTATAATGAATGCTCTTGAGTGTCTTAAACAACTTGAT
GCAATTAAAATACAACCATCACAAACAACTCCTCAGCTTACACAAATAGGAAAATTAATG
AGTGCTTTTCCAATTCTTCCAATGTACAGCAAATGTATTATATCTGCTGAAAAGTTTAAA
TGTACAAGTGAAATTCTTGATATTATTGCCCTTTTATCATCAGAAAATATATATCTTGAA
CCAAGTGCAAATAATCGTGATGTTGCAGCTACTCAACATGCAAAATTTCATACTTTGTAT
GGTGACCATCTTACAATGCTCAAAATATTTGCTCAATTTAAGAAGAGTGATAAGAATAAG
TGGTGCCAAGATCATTTCTTTAGTTTCAAAAATTTGTCGTATGCACTGGAAGTAAGGAAG
CAATTAGAAGAAATTTGCCAAAATAACAAAATACCTATTAATAAATCAGAACCAGTGCAT
CCTGATCAGATTCTTAAATGCTTAATAACGGGGTTATTCAATAATATTGCGGAGTACAAT
CAAAGAGATAATAATTACATAGTACTAGTAAATCGTCAACGAGCTCAGATTCATCCATCT
AGCACACTTTCGGGCTATAATGCAAACTTTAATGGTATAAGTTCGAATGGTAGTGGTAAT
GGAATAATAGCTGTTGGTGGTAAAATGAAAAGTGATCATAATCAAAAACCTGCATTTATA
TTGTTCACTGATATTGTTTCAACAACTAACATCTATTTACGAACAGTGTCTAGAATAAAT
CCCGAATGGATAAATGAAGTCATATCATCAGATAGTGATTTTGTGAATCGAATAAATGCT
AATCATTTTTAG
>g6648.t1 Gene=g6648 Length=683
MMEKAFTLDEQRRKLPVFQYRQHIINCIQQHATLILLAETGSGKSTQICQYIYESNLLKN
GMIAITQPRRVAAVTLAQRVTREKNRHLGELVSYAIRFEDTTTGTTKIKFMTEGILLREA
INDKYLKKYDFIILDEAHERTINTDVLFGLVKTVQRDRKFVNLPELKIIIMSATMDVDHF
SKYFNNCNVLYLPGRTHNVTVKHTKIKQDDYMFAALATLFDIHLKAPPQEDVLIFLTGKD
EIESMAQQIRTIVKSPDLEGKIPLKVFPLHASLPQKKQMDAFVRSSENQRRVVIATNIAE
TSLTLPGIKYVIDTGVVKFKSYDPKTGLESLKIHKISQAQAWQRSGRAGRESDGVCYRTY
TKAEMDSWEKMTIPEILRCNLASTMLNLLAINLNVEKFDFIDKPPKNAIMNALECLKQLD
AIKIQPSQTTPQLTQIGKLMSAFPILPMYSKCIISAEKFKCTSEILDIIALLSSENIYLE
PSANNRDVAATQHAKFHTLYGDHLTMLKIFAQFKKSDKNKWCQDHFFSFKNLSYALEVRK
QLEEICQNNKIPINKSEPVHPDQILKCLITGLFNNIAEYNQRDNNYIVLVNRQRAQIHPS
STLSGYNANFNGISSNGSGNGIIAVGGKMKSDHNQKPAFILFTDIVSTTNIYLRTVSRIN
PEWINEVISSDSDFVNRINANHF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g6648.t1 | CDD | cd17978 | DEXHc_DHX33 | 15 | 192 | 0.000 |
| 16 | g6648.t1 | CDD | cd18791 | SF2_C_RHA | 187 | 360 | 0.000 |
| 11 | g6648.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 195 | 0.000 |
| 12 | g6648.t1 | Gene3D | G3DSA:3.40.50.300 | - | 196 | 370 | 0.000 |
| 13 | g6648.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 393 | 499 | 0.000 |
| 5 | g6648.t1 | PANTHER | PTHR18934:SF118 | ATP-DEPENDENT RNA HELICASE DHX33 | 8 | 666 | 0.000 |
| 6 | g6648.t1 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 8 | 666 | 0.000 |
| 2 | g6648.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 21 | 178 | 0.000 |
| 3 | g6648.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 225 | 350 | 0.000 |
| 4 | g6648.t1 | Pfam | PF04408 | Helicase associated domain (HA2) | 412 | 505 | 0.000 |
| 1 | g6648.t1 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 564 | 666 | 0.000 |
| 15 | g6648.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 25 | 193 | 20.651 |
| 14 | g6648.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 218 | 392 | 16.280 |
| 9 | g6648.t1 | SMART | SM00487 | ultradead3 | 13 | 202 | 0.000 |
| 8 | g6648.t1 | SMART | SM00490 | helicmild6 | 243 | 352 | 0.000 |
| 10 | g6648.t1 | SMART | SM00847 | ha2_5 | 411 | 507 | 0.000 |
| 7 | g6648.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 9 | 547 | 0.000 |
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 transcript has been annotated with K17820 (ATP-dependent RNA helicase DHX33)
Pathway
- This transcript belongs to the following pathways
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.
