General information for g7724.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable ATP-dependent RNA helicase DDX17.
Parent gene
- The parent gene g7724 is located on chr_2: 25481557..25488530 (+ 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 | g7724 | g7724.t1 | TSS | g7724.t1 | 25477585 | 25477585 |
| chr_2 | g7724 | g7724.t1 | isoform | g7724.t1 | 25477952 | 25481802 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon1 | 25477952 | 25478085 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS1 | 25477952 | 25478085 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon2 | 25478156 | 25478663 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS2 | 25478156 | 25478663 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon3 | 25478725 | 25478953 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS3 | 25478725 | 25478953 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon4 | 25479008 | 25479562 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS4 | 25479008 | 25479562 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon5 | 25481168 | 25481234 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS5 | 25481168 | 25481234 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon6 | 25481302 | 25481413 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS6 | 25481302 | 25481413 |
| chr_2 | g7724 | g7724.t1 | exon | g7724.t1.exon7 | 25481506 | 25481802 |
| chr_2 | g7724 | g7724.t1 | cds | g7724.t1.CDS7 | 25481506 | 25481802 |
| chr_2 | g7724 | g7724.t1 | TTS | g7724.t1 | 25482118 | 25482118 |
Sequences
>g7724.t1 Gene=g7724 Length=1902
ATGAATAGTTTATTAAGAAATATTTGTTCACATAGTGCATTAGTTTATAGATATTCGAAG
CAAACGCCAAATTTACTCTTGAAAAATTCTAACAAAAATTTCATCACAAGTTTAACCTCA
AAATTTTGTTCAATGTATATTAAAAGCGAATCACGTTATGGTGGAGCAGGGAATTCAAAT
GGTTTTGGAAATAGTGGATCTCGATCAATGAATGGTAATGGTAGAGACGGAATTGCTAGA
CGAAATGATCGATTTAATGGACGTGTTGAGAAAAATGGATTCGGAGGTATGGGATCATCA
CGGCAAAAGAACAGTCTTGATGAGCAAGTTTTAAAACGTATTAATTGGAATCAAGAGACA
TTGGCACCATTACGTAAAAATTTTTACAAACCATCAACTACAGTTATTGATCGTGCACGC
GCGGAAGTTGATACTTTTCATCGTAAAAATGAAATTACTGTACATGGTCGAGATAATCCA
GCTCCAATATTTGAATTCCATGAAGTTGGTTTCCCATCTTACATTACAAGTGAAATGACT
CGTCAAGGATTCACTAATCCAACAATCATTCAATCAATGGCTTGGCCAGTTGCTATGAGC
GGTCGTGATCTTGTTGGTATTGCACAAACTGGTTCTGGCAAGACTTTGGCATATATTTTA
CCTGCTCTAGTGCACATCACTTATCAAGAAAAAATGCAAAGAGGTGATGGTCCAATTGCT
CTCGTTCTCGCACCAACTAGAGAACTTGCACAACAAATTCAAGCTGTTGCCACAGAATTT
GGCAAACGTATTGGCATTCGTAATACATGCGTATTTGGTGGTGCTCCAAAGCGACCACAA
CAAAATGATTTACAACGTGGAAGCGAAATTGTGATTGCTACTCCTGGTCGACTTATTGAC
TTTTTGCAACAAGAAACTACCAACTTGAAACGTTGTTCATATCTTGTTCTTGACGAAGCT
GACAGAATGTTAGATATGGGTTTTGAACCACAAATTCGTAAAATTATTGAACAAATTCGT
CCAGATCGTCAAGTTTTAATGTGGAGTGCTACATGGCCAAAAGAAGTCAGAAATTTGGCT
GAAGAGTTCTTGAATGACTACGTTCAAATCAATATTGGCTCAATGAACTTATCAGCTAAT
CAAAACATTCTACAAATTGTTGACGTTTGTGATGATGCTGAAAAAGACGCTAAATTAATC
AAATTACTTTCGGAAATTCAATCAGATCGCGAGAGCAAGACCATCATTTTTTCAGAAACA
AAAAGAAAAGTTGATGACATTAGAAACTTTTTGATGAAGAATCATTTCAGAGCAGTTGCT
ATTCATGGCGATAAATCTCAACGCGAACGTGACTTTGTGTTGGGCAAATTCAGACAAGAT
CGTCAAAGTATTCTAATTGCTACTGATGTAGCAAGTCGTGGATTGGACGTGGATGATGTT
AAATTCGTTATCAACTATGATTTCCCATCAAATATTGAGGATTACATTCATCGTATTGGA
AGAACAGGCCGTTCAAATAACAAAGGTACATCTTACACTTTTTTTACACCAACAAATGCT
GGAAAAGTTGATGAACTTGTCAACATTCTGAATGAGACCAATCAGTATGTGAATCCTGAA
TTGTATCAACTTAAAAAATATAATTCAAAAGCTAGCAGTAATAATCGTCGTGGTGGTAAC
AGTCGTGGATTTGGTGGAGGCTTTAAAAAATCATTCGGTCAATCAGGAAGTTATGGTGGA
AATCGCTCATCAAATTACGAAAATGGTGGTGGATACAAAAAGAATTACAATAACAATTAC
AGTAATGGTGGAGAACGAAAATACACACGATTCGATAACAATGATCGTGCGACAGCAACT
AACGGAAATGCATATAGTAATGGTAGCTCACGATTTCAATAA
>g7724.t1 Gene=g7724 Length=633
MNSLLRNICSHSALVYRYSKQTPNLLLKNSNKNFITSLTSKFCSMYIKSESRYGGAGNSN
GFGNSGSRSMNGNGRDGIARRNDRFNGRVEKNGFGGMGSSRQKNSLDEQVLKRINWNQET
LAPLRKNFYKPSTTVIDRARAEVDTFHRKNEITVHGRDNPAPIFEFHEVGFPSYITSEMT
RQGFTNPTIIQSMAWPVAMSGRDLVGIAQTGSGKTLAYILPALVHITYQEKMQRGDGPIA
LVLAPTRELAQQIQAVATEFGKRIGIRNTCVFGGAPKRPQQNDLQRGSEIVIATPGRLID
FLQQETTNLKRCSYLVLDEADRMLDMGFEPQIRKIIEQIRPDRQVLMWSATWPKEVRNLA
EEFLNDYVQINIGSMNLSANQNILQIVDVCDDAEKDAKLIKLLSEIQSDRESKTIIFSET
KRKVDDIRNFLMKNHFRAVAIHGDKSQRERDFVLGKFRQDRQSILIATDVASRGLDVDDV
KFVINYDFPSNIEDYIHRIGRTGRSNNKGTSYTFFTPTNAGKVDELVNILNETNQYVNPE
LYQLKKYNSKASSNNRRGGNSRGFGGGFKKSFGQSGSYGGNRSSNYENGGGYKKNYNNNY
SNGGERKYTRFDNNDRATATNGNAYSNGSSRFQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7724.t1 | CDD | cd17966 | DEADc_DDX5_DDX17 | 175 | 371 | 3.22169E-137 |
| 8 | g7724.t1 | CDD | cd18787 | SF2_C_DEAD | 383 | 515 | 5.51353E-56 |
| 7 | g7724.t1 | Gene3D | G3DSA:3.40.50.300 | - | 130 | 369 | 6.6E-85 |
| 6 | g7724.t1 | Gene3D | G3DSA:3.40.50.300 | - | 370 | 549 | 2.0E-57 |
| 15 | g7724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 64 | 86 | - |
| 14 | g7724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 589 | 607 | - |
| 16 | g7724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 589 | 633 | - |
| 13 | g7724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 614 | 633 | - |
| 3 | g7724.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 81 | 568 | 4.2E-236 |
| 4 | g7724.t1 | PANTHER | PTHR47958:SF73 | LD32873P | 81 | 568 | 4.2E-236 |
| 1 | g7724.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 189 | 358 | 4.9E-50 |
| 2 | g7724.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 395 | 505 | 9.7E-32 |
| 10 | g7724.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 316 | 324 | - |
| 17 | g7724.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 164 | 192 | 9.25 |
| 19 | g7724.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 195 | 370 | 32.804 |
| 18 | g7724.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 398 | 545 | 24.118 |
| 12 | g7724.t1 | SMART | SM00487 | ultradead3 | 183 | 386 | 4.3E-63 |
| 11 | g7724.t1 | SMART | SM00490 | helicmild6 | 425 | 506 | 3.2E-31 |
| 5 | g7724.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 236 | 519 | 8.9E-76 |
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 K12823 (ATP-dependent RNA helicase DDX5/DBP2)
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.
