General information for g7055.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 g7055 is located on chr_2: 20896797..20897781 (+ 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 | g7055 | g7055.t1 | isoform | g7055.t1 | 20890838 | 20897281 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon1 | 20890838 | 20891504 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS1 | 20890838 | 20891504 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon2 | 20891558 | 20891853 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS2 | 20891558 | 20891853 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon3 | 20891911 | 20892642 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS3 | 20891911 | 20892642 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon4 | 20892706 | 20892852 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS4 | 20892706 | 20892852 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon5 | 20893160 | 20893218 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS5 | 20893160 | 20893218 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon6 | 20893434 | 20893845 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS6 | 20893434 | 20893845 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon7 | 20893905 | 20894234 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS7 | 20893905 | 20894234 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon8 | 20894299 | 20894758 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS8 | 20894299 | 20894758 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon9 | 20896513 | 20896737 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS9 | 20896513 | 20896737 |
| chr_2 | g7055 | g7055.t1 | exon | g7055.t1.exon10 | 20896797 | 20897281 |
| chr_2 | g7055 | g7055.t1 | cds | g7055.t1.CDS10 | 20896797 | 20897281 |
| chr_2 | g7055 | g7055.t1 | TTS | g7055.t1 | 20897758 | 20897758 |
| chr_2 | g7055 | g7055.t1 | TSS | g7055.t1 | NA | NA |
Sequences
>g7055.t1 Gene=g7055 Length=3813
ATGTCAACGTCAAATACAACTGCGACAGTTTCAACAGCTTCAAATGTAGCAACAAATGTT
CAACAAAAGCGAGCTCTGGGTGATCAACTTGATAAAAATGATGACAATCTCTCGCCAGCA
GATGAAGATTCAAAACGAAAGAAACGAAAAGATTCAGAATTTCCAATTAAAGATAACTCA
AGTGGAAATAGTGTTGGTGGAAACAAGACAAACACATCATCAACATCAAATCAAGGAATA
AATCGAGTGACATCACGCATCGGAAAACCACCTGGACCAGCATCAAAAACAATGGGACTT
ATGAATAAAACTGGCAATCAACTTGATCGTAAAAGTGAAAGTCCCAAAATGTCTACTGTA
AAATCACCAGCTGAAACAGTAGAAATAGAAAATGATGATTTGAAAGGAAATTCAGCAGAA
GGTGGTCCAAAAGTACCGCCATTAAAAATTGTAATTCCACAGCAATCAACTTCATCATCA
AACACAAATGAAACACAAGACGGTTCACAAAGCACAAATCAAAGAACAAATAAAACTACT
GCAGCGAGAAATGCAACATCAGGACTTCCATATGTAATTAATTCAACTTCAAATACAAAT
GAGAATGCTGTTGCAAGTGCAAATGAAAAGGATGGAACAAATTCATCAAATCTGACAGCA
TCATCGACCGATTCAAACAAATCAAATGATGATAGCAAATCAGCAAGTGCAAGTGGTAAA
TCTAAAGAACCTCGTATCTTGAGAAGTTCACAGAGAAGTGGAAAAGATTCGAAAGATGAT
CGAAGTTCAAACAATTCATCACCTCAATTACCAGCAAGTTCAACTCCCTCACCTGCAGCT
CATCATACAGATTCTTCTGTAGGCACTGAATCAGATCATCAACAGTCAACATGGCAAACT
CATCTCAACCCTCAAATTCAGTCACATCTAGCTCGGCAACTACATCTACAGCATCTATAC
AAACAACTAGCTAATTCAAATGCAACCACATCAAGTAATGTTGCGGCATCTTCATCATCA
CAAAGTTCAGTAGAATTGCATCCAAGAAAGAGAAAAATCAAAGCAAGCAGTAAAGAGCCA
CAAAGTTCTTCATCATCATCATCTGCCTCATCAACTGCCGATTTAAAAGATAGCAATTCA
AAGGATGGTCAAGAGAAATCAAATGAACCTGTTCATCCACATGATCAACCTTTTACAAAT
TGCTATCAAATGTACATTGATTTAAGAAAACAAATTCAACAACGTCATAACAGTTTGCAT
CCAATCGAGCCAAGACCTCTCAAAGGACTCGAAGATTATCTCATGAATCGTCGAACATAT
TCTCTACAAGGTAAAACACCTTTAGAGCCGCCAAATATTATCATTCCACCTCTCTTACCA
GCACCAATGAAAGAAACTTTTGTGGAACAAGAAAAAGAAAGACATCGACTCAAATTGAAA
CATATTGTTGAAAAAGAAAAATTAGTTTTATCAAAGGAACAAGAAATTCTTCGTGTTCAT
TGTAAGGCAGCACAAATGATTGCCAATCAATCGCAACCATTCTCAGTGTGCACAATGTTA
AAGGACGAAGAAGTTTATAATATAATTACGCCAGAGCAAGAAGAGAAATATAGAAATAAG
AATCGAGAAAGATCGCATGGAAGAGTCTTCTATCAAGCATTGAAAGAATTAGATGACAAA
TGGGACAAGATTAAGGAAGCAATGATAATCCGGCATACAAATGAGTCAGAGAGTCTACAT
GCAGTGCAGAAGATGGATTGGGGATGGAAATTAAAGGAACTAGCTTTATGTGATTATAAA
GCAACTCCTGAGATTGAAGAACTTCATGTACCAATGGTTGACCAAATATATCGAAAAATA
ATTAAAATCCAACTTATTCTGCTCAAAAACATTATAAAAATGTACGGAATTCAAAATCAC
GGAAATTTTAGAGGAGGATTTCAACAAAATCGCAATGGTGGTGGCAATAATAGCAACTTT
AGTGATTTAAACAGCACAGTTTTGAAAAGTGTTAATTATGAAAATGCACCACCTTTTCGC
AAGAACTTCTACTCTCCAGCTGAGTCTGTTATAACTCGAACACCACAAGAAACTCAAGCA
TTACTATCGAAATACGAGATAACAATGAAAGGAAAAGATTCTGACGTTTATAAGCCACTT
TCGAATTTTAAAGAGTGTAATTTTCCTGATTTTATTACCAATGAAATCAATCGTCAAGGA
TTTGTAGAGCCTACAAGTATTCAAGCTGGAGCTTTACCAACTATAATGAGTGGTCGTAAT
TTAGTTGGAATTGCAAAAACTGGATCTGGCAAGACACTAGCATATGTTTTGCCTTCGTTG
ATTCATTTGAAACATCAACCAAATATCAAACCTAATGAAGGACCAATCGTTTTGATATTA
GCACCAACCAGGGAACTTGCACAGCAAATTCAAAGTGTTGCCAATGATTTTGGAATGCGA
AACAACATCACAAACGTTGCAGTTTTTGGTGGAGCTGCAAAAAGCAATCAAATTCGTGAA
CTTTCTCGTGGTTGTAATATTTGTATCGCAACTCCTGGAAGGTTAATTGATTTTCTTGAG
CGTGGTGTGTTGAACTTGAAAAGATGCACTTATTTGGTTTTGGATGAGGCAGACAGAATG
CTTGATATGGGTTTTGAGCCTCAAATCAGAAAAATCCTCTCACAGATTCGTTCTGATCGT
CAATTATTGATGTTTTCTGCTACATGGCCTAATGAAATTCAAGCATTGGCGAAAGAGTTT
TTGAATGATTACATTCAAATTAACATCGGATCTTTGTGTCTCTCAGCAAATCATAATATT
TTGCAAATCATTGATGTTTGCGATGAAAATGAAAAGGATAGCAAATTGATAAAAATCCTT
GGTGACATTTCAAATGAGAATGATCGCAAGACTATTGTGTTTGTAGAGACAAAACGCCGT
GCAGATGAAATTTCTCGTTCAATTAACCGTCGAGGTTTTAATGCAGTTGCGATTCATGGC
GATAAGAGCCAAAATGAACGCGATTATACATTAAATTCATTTCGGTCTGGACGACATAAC
GTTCAAATTCTGGTTGCTACTGATGTCGCCTCGCGTGGTTTAGATATCGACGTAAAATAT
GTGATCAATTATGATTACCCAAATAGTTCAGATGAGTACATACACAGAATCGGACGTACA
GGTAGAAACAATCGTACAGGAACTGCCTACACCTTCTTCACAGATTCAAATTCTCAGAAA
GCAAATGATTTGATAAATGTATTGCGTGAAGCAAATCAAATCATTAATCCACGTTTGATT
GAAATGAGTCATCGTTCTTTTGGTAGAAAGGGAAACATGCGTAGAAATCCAAATGGCATG
AATGTAGGAGGAATGAATAGTGGTATGCATATGAATAATAAACGACCACGTTCTGATAAT
AGAAGTGATGTGGTTCAAAAGAAACCACGTTGGGATAATGGTGCAAGCAAAAATGATTCA
GCATTGCATAAAGTATCTCGCTTTTCAAATAATGATGGAAATAGAGGATATAAGGTACAA
CAAGGGAGCAATGGCAATAATAATCCATCGTATCGTGCAAATGCTGCATACCAGCCACAA
AAATATTTCAAGCCAGGTTCATATGATAAAAAACCATCACAATCTCAATCACAGCAACAA
CATTCCTCTATGTCTTTAACATCTTTCACGGCTCAAAGTGGTTTTACTAGTTTTCCACCA
CCAATGCCATTTGCTCATTATGCTTTCACTGCATATCCACCACCAACTACAGCTGGTTTA
TTACAACAGCCACCACCACTACCAAAGAACTAA
>g7055.t1 Gene=g7055 Length=1270
MSTSNTTATVSTASNVATNVQQKRALGDQLDKNDDNLSPADEDSKRKKRKDSEFPIKDNS
SGNSVGGNKTNTSSTSNQGINRVTSRIGKPPGPASKTMGLMNKTGNQLDRKSESPKMSTV
KSPAETVEIENDDLKGNSAEGGPKVPPLKIVIPQQSTSSSNTNETQDGSQSTNQRTNKTT
AARNATSGLPYVINSTSNTNENAVASANEKDGTNSSNLTASSTDSNKSNDDSKSASASGK
SKEPRILRSSQRSGKDSKDDRSSNNSSPQLPASSTPSPAAHHTDSSVGTESDHQQSTWQT
HLNPQIQSHLARQLHLQHLYKQLANSNATTSSNVAASSSSQSSVELHPRKRKIKASSKEP
QSSSSSSSASSTADLKDSNSKDGQEKSNEPVHPHDQPFTNCYQMYIDLRKQIQQRHNSLH
PIEPRPLKGLEDYLMNRRTYSLQGKTPLEPPNIIIPPLLPAPMKETFVEQEKERHRLKLK
HIVEKEKLVLSKEQEILRVHCKAAQMIANQSQPFSVCTMLKDEEVYNIITPEQEEKYRNK
NRERSHGRVFYQALKELDDKWDKIKEAMIIRHTNESESLHAVQKMDWGWKLKELALCDYK
ATPEIEELHVPMVDQIYRKIIKIQLILLKNIIKMYGIQNHGNFRGGFQQNRNGGGNNSNF
SDLNSTVLKSVNYENAPPFRKNFYSPAESVITRTPQETQALLSKYEITMKGKDSDVYKPL
SNFKECNFPDFITNEINRQGFVEPTSIQAGALPTIMSGRNLVGIAKTGSGKTLAYVLPSL
IHLKHQPNIKPNEGPIVLILAPTRELAQQIQSVANDFGMRNNITNVAVFGGAAKSNQIRE
LSRGCNICIATPGRLIDFLERGVLNLKRCTYLVLDEADRMLDMGFEPQIRKILSQIRSDR
QLLMFSATWPNEIQALAKEFLNDYIQINIGSLCLSANHNILQIIDVCDENEKDSKLIKIL
GDISNENDRKTIVFVETKRRADEISRSINRRGFNAVAIHGDKSQNERDYTLNSFRSGRHN
VQILVATDVASRGLDIDVKYVINYDYPNSSDEYIHRIGRTGRNNRTGTAYTFFTDSNSQK
ANDLINVLREANQIINPRLIEMSHRSFGRKGNMRRNPNGMNVGGMNSGMHMNNKRPRSDN
RSDVVQKKPRWDNGASKNDSALHKVSRFSNNDGNRGYKVQQGSNGNNNPSYRANAAYQPQ
KYFKPGSYDKKPSQSQSQQQHSSMSLTSFTAQSGFTSFPPPMPFAHYAFTAYPPPTTAGL
LQQPPPLPKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7055.t1 | CDD | cd18787 | SF2_C_DEAD | 940 | 1073 | 6.60287E-57 |
| 6 | g7055.t1 | Gene3D | G3DSA:3.40.50.300 | - | 692 | 932 | 1.3E-82 |
| 7 | g7055.t1 | Gene3D | G3DSA:3.40.50.300 | - | 933 | 1107 | 8.4E-56 |
| 12 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 300 | - |
| 23 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 26 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 27 | 56 | - |
| 14 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 57 | 84 | - |
| 17 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 125 | - |
| 21 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 151 | 235 | - |
| 19 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 262 | - |
| 20 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 263 | 300 | - |
| 24 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 331 | 397 | - |
| 15 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 358 | 377 | - |
| 25 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 378 | 392 | - |
| 16 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1132 | 1188 | - |
| 18 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1134 | 1154 | - |
| 22 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1159 | 1188 | - |
| 27 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1206 | 1228 | - |
| 13 | g7055.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1209 | 1228 | - |
| 3 | g7055.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 681 | 1140 | 9.5E-218 |
| 4 | g7055.t1 | PANTHER | PTHR47958:SF73 | LD32873P | 681 | 1140 | 9.5E-218 |
| 1 | g7055.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 745 | 915 | 1.3E-47 |
| 2 | g7055.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 952 | 1063 | 6.0E-30 |
| 9 | g7055.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 873 | 881 | - |
| 28 | g7055.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 721 | 749 | 10.337 |
| 30 | g7055.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 752 | 927 | 34.452 |
| 29 | g7055.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 955 | 1103 | 20.781 |
| 11 | g7055.t1 | SMART | SM00487 | ultradead3 | 740 | 943 | 5.1E-66 |
| 10 | g7055.t1 | SMART | SM00490 | helicmild6 | 982 | 1064 | 1.3E-31 |
| 5 | g7055.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 753 | 1075 | 5.3E-72 |
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.
