General information for g789.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable ATP-dependent RNA helicase DDX46.
Parent gene
- The parent gene g789 is located on chr_3: 6051930..6053270 (- 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 | g789 | g789.t1 | TTS | g789.t1 | 6048363 | 6048363 |
| chr_3 | g789 | g789.t1 | isoform | g789.t1 | 6048451 | 6051930 |
| chr_3 | g789 | g789.t1 | exon | g789.t1.exon1 | 6048451 | 6048867 |
| chr_3 | g789 | g789.t1 | cds | g789.t1.CDS1 | 6048451 | 6048867 |
| chr_3 | g789 | g789.t1 | exon | g789.t1.exon2 | 6048928 | 6049510 |
| chr_3 | g789 | g789.t1 | cds | g789.t1.CDS2 | 6048928 | 6049510 |
| chr_3 | g789 | g789.t1 | exon | g789.t1.exon3 | 6049570 | 6050085 |
| chr_3 | g789 | g789.t1 | cds | g789.t1.CDS3 | 6049570 | 6050085 |
| chr_3 | g789 | g789.t1 | exon | g789.t1.exon4 | 6050140 | 6051687 |
| chr_3 | g789 | g789.t1 | cds | g789.t1.CDS4 | 6050140 | 6051687 |
| chr_3 | g789 | g789.t1 | exon | g789.t1.exon5 | 6051749 | 6051930 |
| chr_3 | g789 | g789.t1 | cds | g789.t1.CDS5 | 6051749 | 6051930 |
| chr_3 | g789 | g789.t1 | TSS | g789.t1 | 6052070 | 6052070 |
Sequences
>g789.t1 Gene=g789 Length=3246
ATGGACTCGCGTTCAAGAAAACGCTCAAGATCAATATCACCGGAAAAATCAAAGAAAAAA
TCTAAAAACAAAGATCGCGATAGAAGTAGGGATAAAAAGAAAAAGAATCGCTCAAGATCA
AAGGAAAGAAATCGTTCACGATCAAGAGATAGAGATAAAGACAGAGAATCACGTAAACGA
ATTGGAAATGGTAAAGAGAAAAGAAGATCAAAATCGCGCGAAAAATACATTGAAAAATCA
TCATCATCAAAGGATTATAGACAAAGGTCTCCTAAGTTAAAGAGTCCTGCGCCACCACAT
TCACTTCCAACTGTTGCTAAAGAATCAAAAGATGTGATTGAAATCAAGGATGAATTTAAT
CCAGCTCAATTCGATAAAGAAGAAGAGCAAAGACGATTGGAGTTAGAAATGATTAAAAGA
AAAGAGCGAATTGAGAGATGGCGAGCAGAACGCAAAATGAAAGAAAATGAACTTCAGAAA
AAACCAACCAGTCTGGCACAATCAACAATAAGAAATCCTTCAGCAAAACCTTGGAGTTTA
GAGGATGATGATGAAGATGAAGAAGCAAAAGTTATTGAAATACAAGATAGTCCAAAAGAA
GAAGATGGCAAAGAAGTACAAAAAAATGAGCTTCCTCCCCCTAAAAAGATTGAAAAAATT
GTCATTGATGACGATGATGATGATGTGCTTATTGTTAGATCTGAGCCGTCTAAGAAAGTT
GTAAAAGAAATTATTGAAGCAAAGAAACCAATTGAGCAAACAAAACAACAAGTTGAAGCA
ATGGAAGTTGAAGAAGAAGATGAAGATATCGATCCACTTGATGCTTTCATGAAAGGTGTT
GATGAGGAAGTTCGAAAAATTAACAAAAAAGCTGTCTCGTCAGGAAAAACAGCTTCTTCT
GCTGCAGGTCAAAGTGGATTAGTTATTGTGACAGGAAATGCAAAGAAGCAGCAGAAAGAA
ATCAAAAAAGGTGAACTAATTGAGCAAGACCAAGATGCTTTAGAATATTCAAGTGAAGAA
GAACTGGAGGATATTAAAGATACAGCTGCAAATTTTGCTGCAGCCAAGCAAAAGAAAGAA
CTGCCAAAAGTTGATCATTCGCAGGTCAACTATGAAACATTTAAAAAGTGTTTCTATGTT
GAAGTACCAGAAATTGCAAAAATGACTCAAGAAGAAGTTGATGCTTATAGGAATGAACTT
GAGGGAATACAAGTGAAAGGCAAAGGATGTCCTAAGCCGATTAAAACATGGGCACAATGT
GGTGTTTCAAAGAAAGAAATGGACATTCTGAAAAAGCTTAATTTTGAAAAACCCACTCCA
ATTCAATGCCAAGCTATTCCAGCTATAATGAGTGGTCGTGATCTAATTGGAATTGCAAAA
ACAGGTTCTGGAAAAACAATAGCATTTATTCTCCCTATGTTTAGACATATTCTTGATCAA
CCACCTTTAGAGGATGGTGAAGGTCCGATTGCTATAATTATGACCCCAACAAGAGAACTT
TGTATGCAAATTGGTAAAGATATCAAAAAATTCTCAAAATCACTTAATCTTCGTGCTGTA
TGTGTATATGGCGGAACAGGAATAAGTGAACAGATAGCAGAATTGAAACGAGGCGCAGAA
ATTATAGTTTGTACGCCAGGACGTATGATTGATATGTTAGCAGCAAATTCTGGACGTGTG
ACAAATTTAAGAAGAGTTACATATATCGTTTGTGATGAAGCTGATCGTATGTTTGATATG
GGATTTGAACCACAAGTCGTAAGAATTATTGAAAATGTTCGACCAGATCGTCAGACTGTC
ATGTTTTCAGCTACTTTCCCTCGACAAATGGAAGCATTGGCTAGAAGATTCCTGAAAAAA
CCAATTGAAATTCAAGTTGGAGGCCGCTCAATTGTTTGTAAAGACGTCGAGCAGCATATT
GCGATTCTAGATGATGAAGCCAAGTTCTTTAAGCTTCTTGAATTACTTGGTCATTATCAA
GAACATGGTTCGATTATTGTATTTGTTGATAAACAAGAAAATGCAGATACATTACTAAAG
GAACTGATGAAAGCTTCTTATCCATGCATGAGTTTACATGGAGGAATTGATCAATATGAT
CGTGATTCAACAATATCAGATTTCAAAAGTGGAAGATGTAAATTATTAATTGCAACATCT
GTAGCAGCTCGTGGTTTAGATGTAAAGCAACTAATTCTTGTAGTAAATTATGATGCTCCA
AATCATTATGAAGATTATGTTCACAGAGTGGGACGTACAGGACGTGCTGGAAAGAAAGGA
TTTTCGTGGACATTCTTAACTCCAGATCAAGGAAGATATGCTGGAGATATTTTGAGAGCA
TTAGAGTTATCAGGCGCAGAAGTACCCGAAGATTTGAAAAAACTATGGGAAACATATAAA
CAAGAGCAAGAAGCAATTGGAAAGAAGGTTTATAGTGGCGGTGGGTTTAGTGGAAAAGGT
TTTAAATTCGATGAACAAGAAGCTGCCGAAGCAAATGAGAAGAAAAGGTTACAAAAAGCT
GCACTCGGTCTCGTTGACTCTGATGATGAAGATGATTTAGAAAATGACATTGATCAAACA
ATTGAAAGCATGTTTGCAACTAAACGAACTGTTAAAGAAATTCAAGCTCCAATTATTCCA
ACAGCGACACCTGCTGCATCAATAATCACTCCAACTCCTGCTGCATCGACTGACAAACTA
GAACTCGCTAAACGTCTTGCATCTCGAATAAATATTGCAAAGAATTTAGGAGTTGAAGCT
AAAGGTGCCTCGCAACAAGCTGCGGAAGCTATTTTCAAAGGTGGTGTTACTGCTCATCAA
TTGATAACTAATAAAACAATAGCTGAGCAAATAGCATCAAAATTAAATACAAAACTCAAC
TATCAACCGAAAGATGATGAAGATGCAATGATGGAGCAATCGGATGGTCTTTTCAAAAAA
TATGAGGAAGAATTAGAAATTAATGATTTTCCACAGCAAGCAAGATGGAAAGTTACATCG
AAAGAAGCACTTGCACAAATATCAGAATATTCAGAAGCTGGCCTTACTGTCCGTGGAACA
TATGTGCCGCAAGGAAAACCAGTACCGGAAGGTGAACGCAAACTTTATCTTGCAATTGAG
AGTTGTAGCGAATTAGCTGTATCGAAGGCTAAACGTGAAATTACAAGATTAATTAAGGAA
GAATTATTAAAGATTAAAAACGTGTCTCATCATCTTATTAATAAGGCGCGCTATAAGGTT
ATTTAA
>g789.t1 Gene=g789 Length=1081
MDSRSRKRSRSISPEKSKKKSKNKDRDRSRDKKKKNRSRSKERNRSRSRDRDKDRESRKR
IGNGKEKRRSKSREKYIEKSSSSKDYRQRSPKLKSPAPPHSLPTVAKESKDVIEIKDEFN
PAQFDKEEEQRRLELEMIKRKERIERWRAERKMKENELQKKPTSLAQSTIRNPSAKPWSL
EDDDEDEEAKVIEIQDSPKEEDGKEVQKNELPPPKKIEKIVIDDDDDDVLIVRSEPSKKV
VKEIIEAKKPIEQTKQQVEAMEVEEEDEDIDPLDAFMKGVDEEVRKINKKAVSSGKTASS
AAGQSGLVIVTGNAKKQQKEIKKGELIEQDQDALEYSSEEELEDIKDTAANFAAAKQKKE
LPKVDHSQVNYETFKKCFYVEVPEIAKMTQEEVDAYRNELEGIQVKGKGCPKPIKTWAQC
GVSKKEMDILKKLNFEKPTPIQCQAIPAIMSGRDLIGIAKTGSGKTIAFILPMFRHILDQ
PPLEDGEGPIAIIMTPTRELCMQIGKDIKKFSKSLNLRAVCVYGGTGISEQIAELKRGAE
IIVCTPGRMIDMLAANSGRVTNLRRVTYIVCDEADRMFDMGFEPQVVRIIENVRPDRQTV
MFSATFPRQMEALARRFLKKPIEIQVGGRSIVCKDVEQHIAILDDEAKFFKLLELLGHYQ
EHGSIIVFVDKQENADTLLKELMKASYPCMSLHGGIDQYDRDSTISDFKSGRCKLLIATS
VAARGLDVKQLILVVNYDAPNHYEDYVHRVGRTGRAGKKGFSWTFLTPDQGRYAGDILRA
LELSGAEVPEDLKKLWETYKQEQEAIGKKVYSGGGFSGKGFKFDEQEAAEANEKKRLQKA
ALGLVDSDDEDDLENDIDQTIESMFATKRTVKEIQAPIIPTATPAASIITPTPAASTDKL
ELAKRLASRINIAKNLGVEAKGASQQAAEAIFKGGVTAHQLITNKTIAEQIASKLNTKLN
YQPKDDEDAMMEQSDGLFKKYEEELEINDFPQQARWKVTSKEALAQISEYSEAGLTVRGT
YVPQGKPVPEGERKLYLAIESCSELAVSKAKREITRLIKEELLKIKNVSHHLINKARYKV
I
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g789.t1 | CDD | cd17953 | DEADc_DDX46 | 404 | 625 | 3.4997E-155 |
| 12 | g789.t1 | CDD | cd18787 | SF2_C_DEAD | 636 | 766 | 6.82738E-53 |
| 10 | g789.t1 | Coils | Coil | Coil | 130 | 157 | - |
| 9 | g789.t1 | Coils | Coil | Coil | 251 | 271 | - |
| 11 | g789.t1 | Coils | Coil | Coil | 386 | 406 | - |
| 8 | g789.t1 | Gene3D | G3DSA:3.40.50.300 | - | 366 | 626 | 5.0E-91 |
| 7 | g789.t1 | Gene3D | G3DSA:3.40.50.300 | - | 627 | 800 | 3.2E-47 |
| 17 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 110 | - |
| 22 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 18 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 42 | - |
| 19 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 43 | 91 | - |
| 23 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 153 | 217 | - |
| 16 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 160 | 175 | - |
| 20 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 192 | 217 | - |
| 21 | g789.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 273 | - |
| 3 | g789.t1 | PANTHER | PTHR47958:SF35 | LOW QUALITY PROTEIN: DEAD-BOX ATP-DEPENDENT RNA HELICASE 42-LIKE | 55 | 863 | 1.7E-256 |
| 4 | g789.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 55 | 863 | 1.7E-256 |
| 1 | g789.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 439 | 612 | 7.9E-48 |
| 2 | g789.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 649 | 757 | 1.6E-26 |
| 24 | g789.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 415 | 443 | 10.617 |
| 26 | g789.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 446 | 624 | 32.069 |
| 25 | g789.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 635 | 796 | 22.061 |
| 15 | g789.t1 | SMART | SM00487 | ultradead3 | 434 | 639 | 8.1E-67 |
| 14 | g789.t1 | SMART | SM00490 | helicmild6 | 676 | 757 | 8.2E-29 |
| 6 | g789.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 403 | 626 | 1.42E-72 |
| 5 | g789.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 562 | 798 | 5.08E-52 |
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 K12811 (ATP-dependent RNA helicase DDX46/PRP5)
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.
