General information for g10716.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent RNA helicase bel.
Parent gene
- The parent gene g10716 is located on chr_1: 11564986..11566152 (- 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_1 | g10716 | g10716.t1 | TTS | g10716.t1 | 11562534 | 11562534 |
| chr_1 | g10716 | g10716.t1 | isoform | g10716.t1 | 11562995 | 11566152 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon1 | 11562995 | 11563122 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS1 | 11562995 | 11563122 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon2 | 11563185 | 11563511 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS2 | 11563185 | 11563511 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon3 | 11563572 | 11564121 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS3 | 11563572 | 11564121 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon4 | 11564177 | 11564413 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS4 | 11564177 | 11564413 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon5 | 11564487 | 11564613 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS5 | 11564487 | 11564613 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon6 | 11564683 | 11565399 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS6 | 11564683 | 11565399 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon7 | 11565687 | 11565862 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS7 | 11565687 | 11565862 |
| chr_1 | g10716 | g10716.t1 | exon | g10716.t1.exon8 | 11566108 | 11566152 |
| chr_1 | g10716 | g10716.t1 | cds | g10716.t1.CDS8 | 11566108 | 11566152 |
| chr_1 | g10716 | g10716.t1 | TSS | g10716.t1 | 11566414 | 11566414 |
Sequences
>g10716.t1 Gene=g10716 Length=2307
ATGAATAATTATGCAAACGAAAATGGCATGAGTCTAGAGCAGCAGGTTGCTGGTCTGGAC
TTGAATGAATCTCGTAATAAAGGTTCATCTCTACGCTATATTCCACCTCATTTGAGAGGA
GGCGAAAGTAGTAACGATTCTTCTTCTAATAATCAAAATAATCAAGGAGAAAACTTCAGG
GAGTACAACAATCGTGGTGGTGATCGCGATTATAATAATCGAAACAATAATCGTCGCTTT
AATAGCAACAATAATTATAATCAACGAGATAATTATCATCAACGCAGCGGCGGTGATTAC
AATCACTCGAATTATAACAACAATCGTTATCAGAACGGAGATTCAGGTGATCGTGGTGGT
TCTAATTGGAATAATCGCGGAGGATCAAGAACTTTTAATAATCGCTCGCAGCAAGGAGGC
GAGCCTCGTTTTTCTCAAAACAATTATCAACAGCAGCAGTATCCACCGCAACAAAATTAT
CGCGATGATTCTCAGCAATCACCGGCGCCACAAAATCAACGCGAAGAGCCTGTCAATACA
CGTTGGCAAGAGCCACCATCACAACAGAAGCAACAACAAGATGATCGCTATGGAAGACAA
CAAAATAATGGCAGCGGATTTGGCGGAAAATGGAATCAACGCGGAGGTGAAATTGATTAC
ACTGTACCGCTACCACGTGATGAACGTCTTGAACAGGAGCTGTTCGGCACTGCGAATACC
GGTATCAATTTTAGCAAATACGAAGACATTCCCGTGGAGGCGACGGGACATCAAGTTCCT
GATCACATCACATCATTCGATGATATCAAGTTGACGGAAATTATTCGTAGCAATATTAAA
TTGGCAAGATACGACAAACCGACTCCGGTGCAGAAATATGCCATACCGATCATTCTATCA
GGACGCGATCTCATGTCATGCGCTCAAACTGGTTCAGGCAAAACTGCCGCTTTTCTTGTT
CCGATTTTGAATCGCATGCTTGAACAAGGAGCAAGCATGAATCCTCCTTCAAATCGTCCT
TATAACAGACGCAAACAATATCCACTTGGTTTAGTACTAGCACCAACGCGTGAGTTGGCT
ACACAAATTTATGAAGAAGCAAAGAAGTTTTCTTATCGTTCGCGCATGCGTCCAGCTGTT
TTATATGGCGGTAATAATACTAGCGAGCAAATGCGTGAACTTGACCGTGGATGTCACTTA
ATTGTCGCAACTCCGGGTCGTCTTGATGATATTATCAATCGTGGAAAAATTGGATTGGAA
AATTTACGTTTTCTTGTGCTTGATGAGGCCGATAGAATGCTTGATATGGGTTTCGAACCT
CAAATTCGTCACATTATTGAAAATCGCGATATGCCTCCAACTGGTCAACGTCAAACATTA
ATGTTTTCTGCTACATTTCCGAAGAATATTCAAGAGTTGGCGAGTGATTTTCTATCAAAT
TACATTTTCTTGGCCGTTGGACGTGTTGGTTCAACTTCTGAAAATATTACACAGACAATT
TTGTGGGTTAATGAGCATGAGAAACGTTCATATTTACTTGACTTATTGAGCCGCTTACGC
GAAGGATCGCCTGATTATTCACCTGACAGTTTAACTTTGATTTTTGTTGAAACGAAAAAG
GGTGCTGATGCATTAGAAGAATTCTTGTATCAAAATAAGCATCCAGTCACTTCTATTCAT
GGTGATCGTAGTCAACGTGAGCGTGAAGATGCATTAAAATGTTTCCGTTCTGGTGATTGT
CCTATTCTCGTTGCAACTGCAGTCGCTGCTCGTGGATTAGATATTCCACATGTTAAGCAT
GTCATAAACTATGATTTGCCTTCAGATGTTGAAGAATATGTTCATCGTATTGGTCGAACA
GGTCGTATGGGTAATCTTGGAATTGCAACAAGTTTCTTCAATGAAAAGAATCGCAATATT
GTCTCTGATCTAGTTGAACTTTTGATTGAGACAAATCAAGAATTGCCAGGTTTTCTTGAA
GAAATGGCCAATGATCGTTATAGTGGACCAAGACGAAGCAACAATAATAGAGGTGGCAAT
AGTCGTTATGGTGGTAGTGGTTTTGGCTCACGCGATTATCGTCAACCACAAGGCAACCAA
CGTTATGGTAGTGGTGGTGCTGGAAGCAACAGTGGAAATAGCGGAAATCGTTCATATGGA
GGTGGAAATCGATCATATGGAAACAATGATGGAAGTTATCGTAATGGAGGAGGTGGTGGA
AATAATAGCAGTGGTAGTTATGGAGGAAGCTACAACAATTACAACAACAATCATGCAAGC
TCTGGTCCAGACTGGTGGGAAGATTAA
>g10716.t1 Gene=g10716 Length=768
MNNYANENGMSLEQQVAGLDLNESRNKGSSLRYIPPHLRGGESSNDSSSNNQNNQGENFR
EYNNRGGDRDYNNRNNNRRFNSNNNYNQRDNYHQRSGGDYNHSNYNNNRYQNGDSGDRGG
SNWNNRGGSRTFNNRSQQGGEPRFSQNNYQQQQYPPQQNYRDDSQQSPAPQNQREEPVNT
RWQEPPSQQKQQQDDRYGRQQNNGSGFGGKWNQRGGEIDYTVPLPRDERLEQELFGTANT
GINFSKYEDIPVEATGHQVPDHITSFDDIKLTEIIRSNIKLARYDKPTPVQKYAIPIILS
GRDLMSCAQTGSGKTAAFLVPILNRMLEQGASMNPPSNRPYNRRKQYPLGLVLAPTRELA
TQIYEEAKKFSYRSRMRPAVLYGGNNTSEQMRELDRGCHLIVATPGRLDDIINRGKIGLE
NLRFLVLDEADRMLDMGFEPQIRHIIENRDMPPTGQRQTLMFSATFPKNIQELASDFLSN
YIFLAVGRVGSTSENITQTILWVNEHEKRSYLLDLLSRLREGSPDYSPDSLTLIFVETKK
GADALEEFLYQNKHPVTSIHGDRSQREREDALKCFRSGDCPILVATAVAARGLDIPHVKH
VINYDLPSDVEEYVHRIGRTGRMGNLGIATSFFNEKNRNIVSDLVELLIETNQELPGFLE
EMANDRYSGPRRSNNNRGGNSRYGGSGFGSRDYRQPQGNQRYGSGGAGSNSGNSGNRSYG
GGNRSYGNNDGSYRNGGGGGNNSSGSYGGSYNNYNNNHASSGPDWWED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10716.t1 | CDD | cd18787 | SF2_C_DEAD | 496 | 633 | 1.981E-60 |
| 7 | g10716.t1 | Gene3D | G3DSA:3.40.50.300 | - | 222 | 485 | 1.2E-86 |
| 6 | g10716.t1 | Gene3D | G3DSA:3.40.50.300 | - | 486 | 668 | 2.6E-59 |
| 13 | g10716.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 90 | - |
| 17 | g10716.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 41 | 61 | - |
| 16 | g10716.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 90 | - |
| 12 | g10716.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 135 | 199 | - |
| 14 | g10716.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 668 | 692 | - |
| 15 | g10716.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 668 | 683 | - |
| 3 | g10716.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 218 | 708 | 9.4E-230 |
| 4 | g10716.t1 | PANTHER | PTHR47958:SF98 | DEAD-BOX HELICASE 3 X-LINKED A | 218 | 708 | 9.4E-230 |
| 1 | g10716.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 288 | 473 | 5.5E-53 |
| 2 | g10716.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 524 | 624 | 4.9E-30 |
| 9 | g10716.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 426 | 434 | - |
| 18 | g10716.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 264 | 292 | 9.657 |
| 20 | g10716.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 295 | 484 | 31.924 |
| 19 | g10716.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 511 | 663 | 23.241 |
| 11 | g10716.t1 | SMART | SM00487 | ultradead3 | 283 | 499 | 7.8E-63 |
| 10 | g10716.t1 | SMART | SM00490 | helicmild6 | 543 | 624 | 6.7E-36 |
| 5 | g10716.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 349 | 641 | 1.51E-74 |
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 K11594 (ATP-dependent RNA helicase DDX3X)
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.
