General information for g10716.t4
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.t4 | TTS | g10716.t4 | 11561948 | 11561948 |
| chr_1 | g10716 | g10716.t4 | isoform | g10716.t4 | 11562410 | 11564986 |
| chr_1 | g10716 | g10716.t4 | exon | g10716.t4.exon1 | 11562410 | 11563122 |
| chr_1 | g10716 | g10716.t4 | cds | g10716.t4.CDS1 | 11562995 | 11563122 |
| chr_1 | g10716 | g10716.t4 | exon | g10716.t4.exon2 | 11563185 | 11563511 |
| chr_1 | g10716 | g10716.t4 | cds | g10716.t4.CDS2 | 11563185 | 11563511 |
| chr_1 | g10716 | g10716.t4 | exon | g10716.t4.exon3 | 11563572 | 11564121 |
| chr_1 | g10716 | g10716.t4 | cds | g10716.t4.CDS3 | 11563572 | 11564121 |
| chr_1 | g10716 | g10716.t4 | exon | g10716.t4.exon4 | 11564177 | 11564413 |
| chr_1 | g10716 | g10716.t4 | cds | g10716.t4.CDS4 | 11564177 | 11564413 |
| chr_1 | g10716 | g10716.t4 | exon | g10716.t4.exon5 | 11564487 | 11564613 |
| chr_1 | g10716 | g10716.t4 | cds | g10716.t4.CDS5 | 11564487 | 11564613 |
| chr_1 | g10716 | g10716.t4 | exon | g10716.t4.exon6 | 11564683 | 11564986 |
| chr_1 | g10716 | g10716.t4 | cds | g10716.t4.CDS6 | 11564683 | 11564708 |
| chr_1 | g10716 | g10716.t4 | TSS | g10716.t4 | NA | NA |
Sequences
>g10716.t4 Gene=g10716 Length=2258
ATCAACGCGGAGGTGAAATTGATTACACTGTACCGCTACCACGTGATGAACGTCTTGAAC
AGGAGCTGTTCGGCACTGCGAATACCGGTATCAATTTTAGCAAATACGAAGACATTCCCG
TGGAGGCGACGGGACATCAAGTTCCTGATCACATCACATCATTCGATGATATCAAGTTGA
CGGAAATTATTCGTAGCAATATTAAATTGGCAAGATACGACAAACCGACTCCGGTGCAGA
AATATGCCATACCGATCATTCTATCAGGACGCGATCTCATGTCATGCGCTCAAACTGGTT
CAGGCAAAACTGCCGCTTTTCTTGTTCCGATTTTGAATCGCATGCTTGAACAAGGAGCAA
GCATGAATCCTCCTTCAAATCGTCCTTATAACAGACGCAAACAATATCCACTTGGTTTAG
TACTAGCACCAACGCGTGAGTTGGCTACACAAATTTATGAAGAAGCAAAGAAGTTTTCTT
ATCGTTCGCGCATGCGTCCAGCTGTTTTATATGGCGGTAATAATACTAGCGAGCAAATGC
GTGAACTTGACCGTGGATGTCACTTAATTGTCGCAACTCCGGGTCGTCTTGATGATATTA
TCAATCGTGGAAAAATTGGATTGGAAAATTTACGTTTTCTTGTGCTTGATGAGGCCGATA
GAATGCTTGATATGGGTTTCGAACCTCAAATTCGTCACATTATTGAAAATCGCGATATGC
CTCCAACTGGTCAACGTCAAACATTAATGTTTTCTGCTACATTTCCGAAGAATATTCAAG
AGTTGGCGAGTGATTTTCTATCAAATTACATTTTCTTGGCCGTTGGACGTGTTGGTTCAA
CTTCTGAAAATATTACACAGACAATTTTGTGGGTTAATGAGCATGAGAAACGTTCATATT
TACTTGACTTATTGAGCCGCTTACGCGAAGGATCGCCTGATTATTCACCTGACAGTTTAA
CTTTGATTTTTGTTGAAACGAAAAAGGGTGCTGATGCATTAGAAGAATTCTTGTATCAAA
ATAAGCATCCAGTCACTTCTATTCATGGTGATCGTAGTCAACGTGAGCGTGAAGATGCAT
TAAAATGTTTCCGTTCTGGTGATTGTCCTATTCTCGTTGCAACTGCAGTCGCTGCTCGTG
GATTAGATATTCCACATGTTAAGCATGTCATAAACTATGATTTGCCTTCAGATGTTGAAG
AATATGTTCATCGTATTGGTCGAACAGGTCGTATGGGTAATCTTGGAATTGCAACAAGTT
TCTTCAATGAAAAGAATCGCAATATTGTCTCTGATCTAGTTGAACTTTTGATTGAGACAA
ATCAAGAATTGCCAGGTTTTCTTGAAGAAATGGCCAATGATCGTTATAGTGGACCAAGAC
GAAGCAACAATAATAGAGGTGGCAATAGTCGTTATGGTGGTAGTGGTTTTGGCTCACGCG
ATTATCGTCAACCACAAGGCAACCAACGTTATGGTAGTGGTGGTGCTGGAAGCAACAGTG
GAAATAGCGGAAATCGTTCATATGGAGGTGGAAATCGATCATATGGAAACAATGATGGAA
GTTATCGTAATGGAGGAGGTGGTGGAAATAATAGCAGTGGTAGTTATGGAGGAAGCTACA
ACAATTACAACAACAATCATGCAAGCTCTGGTCCAGACTGGTGGGAAGATTAAGCAGTTT
TCTCACTGCCATTTTCTCTTTCTTTTAATCATCATATATAATTTTGTAGCAGAGTTAATT
TATCAATAGCAAAATCATTCTTCAACAGATTTTAAAATAATAATGTTTTAAATGCTTAAT
TTCTGTTGAAGAATGATTTTTGAAATGATTTTTTCTATAGATAAATTCTCGTGTGACCCT
GTCTCATTAACTACACACATACATACACACACATAAAACATACATACACTATTTAGTTTC
CAATTAAGATTATCTAATATTGATGAGCTATATGAATACAAGATAAAGAAACCCTTTTCA
AATTTTTACATTGACATTGTAAAAATTTTAAATTATGACAAAAAATGAGCAAGAAAAAGC
TAGCAGTGAATATGAATATTAAAAAGCATAGATTGTGGAAACAAATTTTATAAATCTCTT
AAACATGAAAAATAATTGTCATTTAAAAATGGATAAAAAAGAAGAAAGAATTTCTACAGG
TAAATCTCTAAATAAGATGGCGATTTCGCTTGTACTATTATTTAAATGGATAAAAAGAGA
CAACTGTAGAAAAGAAAGAAATAAATAATAAAACATAC
>g10716.t4 Gene=g10716 Length=464
MSCAQTGSGKTAAFLVPILNRMLEQGASMNPPSNRPYNRRKQYPLGLVLAPTRELATQIY
EEAKKFSYRSRMRPAVLYGGNNTSEQMRELDRGCHLIVATPGRLDDIINRGKIGLENLRF
LVLDEADRMLDMGFEPQIRHIIENRDMPPTGQRQTLMFSATFPKNIQELASDFLSNYIFL
AVGRVGSTSENITQTILWVNEHEKRSYLLDLLSRLREGSPDYSPDSLTLIFVETKKGADA
LEEFLYQNKHPVTSIHGDRSQREREDALKCFRSGDCPILVATAVAARGLDIPHVKHVINY
DLPSDVEEYVHRIGRTGRMGNLGIATSFFNEKNRNIVSDLVELLIETNQELPGFLEEMAN
DRYSGPRRSNNNRGGNSRYGGSGFGSRDYRQPQGNQRYGSGGAGSNSGNSGNRSYGGGNR
SYGNNDGSYRNGGGGGNNSSGSYGGSYNNYNNNHASSGPDWWED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10716.t4 | CDD | cd18787 | SF2_C_DEAD | 192 | 329 | 3.2196E-62 |
| 7 | g10716.t4 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 181 | 1.2E-66 |
| 6 | g10716.t4 | Gene3D | G3DSA:3.40.50.300 | - | 182 | 364 | 9.3E-60 |
| 12 | g10716.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 364 | 379 | - |
| 13 | g10716.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 364 | 388 | - |
| 3 | g10716.t4 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 405 | 8.3E-192 |
| 4 | g10716.t4 | PANTHER | PTHR47958:SF98 | DEAD-BOX HELICASE 3 X-LINKED A | 1 | 405 | 8.3E-192 |
| 1 | g10716.t4 | Pfam | PF00270 | DEAD/DEAH box helicase | 3 | 169 | 2.6E-46 |
| 2 | g10716.t4 | Pfam | PF00271 | Helicase conserved C-terminal domain | 220 | 320 | 2.2E-30 |
| 9 | g10716.t4 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 122 | 130 | - |
| 15 | g10716.t4 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 180 | 29.824 |
| 14 | g10716.t4 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 207 | 359 | 23.241 |
| 11 | g10716.t4 | SMART | SM00487 | ultradead3 | 1 | 195 | 3.6E-43 |
| 10 | g10716.t4 | SMART | SM00490 | helicmild6 | 239 | 320 | 6.7E-36 |
| 5 | g10716.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 45 | 337 | 4.18E-75 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
