General information for g9611.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Endoribonuclease dcr-1.
Parent gene
- The parent gene g9611 is located on chr_1: 4281465..4282986 (- 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 | g9611 | g9611.t4 | isoform | g9611.t4 | 4279509 | 4281465 |
| chr_1 | g9611 | g9611.t4 | exon | g9611.t4.exon1 | 4279509 | 4280312 |
| chr_1 | g9611 | g9611.t4 | cds | g9611.t4.CDS1 | 4279511 | 4280312 |
| chr_1 | g9611 | g9611.t4 | exon | g9611.t4.exon2 | 4280379 | 4281178 |
| chr_1 | g9611 | g9611.t4 | cds | g9611.t4.CDS2 | 4280379 | 4281178 |
| chr_1 | g9611 | g9611.t4 | exon | g9611.t4.exon3 | 4281246 | 4281341 |
| chr_1 | g9611 | g9611.t4 | cds | g9611.t4.CDS3 | 4281246 | 4281341 |
| chr_1 | g9611 | g9611.t4 | exon | g9611.t4.exon4 | 4281445 | 4281465 |
| chr_1 | g9611 | g9611.t4 | cds | g9611.t4.CDS4 | 4281445 | 4281465 |
| chr_1 | g9611 | g9611.t4 | TSS | g9611.t4 | 4281719 | 4281719 |
| chr_1 | g9611 | g9611.t4 | TTS | g9611.t4 | NA | NA |
Sequences
>g9611.t4 Gene=g9611 Length=1721
ATGACAAAAGAAGAAAATATTGTTCAAACATTCTTAACAAGAGATTATCAAAGAAACATT
ATTGATGTATGTCTTAAAAGAAACTCAATTGTTTTTCTCCCAACTGGAGCTGGCAAGACA
TACATCGCTATTCAAGTGATCAAGCACTTCTCAAATCAGCTTGGAATAAAATATTCTGAA
GGTGGAAAGCGTTCTGTTTTCTTAGTAAACACAGTGTATCTTGCAAAGCAACAAGCTGAA
GCTATACAATTTCATATTCCATTTAATGTTCGTGTCGTTACTGGCGAAGAAAATGTTGAT
GCGTTTGAAGAAAGCGATTGGTTAAAAATTTTAGACAACAATGAAGTTTTAGTGATGACA
GCTCAATGCTTTCATGACGCTGTAAATCGCACTTTCATTAAAATGAATCAAATTCGAGTT
GTAATTTTTGATGAATGTCATCATGGTCGTAAAGATCATGTATATCATCAACTTATGCAA
AGCATATCAAACAAACTTGATGAAAACGAATTCAAGAATTTACGAATAATTGGACTTTCA
GGAATGCTTATAGGCGTCGATAACAGTATAAAACCTTACCTAGTTGCTGATGAAATGAAA
CGATTGGAAAGTACTTTTCAGAGTGTAATCATTACAGTTAATAATCTTGATGATCACAAA
AATGTTATTCTTTATTCAACCAAAGCTATCAAGACTGCCATTCTCTTTAATATGACTGCA
TGTTCAAAAACACTTGTTGAAGTAAAGGATTCTCTTTTATGTTTTCAAACAAAATTAGAA
ATGATAAAACTAGACAATTTGGATTATATCAATCCTAGAAATTTACGAAAAACAATTCCA
AAACGAATCAAGGAGCTTATTAACATACTCAAAGATTTTGAACATCAAGCTTTAATGATG
GGAAATTTTGGCGCATATATATCACTTGTAAGCATAATAGTACAACTCGAATTGAACAAA
AGAGCAGCAGATTCTGAACGCTATCGCGATGTATTAAAAATGTGCATCACAAAGGTTGAA
GAATGCATAAAAAAAGTAGACTATGAATTATGCTTGAATAGAGATAATGCAACAAACATA
ATTGCAAATTCATCACATAAAGTTCAAACATTGATCGAATTGCTTCAAAAAAGTTTTACT
GATGAAAACAGAGAAAAAGACTTGCAGTGCATAATTTTCGTTGAACGTCGTTCAACTGCA
AAAATACTCTATCATATTATCAAAATGTTGGCAAACTCTATGTTTAATTTTCCACTTCGA
CCTGATTTTATAGTTGGATGCAATAATGATATGCCAGAATCCATTGATGCTATTCTAAAT
AAATCTTTCAATAAGATGGCCTTGGATAAATTCAACAGGAACGAAACAAATTGCGTTATT
TGTACTAATGTTCTTGAGGAAGGGATTGATGTGCAAGCTTGTAATCTTGTTATTATGTAT
GATAAATCAACCACTCCACGAAGTTTCTTTCAATCATGTGGAAGAGCTCGCGACAACAAA
AGCAAATACATAGTGATGCTTGAACAAAGAGATATTGAAAAATTTAAAAAAAATGTTAAC
AACTGGAATTGTATTAACGATGAAATGAAGAAGCAGTTGATTGGAAAAACCTTAGATAGA
GAACTACCAAGTGATGAAAGTATTCAGAATGAACAACAACAATCATGGGAGCCTTATTTA
ACCAAAAGTGGAAGTGAATTAAATGCCTTAAATGCAATTAA
>g9611.t4 Gene=g9611 Length=573
MTKEENIVQTFLTRDYQRNIIDVCLKRNSIVFLPTGAGKTYIAIQVIKHFSNQLGIKYSE
GGKRSVFLVNTVYLAKQQAEAIQFHIPFNVRVVTGEENVDAFEESDWLKILDNNEVLVMT
AQCFHDAVNRTFIKMNQIRVVIFDECHHGRKDHVYHQLMQSISNKLDENEFKNLRIIGLS
GMLIGVDNSIKPYLVADEMKRLESTFQSVIITVNNLDDHKNVILYSTKAIKTAILFNMTA
CSKTLVEVKDSLLCFQTKLEMIKLDNLDYINPRNLRKTIPKRIKELINILKDFEHQALMM
GNFGAYISLVSIIVQLELNKRAADSERYRDVLKMCITKVEECIKKVDYELCLNRDNATNI
IANSSHKVQTLIELLQKSFTDENREKDLQCIIFVERRSTAKILYHIIKMLANSMFNFPLR
PDFIVGCNNDMPESIDAILNKSFNKMALDKFNRNETNCVICTNVLEEGIDVQACNLVIMY
DKSTTPRSFFQSCGRARDNKSKYIVMLEQRDIEKFKKNVNNWNCINDEMKKQLIGKTLDR
ELPSDESIQNEQQQSWEPYLTKSGSELNALNAI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9611.t4 | CDD | cd18034 | DEXHc_dicer | 14 | 214 | 2.23639E-67 |
| 10 | g9611.t4 | CDD | cd15903 | Dicer_PBD | 262 | 350 | 5.77473E-11 |
| 8 | g9611.t4 | Coils | Coil | Coil | 512 | 532 | - |
| 6 | g9611.t4 | Gene3D | G3DSA:3.40.50.300 | - | 13 | 264 | 2.3E-50 |
| 7 | g9611.t4 | Gene3D | G3DSA:3.40.50.300 | - | 355 | 533 | 2.5E-35 |
| 3 | g9611.t4 | PANTHER | PTHR14950:SF36 | DICER-2, ISOFORM A | 11 | 573 | 4.3E-106 |
| 4 | g9611.t4 | PANTHER | PTHR14950 | DICER-RELATED | 11 | 573 | 4.3E-106 |
| 1 | g9611.t4 | Pfam | PF04851 | Type III restriction enzyme, res subunit | 14 | 165 | 7.4E-17 |
| 2 | g9611.t4 | Pfam | PF00271 | Helicase conserved C-terminal domain | 367 | 496 | 4.5E-15 |
| 14 | g9611.t4 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 20 | 181 | 17.683 |
| 13 | g9611.t4 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 367 | 537 | 13.223 |
| 12 | g9611.t4 | SMART | SM00487 | ultradead3 | 9 | 210 | 3.0E-14 |
| 11 | g9611.t4 | SMART | SM00490 | helicmild6 | 422 | 499 | 3.4E-10 |
| 5 | g9611.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 21 | 497 | 4.37E-36 |
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:0003677 | DNA binding | MF |
| GO:0016787 | hydrolase activity | MF |
| GO:0005524 | ATP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12649 (ATP-dependent RNA helicase DHX58)
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. There were no conditions that were differentially expressed