General information for g1103.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent RNA helicase DDX42.
Parent gene
- The parent gene g1103 is located on chr_3: 8203023..8203761 (+ 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 | g1103 | g1103.t1 | TSS | g1103.t1 | 8200430 | 8200430 |
| chr_3 | g1103 | g1103.t1 | isoform | g1103.t1 | 8200567 | 8203023 |
| chr_3 | g1103 | g1103.t1 | exon | g1103.t1.exon1 | 8200567 | 8201422 |
| chr_3 | g1103 | g1103.t1 | cds | g1103.t1.CDS1 | 8200567 | 8201422 |
| chr_3 | g1103 | g1103.t1 | exon | g1103.t1.exon2 | 8201523 | 8201643 |
| chr_3 | g1103 | g1103.t1 | cds | g1103.t1.CDS2 | 8201523 | 8201643 |
| chr_3 | g1103 | g1103.t1 | exon | g1103.t1.exon3 | 8201702 | 8202381 |
| chr_3 | g1103 | g1103.t1 | cds | g1103.t1.CDS3 | 8201702 | 8202381 |
| chr_3 | g1103 | g1103.t1 | exon | g1103.t1.exon4 | 8202443 | 8203023 |
| chr_3 | g1103 | g1103.t1 | cds | g1103.t1.CDS4 | 8202443 | 8203023 |
| chr_3 | g1103 | g1103.t1 | TTS | g1103.t1 | 8203078 | 8203078 |
Sequences
>g1103.t1 Gene=g1103 Length=2238
ATGAGTAAAAATTACAATTTTACTCCATTCAATTATGGATCGAAAAATACACAAAAGCCA
CAAAATTACAGTGCTATGCCGCCTCCTGATTCTTTAACAACAAATTCAAAGCAATTTGGT
CGTGCAAAAGCATCTTATACACCGATTGAAACAATTGCTCAACATACAATTCCAACTTAT
GGAAGGAAGAAAAATTCTTATATAGAAGACGATTATTTTGACGATGATGATGCTACAGAT
AGCAGCAGTTTACAGTATATACCAGCAGAAGGATCACCGAGTGCAAAGAAAAATGACTCA
GATTCAGAAGAAGATGAACTTGATGCATTTATGGCAAATTTAGAGAAAGAACAGAATAAA
ACAGCTAACAAAAGCAAACAGACATCCAACAATGAACAACAGCAGTCACAATCGCAAAGT
AAGGGCATTCGAGCTGATATCGATGAACTTGATGATGAGGAAAGTTATTATAAGTACATG
GAAGAAAATCCAATGGCAGGCGTACTCGATAATAACTCAGAAGATGAAATGGAATACGAT
GAAGAGGGCTATCCAATTGCACAAAGAAAAAAAGAAATTGATCCTTTACCACCCATTGAT
CACTCGCAAATTGAATATAAGCCATTTGAGAAAAATTTTTATACTCCACATGAAGAGATT
GCATCACTCAATCGTGTAAAAACAATTGAATTGAGACAAAAATTAGGAATTAAAGTTACA
GGCGCATCAGCACCAGCACCAGTTTGTTCTTTTGCCCATTTTGGATTTGATGAAGCATTA
ATGAAAGCGATAAGAAAAAGTGAATACATTTCACCAACTCCGATTCAGGCTCAAGCAATT
CCTGTAGCGCTATCAGGACGAGATATCATCGGAATTGCTAAAACAGGAAGTGGTAAAACT
GCAGCATTTCTTTGGCCAATGCTTGTGCATATAATGGATCAAGAAAATTTAAAAAGCGGA
GAAGGTCCAATTGGATTAATCCTCGCTCCAACACGTGAACTTTCAATTCAAATTTATAAT
GAAGCTAAGAAATTTGGTAAAGTGTATAATATTCATGTGGTATGTTGCTATGGCGGTGGA
AATAAATTTGAACAGTCAAAGGCATTAGAAGAACGCCCGGAAATTGTAGTAGCGACTCCG
GGTCGTATGATTGATATGATAAAGATCAAAGCTACAAATTTACTTCGATGTTCATATCTT
GTTCTTGATGAAGCAGACAAAATGTTCAATTTAGGCTTCGAACCACAAGTTCGCTCAATT
TGTAATCATGTAAATCCGTTAAGACAAACACTACTTTTTAGTGCTACATTCAAGAAGCGA
ATAGAAAAACTCGCAAGAGACATTCTTACTGATCCAATTAGAATTGTTCAAGGAGACATT
GGTGAAGCAAATCAAGATATCACACAACATGCTATCATTTTTGAAAAACCAGAACATAAA
TTCAATTGGCTTCTCTTGCGACTTGTTGAATTTCTATCAGAAGGATCTGTACTAATTTTT
GTAACAAAAAAACTTGAAGCTGAAAAACTAGCAAGTGACATACAATTGAAAGAATTTCCT
TGCTTATTGCTTCATGGTGATATAGAACAAGCTGAAAGAAACAAAGTTATTACTGCATTT
AAAAAAAAAGAGTGTGATATTCTCGTTGCAACTGATGTCGCTAGTAGAGGTCTTGATATA
CATCACATTAAAAACGTCATAAATTATGATATGGCTCGAGATATTGATACACACACGCAT
AGAATCGGCAGAACAGCGCGTGGTGGTGAAAAAGGAACAGCATATACACTTGTAACTGAA
AAAGATAAAGAAATGGTTGGTCATTTAGTGCGAAATTTAGAAGGAGCTAATCAAATTGTT
CCTGATGATTTGATGAAGTTAGCTATGCAATCATCATGGTTCAGAAAGTCTCGATTTAGT
GGTGGTAAAGGAAAGTCAATTATTGGTGGTGCTGGTTTGGGATTTAAAGAAAGACCGAGC
ACTTCTTCTTCATCAAATGCTTCATCATCAACAGGAGGCTACAAACAGTCATTTGTCGCT
GCAAGTGAAAATAAATCTACAAATCGACTTGAAGCCCTTAAAAATGCATTCAAATCACAG
TACACATCAAATTTTAAATCAAGTAGCGATAAAACTTGGGAAACACCTTCAGCGCCAAGT
TTCGTGAGACCTCAAGCATCTTTAAATGAAAATTCAGAAGATGGTGGTTCAAAGAAAAAG
AAAAGTCGATGGAATTAA
>g1103.t1 Gene=g1103 Length=745
MSKNYNFTPFNYGSKNTQKPQNYSAMPPPDSLTTNSKQFGRAKASYTPIETIAQHTIPTY
GRKKNSYIEDDYFDDDDATDSSSLQYIPAEGSPSAKKNDSDSEEDELDAFMANLEKEQNK
TANKSKQTSNNEQQQSQSQSKGIRADIDELDDEESYYKYMEENPMAGVLDNNSEDEMEYD
EEGYPIAQRKKEIDPLPPIDHSQIEYKPFEKNFYTPHEEIASLNRVKTIELRQKLGIKVT
GASAPAPVCSFAHFGFDEALMKAIRKSEYISPTPIQAQAIPVALSGRDIIGIAKTGSGKT
AAFLWPMLVHIMDQENLKSGEGPIGLILAPTRELSIQIYNEAKKFGKVYNIHVVCCYGGG
NKFEQSKALEERPEIVVATPGRMIDMIKIKATNLLRCSYLVLDEADKMFNLGFEPQVRSI
CNHVNPLRQTLLFSATFKKRIEKLARDILTDPIRIVQGDIGEANQDITQHAIIFEKPEHK
FNWLLLRLVEFLSEGSVLIFVTKKLEAEKLASDIQLKEFPCLLLHGDIEQAERNKVITAF
KKKECDILVATDVASRGLDIHHIKNVINYDMARDIDTHTHRIGRTARGGEKGTAYTLVTE
KDKEMVGHLVRNLEGANQIVPDDLMKLAMQSSWFRKSRFSGGKGKSIIGGAGLGFKERPS
TSSSSNASSSTGGYKQSFVAASENKSTNRLEALKNAFKSQYTSNFKSSSDKTWETPSAPS
FVRPQASLNENSEDGGSKKKKSRWN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1103.t1 | CDD | cd17952 | DEADc_DDX42 | 260 | 456 | 4.33457E-130 |
| 10 | g1103.t1 | CDD | cd18787 | SF2_C_DEAD | 467 | 598 | 3.40924E-54 |
| 9 | g1103.t1 | Coils | Coil | Coil | 100 | 131 | - |
| 8 | g1103.t1 | Gene3D | G3DSA:3.40.50.300 | - | 212 | 458 | 2.0E-81 |
| 7 | g1103.t1 | Gene3D | G3DSA:3.40.50.300 | - | 461 | 640 | 1.0E-48 |
| 21 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 40 | - |
| 16 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 71 | 148 | - |
| 20 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 113 | - |
| 15 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 123 | 143 | - |
| 19 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 652 | 673 | - |
| 18 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 657 | 673 | - |
| 17 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 701 | 745 | - |
| 22 | g1103.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 701 | 732 | - |
| 3 | g1103.t1 | PANTHER | PTHR24031:SF125 | ATP-DEPENDENT RNA HELICASE DDX42 | 54 | 716 | 6.6E-214 |
| 4 | g1103.t1 | PANTHER | PTHR24031 | RNA HELICASE | 54 | 716 | 6.6E-214 |
| 1 | g1103.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 273 | 444 | 4.3E-47 |
| 2 | g1103.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 487 | 589 | 4.7E-27 |
| 14 | g1103.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 401 | 409 | - |
| 23 | g1103.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 249 | 277 | 10.825 |
| 25 | g1103.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 280 | 455 | 31.371 |
| 24 | g1103.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 484 | 628 | 21.752 |
| 13 | g1103.t1 | SMART | SM00487 | ultradead3 | 268 | 470 | 7.3E-60 |
| 12 | g1103.t1 | SMART | SM00490 | helicmild6 | 508 | 589 | 2.7E-29 |
| 5 | g1103.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 232 | 456 | 6.48E-71 |
| 6 | g1103.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 393 | 636 | 2.08E-51 |
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 K12835 (ATP-dependent RNA helicase DDX42)
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.
