Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative ATP-dependent RNA helicase DDX42.

Parent gene

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.t2 TSS g1103.t2 8200430 8200430
chr_3 g1103 g1103.t2 isoform g1103.t2 8200567 8201415
chr_3 g1103 g1103.t2 exon g1103.t2.exon1 8200567 8201415
chr_3 g1103 g1103.t2 cds g1103.t2.CDS1 8200567 8201415
chr_3 g1103 g1103.t2 TTS g1103.t2 8202340 8202340

Sequences

>g1103.t2 Gene=g1103 Length=849
ATGAGTAAAAATTACAATTTTACTCCATTCAATTATGGATCGAAAAATACACAAAAGCCA
CAAAATTACAGTGCTATGCCGCCTCCTGATTCTTTAACAACAAATTCAAAGCAATTTGGT
CGTGCAAAAGCATCTTATACACCGATTGAAACAATTGCTCAACATACAATTCCAACTTAT
GGAAGGAAGAAAAATTCTTATATAGAAGACGATTATTTTGACGATGATGATGCTACAGAT
AGCAGCAGTTTACAGTATATACCAGCAGAAGGATCACCGAGTGCAAAGAAAAATGACTCA
GATTCAGAAGAAGATGAACTTGATGCATTTATGGCAAATTTAGAGAAAGAACAGAATAAA
ACAGCTAACAAAAGCAAACAGACATCCAACAATGAACAACAGCAGTCACAATCGCAAAGT
AAGGGCATTCGAGCTGATATCGATGAACTTGATGATGAGGAAAGTTATTATAAGTACATG
GAAGAAAATCCAATGGCAGGCGTACTCGATAATAACTCAGAAGATGAAATGGAATACGAT
GAAGAGGGCTATCCAATTGCACAAAGAAAAAAAGAAATTGATCCTTTACCACCCATTGAT
CACTCGCAAATTGAATATAAGCCATTTGAGAAAAATTTTTATACTCCACATGAAGAGATT
GCATCACTCAATCGTGTAAAAACAATTGAATTGAGACAAAAATTAGGAATTAAAGTTACA
GGCGCATCAGCACCAGCACCAGTTTGTTCTTTTGCCCATTTTGGATTTGATGAAGCATTA
ATGAAAGCGATAAGAAAAAGTGAATACATTTCACCAACTCCGATTCAGGCTCAAGCAATT
CCTGTAGCG

>g1103.t2 Gene=g1103 Length=283
MSKNYNFTPFNYGSKNTQKPQNYSAMPPPDSLTTNSKQFGRAKASYTPIETIAQHTIPTY
GRKKNSYIEDDYFDDDDATDSSSLQYIPAEGSPSAKKNDSDSEEDELDAFMANLEKEQNK
TANKSKQTSNNEQQQSQSQSKGIRADIDELDDEESYYKYMEENPMAGVLDNNSEDEMEYD
EEGYPIAQRKKEIDPLPPIDHSQIEYKPFEKNFYTPHEEIASLNRVKTIELRQKLGIKVT
GASAPAPVCSFAHFGFDEALMKAIRKSEYISPTPIQAQAIPVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1103.t2 Coils Coil Coil 100 131 -
8 g1103.t2 Gene3D G3DSA:3.40.50.300 - 212 283 1.3E-10
7 g1103.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 40 -
5 g1103.t2 MobiDBLite mobidb-lite consensus disorder prediction 71 152 -
6 g1103.t2 MobiDBLite mobidb-lite consensus disorder prediction 96 113 -
4 g1103.t2 MobiDBLite mobidb-lite consensus disorder prediction 123 143 -
1 g1103.t2 PANTHER PTHR24031:SF125 ATP-DEPENDENT RNA HELICASE DDX42 53 283 2.8E-15
2 g1103.t2 PANTHER PTHR24031 RNA HELICASE 53 283 2.8E-15
10 g1103.t2 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 249 277 10.825
3 g1103.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 232 282 2.78E-6

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:0004386 helicase activity 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.

Raw TPM values