Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable ATP-dependent RNA helicase DDX5.

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_1 g13653 g13653.t3 TSS g13653.t3 31414466 31414466
chr_1 g13653 g13653.t3 isoform g13653.t3 31414567 31415835
chr_1 g13653 g13653.t3 exon g13653.t3.exon1 31414567 31414610
chr_1 g13653 g13653.t3 cds g13653.t3.CDS1 31414567 31414610
chr_1 g13653 g13653.t3 exon g13653.t3.exon2 31414953 31415835
chr_1 g13653 g13653.t3 cds g13653.t3.CDS2 31414953 31415835
chr_1 g13653 g13653.t3 TTS g13653.t3 31416125 31416125

Sequences

>g13653.t3 Gene=g13653 Length=927
ATGTATCAAGGCGGTTATCAAGGAAATTTCAACCAAAACCATGGTTTTCGTCCACCTCGT
CCAGATTTCAATGCGGATAATCGTTGGAATCGAAACAATCCGAACAATCCACAATTCAAT
AATCACTTCAATCCAAATTTCATGAGTAATGGAGCGTTTAATGGTAACTTTGTTCCAAAT
AATCGCACCTACCCACCGAAGAAAGATTTTGGCGGCCCTAAAAGCAACCAACCAAACCAT
ATAAGGAAGAATAAATCTCCTGATTTGGATGATATGACAAAAGAAGAACGTGCAAAATTG
CAAAGCATGAAAGCAAAATGTCCGGGACAAAATCTCGTTCGTCCTAATTGGGAATCGATT
AAACTTGAACCATTCAAAAAAGATTTTAACAAAATTCACGAAAATAATGCTAATCGTACA
CTCGAAGAAGTCATGGCATGGCGTGCTAGCATGGAAATTACTGTCAAAGGAAAAGATGTT
CCATATCCACATCAAGATTTTGATGAAGCCGGTTTTTCACAAAGTATCATCAATGAAGTC
ACTCGACAAGGTTTCACTACTCCAACTCCCATACAGTCGCAAGGATGGCCAATTGCTATG
AAGGGGCGAGATTTGCTCGGTATTGCCCAAACAGGTTCTGGAAAAACTCTGGCTTATATG
CTGCCAGCAATTGTTCATATTAATAATCAACGACCTTTGATGAGAGGTGAAGGTCCAATT
GTTCTTGTTCTTGCACCTACACGAGAACTTGCACAGCAAATACAAACAGTTGCACGTGAT
TTTGGATCTCATGTGAAACCATATGTTCGTAATACTTGTATTTTCGGTGGTTCACCAAAA
GGACCACAAATCAGAGATTTAGAGCGAGGAATTGAAATTTGTATTGCAACACCGGGTCGT
CTTATTGATTTCCTCGAACGTGGAGTT

>g13653.t3 Gene=g13653 Length=309
MYQGGYQGNFNQNHGFRPPRPDFNADNRWNRNNPNNPQFNNHFNPNFMSNGAFNGNFVPN
NRTYPPKKDFGGPKSNQPNHIRKNKSPDLDDMTKEERAKLQSMKAKCPGQNLVRPNWESI
KLEPFKKDFNKIHENNANRTLEEVMAWRASMEITVKGKDVPYPHQDFDEAGFSQSIINEV
TRQGFTTPTPIQSQGWPIAMKGRDLLGIAQTGSGKTLAYMLPAIVHINNQRPLMRGEGPI
VLVLAPTRELAQQIQTVARDFGSHVKPYVRNTCIFGGSPKGPQIRDLERGIEICIATPGR
LIDFLERGV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13653.t3 Gene3D G3DSA:3.40.50.300 - 127 309 6.0E-55
7 g13653.t3 MobiDBLite mobidb-lite consensus disorder prediction 69 95 -
6 g13653.t3 MobiDBLite mobidb-lite consensus disorder prediction 81 95 -
2 g13653.t3 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 63 308 1.4E-114
3 g13653.t3 PANTHER PTHR47958:SF73 LD32873P 63 308 1.4E-114
1 g13653.t3 Pfam PF00270 DEAD/DEAH box helicase 189 308 2.5E-28
9 g13653.t3 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 165 193 11.137
10 g13653.t3 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 196 309 17.828
5 g13653.t3 SMART SM00487 ultradead3 184 309 1.4E-9
4 g13653.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 147 308 2.37E-45

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 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. There were no conditions that were differentially expressed