Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative ATP-dependent RNA helicase dhx8.

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_4 g16603 g16603.t4 TSS g16603.t4 10171303 10171303
chr_4 g16603 g16603.t4 isoform g16603.t4 10172107 10172787
chr_4 g16603 g16603.t4 exon g16603.t4.exon1 10172107 10172787
chr_4 g16603 g16603.t4 cds g16603.t4.CDS1 10172294 10172785
chr_4 g16603 g16603.t4 TTS g16603.t4 10173425 10173425

Sequences

>g16603.t4 Gene=g16603 Length=681
CGAGACAGGATCTGGCAAGACAACCCAAGTTGCACAGTATTTATTTGAAGGTGGATTAAA
TTTGAAAGGAAAAATTGCTTGCACTCAACCACGACGTGTTGCTGCTGTAACTGTTGCAAA
ACGTGTCGCAGAAGAATATGGATGCATTTTAGGTCAAGAAGTTGGCTATAAAATTCGATT
TGTTGATATGACTTCACCAAATACTGTCATTAAATACATGACTGATGGAATTTTACTTCG
TGAATGTTTATCAGATGCAAACCTTGACAATTATTCAGTTATAATTCTCGATGAAGCTCA
TGAAAGATCAATTTATACTGATGTTTTATTTGGTGTTCTTAAAAAAGCTGCTAAAAGACG
ACCAAAATTAAGAGTTGTCATTTCCTCAGCAACTTTGAATACTGACCAATTTTCTAAATT
TTTCAACAATGCAAAAGTTTTAAAAATTCCTGGCAAAATGTTTCCAGTTGAAATCAAATA
TCAAGCAAATCCAGTACGTGATTATTTTAATGCTGCTGTCAATACAGTTTTGAATATTCA
CTTGCAAGAACCTGAAGGTGATATTTTATGTTTTCTAACTGGACAAGATGAAATTGATTA
TGCATGTGAAATAATTGATGAAATTGCTGAAGCTGATGATGAAAACTTTGGCAATCTTTA
TGCTTATGCTCTCTATTCAGC

>g16603.t4 Gene=g16603 Length=164
MTSPNTVIKYMTDGILLRECLSDANLDNYSVIILDEAHERSIYTDVLFGVLKKAAKRRPK
LRVVISSATLNTDQFSKFFNNAKVLKIPGKMFPVEIKYQANPVRDYFNAAVNTVLNIHLQ
EPEGDILCFLTGQDEIDYACEIIDEIAEADDENFGNLYAYALYS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g16603.t4 CDD cd17917 DEXHc_RHA-like 2 87 2.61709E-49
6 g16603.t4 Gene3D G3DSA:3.40.50.300 - 1 90 7.8E-39
5 g16603.t4 Gene3D G3DSA:3.40.50.300 - 91 164 1.8E-16
1 g16603.t4 PANTHER PTHR18934:SF120 OS06G0343100 PROTEIN 2 164 1.4E-60
2 g16603.t4 PANTHER PTHR18934 ATP-DEPENDENT RNA HELICASE 2 164 1.4E-60
4 g16603.t4 ProSitePatterns PS00690 DEAH-box subfamily ATP-dependent helicases signature. 30 39 -
7 g16603.t4 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 88 13.483
3 g16603.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 161 1.93E-29

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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