Gene loci information

Transcript annotation

  • This transcript has been annotated as DEAD-box helicase Dbp80.

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 g1800 g1800.t16 TSS g1800.t16 13076692 13076692
chr_3 g1800 g1800.t16 isoform g1800.t16 13077634 13078704
chr_3 g1800 g1800.t16 exon g1800.t16.exon1 13077634 13077643
chr_3 g1800 g1800.t16 exon g1800.t16.exon2 13077712 13077806
chr_3 g1800 g1800.t16 cds g1800.t16.CDS1 13077804 13077806
chr_3 g1800 g1800.t16 exon g1800.t16.exon3 13077878 13078426
chr_3 g1800 g1800.t16 cds g1800.t16.CDS2 13077878 13078426
chr_3 g1800 g1800.t16 exon g1800.t16.exon4 13078560 13078704
chr_3 g1800 g1800.t16 cds g1800.t16.CDS3 13078560 13078586
chr_3 g1800 g1800.t16 TTS g1800.t16 13078912 13078912

Sequences

>g1800.t16 Gene=g1800 Length=799
GTGATAATAGGTACACCTGGAAAAGTTCAGGATTGGTCTCTTAAATATCATGCTTTTGAT
TTATCAAAAATCACTGTATTTGTTCTCGATGAAGCCGATGTTATGATTGCACAACAAGGA
CATCAAGATCAATGTACTCGTTTAAATAAGCATATCTCAAAGAAAACGTGTCAATATATG
CTTTTTAGTGCTACATACGATAAGAAAGTTATGGAATTTGCAGAATACATTGTTCCATCT
CCAATTACCATTCGTTTGAAAAAAGAAGAAGAAGTATTGGATAATATCAAACAATACTAT
GTGCGTTGTGCAAATCAAGAAATTAAATATCAAGCTATTGCAAATATCTATGGAGTAGTT
ACAATCGGTCAGGCAATTATTTTCTGTCATACTCGCAAAACGGCATCTTGGTTATCTAGT
AAAATGGCTAAAGAAGGTCATTCAGTTGGTGTTTTATCAGGAGAATTGACCGTTGAACAA
CGTTTAGCAGTGCTCGATCGTTTCCGTGAAGGCCATGAAAAAGTTTTGATTACCACTAAT
GTTCTATCTCGTGGCATTGATATTGAACAAGTCAATATTGTTGTGAATTTTGACTTACCT
GTTGATCGAGACGATAATGCTGATTGTGAGACTTACTTGCATAGAATAGGTAAAATTTGG
CAAACATGGCATCGCTATTAATTTGATTGATTCTGAAAAATCAATGCAAATTTGTCGCGA
TATTGAAAAACATTTTGGTAAAAAGATAATGCTCCTCGATGTTGAAAACTCAGATGAAAT
TGAAAAAATTGGATCATAA

>g1800.t16 Gene=g1800 Length=192
MIAQQGHQDQCTRLNKHISKKTCQYMLFSATYDKKVMEFAEYIVPSPITIRLKKEEEVLD
NIKQYYVRCANQEIKYQAIANIYGVVTIGQAIIFCHTRKTASWLSSKMAKEGHSVGVLSG
ELTVEQRLAVLDRFREGHEKVLITTNVLSRGIDIEQVNIVVNFDLPVDRDDNADCETYLH
RIGKIWQTWHRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1800.t16 CDD cd18787 SF2_C_DEAD 62 183 0.0000000
6 g1800.t16 Gene3D G3DSA:3.40.50.300 - 1 61 0.0000001
7 g1800.t16 Gene3D G3DSA:3.40.50.300 - 62 188 0.0000000
2 g1800.t16 PANTHER PTHR47958:SF84 DEAD-BOX HELICASE 19A 1 184 0.0000000
3 g1800.t16 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 1 184 0.0000000
1 g1800.t16 Pfam PF00271 Helicase conserved C-terminal domain 79 185 0.0000000
9 g1800.t16 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 50 7.7430000
8 g1800.t16 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 61 192 16.7980000
5 g1800.t16 SMART SM00490 helicmild6 102 184 0.0000000
4 g1800.t16 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 8 185 0.0000000

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. There were no conditions that were differentially expressed