General information for g1800.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DEAD-box helicase Dbp80.
Parent gene
- The parent gene g1800 is located on chr_3: 13077910..13078704 (+ 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 | g1800 | g1800.t17 | isoform | g1800.t17 | 13077910 | 13078704 |
| chr_3 | g1800 | g1800.t17 | exon | g1800.t17.exon1 | 13077910 | 13078426 |
| chr_3 | g1800 | g1800.t17 | cds | g1800.t17.CDS1 | 13077950 | 13078426 |
| chr_3 | g1800 | g1800.t17 | exon | g1800.t17.exon2 | 13078560 | 13078704 |
| chr_3 | g1800 | g1800.t17 | cds | g1800.t17.CDS2 | 13078560 | 13078586 |
| chr_3 | g1800 | g1800.t17 | TTS | g1800.t17 | 13078912 | 13078912 |
| chr_3 | g1800 | g1800.t17 | TSS | g1800.t17 | NA | NA |
Sequences
>g1800.t17 Gene=g1800 Length=662
TCGTTTAAATAAGCATATCTCAAAGAAAACGTGTCAATATATGCTTTTTAGTGCTACATA
CGATAAGAAAGTTATGGAATTTGCAGAATACATTGTTCCATCTCCAATTACCATTCGTTT
GAAAAAAGAAGAAGAAGTATTGGATAATATCAAACAATACTATGTGCGTTGTGCAAATCA
AGAAATTAAATATCAAGCTATTGCAAATATCTATGGAGTAGTTACAATCGGTCAGGCAAT
TATTTTCTGTCATACTCGCAAAACGGCATCTTGGTTATCTAGTAAAATGGCTAAAGAAGG
TCATTCAGTTGGTGTTTTATCAGGAGAATTGACCGTTGAACAACGTTTAGCAGTGCTCGA
TCGTTTCCGTGAAGGCCATGAAAAAGTTTTGATTACCACTAATGTTCTATCTCGTGGCAT
TGATATTGAACAAGTCAATATTGTTGTGAATTTTGACTTACCTGTTGATCGAGACGATAA
TGCTGATTGTGAGACTTACTTGCATAGAATAGGTAAAATTTGGCAAACATGGCATCGCTA
TTAATTTGATTGATTCTGAAAAATCAATGCAAATTTGTCGCGATATTGAAAAACATTTTG
GTAAAAAGATAATGCTCCTCGATGTTGAAAACTCAGATGAAATTGAAAAAATTGGATCAT
AA
>g1800.t17 Gene=g1800 Length=167
MLFSATYDKKVMEFAEYIVPSPITIRLKKEEEVLDNIKQYYVRCANQEIKYQAIANIYGV
VTIGQAIIFCHTRKTASWLSSKMAKEGHSVGVLSGELTVEQRLAVLDRFREGHEKVLITT
NVLSRGIDIEQVNIVVNFDLPVDRDDNADCETYLHRIGKIWQTWHRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1800.t17 | CDD | cd18787 | SF2_C_DEAD | 37 | 158 | 0.000 |
| 6 | g1800.t17 | Gene3D | G3DSA:3.40.50.300 | - | 32 | 163 | 0.000 |
| 2 | g1800.t17 | PANTHER | PTHR47958:SF84 | DEAD-BOX HELICASE 19A | 1 | 159 | 0.000 |
| 3 | g1800.t17 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 159 | 0.000 |
| 1 | g1800.t17 | Pfam | PF00271 | Helicase conserved C-terminal domain | 53 | 160 | 0.000 |
| 8 | g1800.t17 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 25 | 6.875 |
| 7 | g1800.t17 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 36 | 167 | 16.798 |
| 5 | g1800.t17 | SMART | SM00490 | helicmild6 | 77 | 159 | 0.000 |
| 4 | g1800.t17 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 161 | 0.000 |
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.
