General information for g1800.t13
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.t13 | TSS | g1800.t13 | 13076692 | 13076692 |
| chr_3 | g1800 | g1800.t13 | isoform | g1800.t13 | 13076803 | 13078704 |
| chr_3 | g1800 | g1800.t13 | exon | g1800.t13.exon1 | 13076803 | 13077038 |
| chr_3 | g1800 | g1800.t13 | exon | g1800.t13.exon2 | 13077101 | 13077232 |
| chr_3 | g1800 | g1800.t13 | exon | g1800.t13.exon3 | 13077294 | 13077643 |
| chr_3 | g1800 | g1800.t13 | cds | g1800.t13.CDS1 | 13077325 | 13077643 |
| chr_3 | g1800 | g1800.t13 | exon | g1800.t13.exon4 | 13077712 | 13077800 |
| chr_3 | g1800 | g1800.t13 | cds | g1800.t13.CDS2 | 13077712 | 13077800 |
| chr_3 | g1800 | g1800.t13 | exon | g1800.t13.exon5 | 13077878 | 13078426 |
| chr_3 | g1800 | g1800.t13 | cds | g1800.t13.CDS3 | 13077878 | 13078426 |
| chr_3 | g1800 | g1800.t13 | exon | g1800.t13.exon6 | 13078560 | 13078704 |
| chr_3 | g1800 | g1800.t13 | cds | g1800.t13.CDS4 | 13078560 | 13078586 |
| chr_3 | g1800 | g1800.t13 | TTS | g1800.t13 | 13078912 | 13078912 |
Sequences
>g1800.t13 Gene=g1800 Length=1501
ATGGCAGATACATGGACAAAAGCTGCAGAAAATCAAGAACAGCTCGAACAGCAAGAAATT
CAAAAATTAGTAAGTAGAAAGAGCGGCATTTTTGGCTCGGTTTGCAAAAATTGTGAAACA
TGCTTATAATTGATTTAAAATATTATTTTCTATAGAACGAAAATGTTAATAATGTGTCAA
TAAGTAATGATACAAAGACAATTAACAAAGATGATGAGCCTGATGAAGTGAAGTAATTTG
GCAGAAGCTTCATTGCTTGTTAAAATTATTCGAAAGGGGCTAATCGAAACTGGAACAAGC
CTTGACATTCAAAGAAAAGATCCGAATTCTCCATTGTATTCAGTTAAATCGTTTGAAGCT
CTTCATTTAAAACCAGAACTTTTACGTGGTGTATATGGAATGGGATATAACGCTCCTTCA
AAAATTCAAGAGACTGCACTTCCAACACTGATTGCTGATCCACCTCAAAATATGATTGCA
CAATCACAATCTGGTACTGGAAAAACAGCCTGCTTTACTTTAGCTATGTTGACTCGTGTA
GATACAACAAAAGACTATCCGCAAGTGCTATGTTTAAGTCCAACTTATGAACTTGCAATT
CAGACTGGAGAAGTTGCTGCACGAATGGCAAAATTTTGTCCTGAAATTCGTATTCGTTAT
GCAGTTAGAGGAGAAGATATCCAAAGAGGAACGAAATTAACAGATCATGTGATAATAGGT
ACACCTGGAAAAGTTCAGGATTGGTCTCTTAAATATCATGCTTTTGATTTATCAAAAATC
ACTGTATTTGTTCTCGATGAAGCCGATATTGCACAACAAGGACATCAAGATCAATGTACT
CGTTTAAATAAGCATATCTCAAAGAAAACGTGTCAATATATGCTTTTTAGTGCTACATAC
GATAAGAAAGTTATGGAATTTGCAGAATACATTGTTCCATCTCCAATTACCATTCGTTTG
AAAAAAGAAGAAGAAGTATTGGATAATATCAAACAATACTATGTGCGTTGTGCAAATCAA
GAAATTAAATATCAAGCTATTGCAAATATCTATGGAGTAGTTACAATCGGTCAGGCAATT
ATTTTCTGTCATACTCGCAAAACGGCATCTTGGTTATCTAGTAAAATGGCTAAAGAAGGT
CATTCAGTTGGTGTTTTATCAGGAGAATTGACCGTTGAACAACGTTTAGCAGTGCTCGAT
CGTTTCCGTGAAGGCCATGAAAAAGTTTTGATTACCACTAATGTTCTATCTCGTGGCATT
GATATTGAACAAGTCAATATTGTTGTGAATTTTGACTTACCTGTTGATCGAGACGATAAT
GCTGATTGTGAGACTTACTTGCATAGAATAGGTAAAATTTGGCAAACATGGCATCGCTAT
TAATTTGATTGATTCTGAAAAATCAATGCAAATTTGTCGCGATATTGAAAAACATTTTGG
TAAAAAGATAATGCTCCTCGATGTTGAAAACTCAGATGAAATTGAAAAAATTGGATCATA
A
>g1800.t13 Gene=g1800 Length=327
MGYNAPSKIQETALPTLIADPPQNMIAQSQSGTGKTACFTLAMLTRVDTTKDYPQVLCLS
PTYELAIQTGEVAARMAKFCPEIRIRYAVRGEDIQRGTKLTDHVIIGTPGKVQDWSLKYH
AFDLSKITVFVLDEADIAQQGHQDQCTRLNKHISKKTCQYMLFSATYDKKVMEFAEYIVP
SPITIRLKKEEEVLDNIKQYYVRCANQEIKYQAIANIYGVVTIGQAIIFCHTRKTASWLS
SKMAKEGHSVGVLSGELTVEQRLAVLDRFREGHEKVLITTNVLSRGIDIEQVNIVVNFDL
PVDRDDNADCETYLHRIGKIWQTWHRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g1800.t13 | CDD | cd17963 | DEADc_DDX19_DDX25 | 1 | 186 | 0.000 |
| 13 | g1800.t13 | CDD | cd18787 | SF2_C_DEAD | 197 | 318 | 0.000 |
| 9 | g1800.t13 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 192 | 0.000 |
| 8 | g1800.t13 | Gene3D | G3DSA:3.40.50.300 | - | 193 | 323 | 0.000 |
| 3 | g1800.t13 | PANTHER | PTHR47958:SF33 | ATP-DEPENDENT RNA HELICASE DDX25 | 1 | 319 | 0.000 |
| 4 | g1800.t13 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 319 | 0.000 |
| 1 | g1800.t13 | Pfam | PF00270 | DEAD/DEAH box helicase | 8 | 172 | 0.000 |
| 2 | g1800.t13 | Pfam | PF00271 | Helicase conserved C-terminal domain | 214 | 320 | 0.000 |
| 11 | g1800.t13 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 16 | 185 | 20.192 |
| 10 | g1800.t13 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 196 | 327 | 16.798 |
| 7 | g1800.t13 | SMART | SM00487 | ultradead3 | 2 | 200 | 0.000 |
| 6 | g1800.t13 | SMART | SM00490 | helicmild6 | 237 | 319 | 0.000 |
| 5 | g1800.t13 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 54 | 320 | 0.000 |
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: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