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.t1 TSS g1800.t1 13076692 13076692
chr_3 g1800 g1800.t1 isoform g1800.t1 13076803 13078704
chr_3 g1800 g1800.t1 exon g1800.t1.exon1 13076803 13076871
chr_3 g1800 g1800.t1 cds g1800.t1.CDS1 13076803 13076871
chr_3 g1800 g1800.t1 exon g1800.t1.exon2 13076958 13077034
chr_3 g1800 g1800.t1 cds g1800.t1.CDS2 13076958 13077034
chr_3 g1800 g1800.t1 exon g1800.t1.exon3 13077101 13077232
chr_3 g1800 g1800.t1 cds g1800.t1.CDS3 13077101 13077232
chr_3 g1800 g1800.t1 exon g1800.t1.exon4 13077294 13077643
chr_3 g1800 g1800.t1 cds g1800.t1.CDS4 13077294 13077643
chr_3 g1800 g1800.t1 exon g1800.t1.exon5 13077712 13077806
chr_3 g1800 g1800.t1 cds g1800.t1.CDS5 13077712 13077806
chr_3 g1800 g1800.t1 exon g1800.t1.exon6 13077878 13078421
chr_3 g1800 g1800.t1 cds g1800.t1.CDS6 13077878 13078421
chr_3 g1800 g1800.t1 exon g1800.t1.exon7 13078487 13078499
chr_3 g1800 g1800.t1 cds g1800.t1.CDS7 13078487 13078499
chr_3 g1800 g1800.t1 exon g1800.t1.exon8 13078560 13078704
chr_3 g1800 g1800.t1 cds g1800.t1.CDS8 13078560 13078704
chr_3 g1800 g1800.t1 TTS g1800.t1 13078912 13078912

Sequences

>g1800.t1 Gene=g1800 Length=1425
ATGGCAGATACATGGACAAAAGCTGCAGAAAATCAAGAACAGCTCGAACAGCAAGAAATT
CAAAAATTAAACGAAAATGTTAATAATGTGTCAATAAGTAATGATACAAAGACAATTAAC
AAAGATGATGAGCCTGATGAAGTGAATTTGGCAGAAGCTTCATTGCTTGTTAAAATTATT
CGAAAGGGGCTAATCGAAACTGGAACAAGCCTTGACATTCAAAGAAAAGATCCGAATTCT
CCATTGTATTCAGTTAAATCGTTTGAAGCTCTTCATTTAAAACCAGAACTTTTACGTGGT
GTATATGGAATGGGATATAACGCTCCTTCAAAAATTCAAGAGACTGCACTTCCAACACTG
ATTGCTGATCCACCTCAAAATATGATTGCACAATCACAATCTGGTACTGGAAAAACAGCC
TGCTTTACTTTAGCTATGTTGACTCGTGTAGATACAACAAAAGACTATCCGCAAGTGCTA
TGTTTAAGTCCAACTTATGAACTTGCAATTCAGACTGGAGAAGTTGCTGCACGAATGGCA
AAATTTTGTCCTGAAATTCGTATTCGTTATGCAGTTAGAGGAGAAGATATCCAAAGAGGA
ACGAAATTAACAGATCATGTGATAATAGGTACACCTGGAAAAGTTCAGGATTGGTCTCTT
AAATATCATGCTTTTGATTTATCAAAAATCACTGTATTTGTTCTCGATGAAGCCGATGTT
ATGATTGCACAACAAGGACATCAAGATCAATGTACTCGTTTAAATAAGCATATCTCAAAG
AAAACGTGTCAATATATGCTTTTTAGTGCTACATACGATAAGAAAGTTATGGAATTTGCA
GAATACATTGTTCCATCTCCAATTACCATTCGTTTGAAAAAAGAAGAAGAAGTATTGGAT
AATATCAAACAATACTATGTGCGTTGTGCAAATCAAGAAATTAAATATCAAGCTATTGCA
AATATCTATGGAGTAGTTACAATCGGTCAGGCAATTATTTTCTGTCATACTCGCAAAACG
GCATCTTGGTTATCTAGTAAAATGGCTAAAGAAGGTCATTCAGTTGGTGTTTTATCAGGA
GAATTGACCGTTGAACAACGTTTAGCAGTGCTCGATCGTTTCCGTGAAGGCCATGAAAAA
GTTTTGATTACCACTAATGTTCTATCTCGTGGCATTGATATTGAACAAGTCAATATTGTT
GTGAATTTTGACTTACCTGTTGATCGAGACGATAATGCTGATTGTGAGACTTACTTGCAT
AGAATAGGTCGTACTGGACGATTTGGCAAACATGGCATCGCTATTAATTTGATTGATTCT
GAAAAATCAATGCAAATTTGTCGCGATATTGAAAAACATTTTGGTAAAAAGATAATGCTC
CTCGATGTTGAAAACTCAGATGAAATTGAAAAAATTGGATCATAA

>g1800.t1 Gene=g1800 Length=474
MADTWTKAAENQEQLEQQEIQKLNENVNNVSISNDTKTINKDDEPDEVNLAEASLLVKII
RKGLIETGTSLDIQRKDPNSPLYSVKSFEALHLKPELLRGVYGMGYNAPSKIQETALPTL
IADPPQNMIAQSQSGTGKTACFTLAMLTRVDTTKDYPQVLCLSPTYELAIQTGEVAARMA
KFCPEIRIRYAVRGEDIQRGTKLTDHVIIGTPGKVQDWSLKYHAFDLSKITVFVLDEADV
MIAQQGHQDQCTRLNKHISKKTCQYMLFSATYDKKVMEFAEYIVPSPITIRLKKEEEVLD
NIKQYYVRCANQEIKYQAIANIYGVVTIGQAIIFCHTRKTASWLSSKMAKEGHSVGVLSG
ELTVEQRLAVLDRFREGHEKVLITTNVLSRGIDIEQVNIVVNFDLPVDRDDNADCETYLH
RIGRTGRFGKHGIAINLIDSEKSMQICRDIEKHFGKKIMLLDVENSDEIEKIGS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1800.t1 CDD cd17963 DEADc_DDX19_DDX25 93 291 1.99521E-111
10 g1800.t1 CDD cd18787 SF2_C_DEAD 302 438 2.1413E-50
8 g1800.t1 Coils Coil Coil 6 26 -
6 g1800.t1 Gene3D G3DSA:3.40.50.300 - 63 297 3.2E-62
7 g1800.t1 Gene3D G3DSA:3.40.50.300 - 298 474 8.6E-52
3 g1800.t1 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 39 465 3.0E-185
4 g1800.t1 PANTHER PTHR47958:SF93 ATP-DEPENDENT RNA HELICASE DDX19B 39 465 3.0E-185
1 g1800.t1 Pfam PF00270 DEAD/DEAH box helicase 111 277 2.6E-29
2 g1800.t1 Pfam PF00271 Helicase conserved C-terminal domain 319 429 9.9E-27
13 g1800.t1 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 86 114 10.081
15 g1800.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 119 290 21.493
14 g1800.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 301 469 21.976
12 g1800.t1 SMART SM00487 ultradead3 105 305 4.8E-40
11 g1800.t1 SMART SM00490 helicmild6 342 429 2.0E-27
5 g1800.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 157 443 2.94E-56

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

Pathway

  • This transcript belongs to the following pathways

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