Gene loci information

Transcript annotation

  • This transcript has been annotated as Spliceosome RNA helicase DDX39B.

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_2 g6095 g6095.t5 TSS g6095.t5 14092094 14092094
chr_2 g6095 g6095.t5 isoform g6095.t5 14092805 14095797
chr_2 g6095 g6095.t5 exon g6095.t5.exon1 14092805 14092952
chr_2 g6095 g6095.t5 exon g6095.t5.exon2 14093205 14093442
chr_2 g6095 g6095.t5 exon g6095.t5.exon3 14093632 14093931
chr_2 g6095 g6095.t5 cds g6095.t5.CDS1 14093697 14093931
chr_2 g6095 g6095.t5 exon g6095.t5.exon4 14093994 14094098
chr_2 g6095 g6095.t5 cds g6095.t5.CDS2 14093994 14094098
chr_2 g6095 g6095.t5 exon g6095.t5.exon5 14094284 14094402
chr_2 g6095 g6095.t5 cds g6095.t5.CDS3 14094284 14094402
chr_2 g6095 g6095.t5 exon g6095.t5.exon6 14095120 14095398
chr_2 g6095 g6095.t5 cds g6095.t5.CDS4 14095120 14095398
chr_2 g6095 g6095.t5 exon g6095.t5.exon7 14095468 14095797
chr_2 g6095 g6095.t5 cds g6095.t5.CDS5 14095468 14095746
chr_2 g6095 g6095.t5 TTS g6095.t5 14096130 14096130

Sequences

>g6095.t5 Gene=g6095 Length=1519
TAAAAATTTCAAATCCACTTTTGGAATGAGAGCGCATTTTTCAAAAAAAACTAATTTAAC
GTATAAAAAATTCAAATATTTTGAAAATTTTTGATGCGAAAATATTCTGCTTCATTGACG
CTAAAACATTCAAAACGCTAATTTTATCTTCAAGTATTACAAGAGCATTAAATAAATAAT
TGCAACAATATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAA
CAAGCCGTTGTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCAC
AGTTCTGGTTTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGT
GGTTTCGAACATCCTTCGGCCGGTATTACAACATGAGTGCATTCCACAAGCTGTTTTGGG
CATGGACATTCTGTGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGC
AACATTACAGCAACTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACAC
TCGTGAACTAGCTTTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGG
AGTTAAAGTCGGAGTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAA
AACAACAACACCACACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGG
CAAAAATTTAAATTTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTT
GGAACAGTTAGATATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAA
ACAAGTCATGATGTTCTCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATT
TATGCAAGATCCTATGGAAGTATATGTGGACGATGAAACGAAATTGACTTTACACGGATT
GCAACAACACTATGTCAAATTGAAGGAAAATGAAAAGAATAAGAAGCTTTTTGAATTACT
TGATGTATTGGAATTCAATCAAGTGGTCATCTTTGTGAAATCAGTTCAAAGATGTGAAGC
TTTAGCCACTCTTTTGACAGATCAGAATTTTCCAGCAATTGCAATTCATCGTGGTATGGC
ACAAGATGAGCGTTTGGCTAAATATCAGCAATTTAAAGATTTTCAAAAGCGTATTTTGGT
GGCAACAAACTTATTTGGACGTGGAATGGATATTGAACGTGTTAATATCGTTTTCAACTA
TGATATGCCTGAAGATTCTGATACTTATCTTCATCGAGTCGCTCGTGCTGGTCGTTTTGG
TACAAAAGGTCTCGCCATCACTTTTGTTTCTGATGAAAATGATGCAAAGATTTTGAATAA
TGTTCAGGATCGCTTCGATGTCAACATAACAGAGTTGCCCGACGAAATAGATCTCAGTTC
ATACAGTAAGTCTTATATTCATTATTAATTTGAATCGTTTACTAATACTTGTTTTCTTTT
ATTAGTTGAAGGACGATAA

>g6095.t5 Gene=g6095 Length=338
MGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELAFQISKEYERFSKYMSGVKVGVFFGGM
PIQKDEATLKTTTPHIVVGTPGRILALIRGKNLNLKHLKHFILDECDKMLEQLDMRKDVQ
EIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDPMEVYVDDETKLTLHGLQQHYVKLKEN
EKNKKLFELLDVLEFNQVVIFVKSVQRCEALATLLTDQNFPAIAIHRGMAQDERLAKYQQ
FKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVS
DENDAKILNNVQDRFDVNITELPDEIDLSSYSKSYIHY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g6095.t5 CDD cd18787 SF2_C_DEAD 170 299 9.39937E-48
7 g6095.t5 Gene3D G3DSA:3.40.50.300 - 1 159 6.1E-49
6 g6095.t5 Gene3D G3DSA:3.40.50.300 - 171 335 3.5E-53
3 g6095.t5 PANTHER PTHR47958:SF10 ATP-DEPENDENT RNA HELICASE DDX39A 1 329 3.1E-191
4 g6095.t5 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 1 329 3.1E-191
1 g6095.t5 Pfam PF00270 DEAD/DEAH box helicase 1 143 5.6E-31
2 g6095.t5 Pfam PF00271 Helicase conserved C-terminal domain 182 290 1.3E-24
9 g6095.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
10 g6095.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
11 g6095.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
12 g6095.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
8 g6095.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 338 -
17 g6095.t5 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 157 24.272
16 g6095.t5 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 169 330 21.713
15 g6095.t5 SMART SM00487 ultradead3 1 173 2.5E-28
14 g6095.t5 SMART SM00490 helicmild6 209 290 5.5E-25
5 g6095.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 21 305 1.61E-65

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.

Raw TPM values