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.t9 TSS g6095.t9 14092094 14092094
chr_2 g6095 g6095.t9 isoform g6095.t9 14092941 14095393
chr_2 g6095 g6095.t9 exon g6095.t9.exon1 14092941 14092952
chr_2 g6095 g6095.t9 exon g6095.t9.exon2 14093205 14093442
chr_2 g6095 g6095.t9 exon g6095.t9.exon3 14093632 14093931
chr_2 g6095 g6095.t9 cds g6095.t9.CDS1 14093697 14093931
chr_2 g6095 g6095.t9 exon g6095.t9.exon4 14093994 14094098
chr_2 g6095 g6095.t9 cds g6095.t9.CDS2 14093994 14094098
chr_2 g6095 g6095.t9 exon g6095.t9.exon5 14094284 14094402
chr_2 g6095 g6095.t9 cds g6095.t9.CDS3 14094284 14094402
chr_2 g6095 g6095.t9 exon g6095.t9.exon6 14095120 14095393
chr_2 g6095 g6095.t9 cds g6095.t9.CDS4 14095120 14095392
chr_2 g6095 g6095.t9 TTS g6095.t9 14096130 14096130

Sequences

>g6095.t9 Gene=g6095 Length=1048
GCTAATTTTATCTTCAAGTATTACAAGAGCATTAAATAAATAATTGCAACAATATGGCTG
ATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCGTTGTCGACG
CTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTGGTTTTCGCG
ATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCGAACATCCTT
CGGCCGGTATTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGACATTCTGTGT
CAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTACAGCAACTT
GAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAACTAGCTTTT
CAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAAGTCGGAGTA
TTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACAACACCACAC
ATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAATTTAAATTTG
AAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAGTTAGATATG
CGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTCATGATGTTC
TCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTATGCAAGATCCTATG
GAAGTATATGTGGACGATGAAACGAAATTGACTTTACACGGATTGCAACAACACTATGTC
AAATTGAAGGAAAATGAAAAGAATAAGAAGCTTTTTGAATTACTTGATGTATTGGAATTC
AATCAAGTGGTCATCTTTGTGAAATCAGTTCAAAGATGTGAAGCTTTAGCCACTCTTTTG
ACAGATCAGAATTTTCCAGCAATTGCAATTCATCGTGGTATGGCACAAGATGAGCGTTTG
GCTAAATATCAGCAATTTAAAGATTTTC

>g6095.t9 Gene=g6095 Length=244
MGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELAFQISKEYERFSKYMSGVKVGVFFGGM
PIQKDEATLKTTTPHIVVGTPGRILALIRGKNLNLKHLKHFILDECDKMLEQLDMRKDVQ
EIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDPMEVYVDDETKLTLHGLQQHYVKLKEN
EKNKKLFELLDVLEFNQVVIFVKSVQRCEALATLLTDQNFPAIAIHRGMAQDERLAKYQQ
FKDF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6095.t9 Gene3D G3DSA:3.40.50.300 - 1 159 2.6E-49
8 g6095.t9 Gene3D G3DSA:3.40.50.300 - 171 244 1.6E-16
3 g6095.t9 PANTHER PTHR47958:SF10 ATP-DEPENDENT RNA HELICASE DDX39A 1 244 1.1E-134
4 g6095.t9 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 1 244 1.1E-134
1 g6095.t9 Pfam PF00270 DEAD/DEAH box helicase 1 143 2.4E-31
2 g6095.t9 Pfam PF00271 Helicase conserved C-terminal domain 182 242 1.4E-5
13 g6095.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
14 g6095.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
15 g6095.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
16 g6095.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
12 g6095.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 244 -
11 g6095.t9 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 157 24.272
10 g6095.t9 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 169 244 8.039
7 g6095.t9 SMART SM00487 ultradead3 1 173 2.5E-28
5 g6095.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 160 3.26E-42
6 g6095.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 165 243 5.1E-13

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