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.t7 TSS g6095.t7 14092094 14092094
chr_2 g6095 g6095.t7 isoform g6095.t7 14092941 14094402
chr_2 g6095 g6095.t7 exon g6095.t7.exon1 14092941 14092952
chr_2 g6095 g6095.t7 exon g6095.t7.exon2 14093205 14093442
chr_2 g6095 g6095.t7 exon g6095.t7.exon3 14093632 14093931
chr_2 g6095 g6095.t7 cds g6095.t7.CDS1 14093697 14093931
chr_2 g6095 g6095.t7 exon g6095.t7.exon4 14093994 14094098
chr_2 g6095 g6095.t7 cds g6095.t7.CDS2 14093994 14094098
chr_2 g6095 g6095.t7 exon g6095.t7.exon5 14094284 14094402
chr_2 g6095 g6095.t7 cds g6095.t7.CDS3 14094284 14094402
chr_2 g6095 g6095.t7 TTS g6095.t7 NA NA

Sequences

>g6095.t7 Gene=g6095 Length=774
GCTAATTTTATCTTCAAGTATTACAAGAGCATTAAATAAATAATTGCAACAATATGGCTG
ATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCGTTGTCGACG
CTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTGGTTTTCGCG
ATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCGAACATCCTT
CGGCCGGTATTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGACATTCTGTGT
CAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTACAGCAACTT
GAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAACTAGCTTTT
CAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAAGTCGGAGTA
TTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACAACACCACAC
ATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAATTTAAATTTG
AAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAGTTAGATATG
CGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTCATGATGTTC
TCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTATGCAAGAT

>g6095.t7 Gene=g6095 Length=153
MGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELAFQISKEYERFSKYMSGVKVGVFFGGM
PIQKDEATLKTTTPHIVVGTPGRILALIRGKNLNLKHLKHFILDECDKMLEQLDMRKDVQ
EIFRNTPHGKQVMMFSATLSKEIRPICKKFMQD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g6095.t7 Gene3D G3DSA:3.40.50.300 - 1 153 2.4E-48
2 g6095.t7 PANTHER PTHR47958:SF10 ATP-DEPENDENT RNA HELICASE DDX39A 1 153 2.0E-83
3 g6095.t7 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 1 153 2.0E-83
1 g6095.t7 Pfam PF00270 DEAD/DEAH box helicase 1 143 5.3E-32
9 g6095.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
10 g6095.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
11 g6095.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
12 g6095.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
8 g6095.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 153 -
7 g6095.t7 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 153 23.713
5 g6095.t7 SMART SM00487 ultradead3 1 153 2.3E-17
4 g6095.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 153 1.09E-40

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