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.t15 TSS g6095.t15 14092094 14092094
chr_2 g6095 g6095.t15 isoform g6095.t15 14092958 14095125
chr_2 g6095 g6095.t15 exon g6095.t15.exon1 14092958 14093054
chr_2 g6095 g6095.t15 exon g6095.t15.exon2 14093205 14093438
chr_2 g6095 g6095.t15 cds g6095.t15.CDS1 14093246 14093438
chr_2 g6095 g6095.t15 exon g6095.t15.exon3 14093632 14093931
chr_2 g6095 g6095.t15 cds g6095.t15.CDS2 14093632 14093931
chr_2 g6095 g6095.t15 exon g6095.t15.exon4 14093994 14094098
chr_2 g6095 g6095.t15 cds g6095.t15.CDS3 14093994 14094098
chr_2 g6095 g6095.t15 exon g6095.t15.exon5 14094284 14094402
chr_2 g6095 g6095.t15 cds g6095.t15.CDS4 14094284 14094402
chr_2 g6095 g6095.t15 exon g6095.t15.exon6 14095120 14095125
chr_2 g6095 g6095.t15 cds g6095.t15.CDS5 14095120 14095125
chr_2 g6095 g6095.t15 TTS g6095.t15 14096130 14096130

Sequences

>g6095.t15 Gene=g6095 Length=861
TTTTTCTTTGGATTTTATTAAGTTAATAACTTATTTTGTACCTTTTAAATATAAGATTAT
TTTTGTTTAGCCGCTATATTTTTAGAATATAATTATTTTCAAGTATTACAAGAGCATTAA
ATAAATAATTGCAACAATATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAA
CAAAATGAACAAGCCGTTGTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTT
TCTATTCACAGTTCTGGTTTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATT
GTTGATTGTGGTTTCGAACATCCTTCGGCCGTACAACATGAGTGCATTCCACAAGCTGTT
TTGGGCATGGACATTCTGTGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTT
TTGGCAACATTACAGCAACTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGT
CACACTCGTGAACTAGCTTTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATG
TCTGGAGTTAAAGTCGGAGTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACA
CTGAAAACAACAACACCACACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATT
CGTGGCAAAAATTTAAATTTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAA
ATGTTGGAACAGTTAGATATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACAC
GGAAAACAAGTCATGATGTTCTCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAG
AAATTTATGCAAGATCCTATG

>g6095.t15 Gene=g6095 Length=241
MADNDDLLDYEDEEQNEQAVVDAGEKKDVKGTYVSIHSSGFRDFLLKPEILRAIVDCGFE
HPSAVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELA
FQISKEYERFSKYMSGVKVGVFFGGMPIQKDEATLKTTTPHIVVGTPGRILALIRGKNLN
LKHLKHFILDECDKMLEQLDMRKDVQEIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDP
M

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6095.t15 CDD cd17950 DEADc_DDX39 38 241 0.000
6 g6095.t15 Gene3D G3DSA:3.40.50.300 - 27 241 0.000
2 g6095.t15 PANTHER PTHR47958:SF10 ATP-DEPENDENT RNA HELICASE DDX39A 22 240 0.000
3 g6095.t15 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 22 240 0.000
1 g6095.t15 Pfam PF00270 DEAD/DEAH box helicase 64 229 0.000
7 g6095.t15 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 39 67 9.298
8 g6095.t15 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 70 241 26.429
5 g6095.t15 SMART SM00487 ultradead3 58 240 0.000
4 g6095.t15 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 27 240 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:0004386 helicase activity 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