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.t11 TSS g6095.t11 14092094 14092094
chr_2 g6095 g6095.t11 isoform g6095.t11 14092941 14096224
chr_2 g6095 g6095.t11 exon g6095.t11.exon1 14092941 14092952
chr_2 g6095 g6095.t11 exon g6095.t11.exon2 14093205 14093438
chr_2 g6095 g6095.t11 cds g6095.t11.CDS1 14093246 14093438
chr_2 g6095 g6095.t11 exon g6095.t11.exon3 14093632 14093931
chr_2 g6095 g6095.t11 cds g6095.t11.CDS2 14093632 14093931
chr_2 g6095 g6095.t11 exon g6095.t11.exon4 14093994 14094098
chr_2 g6095 g6095.t11 cds g6095.t11.CDS3 14093994 14094098
chr_2 g6095 g6095.t11 exon g6095.t11.exon5 14094284 14094797
chr_2 g6095 g6095.t11 cds g6095.t11.CDS4 14094284 14094435
chr_2 g6095 g6095.t11 exon g6095.t11.exon6 14094863 14095398
chr_2 g6095 g6095.t11 exon g6095.t11.exon7 14095468 14095723
chr_2 g6095 g6095.t11 exon g6095.t11.exon8 14095784 14096224
chr_2 g6095 g6095.t11 TTS g6095.t11 NA NA

Sequences

>g6095.t11 Gene=g6095 Length=2398
GCTAATTTTATCTTCAAGTATTACAAGAGCATTAAATAAATAATTGCAACAATATGGCTG
ATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGAACAAGCCGTTGTCGACG
CTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCACAGTTCTGGTTTTCGCG
ATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTGTGGTTTCGAACATCCTT
CGGCCGTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCATGGACATTCTGTGTCAGG
CAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAACATTACAGCAACTTGAAC
CAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCGTGAACTAGCTTTTCAAA
TCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGTTAAAGTCGGAGTATTTT
TCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAACAACAACACCACACATTG
TTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAAAAATTTAAATTTGAAGC
ATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGAACAGTTAGATATGCGCA
AAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACAAGTCATGATGTTCTCAG
CTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTATGCAAGATGTAAATCGCG
TTCCAATAATGTTAAGAACATGAAACCAAAATTATTAATCTGAGAAAAGAGTAATTGCGC
GAAAAAAATATTAACGGGTTGCGACTTGATGGCGATAGAAATACAACTGACGGTCTCTGG
AATAATAAAAGCCTAATATAATACAAATTGATAATATTAAGTCCATGTCCACCAATATAA
ATTATATTTATACCATAATATAGAGTTATAATATATTATTAAATCGTTACCCAGAGATCG
AACGCGATTAGTCAGTAGCCATATACAAAATTGGGAAAATATTAGGGAAAAGGGGAATTG
TAATTTGGGATTTTAAAAAAATTGAAATGCTCAAAACATCAATCAATTTATTATAAGAAG
ATATCAACTGTTCCCGGATATAATGATAATTGTTTTCCATTTTTGTGCACTAATTGTGTG
ATCTTCGCTCTTGGATGACGAGTCTAATATCACGATGTTACCAGCTTGATGGTACCTAAA
TCGCCCGAGTTAAATCAATTGCAGCATATTTTAAAATGCCTCATTAATTTCCATCACGCT
CCCGCGCTTTAAAATTTTTTCTCTTCTCAAATCAAACGTTTTTAAATTTTGTCGTTTTTT
TAACATATTTTTTCTCATCTTTATTTTTCTAAAAAAAAATAGCCTATGGAAGTATATGTG
GACGATGAAACGAAATTGACTTTACACGGATTGCAACAACACTATGTCAAATTGAAGGAA
AATGAAAAGAATAAGAAGCTTTTTGAATTACTTGATGTATTGGAATTCAATCAAGTGGTC
ATCTTTGTGAAATCAGTTCAAAGATGTGAAGCTTTAGCCACTCTTTTGACAGATCAGAAT
TTTCCAGCAATTGCAATTCATCGTGGTATGGCACAAGATGAGCGTTTGGCTAAATATCAG
CAATTTAAAGATTTTCAAAAGCGTATTTTGGTGGCAACAAACTTATTTGGACGTGGAATG
GATATTGAACGTGTTAATATCGTTTTCAACTATGATATGCCTGAAGATTCTGATACTTAT
CTTCATCGAGTCGCTCGTGCTGGTCGTTTTGGTACAAAAGGTCTCGCCATCACTTTTGTT
TCTGATGAAAATGATGCAAAGATTTTGAATAATGTTCAGGATCGCTTCGATGTCAACATA
ACAGAGTTGCCCGACGAAATAGATCTCAGTTCATACATTGAAGGACGATAAACAGCTGAC
GTAAAATTGGCAATATTGAGAATACGCTACATTAAAAAAGAGCTCAAAGTAGCTTAATAC
ATTCTCTTCATACATAATTTTTAGATCTTAAGCATTTTTTTCTTAAATTTTGAATTTTCT
CACTCTATTTGTGTGTGCAAAAGAGCAAGATATTTAATTATTTTTCATTAAAGAACTATC
AAAACACACACTTTTCAATTGGAATTCAACAAGTGAAATAGACTTTCTACACATACACAA
ACCAAAACCAATATTCATTTTAAAATTAACATAATGTGAAACCTTCAGAAATAAATAAAA
ATTTGATTAAATTTTTCTGATTGTAGGACAAACATTTTTTATTCATCTAATAATTTCTTA
TCACATCATTACTGCAACTTTTTTAATAATTTGATTTTTCTTATCGAAAAAATAATTT

>g6095.t11 Gene=g6095 Length=249
MADNDDLLDYEDEEQNEQAVVDAGEKKDVKGTYVSIHSSGFRDFLLKPEILRAIVDCGFE
HPSAVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELA
FQISKEYERFSKYMSGVKVGVFFGGMPIQKDEATLKTTTPHIVVGTPGRILALIRGKNLN
LKHLKHFILDECDKMLEQLDMRKDVQEIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDV
NRVPIMLRT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6095.t11 CDD cd17950 DEADc_DDX39 38 239 0.000
6 g6095.t11 Gene3D G3DSA:3.40.50.300 - 27 244 0.000
2 g6095.t11 PANTHER PTHR47958:SF10 ATP-DEPENDENT RNA HELICASE DDX39A 22 245 0.000
3 g6095.t11 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 22 245 0.000
1 g6095.t11 Pfam PF00270 DEAD/DEAH box helicase 64 229 0.000
7 g6095.t11 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 39 67 9.298
8 g6095.t11 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 70 243 26.347
5 g6095.t11 SMART SM00487 ultradead3 58 248 0.000
4 g6095.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 27 242 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