Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-dependent RNA helicase WM6.

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.t3 TSS g6095.t3 14092094 14092094
chr_2 g6095 g6095.t3 isoform g6095.t3 14092204 14095713
chr_2 g6095 g6095.t3 exon g6095.t3.exon1 14092204 14092952
chr_2 g6095 g6095.t3 exon g6095.t3.exon2 14093205 14093438
chr_2 g6095 g6095.t3 cds g6095.t3.CDS1 14093246 14093438
chr_2 g6095 g6095.t3 exon g6095.t3.exon3 14093632 14093931
chr_2 g6095 g6095.t3 cds g6095.t3.CDS2 14093632 14093931
chr_2 g6095 g6095.t3 exon g6095.t3.exon4 14093994 14094098
chr_2 g6095 g6095.t3 cds g6095.t3.CDS3 14093994 14094098
chr_2 g6095 g6095.t3 exon g6095.t3.exon5 14094284 14094402
chr_2 g6095 g6095.t3 cds g6095.t3.CDS4 14094284 14094402
chr_2 g6095 g6095.t3 exon g6095.t3.exon6 14095120 14095398
chr_2 g6095 g6095.t3 cds g6095.t3.CDS5 14095120 14095398
chr_2 g6095 g6095.t3 exon g6095.t3.exon7 14095468 14095713
chr_2 g6095 g6095.t3 cds g6095.t3.CDS6 14095468 14095713
chr_2 g6095 g6095.t3 TTS g6095.t3 14096130 14096130

Sequences

>g6095.t3 Gene=g6095 Length=2032
GGTTGGTATGAATCAGATTAATCTTGATTATTTCCTTTTTGTTCACTTGTATGCTCTATT
TTTTGCAACATCATTTAATAAAAGTACATAATTGAACTTTGACAGTTATCATAATCATCA
ATCGTTATCAATGAATCATACGCATTTACACAGAACGATGAATTTTTCTCAAATAAAGTG
TAATTGGACAACAGGTCTTAAATTTTAGTTTTTTTCTCTTTCTATTCATCATCAATAATG
CATAAAATTCTTTTTCGATTGATGCATATGTGTTATACAAAACTATTGTTCATTAATAAC
GACGACATAAAACAGTTAAGGTAATGAAAAATGAAGTAAATAATTGAAAAGTGTGGGAGA
TACGAGTGGTAGCGAAAAAAGTAAAATTAAAATTTAATTAATTTCAGTTGTTGTTGCTTA
CCCAATTAAACTATTTTACGAAATATCCTATATCTCAAGATTATTCCTAGAGTTGTTCGA
TATCACCCAATAGCCACCGATTGTTAATACTATTTAATATACGTTTATGGCGTTAATATT
AGTTGAAATTACGAAAATAACAAAAATTTCTCTCACAAGCAATTCTTTTTTTACACAAAA
CTAAAAATTTCAAATCCACTTTTGGAATGAGAGCGCATTTTTCAAAAAAAACTAATTTAA
CGTATAAAAAATTCAAATATTTTGAAAATTTTTGATGCGAAAATATTCTGCTTCATTGAC
GCTAAAACATTCAAAACGCTAATTTTATCTTCAAGTATTACAAGAGCATTAAATAAATAA
TTGCAACAATATGGCTGATAATGACGATCTTCTCGACTATGAGGATGAAGAACAAAATGA
ACAAGCCGTTGTCGACGCTGGCGAAAAGAAAGATGTAAAAGGAACTTATGTTTCTATTCA
CAGTTCTGGTTTTCGCGATTTCCTTTTAAAACCTGAAATCTTGAGAGCTATTGTTGATTG
TGGTTTCGAACATCCTTCGGCCGTACAACATGAGTGCATTCCACAAGCTGTTTTGGGCAT
GGACATTCTGTGTCAGGCAAAATCCGGCATGGGAAAAACAGCTGTCTTTGTTTTGGCAAC
ATTACAGCAACTTGAACCAACAGATAATCATGTTTATGTTCTTGTAATGTGTCACACTCG
TGAACTAGCTTTTCAAATCAGTAAAGAGTACGAAAGATTTAGCAAGTACATGTCTGGAGT
TAAAGTCGGAGTATTTTTCGGTGGAATGCCTATTCAAAAAGACGAAGCTACACTGAAAAC
AACAACACCACACATTGTTGTTGGTACTCCTGGAAGAATTCTTGCCCTCATTCGTGGCAA
AAATTTAAATTTGAAGCATTTGAAACACTTCATTTTGGATGAATGCGATAAAATGTTGGA
ACAGTTAGATATGCGCAAAGATGTACAAGAAATTTTCCGAAACACTCCACACGGAAAACA
AGTCATGATGTTCTCAGCTACGCTTAGCAAAGAAATAAGACCTATCTGCAAGAAATTTAT
GCAAGATCCTATGGAAGTATATGTGGACGATGAAACGAAATTGACTTTACACGGATTGCA
ACAACACTATGTCAAATTGAAGGAAAATGAAAAGAATAAGAAGCTTTTTGAATTACTTGA
TGTATTGGAATTCAATCAAGTGGTCATCTTTGTGAAATCAGTTCAAAGATGTGAAGCTTT
AGCCACTCTTTTGACAGATCAGAATTTTCCAGCAATTGCAATTCATCGTGGTATGGCACA
AGATGAGCGTTTGGCTAAATATCAGCAATTTAAAGATTTTCAAAAGCGTATTTTGGTGGC
AACAAACTTATTTGGACGTGGAATGGATATTGAACGTGTTAATATCGTTTTCAACTATGA
TATGCCTGAAGATTCTGATACTTATCTTCATCGAGTCGCTCGTGCTGGTCGTTTTGGTAC
AAAAGGTCTCGCCATCACTTTTGTTTCTGATGAAAATGATGCAAAGATTTTGAATAATGT
TCAGGATCGCTTCGATGTCAACATAACAGAGTTGCCCGACGAAATAGATCTC

>g6095.t3 Gene=g6095 Length=414
MADNDDLLDYEDEEQNEQAVVDAGEKKDVKGTYVSIHSSGFRDFLLKPEILRAIVDCGFE
HPSAVQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLEPTDNHVYVLVMCHTRELA
FQISKEYERFSKYMSGVKVGVFFGGMPIQKDEATLKTTTPHIVVGTPGRILALIRGKNLN
LKHLKHFILDECDKMLEQLDMRKDVQEIFRNTPHGKQVMMFSATLSKEIRPICKKFMQDP
MEVYVDDETKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVQRCEALATL
LTDQNFPAIAIHRGMAQDERLAKYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPE
DSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNNVQDRFDVNITELPDEIDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g6095.t3 CDD cd17950 DEADc_DDX39 38 245 0.000
14 g6095.t3 CDD cd18787 SF2_C_DEAD 256 385 0.000
9 g6095.t3 Gene3D G3DSA:3.40.50.300 - 27 245 0.000
8 g6095.t3 Gene3D G3DSA:3.40.50.300 - 257 414 0.000
3 g6095.t3 PANTHER PTHR47958:SF10 ATP-DEPENDENT RNA HELICASE DDX39A 23 412 0.000
4 g6095.t3 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 23 412 0.000
1 g6095.t3 Pfam PF00270 DEAD/DEAH box helicase 64 229 0.000
2 g6095.t3 Pfam PF00271 Helicase conserved C-terminal domain 268 376 0.000
10 g6095.t3 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 39 67 9.298
12 g6095.t3 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 70 243 26.592
11 g6095.t3 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 255 414 21.767
7 g6095.t3 SMART SM00487 ultradead3 58 259 0.000
6 g6095.t3 SMART SM00490 helicmild6 295 376 0.000
5 g6095.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 107 391 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

Pathway

  • This transcript belongs to the following pathways

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