Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable ATP-dependent RNA helicase DDX20.

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_3 g3780 g3780.t1 TSS g3780.t1 27946756 27946756
chr_3 g3780 g3780.t1 isoform g3780.t1 27946872 27948918
chr_3 g3780 g3780.t1 exon g3780.t1.exon1 27946872 27947301
chr_3 g3780 g3780.t1 cds g3780.t1.CDS1 27946872 27947301
chr_3 g3780 g3780.t1 exon g3780.t1.exon2 27947372 27948918
chr_3 g3780 g3780.t1 cds g3780.t1.CDS2 27947372 27948918
chr_3 g3780 g3780.t1 TTS g3780.t1 NA NA

Sequences

>g3780.t1 Gene=g3780 Length=1977
ATGGTGGATGAAGAAGAAAAGAAATTTCATACCGCTGATGTGCTCGTTTCGCAAAATTAT
CTATTTTCAAATTTCTTGCTTTCGGAAAAACTTTTAAAATCTCTCCATGAAATGAAATAC
ATTAAACCGTCACCTATTCAAGTTAAAACTATTCCTCTAGCAAGAAGTCGATTAGATATG
ATAATACAATCAAAATCCGGCACAGGAAAGACATTGAGTTTTGCAATTTGTTTACTTGAA
ACATACGATGAAGATATTAAGTTTCCTCAAGCTTTAATTGTTGTACCAACAAGAGAGATT
GCTGTACAAATCACAAATAATCTTGAAAGTTTAGGTATACACATGAAGTATTTTAAAGCT
TGTGAATTTATTGGAGGAACTGATATGAAAAATGATCGTAAACGAATTCAAACCGCCAAA
ATTGTTATTGGTACCCCAGGACGAATATTGCATTTAATTAATAATGCAATTTTCAATACA
ACATGTATAAAGACAATTGTACTTGATGAAGCTGATAAATTACTCGAAAGCGGTCAAATG
GCTAAAGATGTACAATCAATATTAAAAAAAGTCAGAGAGAATAATGATTTGCAAATTATT
GCTGCAACTGCAACTGTTTCAACTCAATTTGAAGAACATATTAAGCGATTTATGAAAAAT
CCTATAGGCATTACTCCAAAACATGAAGCTCCAATTTTACTTGGAATCAAACAATTTGCT
ATCCAATTACAAGAGCAAACTGATAATATTGAACTTATGCGAATGAAGGTTGCAGAGCTT
GAGAAAATTTTTACAAAAGTATCATTTAAGCAATGTCTTCTATTCACTGATTCTCAACTG
AGAACTGAATCCTATGGAAACTATTTAAAGAAGTTGGGATGGAAAAATGAAGTGATAAAT
GGCTCTCAAGAGCAAACAAAAAGACTTAGAGTCTTAGATAAACTTACAAAATTTAAATGT
AGAGTACTAATCACAACCGATCTTATGGCAAGAGGAATTGATATAGAAAATGTTAATTTA
GTAATAAATCTAGATCTACCATATGATTGTTTTACATACTTGCACAGAATAGGAAGAGCT
GGTCGATTTGGAACTCTCGGTTTAGCAATTACTTTCTTAAATGGTGAAAAAGATAAAGAA
AAGTTCAAGAAAATGTTGGGCGAAATCGGAAGTAGTAAATCGTTGGTTTATGAGTTTCCT
GATGAAAATGTTTCGTACAACTTCTGGGATTTTAATAATACTAAACAAGATGAAAAATTA
AAGAGAGTTGATGTAGAAGTAGTAAATGATATCGATGAAAATACAAATCTTGAACAAAAT
AGTGATGATAAAGATAAAAGTTTACTTCAAGAGATTGAAAAGATGCTTATTGGAAATAAT
GGTGCTGATTCGTATAAATGTAGTAATAATGGCTCATTAGATAAAAACAGTAAAATTGAT
TCTAATAGAAAATTTGAAGAAAAAACATCGGAAGATGATATTGTGGAGAGAAATTTGATG
CTTCTTGATATTTCCAAAAAATTAATTGATGATACTCAAAATGAACAAAATTCAAATTTA
TTTGATGCATCTATTTTGTTGAATGACTATGAAAAATTTTGTGAAAATGAAAATGAAAAT
TTGCCACCTGAAGAACAACAAGAATCACCAAAGAGCGATTTTAGGAAAGTTATTTTCAAA
CGAAATCCTCTTGATGAAGAATATGAAGAATCCATTTCATCGAAAAGTGATTATTCTAAA
CAAGAAAGTGAAGAGTCAGTTGGAGATGAAATTGAGTTTGATGAAGAGAAGTCAATATGT
GAAGAGAGTCAGCCAAATTTACAAAATTTATCAAGAACATTTGAAGAAAATGCTTCGGGA
TACGAAAATTATAATCAATACGTTGCACATTATTACAATCAATGGAGAAACACATTTCAT
TTTCAATTGGCAAACATTGAAAACTATGTCAAATATAATAAATCAAATTTAACATAA

>g3780.t1 Gene=g3780 Length=658
MVDEEEKKFHTADVLVSQNYLFSNFLLSEKLLKSLHEMKYIKPSPIQVKTIPLARSRLDM
IIQSKSGTGKTLSFAICLLETYDEDIKFPQALIVVPTREIAVQITNNLESLGIHMKYFKA
CEFIGGTDMKNDRKRIQTAKIVIGTPGRILHLINNAIFNTTCIKTIVLDEADKLLESGQM
AKDVQSILKKVRENNDLQIIAATATVSTQFEEHIKRFMKNPIGITPKHEAPILLGIKQFA
IQLQEQTDNIELMRMKVAELEKIFTKVSFKQCLLFTDSQLRTESYGNYLKKLGWKNEVIN
GSQEQTKRLRVLDKLTKFKCRVLITTDLMARGIDIENVNLVINLDLPYDCFTYLHRIGRA
GRFGTLGLAITFLNGEKDKEKFKKMLGEIGSSKSLVYEFPDENVSYNFWDFNNTKQDEKL
KRVDVEVVNDIDENTNLEQNSDDKDKSLLQEIEKMLIGNNGADSYKCSNNGSLDKNSKID
SNRKFEEKTSEDDIVERNLMLLDISKKLIDDTQNEQNSNLFDASILLNDYEKFCENENEN
LPPEEQQESPKSDFRKVIFKRNPLDEEYEESISSKSDYSKQESEESVGDEIEFDEEKSIC
EESQPNLQNLSRTFEENASGYENYNQYVAHYYNQWRNTFHFQLANIENYVKYNKSNLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3780.t1 CDD cd18787 SF2_C_DEAD 236 373 2.15789E-41
8 g3780.t1 Coils Coil Coil 243 263 -
6 g3780.t1 Gene3D G3DSA:3.40.50.300 - 21 226 7.4E-59
7 g3780.t1 Gene3D G3DSA:3.40.50.300 - 233 398 1.0E-36
13 g3780.t1 MobiDBLite mobidb-lite consensus disorder prediction 567 586 -
14 g3780.t1 MobiDBLite mobidb-lite consensus disorder prediction 567 592 -
3 g3780.t1 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 32 409 6.0E-97
4 g3780.t1 PANTHER PTHR47958:SF89 ATP-DEPENDENT RNA HELICASE DDX20-RELATED 32 409 6.0E-97
1 g3780.t1 Pfam PF00270 DEAD/DEAH box helicase 45 210 8.6E-34
2 g3780.t1 Pfam PF00271 Helicase conserved C-terminal domain 257 364 5.9E-22
12 g3780.t1 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 167 175 -
15 g3780.t1 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 20 48 9.554
17 g3780.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 51 224 23.826
16 g3780.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 259 405 19.452
11 g3780.t1 SMART SM00487 ultradead3 39 239 1.6E-45
10 g3780.t1 SMART SM00490 helicmild6 283 364 8.0E-27
5 g3780.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 89 379 1.59E-55

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 gene does not belong to any 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