Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable ATP-dependent RNA helicase DDX5.

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_1 g13653 g13653.t1 TSS g13653.t1 31414466 31414466
chr_1 g13653 g13653.t1 isoform g13653.t1 31414567 31422253
chr_1 g13653 g13653.t1 exon g13653.t1.exon1 31414567 31414610
chr_1 g13653 g13653.t1 cds g13653.t1.CDS1 31414567 31414610
chr_1 g13653 g13653.t1 exon g13653.t1.exon2 31414953 31416397
chr_1 g13653 g13653.t1 cds g13653.t1.CDS2 31414953 31416397
chr_1 g13653 g13653.t1 exon g13653.t1.exon3 31416464 31416476
chr_1 g13653 g13653.t1 cds g13653.t1.CDS3 31416464 31416476
chr_1 g13653 g13653.t1 exon g13653.t1.exon4 31416554 31417641
chr_1 g13653 g13653.t1 cds g13653.t1.CDS4 31416554 31417641
chr_1 g13653 g13653.t1 exon g13653.t1.exon5 31417700 31417883
chr_1 g13653 g13653.t1 cds g13653.t1.CDS5 31417700 31417883
chr_1 g13653 g13653.t1 exon g13653.t1.exon6 31422166 31422253
chr_1 g13653 g13653.t1 cds g13653.t1.CDS6 31422166 31422253
chr_1 g13653 g13653.t1 TTS g13653.t1 31422346 31422346

Sequences

>g13653.t1 Gene=g13653 Length=2862
ATGTATCAAGGCGGTTATCAAGGAAATTTCAACCAAAACCATGGTTTTCGTCCACCTCGT
CCAGATTTCAATGCGGATAATCGTTGGAATCGAAACAATCCGAACAATCCACAATTCAAT
AATCACTTCAATCCAAATTTCATGAGTAATGGAGCGTTTAATGGTAACTTTGTTCCAAAT
AATCGCACCTACCCACCGAAGAAAGATTTTGGCGGCCCTAAAAGCAACCAACCAAACCAT
ATAAGGAAGAATAAATCTCCTGATTTGGATGATATGACAAAAGAAGAACGTGCAAAATTG
CAAAGCATGAAAGCAAAATGTCCGGGACAAAATCTCGTTCGTCCTAATTGGGAATCGATT
AAACTTGAACCATTCAAAAAAGATTTTAACAAAATTCACGAAAATAATGCTAATCGTACA
CTCGAAGAAGTCATGGCATGGCGTGCTAGCATGGAAATTACTGTCAAAGGAAAAGATGTT
CCATATCCACATCAAGATTTTGATGAAGCCGGTTTTTCACAAAGTATCATCAATGAAGTC
ACTCGACAAGGTTTCACTACTCCAACTCCCATACAGTCGCAAGGATGGCCAATTGCTATG
AAGGGGCGAGATTTGCTCGGTATTGCCCAAACAGGTTCTGGAAAAACTCTGGCTTATATG
CTGCCAGCAATTGTTCATATTAATAATCAACGACCTTTGATGAGAGGTGAAGGTCCAATT
GTTCTTGTTCTTGCACCTACACGAGAACTTGCACAGCAAATACAAACAGTTGCACGTGAT
TTTGGATCTCATGTGAAACCATATGTTCGTAATACTTGTATTTTCGGTGGTTCACCAAAA
GGACCACAAATCAGAGATTTAGAGCGAGGAATTGAAATTTGTATTGCAACACCGGGTCGT
CTTATTGATTTCCTCGAACGTGGAGTTACAAACATGCGTCGAGTTACTTATCTCGTTTTG
GATGAAGCTGATCGCATGTTGGACATGGGTTTTGAGCCTCAAATTCGCAAAATAATTGAA
CAAATTCGTCCTGATCGTCAAGTATTGATGTGGAGCGCAACATGGCCACGAGAAGTACAA
ACACTTGCAGAAGACTTTTTACGCAACTACATTCAAGTCAATATCGGATCTTTGAATCTC
TCAGCTAATAACAATATTGTTCAAAACATTAAAGTTTGCGAAGAAAATGAAAAAGAAGGC
GAACTTATTGCTTTATTAAAAACTGTTGTAACTGACAACTCAAAGAAGGGCATCATTTTT
GTTGAGACAAAGAAAAAAGTTGAAGACATTTTGAAAATTATTCAACGCGAAGGTTATCAG
TCTAACTCGATTCATGGTGACAAGAGCCAAAATGAACGTGACTTTGTCTTGGAAAGTTTT
CGTAATGGACGCATTGCTATTTTGGTTGCTACTGATGTTGCTGCGAGAGGTTTAGATGTT
GAAGATGTTAAATATGTTATTAACTATGATTATCCAAACTCATCAGAAGATTACGTGCAC
AGAATCGGGAGAACTGGACGTTGTGAGCAAACTGGAACAGCTTATACGTTCTTTACACCA
TCAAATGCACGTCAAGCTCGTGAATTGATTGCAGTTTTGAATGAGGCTGGTCAAAGTCCA
ACAAAAGAACTTTTGGATCTTGCAAAAAGTATTCCTGGCAAAGGAAATCAAAGGATCAAT
TCACGATTCGGTCGTCCAGATCAATATAATAAACCAATGAATCATTTTAATAATGGTATG
AAACCGATGAATGGACCAGGAGGTTGGATGAATAATGGTGTAAATCAGAATATGAATGGC
TATCATAACTCGACTAACACTTTCAACAGAACCGGAGATAGATTCAACAATAAGAGTGAT
CAACAACAGCGACCATTCAATAAATACAACAATTCACAGAATAATGACGAAGAGAAAAAG
TATGACGGTTACAAGAGAAATCCTGATTTCAATAATCGATTCAAAAATCCAATGCAAAAT
GGCTTTGTTAATAATCAAACAGTTCCACCACAACAACAACCACAACAGAATGGATATCAA
AAGAATTTTGCTGGTCAAGAAGGTGGCTACAAGCCTCGTAATTCGTTTGTTAAGCCAGAT
TTCAATGGAAATCCGCGCAACAATCAGCATTTTGGTGGTGAAAAGCCTCCATTCCAAAAT
AATTATATGGGCAATAAACCACGTGCTCCATTTAACAGCAATGGACCGGCTCCACGTTTT
GCAAATGGTGGTAATAATTTGAATGGTAACGAATATGCAGGAGGTTCACAAAAGTATAAC
AAATTTGAAAACTATAAAAGTGCTGCATATGGTGAAAAAACTGAGGGCAGCGATGTTTTT
CAAGGTGTGAAAAGTTTCAATTCTCATCAATCGGGTGGACGTCATTACAATTCTGGAAAT
CGCTTCAATGAACATCAAAATGGTACAATCGACGGTCAGACACCACAAGCTGTTCATGCT
CAACAGCCACCACCACAACAGTTTGTTCAAGCTGATGCCATTGATGGTGCTCAAGCTTTT
GATTCCAATATGATTGCTGGTTATCGTATGGTTGCAAATGGAACTATTCCACCATTTCCA
CCAGCATTCGCAACAGCAGATTTTCAACAGCGTCCTCAAGCAAATGGACAACCTATTGCG
GATATCAATAATCCTTGCGCATTCCAGAACATCCAAGGAGCGCCTCAATCGCGTCAACAA
ATGTATGTGATTGGAGCACCACCACCAACTGCAACACCTTACGCAATTCAATTCCAACAT
ACTGCTGTTCAACCGATGTTTTCGTATTATGCTTCGTTGTCACCACCACTGTCGTCGTCG
AATATTAGTGCTTTTATGGATCATAATGATGGCTTCGATTAA

>g13653.t1 Gene=g13653 Length=953
MYQGGYQGNFNQNHGFRPPRPDFNADNRWNRNNPNNPQFNNHFNPNFMSNGAFNGNFVPN
NRTYPPKKDFGGPKSNQPNHIRKNKSPDLDDMTKEERAKLQSMKAKCPGQNLVRPNWESI
KLEPFKKDFNKIHENNANRTLEEVMAWRASMEITVKGKDVPYPHQDFDEAGFSQSIINEV
TRQGFTTPTPIQSQGWPIAMKGRDLLGIAQTGSGKTLAYMLPAIVHINNQRPLMRGEGPI
VLVLAPTRELAQQIQTVARDFGSHVKPYVRNTCIFGGSPKGPQIRDLERGIEICIATPGR
LIDFLERGVTNMRRVTYLVLDEADRMLDMGFEPQIRKIIEQIRPDRQVLMWSATWPREVQ
TLAEDFLRNYIQVNIGSLNLSANNNIVQNIKVCEENEKEGELIALLKTVVTDNSKKGIIF
VETKKKVEDILKIIQREGYQSNSIHGDKSQNERDFVLESFRNGRIAILVATDVAARGLDV
EDVKYVINYDYPNSSEDYVHRIGRTGRCEQTGTAYTFFTPSNARQARELIAVLNEAGQSP
TKELLDLAKSIPGKGNQRINSRFGRPDQYNKPMNHFNNGMKPMNGPGGWMNNGVNQNMNG
YHNSTNTFNRTGDRFNNKSDQQQRPFNKYNNSQNNDEEKKYDGYKRNPDFNNRFKNPMQN
GFVNNQTVPPQQQPQQNGYQKNFAGQEGGYKPRNSFVKPDFNGNPRNNQHFGGEKPPFQN
NYMGNKPRAPFNSNGPAPRFANGGNNLNGNEYAGGSQKYNKFENYKSAAYGEKTEGSDVF
QGVKSFNSHQSGGRHYNSGNRFNEHQNGTIDGQTPQAVHAQQPPPQQFVQADAIDGAQAF
DSNMIAGYRMVANGTIPPFPPAFATADFQQRPQANGQPIADINNPCAFQNIQGAPQSRQQ
MYVIGAPPPTATPYAIQFQHTAVQPMFSYYASLSPPLSSSNISAFMDHNDGFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g13653.t1 CDD cd17966 DEADc_DDX5_DDX17 176 374 7.88704E-139
8 g13653.t1 CDD cd18787 SF2_C_DEAD 386 518 1.9625E-55
6 g13653.t1 Gene3D G3DSA:3.40.50.300 - 138 375 1.0E-85
7 g13653.t1 Gene3D G3DSA:3.40.50.300 - 376 551 2.7E-57
16 g13653.t1 MobiDBLite mobidb-lite consensus disorder prediction 69 95 -
13 g13653.t1 MobiDBLite mobidb-lite consensus disorder prediction 81 95 -
14 g13653.t1 MobiDBLite mobidb-lite consensus disorder prediction 616 632 -
15 g13653.t1 MobiDBLite mobidb-lite consensus disorder prediction 616 641 -
3 g13653.t1 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 63 623 7.8E-294
4 g13653.t1 PANTHER PTHR47958:SF73 LD32873P 63 623 7.8E-294
1 g13653.t1 Pfam PF00270 DEAD/DEAH box helicase 189 362 9.6E-48
2 g13653.t1 Pfam PF00271 Helicase conserved C-terminal domain 403 508 4.0E-30
10 g13653.t1 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 319 327 -
17 g13653.t1 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 165 193 11.137
19 g13653.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 196 373 31.276
18 g13653.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 401 548 24.033
12 g13653.t1 SMART SM00487 ultradead3 184 389 4.5E-63
11 g13653.t1 SMART SM00490 helicmild6 428 509 1.9E-31
5 g13653.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 238 526 1.45E-73

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