Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable ATP-dependent RNA helicase DHX35.

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 g9273 g9273.t1 isoform g9273.t1 1387242 1389369
chr_1 g9273 g9273.t1 exon g9273.t1.exon1 1387242 1389062
chr_1 g9273 g9273.t1 cds g9273.t1.CDS1 1387242 1389062
chr_1 g9273 g9273.t1 exon g9273.t1.exon2 1389124 1389369
chr_1 g9273 g9273.t1 cds g9273.t1.CDS2 1389124 1389369
chr_1 g9273 g9273.t1 TSS g9273.t1 1389949 1389949
chr_1 g9273 g9273.t1 TTS g9273.t1 NA NA

Sequences

>g9273.t1 Gene=g9273 Length=2067
ATGAATAGTGAGAGTCGATTAAAGTTTCTTAAACCGGATGATTCTGACGATGTGTTTGCT
GTTGATCGAGAAACTCAAAATGCCGAAACAACATCATTCGTTTTTAATCCAAATCGAAAT
TTAAGTTTAATTGCTCAACGAGATAAGCTTCCAATAAGAAAATTTGTTAATGACATTTTA
TATTGTCTCAGCAATTATCAAACATTAATACTTTGTGGTGAATGTGGCAGTGGCAAATCA
ACACAGATACCACAAATTCTGTATGAGAAAGGTTATCATGCTAAAGGAATAATTGGAATT
ACACAACCAAGAAGAGTGTCAGCAATAACTTTAGCTAAAAGAGTGGCAGAAGAGATGGGT
CAAGTATTTGGCGAAGAAGTCGGTGTAGCATGTCGATTCTTAAATAAATTCAATGAAGAC
ACAAAAATCAAATTCATGACAGAAGGCATAATTATGAGAGAAATCTTTGCAAATCCACTT
CTTTCCGAATATTCTGTTATTATCATTGATGAAGCACATGAACGTAATTTAATAACAGAC
TGCATTCTTGGATTATTAAAAAAGATTGCAAAAAAGCGAGAATCATTGAAAATCATTATT
TCATCTGCAACGATGGATGCAAAATTATTTAGAGATTTTTACAATTTTCGTAGCAAATCG
AATCCAAAAGATACATCTATTATTTTGACTGTTGAAGGAAGAATGTATGAGAATGAAATT
TTTTATCTTAATGAACCTTGTGCCGATTATGTACAATCAACAGTCGATACGATTATGAAA
ATTCATCATAAAGAACCAGCTGGCGATATTTTAGCTTTTCTTACAGGTCAAGAAGAAATC
ACAAGAGCAATTAGAATGCTTCGAGAGCATATGGAATTGACTAATGTTACCGAAGATGAA
TTAAAAGTTATGCCAATGCATGCATCTCTTACACATCACGATCAATTAAGAGTTTTTTTT
CATACATCAAGAAATACAAGAAAAGTTATTATAGCAACAAATATAGCAGAAACATCAGTT
ACAATTCCAGGAATCGTTTTTGTGATTGATTGTGGATTTATTAAATTAAATTGGTATATG
GCTGATCTACAAATTAATATGCTTGTTGTAACACCTGCATCTCAAGCAACTGCCAGGCAA
CGCGCAGGCAGAGCTGGAAGAATAAAAAATGGTAAAGTTTATAGACTTTTTACTCAAGAA
GAATATCAAAAACTTCCAAATATTACTGCGCCTGAAATGAGAAGAGCAGACTTATCAACT
ACAATTCTAACACTAAAAGCTTTAGGAATTGACAATATTCTTCGGTTTGATTTTCCTTCA
GCACCTCCTGCAAAGAATATGCTTGCATCAATTGAACTTCTCTATGCTCTTGGAGCGATA
GATAGTGAAGGAAATTTAACAAATGATGGTTTAATCATGGCAGAACTTCCTTTGTCACCA
ATTCATTCAAAAATGTTACTAGAATCACGTGAACTGGGATGTAGTGATGAAATATTAAGC
ATTGTTTCAATGATGCAAGTTCAACAAATATTTTCATACCCTAAATCAGGTCAAGGAGCA
ATTACTGCAAGACGTCAAAGAAGAAATTTTGAAGTTGCTGAAGGTGATCTTATCACGTAT
CTCAATGTCTATCAAGCATTTGTTGCAAATGGATGCACGAAAGAATTTTGTGGACAGTTT
TGTCTTATGTATAGGCATTTAAAGCGAGTTGTTGAGATAAGAAATCAATTGGAACTTATG
TTAACAAAGCAATTTAAAATGAAATTCAATTCAACAGCTGCAAGTACAACAATAATTCGT
CGTTGCATTTGTGCAGCAGCTTTTCCATTTGCTGCTTACTTACATCATTCAGGAACTTAT
AGAATGGTGCGAGGTGATACAGAAGTTAACATACATCCCACATCATGTCTTTACACTGAA
AAACAACCTTCTTGGATTGTTTTTGGTGAAGTTGTACACACTACAAAACTTTTTGTTCGT
GATATAACTACAATTGAATCACCATGGCTCTTAGAATTAGCTCAACATTATTATCATAAG
ACTTCTGTTCGAAATAATCAAATTTAA

>g9273.t1 Gene=g9273 Length=688
MNSESRLKFLKPDDSDDVFAVDRETQNAETTSFVFNPNRNLSLIAQRDKLPIRKFVNDIL
YCLSNYQTLILCGECGSGKSTQIPQILYEKGYHAKGIIGITQPRRVSAITLAKRVAEEMG
QVFGEEVGVACRFLNKFNEDTKIKFMTEGIIMREIFANPLLSEYSVIIIDEAHERNLITD
CILGLLKKIAKKRESLKIIISSATMDAKLFRDFYNFRSKSNPKDTSIILTVEGRMYENEI
FYLNEPCADYVQSTVDTIMKIHHKEPAGDILAFLTGQEEITRAIRMLREHMELTNVTEDE
LKVMPMHASLTHHDQLRVFFHTSRNTRKVIIATNIAETSVTIPGIVFVIDCGFIKLNWYM
ADLQINMLVVTPASQATARQRAGRAGRIKNGKVYRLFTQEEYQKLPNITAPEMRRADLST
TILTLKALGIDNILRFDFPSAPPAKNMLASIELLYALGAIDSEGNLTNDGLIMAELPLSP
IHSKMLLESRELGCSDEILSIVSMMQVQQIFSYPKSGQGAITARRQRRNFEVAEGDLITY
LNVYQAFVANGCTKEFCGQFCLMYRHLKRVVEIRNQLELMLTKQFKMKFNSTAASTTIIR
RCICAAAFPFAAYLHHSGTYRMVRGDTEVNIHPTSCLYTEKQPSWIVFGEVVHTTKLFVR
DITTIESPWLLELAQHYYHKTSVRNNQI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g9273.t1 CDD cd18791 SF2_C_RHA 239 397 1.3261E-66
7 g9273.t1 Gene3D G3DSA:3.40.50.300 - 11 234 1.5E-69
8 g9273.t1 Gene3D G3DSA:3.40.50.300 - 235 407 2.4E-59
9 g9273.t1 Gene3D G3DSA:1.20.120.1080 - 432 532 1.5E-25
4 g9273.t1 PANTHER PTHR18934:SF120 OS06G0343100 PROTEIN 37 680 6.4E-182
5 g9273.t1 PANTHER PTHR18934 ATP-DEPENDENT RNA HELICASE 37 680 6.4E-182
2 g9273.t1 Pfam PF00271 Helicase conserved C-terminal domain 257 388 1.8E-13
3 g9273.t1 Pfam PF04408 Helicase associated domain (HA2) 450 532 8.7E-21
1 g9273.t1 Pfam PF07717 Oligonucleotide/oligosaccharide-binding (OB)-fold 599 677 5.2E-18
11 g9273.t1 ProSitePatterns PS00690 DEAH-box subfamily ATP-dependent helicases signature. 165 174 -
16 g9273.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 60 223 18.607
15 g9273.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 254 429 15.653
13 g9273.t1 SMART SM00487 ultradead3 37 237 6.6E-19
12 g9273.t1 SMART SM00490 helicmild6 289 389 8.3E-15
14 g9273.t1 SMART SM00847 ha2_5 449 541 2.9E-27
6 g9273.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 31 561 1.04E-98

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:0004386 helicase activity 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