Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-dependent RNA helicase me31b.

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 g8754 g8754.t4 TSS g8754.t4 32807174 32807174
chr_2 g8754 g8754.t4 isoform g8754.t4 32807240 32809190
chr_2 g8754 g8754.t4 exon g8754.t4.exon1 32807240 32807242
chr_2 g8754 g8754.t4 exon g8754.t4.exon2 32807879 32808001
chr_2 g8754 g8754.t4 cds g8754.t4.CDS1 32807958 32808001
chr_2 g8754 g8754.t4 exon g8754.t4.exon3 32808066 32808135
chr_2 g8754 g8754.t4 cds g8754.t4.CDS2 32808066 32808135
chr_2 g8754 g8754.t4 exon g8754.t4.exon4 32808201 32809190
chr_2 g8754 g8754.t4 cds g8754.t4.CDS3 32808201 32809190
chr_2 g8754 g8754.t4 TTS g8754.t4 32809939 32809939

Sequences

>g8754.t4 Gene=g8754 Length=1186
AAGATCGTTCAAATATTTAATACAAGGAAAGAAAGAGAGAGAAAAAAGCAAGAAAAAAAG
TAAGAGAAAAAAAATCAACAAAATGACGACTAAAACAATGAATAGTAACAATCATTTTAG
TCAAAGCGACCGTATTGATCCCGGATGGAAAGCAAAACTACAAATCCCACCCAAAGATAA
TAGAATTAAGACTAGTGATGTAACTGATACACGTGGCAATGAGTTCGAAGAGTTTTGTGT
TAAGCGAGAATTGCTTATGGGTGTTTTCGAGATGGGCTGGGAAAAACCATCTCCAATTCA
AGAAGCTGCTATTCCAATTGCTCTCGGTGGTAAGGATATTTTAGCAAGAGCTAAAAATGG
AACTGGGAAAACTGGGGCCTATTGTATTCCTATTTTGGAACAAGTCGATGAAAAAAAAGA
TTGTATTCAAGCATTGATTATTGTACCAACGAGAGAATTGGCACTTCAGACTTCACAAAT
CTGCATTGAATTGGCTAAGCATTTGGACATTAAAGTTATGGTGACAACAGGAGGAACTAA
TTTGAAAGATGATATCATGAGGTTGTATCAGAAAGTACAAGTTATTATTGCTACTCCGGG
ACGTATTCTTGATTTGATGGACAAAGAAGTTGCTATAATGGACAATTGCAAAATGCTCGT
ACTCGATGAGGCCGATAAACTGCTGTCACAAGATTTTAAAGGCATGCTAGATCATGTCAT
CATGAAGCTACCGCGCGAACGTCAAATTCTGCTCTTTTCGGCCACATTCCCGCTCACTGT
TAAACAGTTCATGGACAAGCACTTGCGCAATCCATACGAGATCAATTTAATGGAAGAGTT
GACACTGAAAGGTGTTACACAATATTATGCATTCGTTCAAGAACGCCAGAAAGTTCACTG
CTTAAATACACTTTTTAGCAAGCTTCAAATCAATCAGTCCATCATTTTCTGCAATTCGAC
ACAACGCGTCGAACTATTGGCGAAAAAAATTACAGAATTGGGCTATTGTTGCTATTATAT
TCATGCAAAAATGGCTCAAGTACATCGTAATCGTGTTTTCCACGATTTCCGTTCTGGGTT
ATGTCGTAATCTTGTGTGCTCGGATCTTTTTACACGTGGTATTGATGTTCAGGCTGTGAA
TGTTGTTATAAACTTTGATTTTCCCAAAATGGCCGAGACTTACTTG

>g8754.t4 Gene=g8754 Length=368
MTTKTMNSNNHFSQSDRIDPGWKAKLQIPPKDNRIKTSDVTDTRGNEFEEFCVKRELLMG
VFEMGWEKPSPIQEAAIPIALGGKDILARAKNGTGKTGAYCIPILEQVDEKKDCIQALII
VPTRELALQTSQICIELAKHLDIKVMVTTGGTNLKDDIMRLYQKVQVIIATPGRILDLMD
KEVAIMDNCKMLVLDEADKLLSQDFKGMLDHVIMKLPRERQILLFSATFPLTVKQFMDKH
LRNPYEINLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLA
KKITELGYCCYYIHAKMAQVHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDF
PKMAETYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g8754.t4 CDD cd17940 DEADc_DDX6 48 248 8.04782E-137
9 g8754.t4 CDD cd18787 SF2_C_DEAD 258 368 4.47509E-40
8 g8754.t4 Gene3D G3DSA:3.40.50.300 - 35 250 1.5E-67
7 g8754.t4 Gene3D G3DSA:3.40.50.300 - 251 368 7.7E-35
14 g8754.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 16 -
15 g8754.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
3 g8754.t4 PANTHER PTHR47960:SF8 DEAD (ASP-GLU-ALA-ASP) BOX HELICASE 6 7 368 3.2E-197
4 g8754.t4 PANTHER PTHR47960 DEAD-BOX ATP-DEPENDENT RNA HELICASE 50 7 368 3.2E-197
1 g8754.t4 Pfam PF00270 DEAD/DEAH box helicase 71 235 1.8E-44
2 g8754.t4 Pfam PF00271 Helicase conserved C-terminal domain 272 367 4.2E-19
11 g8754.t4 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 193 201 -
16 g8754.t4 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 46 74 9.673
18 g8754.t4 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 77 247 30.446
17 g8754.t4 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 257 368 16.006
13 g8754.t4 SMART SM00487 ultradead3 65 261 4.0E-55
12 g8754.t4 SMART SM00490 helicmild6 297 368 6.1E-10
6 g8754.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 33 248 1.87E-61
5 g8754.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 187 367 6.06E-34

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