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.t6 TSS g8754.t6 32807174 32807174
chr_2 g8754 g8754.t6 isoform g8754.t6 32807240 32809536
chr_2 g8754 g8754.t6 exon g8754.t6.exon1 32807240 32807242
chr_2 g8754 g8754.t6 exon g8754.t6.exon2 32807879 32808001
chr_2 g8754 g8754.t6 cds g8754.t6.CDS1 32807958 32808001
chr_2 g8754 g8754.t6 exon g8754.t6.exon3 32808066 32808135
chr_2 g8754 g8754.t6 cds g8754.t6.CDS2 32808066 32808135
chr_2 g8754 g8754.t6 exon g8754.t6.exon4 32808201 32809190
chr_2 g8754 g8754.t6 cds g8754.t6.CDS3 32808201 32809190
chr_2 g8754 g8754.t6 exon g8754.t6.exon5 32809247 32809283
chr_2 g8754 g8754.t6 cds g8754.t6.CDS4 32809247 32809283
chr_2 g8754 g8754.t6 exon g8754.t6.exon6 32809349 32809536
chr_2 g8754 g8754.t6 cds g8754.t6.CDS5 32809349 32809536
chr_2 g8754 g8754.t6 TTS g8754.t6 32809939 32809939

Sequences

>g8754.t6 Gene=g8754 Length=1411
AAGATCGTTCAAATATTTAATACAAGGAAAGAAAGAGAGAGAAAAAAGCAAGAAAAAAAG
TAAGAGAAAAAAAATCAACAAAATGACGACTAAAACAATGAATAGTAACAATCATTTTAG
TCAAAGCGACCGTATTGATCCCGGATGGAAAGCAAAACTACAAATCCCACCCAAAGATAA
TAGAATTAAGACTAGTGATGTAACTGATACACGTGGCAATGAGTTCGAAGAGTTTTGTGT
TAAGCGAGAATTGCTTATGGGTGTTTTCGAGATGGGCTGGGAAAAACCATCTCCAATTCA
AGAAGCTGCTATTCCAATTGCTCTCGGTGGTAAGGATATTTTAGCAAGAGCTAAAAATGG
AACTGGGAAAACTGGGGCCTATTGTATTCCTATTTTGGAACAAGTCGATGAAAAAAAAGA
TTGTATTCAAGCATTGATTATTGTACCAACGAGAGAATTGGCACTTCAGACTTCACAAAT
CTGCATTGAATTGGCTAAGCATTTGGACATTAAAGTTATGGTGACAACAGGAGGAACTAA
TTTGAAAGATGATATCATGAGGTTGTATCAGAAAGTACAAGTTATTATTGCTACTCCGGG
ACGTATTCTTGATTTGATGGACAAAGAAGTTGCTATAATGGACAATTGCAAAATGCTCGT
ACTCGATGAGGCCGATAAACTGCTGTCACAAGATTTTAAAGGCATGCTAGATCATGTCAT
CATGAAGCTACCGCGCGAACGTCAAATTCTGCTCTTTTCGGCCACATTCCCGCTCACTGT
TAAACAGTTCATGGACAAGCACTTGCGCAATCCATACGAGATCAATTTAATGGAAGAGTT
GACACTGAAAGGTGTTACACAATATTATGCATTCGTTCAAGAACGCCAGAAAGTTCACTG
CTTAAATACACTTTTTAGCAAGCTTCAAATCAATCAGTCCATCATTTTCTGCAATTCGAC
ACAACGCGTCGAACTATTGGCGAAAAAAATTACAGAATTGGGCTATTGTTGCTATTATAT
TCATGCAAAAATGGCTCAAGTACATCGTAATCGTGTTTTCCACGATTTCCGTTCTGGGTT
ATGTCGTAATCTTGTGTGCTCGGATCTTTTTACACGTGGTATTGATGTTCAGGCTGTGAA
TGTTGTTATAAACTTTGATTTTCCCAAAATGGCCGAGACTTACTTGCACCGTATCGGACG
TAGCGGTAGATTTGGTCATTTGGGTATTGCCATCAATCTAATCACGTACGAAGACCGATA
TGATCTTCATCGTATTGAAAAAGAATTGGGTACAGAAATCAAGCCAATTCCAAAAGTTAT
TGATCCTGCACTATATGTGGCATCGAAGCTTGATGAACAACAACAACAAGAAGAGCAGCA
ACAACAGCAAAATGCCAACAATAATAAGTAA

>g8754.t6 Gene=g8754 Length=442
MTTKTMNSNNHFSQSDRIDPGWKAKLQIPPKDNRIKTSDVTDTRGNEFEEFCVKRELLMG
VFEMGWEKPSPIQEAAIPIALGGKDILARAKNGTGKTGAYCIPILEQVDEKKDCIQALII
VPTRELALQTSQICIELAKHLDIKVMVTTGGTNLKDDIMRLYQKVQVIIATPGRILDLMD
KEVAIMDNCKMLVLDEADKLLSQDFKGMLDHVIMKLPRERQILLFSATFPLTVKQFMDKH
LRNPYEINLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVELLA
KKITELGYCCYYIHAKMAQVHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINFDF
PKMAETYLHRIGRSGRFGHLGIAINLITYEDRYDLHRIEKELGTEIKPIPKVIDPALYVA
SKLDEQQQQEEQQQQQNANNNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8754.t6 CDD cd17940 DEADc_DDX6 48 248 6.52876E-136
8 g8754.t6 CDD cd18787 SF2_C_DEAD 258 387 9.03353E-53
7 g8754.t6 Gene3D G3DSA:3.40.50.300 - 35 250 2.4E-67
6 g8754.t6 Gene3D G3DSA:3.40.50.300 - 251 432 3.1E-51
13 g8754.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 16 -
14 g8754.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
3 g8754.t6 PANTHER PTHR47960:SF8 DEAD (ASP-GLU-ALA-ASP) BOX HELICASE 6 7 421 7.6E-229
4 g8754.t6 PANTHER PTHR47960 DEAD-BOX ATP-DEPENDENT RNA HELICASE 50 7 421 7.6E-229
1 g8754.t6 Pfam PF00270 DEAD/DEAH box helicase 71 235 2.7E-44
2 g8754.t6 Pfam PF00271 Helicase conserved C-terminal domain 272 378 1.9E-25
10 g8754.t6 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 193 201 -
15 g8754.t6 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 46 74 9.673
17 g8754.t6 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 77 247 30.446
16 g8754.t6 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 257 417 22.694
12 g8754.t6 SMART SM00487 ultradead3 65 261 4.0E-55
11 g8754.t6 SMART SM00490 helicmild6 297 378 1.5E-26
5 g8754.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 115 400 7.71E-67

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