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.t5 TSS g8754.t5 32807174 32807174
chr_2 g8754 g8754.t5 isoform g8754.t5 32807240 32809190
chr_2 g8754 g8754.t5 exon g8754.t5.exon1 32807240 32807242
chr_2 g8754 g8754.t5 exon g8754.t5.exon2 32807879 32808001
chr_2 g8754 g8754.t5 exon g8754.t5.exon3 32808066 32808139
chr_2 g8754 g8754.t5 exon g8754.t5.exon4 32808201 32809190
chr_2 g8754 g8754.t5 cds g8754.t5.CDS1 32808261 32809190
chr_2 g8754 g8754.t5 TTS g8754.t5 32809939 32809939

Sequences

>g8754.t5 Gene=g8754 Length=1190
AAGATCGTTCAAATATTTAATACAAGGAAAGAAAGAGAGAGAAAAAAGCAAGAAAAAAAG
TAAGAGAAAAAAAATCAACAAAATGACGACTAAAACAATGAATAGTAACAATCATTTTAG
TCAAAGCGACCGTATTGATCCCGGATGGAAAGCAAAACTACAAATCCCACCCAAAGATAA
TAGAATTAAGACTAGTGTAAGATGTAACTGATACACGTGGCAATGAGTTCGAAGAGTTTT
GTGTTAAGCGAGAATTGCTTATGGGTGTTTTCGAGATGGGCTGGGAAAAACCATCTCCAA
TTCAAGAAGCTGCTATTCCAATTGCTCTCGGTGGTAAGGATATTTTAGCAAGAGCTAAAA
ATGGAACTGGGAAAACTGGGGCCTATTGTATTCCTATTTTGGAACAAGTCGATGAAAAAA
AAGATTGTATTCAAGCATTGATTATTGTACCAACGAGAGAATTGGCACTTCAGACTTCAC
AAATCTGCATTGAATTGGCTAAGCATTTGGACATTAAAGTTATGGTGACAACAGGAGGAA
CTAATTTGAAAGATGATATCATGAGGTTGTATCAGAAAGTACAAGTTATTATTGCTACTC
CGGGACGTATTCTTGATTTGATGGACAAAGAAGTTGCTATAATGGACAATTGCAAAATGC
TCGTACTCGATGAGGCCGATAAACTGCTGTCACAAGATTTTAAAGGCATGCTAGATCATG
TCATCATGAAGCTACCGCGCGAACGTCAAATTCTGCTCTTTTCGGCCACATTCCCGCTCA
CTGTTAAACAGTTCATGGACAAGCACTTGCGCAATCCATACGAGATCAATTTAATGGAAG
AGTTGACACTGAAAGGTGTTACACAATATTATGCATTCGTTCAAGAACGCCAGAAAGTTC
ACTGCTTAAATACACTTTTTAGCAAGCTTCAAATCAATCAGTCCATCATTTTCTGCAATT
CGACACAACGCGTCGAACTATTGGCGAAAAAAATTACAGAATTGGGCTATTGTTGCTATT
ATATTCATGCAAAAATGGCTCAAGTACATCGTAATCGTGTTTTCCACGATTTCCGTTCTG
GGTTATGTCGTAATCTTGTGTGCTCGGATCTTTTTACACGTGGTATTGATGTTCAGGCTG
TGAATGTTGTTATAAACTTTGATTTTCCCAAAATGGCCGAGACTTACTTG

>g8754.t5 Gene=g8754 Length=310
MGVFEMGWEKPSPIQEAAIPIALGGKDILARAKNGTGKTGAYCIPILEQVDEKKDCIQAL
IIVPTRELALQTSQICIELAKHLDIKVMVTTGGTNLKDDIMRLYQKVQVIIATPGRILDL
MDKEVAIMDNCKMLVLDEADKLLSQDFKGMLDHVIMKLPRERQILLFSATFPLTVKQFMD
KHLRNPYEINLMEELTLKGVTQYYAFVQERQKVHCLNTLFSKLQINQSIIFCNSTQRVEL
LAKKITELGYCCYYIHAKMAQVHRNRVFHDFRSGLCRNLVCSDLFTRGIDVQAVNVVINF
DFPKMAETYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g8754.t5 CDD cd17940 DEADc_DDX6 1 190 1.12814E-128
9 g8754.t5 CDD cd18787 SF2_C_DEAD 200 310 2.41708E-40
8 g8754.t5 Gene3D G3DSA:3.40.50.300 - 2 192 2.2E-64
7 g8754.t5 Gene3D G3DSA:3.40.50.300 - 193 310 5.4E-35
3 g8754.t5 PANTHER PTHR47960 DEAD-BOX ATP-DEPENDENT RNA HELICASE 50 1 310 4.6E-175
4 g8754.t5 PANTHER PTHR47960:SF17 ATP-DEPENDENT RNA HELICASE DDX6-RELATED 1 310 4.6E-175
1 g8754.t5 Pfam PF00270 DEAD/DEAH box helicase 13 177 1.1E-44
2 g8754.t5 Pfam PF00271 Helicase conserved C-terminal domain 214 309 3.0E-19
11 g8754.t5 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 135 143 -
14 g8754.t5 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 1 16 6.867
16 g8754.t5 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 19 189 30.446
15 g8754.t5 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 199 310 16.006
13 g8754.t5 SMART SM00487 ultradead3 7 203 4.0E-55
12 g8754.t5 SMART SM00490 helicmild6 239 310 6.1E-10
5 g8754.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 190 2.04E-58
6 g8754.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 129 309 3.84E-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