Gene loci information

Transcript annotation

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

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 g10716 g10716.t2 isoform g10716.t2 11561938 11564120
chr_1 g10716 g10716.t2 exon g10716.t2.exon1 11561938 11564120
chr_1 g10716 g10716.t2 TTS g10716.t2 11561948 11561948
chr_1 g10716 g10716.t2 cds g10716.t2.CDS1 11563174 11564118
chr_1 g10716 g10716.t2 TSS g10716.t2 NA NA

Sequences

>g10716.t2 Gene=g10716 Length=2183
ATATGGGTTTCGAACCTCAAATTCGTCACATTATTGAAAATCGCGATATGCCTCCAACTG
GTCAACGTCAAACATTAATGTTTTCTGCTACATTTCCGAAGAATATTCAAGAGTTGGCGA
GTGATTTTCTATCAAATTACATTTTCTTGGCCGTTGGACGTGTTGGTTCAACTTCTGAAA
ATATTACACAGACAATTTTGTGGGTTAATGAGCATGAGAAACGTTCATATTTACTTGACT
TATTGAGCCGCTTACGCGAAGGATCGCCTGATTATTCACCTGACAGTTTAACTTTGATTT
TTGTTGAAACGAAAAAGGGTGCTGATGCATTAGAAGAATTCTTGTATCAAAATAAGCATC
CAGTCACTTCTATTCATGGTGATCGTAGTCAACGTGAGCGTGAAGATGCATTAAAATGTT
TCCGTTCTGGTGATTGTCCTATTCTCGTTGCAACTGCAGTCGCTGCTCGTGGATTAGATA
TTCCACATGTTAAGCATGTCATAAACTATGATTTGCCTTCAGATGTTGAAGAATATGTTC
ATCGTATTGGTAAGAATTGCGTAATTTGTATATTTTTTATGACAATATTTAATTTAATTT
TAATCATAGGTCGAACAGGTCGTATGGGTAATCTTGGAATTGCAACAAGTTTCTTCAATG
AAAAGAATCGCAATATTGTCTCTGATCTAGTTGAACTTTTGATTGAGACAAATCAAGAAT
TGCCAGGTTTTCTTGAAGAAATGGCCAATGATCGTTATAGTGGACCAAGACGAAGCAACA
ATAATAGAGGTGGCAATAGTCGTTATGGTGGTAGTGGTTTTGGCTCACGCGATTATCGTC
AACCACAAGGCAACCAACGTTATGGTAGTGGTGGTGCTGGAAGCAACAGTGGAAATAGCG
GAAATCGTTCATATGGAGGTGGAAATCGATCATATGGTATGTTTTAATCTTTCTTTTGAT
TGAAATGATTTTAATTATCTTTTTTCTTATTTAAATAGGAAACAATGATGGAAGTTATCG
TAATGGAGGAGGTGGTGGAAATAATAGCAGTGGTAGTTATGGAGGAAGCTACAACAATTA
CAACAACAATCATGCAAGCTCTGGTCCAGACTGGTGGGAAGATTAAGCAGTTTTCTCACT
GCCATTTTCTCTTTCTTTTAATCATCATATATAATTTTGTAGCAGAGTTAATTTATCAAT
AGCAAAATCATTCTTCAACAGATTTTAAAATAATAATGTTTTAAATGCTTAATTTCTGTT
GAAGAATGATTTTTGAAATGATTTTTTCTATAGATAAATTCTCGTGTGACCCTGTCTCAT
TAACTACACACATACATACACACACATAAAACATACATACACTATTTAGTTTCCAATTAA
GATTATCTAATATTGATGAGCTATATGAATACAAGATAAAGAAACCCTTTTCAAATTTTT
ACATTGACATTGTAAAAATTTTAAATTATGACAAAAAATGAGCAAGAAAAAGCTAGCAGT
GAATATGAATATTAAAAAGCATAGATTGTGGAAACAAATTTTATAAATCTCTTAAACATG
AAAAATAATTGTCATTTAAAAATGGATAAAAAAGAAGAAAGAATTTCTACAGGTAAATCT
CTAAATAAGATGGCGATTTCGCTTGTACTATTATTTAAATGGATAAAAAGAGACAACTGT
AGAAAAGAAAGAAATAAATAATAAAACATACAATTTATGGATTTCTATTATAGAATAAAA
GAGGAATAAGTTGTGGACAAATAAAATTACACACACACACATACATGAATGAAGAAAAAT
TTTATGAAACTAATATAATTACTAAACGAAAGATGAAGAAATAATATTAATTTAAAAAAA
AAACATTTTCATATGCACTCAATCTCGTTACTTTTAAAAACGAGATGAAATTATATTTGC
ATTAAGAATACTAAGATGAAAAACCTTTTTTGATTTAGGTAAAAACAATTATTACTACTA
AAATGAATCCCCTCCTATCTTATTTTTCTGTATTTTAAATGAATACGAAGAACACACATA
AACACAAAAGAAGAAAAAGCATAACTAAAATAGTAAAAATTAAATAAGCTATGATGATGA
TTGAAAAATAGATGGAATGATAATGAATCAAATGAAAAAATAAAAATGGAGAATTCATAT
TATAAAGAAAGAGAATACTTTTG

>g10716.t2 Gene=g10716 Length=314
MGFEPQIRHIIENRDMPPTGQRQTLMFSATFPKNIQELASDFLSNYIFLAVGRVGSTSEN
ITQTILWVNEHEKRSYLLDLLSRLREGSPDYSPDSLTLIFVETKKGADALEEFLYQNKHP
VTSIHGDRSQREREDALKCFRSGDCPILVATAVAARGLDIPHVKHVINYDLPSDVEEYVH
RIGKNCVICIFFMTIFNLILIIGRTGRMGNLGIATSFFNEKNRNIVSDLVELLIETNQEL
PGFLEEMANDRYSGPRRSNNNRGGNSRYGGSGFGSRDYRQPQGNQRYGSGGAGSNSGNSG
NRSYGGGNRSYGMF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10716.t2 CDD cd18787 SF2_C_DEAD 61 218 3.90695E-58
7 g10716.t2 Gene3D G3DSA:3.40.50.300 - 1 50 6.6E-12
6 g10716.t2 Gene3D G3DSA:3.40.50.300 - 51 253 1.9E-56
14 g10716.t2 MobiDBLite mobidb-lite consensus disorder prediction 253 268 -
15 g10716.t2 MobiDBLite mobidb-lite consensus disorder prediction 253 314 -
16 g10716.t2 MobiDBLite mobidb-lite consensus disorder prediction 277 306 -
2 g10716.t2 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 1 287 3.1E-120
3 g10716.t2 PANTHER PTHR47958:SF98 DEAD-BOX HELICASE 3 X-LINKED A 1 287 3.1E-120
1 g10716.t2 Pfam PF00271 Helicase conserved C-terminal domain 89 184 1.8E-26
9 g10716.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 181 -
10 g10716.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 182 202 -
8 g10716.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 203 314 -
18 g10716.t2 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 49 9.082
17 g10716.t2 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 76 248 21.09
13 g10716.t2 SMART SM00490 helicmild6 108 209 2.6E-27
5 g10716.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 51 1.02E-7
4 g10716.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 56 241 2.1E-42
12 g10716.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 208 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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