Gene loci information

Transcript annotation

  • This transcript has been annotated as Endoribonuclease dcr-1.

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 g14022 g14022.t1 TTS g14022.t1 34100102 34100102
chr_1 g14022 g14022.t1 isoform g14022.t1 34100258 34102268
chr_1 g14022 g14022.t1 exon g14022.t1.exon1 34100258 34102192
chr_1 g14022 g14022.t1 cds g14022.t1.CDS1 34100258 34102192
chr_1 g14022 g14022.t1 exon g14022.t1.exon2 34102257 34102268
chr_1 g14022 g14022.t1 cds g14022.t1.CDS2 34102257 34102268
chr_1 g14022 g14022.t1 TSS g14022.t1 34102483 34102483

Sequences

>g14022.t1 Gene=g14022 Length=1947
ATGACACTCCCGAACTACGAAATACGAGATTATCAAGAACAAATTTATAATATTTGTTTA
AAACAAAACTCATTAATCTATTTGCCCACAGGAAGTGGAAAGACAATGATTGCCATTAAA
GTAATTAACCACTTTAGAGATGAAATCGTTGAACCTATTAACAAGAATGGTAAAAGAGCA
GTATTTCTGGTAAATACAGTATGTCTTGCTAAACAACATAAAGAAACAATTGAAGAAGTG
TTAGGACTAAAAGTCAGTTGCTGGACTTCAGAATCAAAAAATAAAACATGGAGTAAAGCA
ATGTATTTGGAGAAGTTCAATGAGTGCTCAGTAATTATAGCAACAGCACAATTATTTGTG
GATGCAGTTAAACATTCTTTCATATCTATCGATCAAATTCGAGTGTTAATTTTCGATGAG
TGTCATCACGGAAGAATGAACCATCCATATCACGAATTAATGAAGCAATTTCAATACGTT
GATAAAAAGTTGCATCCTCGTGTAATTGGTTTGTCTGGAATGCTCGTCGGAATTGCAAAC
TCTTTGACAACTGATAATGTTAATGATGAACTAAAGAAACTCGAGAGTACGTATGATGCA
AAGATCGTTACTGTTAACAAAATTCAAGATTATTTAAACGTATTGATTCATAGTACAAAT
CCAAACGAAAGTTTTGTACGATATAAAAAATTCACTAACTGCGAACTTGCAGAAGAATTA
GTGGAAAGAATCAGTGAAATTCGTTGGATATTGGGATCTCTTAAAGTTCCTGGCATGACT
GAAATCAATCCAGAGACATTGAAGCCGTCGAGATCAAGAAAATTAAAGGAACTTGAATTG
TATTTTAATGAAGTTAAAGAAGAATTAGAGCAAATGGGATTATTTGGTGCTTATTTATCT
CTTAAAGCAATTCGCGTTCAATATTTGCTTATAAAAAAGAAACCTGGGCAAAACAAAACT
TTTCTTGAAGTCGTTAACAAATGTATTGATTATGTTGATGAATTGATGACTCTATTGGAT
GAAGAAAAAGATTTTAAAAATTTATCACTTATCAAGATTTTGCAAAACATATCACCCAAA
ATGAGAGCATTAATTCTTTTGCTTAAGATGCAATTCAACATTCAAAAATCTATAAAAAAT
CTTCAATGTTTGCTCTTTGTGACTCGCCGCTATTCTGCAAAATGTCTTTACTGGGTATTG
AAAAAGTATGCTGAGTATGATAAAGAATTCCGGATAATTCCAGATTTTGTTGTTGGCATT
AATTCAGAAATTCCAGAAAGTATTGAAGATGCTTTAAGTCAAAATTTCAATAACCTTGCT
CTTAAGAGATTCCGCGATAGAGAAACTAATTTAATTTGTGCATCTTCTGTTCTCGAAGAA
GGAATTGATTTGCAAATGTGTAATTTGGTTATTATGTTTGATTATCCAACAACTTTCCGC
TGCTACCTACAAACAATGGGTCGTGCAAGAATCAGAAATTCGAACTATATTGTATTGTTA
GAGGACAACAACGTTCCCAATTTTTTGAAAAAACGTGATGAAATGCATGCGATTGATAAG
GAATTGAAGAGAATTTTGGTAACAAAAACAATTGATCGTGTCATAACTAAAGAAGATATT
GAAAGAGAGCAAATGGAAGCTTGGGAACCATTAATTACAGAAAACAGAGCTTTGGTAAAT
TCAATTTCATCGATTGCTCTTCTTAATCGTTTTGTTAGTCGTTACGCAAATGCCAATTTA
TTATGGAGTAGACAAGATTATGGTGTTGGTAGAGTTGTTGCTATTCTCATATTACCAAGT
CAGTTGGATCTTGATAATTATATAATAAGATCGGATCAGATGCCTGATATCAAAACTGCA
AAGCAACATGCAGCATTTAAAGCATGTGAGATTCTTCATGAGAAGGGATATCTTGATTCA
AATTTGATTCCTTCATACATTATTTAA

>g14022.t1 Gene=g14022 Length=648
MTLPNYEIRDYQEQIYNICLKQNSLIYLPTGSGKTMIAIKVINHFRDEIVEPINKNGKRA
VFLVNTVCLAKQHKETIEEVLGLKVSCWTSESKNKTWSKAMYLEKFNECSVIIATAQLFV
DAVKHSFISIDQIRVLIFDECHHGRMNHPYHELMKQFQYVDKKLHPRVIGLSGMLVGIAN
SLTTDNVNDELKKLESTYDAKIVTVNKIQDYLNVLIHSTNPNESFVRYKKFTNCELAEEL
VERISEIRWILGSLKVPGMTEINPETLKPSRSRKLKELELYFNEVKEELEQMGLFGAYLS
LKAIRVQYLLIKKKPGQNKTFLEVVNKCIDYVDELMTLLDEEKDFKNLSLIKILQNISPK
MRALILLLKMQFNIQKSIKNLQCLLFVTRRYSAKCLYWVLKKYAEYDKEFRIIPDFVVGI
NSEIPESIEDALSQNFNNLALKRFRDRETNLICASSVLEEGIDLQMCNLVIMFDYPTTFR
CYLQTMGRARIRNSNYIVLLEDNNVPNFLKKRDEMHAIDKELKRILVTKTIDRVITKEDI
EREQMEAWEPLITENRALVNSISSIALLNRFVSRYANANLLWSRQDYGVGRVVAILILPS
QLDLDNYIIRSDQMPDIKTAKQHAAFKACEILHEKGYLDSNLIPSYII

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g14022.t1 Gene3D G3DSA:3.40.50.300 - 9 219 0.0000000
9 g14022.t1 Gene3D G3DSA:3.40.50.300 - 220 505 0.0000000
12 g14022.t1 Gene3D G3DSA:1.20.1320.30 - 233 357 0.0000000
11 g14022.t1 Gene3D G3DSA:3.30.160.380 - 559 647 0.0000000
4 g14022.t1 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 7 645 0.0000000
5 g14022.t1 PANTHER PTHR14950 DICER-RELATED 7 645 0.0000000
1 g14022.t1 Pfam PF04851 Type III restriction enzyme, res subunit 6 159 0.0000000
2 g14022.t1 Pfam PF00271 Helicase conserved C-terminal domain 428 490 0.0000000
3 g14022.t1 Pfam PF03368 Dicer dimerisation domain 564 645 0.0000000
15 g14022.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 15 193 16.8400000
14 g14022.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 373 526 12.1120000
13 g14022.t1 ProSiteProfiles PS51327 Dicer double-stranded RNA-binding fold domain profile. 554 648 10.6380000
8 g14022.t1 SMART SM00487 ultradead3 4 211 0.0000000
7 g14022.t1 SMART SM00490 helicmild6 401 492 0.0000002
6 g14022.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 56 506 0.0000000

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:0003677 DNA binding MF
GO:0016891 endoribonuclease activity, producing 5’-phosphomonoesters MF
GO:0016787 hydrolase activity MF
GO:0005524 ATP 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