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 g9611 g9611.t2 TTS g9611.t2 4276174 4276174
chr_1 g9611 g9611.t2 isoform g9611.t2 4276297 4281465
chr_1 g9611 g9611.t2 exon g9611.t2.exon1 4276297 4279450
chr_1 g9611 g9611.t2 cds g9611.t2.CDS1 4276297 4279450
chr_1 g9611 g9611.t2 exon g9611.t2.exon2 4279509 4280312
chr_1 g9611 g9611.t2 cds g9611.t2.CDS2 4279509 4280312
chr_1 g9611 g9611.t2 exon g9611.t2.exon3 4280379 4281178
chr_1 g9611 g9611.t2 cds g9611.t2.CDS3 4280379 4281178
chr_1 g9611 g9611.t2 exon g9611.t2.exon4 4281246 4281341
chr_1 g9611 g9611.t2 cds g9611.t2.CDS4 4281246 4281341
chr_1 g9611 g9611.t2 exon g9611.t2.exon5 4281445 4281465
chr_1 g9611 g9611.t2 cds g9611.t2.CDS5 4281445 4281465
chr_1 g9611 g9611.t2 TSS g9611.t2 4281719 4281719

Sequences

>g9611.t2 Gene=g9611 Length=4875
ATGACAAAAGAAGAAAATATTGTTCAAACATTCTTAACAAGAGATTATCAAAGAAACATT
ATTGATGTATGTCTTAAAAGAAACTCAATTGTTTTTCTCCCAACTGGAGCTGGCAAGACA
TACATCGCTATTCAAGTGATCAAGCACTTCTCAAATCAGCTTGGAATAAAATATTCTGAA
GGTGGAAAGCGTTCTGTTTTCTTAGTAAACACAGTGTATCTTGCAAAGCAACAAGCTGAA
GCTATACAATTTCATATTCCATTTAATGTTCGTGTCGTTACTGGCGAAGAAAATGTTGAT
GCGTTTGAAGAAAGCGATTGGTTAAAAATTTTAGACAACAATGAAGTTTTAGTGATGACA
GCTCAATGCTTTCATGACGCTGTAAATCGCACTTTCATTAAAATGAATCAAATTCGAGTT
GTAATTTTTGATGAATGTCATCATGGTCGTAAAGATCATGTATATCATCAACTTATGCAA
AGCATATCAAACAAACTTGATGAAAACGAATTCAAGAATTTACGAATAATTGGACTTTCA
GGAATGCTTATAGGCGTCGATAACAGTATAAAACCTTACCTAGTTGCTGATGAAATGAAA
CGATTGGAAAGTACTTTTCAGAGTGTAATCATTACAGTTAATAATCTTGATGATCACAAA
AATGTTATTCTTTATTCAACCAAAGCTATCAAGACTGCCATTCTCTTTAATATGACTGCA
TGTTCAAAAACACTTGTTGAAGTAAAGGATTCTCTTTTATGTTTTCAAACAAAATTAGAA
ATGATAAAACTAGACAATTTGGATTATATCAATCCTAGAAATTTACGAAAAACAATTCCA
AAACGAATCAAGGAGCTTATTAACATACTCAAAGATTTTGAACATCAAGCTTTAATGATG
GGAAATTTTGGCGCATATATATCACTTGTAAGCATAATAGTACAACTCGAATTGAACAAA
AGAGCAGCAGATTCTGAACGCTATCGCGATGTATTAAAAATGTGCATCACAAAGGTTGAA
GAATGCATAAAAAAAGTAGACTATGAATTATGCTTGAATAGAGATAATGCAACAAACATA
ATTGCAAATTCATCACATAAAGTTCAAACATTGATCGAATTGCTTCAAAAAAGTTTTACT
GATGAAAACAGAGAAAAAGACTTGCAGTGCATAATTTTCGTTGAACGTCGTTCAACTGCA
AAAATACTCTATCATATTATCAAAATGTTGGCAAACTCTATGTTTAATTTTCCACTTCGA
CCTGATTTTATAGTTGGATGCAATAATGATATGCCAGAATCCATTGATGCTATTCTAAAT
AAATCTTTCAATAAGATGGCCTTGGATAAATTCAACAGGAACGAAACAAATTGCGTTATT
TGTACTAATGTTCTTGAGGAAGGGATTGATGTGCAAGCTTGTAATCTTGTTATTATGTAT
GATAAATCAACCACTCCACGAAGTTTCTTTCAATCATGTGGAAGAGCTCGCGACAACAAA
AGCAAATACATAGTGATGCTTGAACAAAGAGATATTGAAAAATTTAAAAAAAATGTTAAC
AACTGGAATTGTATTAACGATGAAATGAAGAAGCAGTTGATTGGAAAAACCTTAGATAGA
GAACTACCAAGTGATGAAAGTATTCAGAATGAACAACAACAATCATGGGAGCCTTATTTA
ACCAAAAGTGGAAGTGAATTAAATGCCTTAAATGCAATTAACATCTTGAATCAATATTGC
ATGTCACTTCCATTTGATAAATATACTAAATATCGTGAATCCTATCGTCGAATTGATCAC
AAAGACGGAACTTGTCAAGTTGCAATTCAAATGCCAATTTCATCAATGATTCGTGAAGAA
ATTTTTGGCGAACCTAAAGAAAATGTACGATTGGCAAAACAACATGCTGCTTTTGAAGCA
TGCAAAATATTAATTGAAAACGGCTCACTTACTGATAAATTGACTCCAATTGATTCTCTG
CAAAAAATTGAAGAATTTAATGATGAATATTTTTCACACTGGGAAAAATATAAAAATGAT
GAAAAATCAAAAGCTGGTACAAAAAATAATCGACGTTATCACAAGTCAAAAGTTCCTGAC
GTGTTAAAAAACTGTGGACCATCATTGACAAAAACAAATTATCTTTATACCATTCGGATC
AAACCAGATTTCGATACTAAAGATGATTTTGATTTAAAAGTATTTCATGAGCTCATTGAT
AATGAAAATACTTTTGGAATTTTAACTACAAAACGAATTCCACGTATATGTAAAATTCCA
CTTTTTCAATCATATGGAAAGATCGTTTGTGAAATAATTTCACCTCCAATTGCAATTTCA
ATAGAAAATGAGAAAGAACTTGATGCTCTTAGACGATTCCATTTGAACATATTTTGTGAT
GTTTTAAAAGTTTTCAAAAGCTTTTTGGCACTTGACAAGTCATCTTACCTAATTGTTCCT
TTAGACAAACAAAATGGAATAAACTGGACATTACTTGAGCAATTTGAGACAATACATTCT
CCTGTTAAACTATCAAAAAACGAAATTATGACAATGTCTTTTAAACCAGATGATTATCTT
TATAAAGTGTTAAATCCTGTTTATCGAGAGACAGATCAAAATTATGTTGTTATCAAAGTT
CTTGAACACAAAAATCCACAAAGCGCATTTCCTTCAGAAAAAGCAAAGACATATTATGAA
TACTATCTTTCAAAAGATCATCAAATTTATCGAAATGATCAATTTTTGGTACAAGTTAAA
GGAATCAGTAAAAATTTAAATTTATTTTTTCCTGGTGCTGGTGTAAGCGGTGATAAAAAA
TCGACTAGAAACTTATTGGAAGAATATGTGCCTGAATTGTGTCACAACTATAAATTTCCT
GCTGCTTATTGGTTAAAAGCAACATTGTTACCATCTATCTGTCATCGACTACATTATTTG
TTGCTTGCACAAGAATTACATACTTGGCTCATTAAAGAGAAAATTGACCTGGGTCGTGGA
ACTCAAAATTATGAGGAGCTTGATATAGATTATGGAAATTATGAAGATCGTAATAAGAAA
GTAGAGCAATATGATGAGCAAATATTAGAACAACTTGATAATTTTGAACAAATATTAAAA
GAACAAAAAAATTTCGATAATCAAGTTGAACAACAAAACAAGAACACACTTTTAATCTGT
AATAGTAAAGGTATGGATATGCCAATTGATTTCGATAGAAATTTGCTTACAGTCACCGAG
GCAGATCTTGATTATTATGCTTACTTTACTGGACAAACAAAATCTTCTGGCTTTAAAACT
GCAAATATTGATACAAATCGTGGATCAAGAAAACAGCTATCACTAAAAGATGATGTTCAT
CGAAAAGACATCAAATTATTAGATTTGACAAGTGCAAATAGTAGCATTCAACAGAGAAAT
TTGATTAAAGTTATTACAACTGCAAAATCTGGTGATGTTTTTGATATGGAGCGATTTGAG
ACACTTGGTGATGCTTTTCTAAAATTTATTTCATCGCTTTATTTGTTCAAAAATCATGTT
AATTTACATGAAGGTCATCTTTCTGCTTTAAAAGGACGATTGGTTAGCAATCGTAATTTA
TTTTATATTGGAAACGAATTTGGTCTTTCAAATCTTTTAAAAACCACTCAATTTTGTTCA
GGTGATGTACTCTGTGGTTTAGCACCAAGTGCAAAAATTCCATCAAGCATTCAAGCATGC
ATTGATGATAAAAAATCTTTAATAAATCATTTAGTGGATGTAAAATTGTCTAAAGAAGAA
ATGCAAACAGAAAAGGTAACAGAACAACATTTGAAAGAGTTTCGCATGGAAGAAAATGAA
AAAAGCAATATGTTCTGTGTGGAAAGCGGCAATGATAATGTTGATACAGGAATGCTCCCT
TATATCAATGAAAATAATATTGGCGATAAAATAATTGCAGATGCTGTTGAAGCATTAATT
GGATGTGTAGTTTCAAGTACAGGACCAACATCAGCTCTCAAATTATGTCATAAATTAAAA
ATTATTCCATCAATGGATGAAAGTTTATTAAATGAAAAAATTCCTCCACGTGTTCCTTTT
GCAGCACAAGTAAACATCGAATCAACTTTTGATAAACTTGAAAAAATAATTGGATATAAA
TTCAATGATAAACTATATTTATGTCAAGCACTTACACATACATCATATCCAATCAAAGAT
GCAGGTACCTATGAAAATTTAGAATTTCTAGGTGATGCTGTTTTAGATTTTCTTATAACA
AGTTATATAAGTGAGCAATGTCCAAAAATGAGCCCTGGAAAATTGACAGATTTGCGATCC
GCATTAGTTAATAATGTTACTCTCGCTTGTATAATTGTGCGTAAGGAAATTTATAAATTT
TTAAAAGCAGAATGTCGCACATTATACGAGATTATCAAGAAATTTGTTGAATTTCAAAAG
GCACAGAATAATAAAGTAACAGATGATGTAATCTTGCTTACAACAGATGAAGAAACAAGT
TCTGCAGAGGCTGTGAATGTTCCAAAAGTTCTGGGCGATATTTTTGAATCAATTATTGGT
GCAGTCTTTTGCGATTCAAATAACTCTCTTTCGAAAACATGGAATGTGATTTACAATCTA
ATGAAAGAAGAAATTCATGAATTTATTTCTAATGTTCCACTTCAAGTTGTTCGTCGTCTT
TATGAATATCATAAAGGTAATGCTGAGCCGAAATTCTATGAATCAAGAGTTCTTCCGGAT
GATGAAGGAGTTGCTGTACCACTGAAATTCAAATGTCGTGGTGAAGAAAAGATTGTTATT
GGCATAGGAAAGAACAGAAAAATTGCAAAAAATGCAGCTGCCAAACGTGCTTTAAATTAT
CTTGAAAAAAAATAA

>g9611.t2 Gene=g9611 Length=1624
MTKEENIVQTFLTRDYQRNIIDVCLKRNSIVFLPTGAGKTYIAIQVIKHFSNQLGIKYSE
GGKRSVFLVNTVYLAKQQAEAIQFHIPFNVRVVTGEENVDAFEESDWLKILDNNEVLVMT
AQCFHDAVNRTFIKMNQIRVVIFDECHHGRKDHVYHQLMQSISNKLDENEFKNLRIIGLS
GMLIGVDNSIKPYLVADEMKRLESTFQSVIITVNNLDDHKNVILYSTKAIKTAILFNMTA
CSKTLVEVKDSLLCFQTKLEMIKLDNLDYINPRNLRKTIPKRIKELINILKDFEHQALMM
GNFGAYISLVSIIVQLELNKRAADSERYRDVLKMCITKVEECIKKVDYELCLNRDNATNI
IANSSHKVQTLIELLQKSFTDENREKDLQCIIFVERRSTAKILYHIIKMLANSMFNFPLR
PDFIVGCNNDMPESIDAILNKSFNKMALDKFNRNETNCVICTNVLEEGIDVQACNLVIMY
DKSTTPRSFFQSCGRARDNKSKYIVMLEQRDIEKFKKNVNNWNCINDEMKKQLIGKTLDR
ELPSDESIQNEQQQSWEPYLTKSGSELNALNAINILNQYCMSLPFDKYTKYRESYRRIDH
KDGTCQVAIQMPISSMIREEIFGEPKENVRLAKQHAAFEACKILIENGSLTDKLTPIDSL
QKIEEFNDEYFSHWEKYKNDEKSKAGTKNNRRYHKSKVPDVLKNCGPSLTKTNYLYTIRI
KPDFDTKDDFDLKVFHELIDNENTFGILTTKRIPRICKIPLFQSYGKIVCEIISPPIAIS
IENEKELDALRRFHLNIFCDVLKVFKSFLALDKSSYLIVPLDKQNGINWTLLEQFETIHS
PVKLSKNEIMTMSFKPDDYLYKVLNPVYRETDQNYVVIKVLEHKNPQSAFPSEKAKTYYE
YYLSKDHQIYRNDQFLVQVKGISKNLNLFFPGAGVSGDKKSTRNLLEEYVPELCHNYKFP
AAYWLKATLLPSICHRLHYLLLAQELHTWLIKEKIDLGRGTQNYEELDIDYGNYEDRNKK
VEQYDEQILEQLDNFEQILKEQKNFDNQVEQQNKNTLLICNSKGMDMPIDFDRNLLTVTE
ADLDYYAYFTGQTKSSGFKTANIDTNRGSRKQLSLKDDVHRKDIKLLDLTSANSSIQQRN
LIKVITTAKSGDVFDMERFETLGDAFLKFISSLYLFKNHVNLHEGHLSALKGRLVSNRNL
FYIGNEFGLSNLLKTTQFCSGDVLCGLAPSAKIPSSIQACIDDKKSLINHLVDVKLSKEE
MQTEKVTEQHLKEFRMEENEKSNMFCVESGNDNVDTGMLPYINENNIGDKIIADAVEALI
GCVVSSTGPTSALKLCHKLKIIPSMDESLLNEKIPPRVPFAAQVNIESTFDKLEKIIGYK
FNDKLYLCQALTHTSYPIKDAGTYENLEFLGDAVLDFLITSYISEQCPKMSPGKLTDLRS
ALVNNVTLACIIVRKEIYKFLKAECRTLYEIIKKFVEFQKAQNNKVTDDVILLTTDEETS
SAEAVNVPKVLGDIFESIIGAVFCDSNNSLSKTWNVIYNLMKEEIHEFISNVPLQVVRRL
YEYHKGNAEPKFYESRVLPDDEGVAVPLKFKCRGEEKIVIGIGKNRKIAKNAAAKRALNY
LEKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g9611.t2 CDD cd18034 DEXHc_dicer 14 214 2.5745E-65
28 g9611.t2 CDD cd15903 Dicer_PBD 262 346 4.40701E-11
27 g9611.t2 CDD cd00593 RIBOc 1141 1233 4.78283E-18
26 g9611.t2 CDD cd00593 RIBOc 1386 1549 1.07851E-32
24 g9611.t2 Coils Coil Coil 512 532 -
18 g9611.t2 Gene3D G3DSA:3.40.50.300 - 13 263 1.6E-49
19 g9611.t2 Gene3D G3DSA:3.40.50.300 - 355 533 1.3E-34
21 g9611.t2 Gene3D G3DSA:3.30.160.380 - 568 668 8.0E-20
20 g9611.t2 Gene3D G3DSA:2.170.260.10 paz domain 847 955 3.5E-19
23 g9611.t2 Gene3D G3DSA:1.10.1520.10 - 1364 1556 3.5E-66
22 g9611.t2 Gene3D G3DSA:3.30.160.20 - 1557 1624 1.3E-10
8 g9611.t2 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 11 989 0.0
11 g9611.t2 PANTHER PTHR14950 DICER-RELATED 11 989 0.0
10 g9611.t2 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 1091 1484 0.0
13 g9611.t2 PANTHER PTHR14950 DICER-RELATED 1091 1484 0.0
9 g9611.t2 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 1489 1623 0.0
12 g9611.t2 PANTHER PTHR14950 DICER-RELATED 1489 1623 0.0
3 g9611.t2 Pfam PF04851 Type III restriction enzyme, res subunit 14 165 3.6E-16
4 g9611.t2 Pfam PF00271 Helicase conserved C-terminal domain 367 496 1.7E-14
6 g9611.t2 Pfam PF03368 Dicer dimerisation domain 572 659 2.2E-18
5 g9611.t2 Pfam PF02170 PAZ domain 852 978 3.5E-17
1 g9611.t2 Pfam PF00636 Ribonuclease III domain 1157 1327 2.6E-20
2 g9611.t2 Pfam PF00636 Ribonuclease III domain 1405 1526 6.0E-22
7 g9611.t2 Pfam PF00035 Double-stranded RNA binding motif 1579 1621 1.2E-4
37 g9611.t2 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 20 181 17.683
36 g9611.t2 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 367 537 13.223
34 g9611.t2 ProSiteProfiles PS51327 Dicer double-stranded RNA-binding fold domain profile. 572 664 22.43
38 g9611.t2 ProSiteProfiles PS50142 Ribonuclease III family domain profile. 1111 1328 19.25
39 g9611.t2 ProSiteProfiles PS50142 Ribonuclease III family domain profile. 1370 1527 34.362
35 g9611.t2 ProSiteProfiles PS50137 Double stranded RNA-binding domain (dsRBD) profile. 1601 1623 10.29
33 g9611.t2 SMART SM00487 ultradead3 9 210 3.0E-14
32 g9611.t2 SMART SM00490 helicmild6 422 499 3.4E-10
31 g9611.t2 SMART SM00949 PAZ_2_a_3 829 982 2.3E-7
30 g9611.t2 SMART SM00535 riboneu5 1125 1350 1.5E-14
29 g9611.t2 SMART SM00535 riboneu5 1385 1550 2.3E-35
17 g9611.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 22 497 5.61E-35
14 g9611.t2 SUPERFAMILY SSF69065 RNase III domain-like 1138 1340 1.22E-23
15 g9611.t2 SUPERFAMILY SSF69065 RNase III domain-like 1369 1549 3.66E-37
16 g9611.t2 SUPERFAMILY SSF54768 dsRNA-binding domain-like 1509 1621 1.19E-7

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:0006396 RNA processing BP
GO:0003677 DNA binding MF
GO:0016891 endoribonuclease activity, producing 5’-phosphomonoesters MF
GO:0016787 hydrolase activity MF
GO:0005524 ATP binding MF
GO:0005515 protein binding MF
GO:0004525 ribonuclease III activity 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