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.t1 TTS g9611.t1 4276174 4276174
chr_1 g9611 g9611.t1 isoform g9611.t1 4276297 4281465
chr_1 g9611 g9611.t1 exon g9611.t1.exon1 4276297 4279450
chr_1 g9611 g9611.t1 cds g9611.t1.CDS1 4276297 4279450
chr_1 g9611 g9611.t1 exon g9611.t1.exon2 4279509 4280312
chr_1 g9611 g9611.t1 cds g9611.t1.CDS2 4279509 4280312
chr_1 g9611 g9611.t1 exon g9611.t1.exon3 4280379 4281178
chr_1 g9611 g9611.t1 cds g9611.t1.CDS3 4280379 4281178
chr_1 g9611 g9611.t1 exon g9611.t1.exon4 4281246 4281341
chr_1 g9611 g9611.t1 cds g9611.t1.CDS4 4281246 4281341
chr_1 g9611 g9611.t1 exon g9611.t1.exon5 4281436 4281465
chr_1 g9611 g9611.t1 cds g9611.t1.CDS5 4281436 4281465
chr_1 g9611 g9611.t1 TSS g9611.t1 4281719 4281719

Sequences

>g9611.t1 Gene=g9611 Length=4884
ATGACAAAAGAAGAAAATATTGTAAGTGAGGTTCAAACATTCTTAACAAGAGATTATCAA
AGAAACATTATTGATGTATGTCTTAAAAGAAACTCAATTGTTTTTCTCCCAACTGGAGCT
GGCAAGACATACATCGCTATTCAAGTGATCAAGCACTTCTCAAATCAGCTTGGAATAAAA
TATTCTGAAGGTGGAAAGCGTTCTGTTTTCTTAGTAAACACAGTGTATCTTGCAAAGCAA
CAAGCTGAAGCTATACAATTTCATATTCCATTTAATGTTCGTGTCGTTACTGGCGAAGAA
AATGTTGATGCGTTTGAAGAAAGCGATTGGTTAAAAATTTTAGACAACAATGAAGTTTTA
GTGATGACAGCTCAATGCTTTCATGACGCTGTAAATCGCACTTTCATTAAAATGAATCAA
ATTCGAGTTGTAATTTTTGATGAATGTCATCATGGTCGTAAAGATCATGTATATCATCAA
CTTATGCAAAGCATATCAAACAAACTTGATGAAAACGAATTCAAGAATTTACGAATAATT
GGACTTTCAGGAATGCTTATAGGCGTCGATAACAGTATAAAACCTTACCTAGTTGCTGAT
GAAATGAAACGATTGGAAAGTACTTTTCAGAGTGTAATCATTACAGTTAATAATCTTGAT
GATCACAAAAATGTTATTCTTTATTCAACCAAAGCTATCAAGACTGCCATTCTCTTTAAT
ATGACTGCATGTTCAAAAACACTTGTTGAAGTAAAGGATTCTCTTTTATGTTTTCAAACA
AAATTAGAAATGATAAAACTAGACAATTTGGATTATATCAATCCTAGAAATTTACGAAAA
ACAATTCCAAAACGAATCAAGGAGCTTATTAACATACTCAAAGATTTTGAACATCAAGCT
TTAATGATGGGAAATTTTGGCGCATATATATCACTTGTAAGCATAATAGTACAACTCGAA
TTGAACAAAAGAGCAGCAGATTCTGAACGCTATCGCGATGTATTAAAAATGTGCATCACA
AAGGTTGAAGAATGCATAAAAAAAGTAGACTATGAATTATGCTTGAATAGAGATAATGCA
ACAAACATAATTGCAAATTCATCACATAAAGTTCAAACATTGATCGAATTGCTTCAAAAA
AGTTTTACTGATGAAAACAGAGAAAAAGACTTGCAGTGCATAATTTTCGTTGAACGTCGT
TCAACTGCAAAAATACTCTATCATATTATCAAAATGTTGGCAAACTCTATGTTTAATTTT
CCACTTCGACCTGATTTTATAGTTGGATGCAATAATGATATGCCAGAATCCATTGATGCT
ATTCTAAATAAATCTTTCAATAAGATGGCCTTGGATAAATTCAACAGGAACGAAACAAAT
TGCGTTATTTGTACTAATGTTCTTGAGGAAGGGATTGATGTGCAAGCTTGTAATCTTGTT
ATTATGTATGATAAATCAACCACTCCACGAAGTTTCTTTCAATCATGTGGAAGAGCTCGC
GACAACAAAAGCAAATACATAGTGATGCTTGAACAAAGAGATATTGAAAAATTTAAAAAA
AATGTTAACAACTGGAATTGTATTAACGATGAAATGAAGAAGCAGTTGATTGGAAAAACC
TTAGATAGAGAACTACCAAGTGATGAAAGTATTCAGAATGAACAACAACAATCATGGGAG
CCTTATTTAACCAAAAGTGGAAGTGAATTAAATGCCTTAAATGCAATTAACATCTTGAAT
CAATATTGCATGTCACTTCCATTTGATAAATATACTAAATATCGTGAATCCTATCGTCGA
ATTGATCACAAAGACGGAACTTGTCAAGTTGCAATTCAAATGCCAATTTCATCAATGATT
CGTGAAGAAATTTTTGGCGAACCTAAAGAAAATGTACGATTGGCAAAACAACATGCTGCT
TTTGAAGCATGCAAAATATTAATTGAAAACGGCTCACTTACTGATAAATTGACTCCAATT
GATTCTCTGCAAAAAATTGAAGAATTTAATGATGAATATTTTTCACACTGGGAAAAATAT
AAAAATGATGAAAAATCAAAAGCTGGTACAAAAAATAATCGACGTTATCACAAGTCAAAA
GTTCCTGACGTGTTAAAAAACTGTGGACCATCATTGACAAAAACAAATTATCTTTATACC
ATTCGGATCAAACCAGATTTCGATACTAAAGATGATTTTGATTTAAAAGTATTTCATGAG
CTCATTGATAATGAAAATACTTTTGGAATTTTAACTACAAAACGAATTCCACGTATATGT
AAAATTCCACTTTTTCAATCATATGGAAAGATCGTTTGTGAAATAATTTCACCTCCAATT
GCAATTTCAATAGAAAATGAGAAAGAACTTGATGCTCTTAGACGATTCCATTTGAACATA
TTTTGTGATGTTTTAAAAGTTTTCAAAAGCTTTTTGGCACTTGACAAGTCATCTTACCTA
ATTGTTCCTTTAGACAAACAAAATGGAATAAACTGGACATTACTTGAGCAATTTGAGACA
ATACATTCTCCTGTTAAACTATCAAAAAACGAAATTATGACAATGTCTTTTAAACCAGAT
GATTATCTTTATAAAGTGTTAAATCCTGTTTATCGAGAGACAGATCAAAATTATGTTGTT
ATCAAAGTTCTTGAACACAAAAATCCACAAAGCGCATTTCCTTCAGAAAAAGCAAAGACA
TATTATGAATACTATCTTTCAAAAGATCATCAAATTTATCGAAATGATCAATTTTTGGTA
CAAGTTAAAGGAATCAGTAAAAATTTAAATTTATTTTTTCCTGGTGCTGGTGTAAGCGGT
GATAAAAAATCGACTAGAAACTTATTGGAAGAATATGTGCCTGAATTGTGTCACAACTAT
AAATTTCCTGCTGCTTATTGGTTAAAAGCAACATTGTTACCATCTATCTGTCATCGACTA
CATTATTTGTTGCTTGCACAAGAATTACATACTTGGCTCATTAAAGAGAAAATTGACCTG
GGTCGTGGAACTCAAAATTATGAGGAGCTTGATATAGATTATGGAAATTATGAAGATCGT
AATAAGAAAGTAGAGCAATATGATGAGCAAATATTAGAACAACTTGATAATTTTGAACAA
ATATTAAAAGAACAAAAAAATTTCGATAATCAAGTTGAACAACAAAACAAGAACACACTT
TTAATCTGTAATAGTAAAGGTATGGATATGCCAATTGATTTCGATAGAAATTTGCTTACA
GTCACCGAGGCAGATCTTGATTATTATGCTTACTTTACTGGACAAACAAAATCTTCTGGC
TTTAAAACTGCAAATATTGATACAAATCGTGGATCAAGAAAACAGCTATCACTAAAAGAT
GATGTTCATCGAAAAGACATCAAATTATTAGATTTGACAAGTGCAAATAGTAGCATTCAA
CAGAGAAATTTGATTAAAGTTATTACAACTGCAAAATCTGGTGATGTTTTTGATATGGAG
CGATTTGAGACACTTGGTGATGCTTTTCTAAAATTTATTTCATCGCTTTATTTGTTCAAA
AATCATGTTAATTTACATGAAGGTCATCTTTCTGCTTTAAAAGGACGATTGGTTAGCAAT
CGTAATTTATTTTATATTGGAAACGAATTTGGTCTTTCAAATCTTTTAAAAACCACTCAA
TTTTGTTCAGGTGATGTACTCTGTGGTTTAGCACCAAGTGCAAAAATTCCATCAAGCATT
CAAGCATGCATTGATGATAAAAAATCTTTAATAAATCATTTAGTGGATGTAAAATTGTCT
AAAGAAGAAATGCAAACAGAAAAGGTAACAGAACAACATTTGAAAGAGTTTCGCATGGAA
GAAAATGAAAAAAGCAATATGTTCTGTGTGGAAAGCGGCAATGATAATGTTGATACAGGA
ATGCTCCCTTATATCAATGAAAATAATATTGGCGATAAAATAATTGCAGATGCTGTTGAA
GCATTAATTGGATGTGTAGTTTCAAGTACAGGACCAACATCAGCTCTCAAATTATGTCAT
AAATTAAAAATTATTCCATCAATGGATGAAAGTTTATTAAATGAAAAAATTCCTCCACGT
GTTCCTTTTGCAGCACAAGTAAACATCGAATCAACTTTTGATAAACTTGAAAAAATAATT
GGATATAAATTCAATGATAAACTATATTTATGTCAAGCACTTACACATACATCATATCCA
ATCAAAGATGCAGGTACCTATGAAAATTTAGAATTTCTAGGTGATGCTGTTTTAGATTTT
CTTATAACAAGTTATATAAGTGAGCAATGTCCAAAAATGAGCCCTGGAAAATTGACAGAT
TTGCGATCCGCATTAGTTAATAATGTTACTCTCGCTTGTATAATTGTGCGTAAGGAAATT
TATAAATTTTTAAAAGCAGAATGTCGCACATTATACGAGATTATCAAGAAATTTGTTGAA
TTTCAAAAGGCACAGAATAATAAAGTAACAGATGATGTAATCTTGCTTACAACAGATGAA
GAAACAAGTTCTGCAGAGGCTGTGAATGTTCCAAAAGTTCTGGGCGATATTTTTGAATCA
ATTATTGGTGCAGTCTTTTGCGATTCAAATAACTCTCTTTCGAAAACATGGAATGTGATT
TACAATCTAATGAAAGAAGAAATTCATGAATTTATTTCTAATGTTCCACTTCAAGTTGTT
CGTCGTCTTTATGAATATCATAAAGGTAATGCTGAGCCGAAATTCTATGAATCAAGAGTT
CTTCCGGATGATGAAGGAGTTGCTGTACCACTGAAATTCAAATGTCGTGGTGAAGAAAAG
ATTGTTATTGGCATAGGAAAGAACAGAAAAATTGCAAAAAATGCAGCTGCCAAACGTGCT
TTAAATTATCTTGAAAAAAAATAA

>g9611.t1 Gene=g9611 Length=1627
MTKEENIVSEVQTFLTRDYQRNIIDVCLKRNSIVFLPTGAGKTYIAIQVIKHFSNQLGIK
YSEGGKRSVFLVNTVYLAKQQAEAIQFHIPFNVRVVTGEENVDAFEESDWLKILDNNEVL
VMTAQCFHDAVNRTFIKMNQIRVVIFDECHHGRKDHVYHQLMQSISNKLDENEFKNLRII
GLSGMLIGVDNSIKPYLVADEMKRLESTFQSVIITVNNLDDHKNVILYSTKAIKTAILFN
MTACSKTLVEVKDSLLCFQTKLEMIKLDNLDYINPRNLRKTIPKRIKELINILKDFEHQA
LMMGNFGAYISLVSIIVQLELNKRAADSERYRDVLKMCITKVEECIKKVDYELCLNRDNA
TNIIANSSHKVQTLIELLQKSFTDENREKDLQCIIFVERRSTAKILYHIIKMLANSMFNF
PLRPDFIVGCNNDMPESIDAILNKSFNKMALDKFNRNETNCVICTNVLEEGIDVQACNLV
IMYDKSTTPRSFFQSCGRARDNKSKYIVMLEQRDIEKFKKNVNNWNCINDEMKKQLIGKT
LDRELPSDESIQNEQQQSWEPYLTKSGSELNALNAINILNQYCMSLPFDKYTKYRESYRR
IDHKDGTCQVAIQMPISSMIREEIFGEPKENVRLAKQHAAFEACKILIENGSLTDKLTPI
DSLQKIEEFNDEYFSHWEKYKNDEKSKAGTKNNRRYHKSKVPDVLKNCGPSLTKTNYLYT
IRIKPDFDTKDDFDLKVFHELIDNENTFGILTTKRIPRICKIPLFQSYGKIVCEIISPPI
AISIENEKELDALRRFHLNIFCDVLKVFKSFLALDKSSYLIVPLDKQNGINWTLLEQFET
IHSPVKLSKNEIMTMSFKPDDYLYKVLNPVYRETDQNYVVIKVLEHKNPQSAFPSEKAKT
YYEYYLSKDHQIYRNDQFLVQVKGISKNLNLFFPGAGVSGDKKSTRNLLEEYVPELCHNY
KFPAAYWLKATLLPSICHRLHYLLLAQELHTWLIKEKIDLGRGTQNYEELDIDYGNYEDR
NKKVEQYDEQILEQLDNFEQILKEQKNFDNQVEQQNKNTLLICNSKGMDMPIDFDRNLLT
VTEADLDYYAYFTGQTKSSGFKTANIDTNRGSRKQLSLKDDVHRKDIKLLDLTSANSSIQ
QRNLIKVITTAKSGDVFDMERFETLGDAFLKFISSLYLFKNHVNLHEGHLSALKGRLVSN
RNLFYIGNEFGLSNLLKTTQFCSGDVLCGLAPSAKIPSSIQACIDDKKSLINHLVDVKLS
KEEMQTEKVTEQHLKEFRMEENEKSNMFCVESGNDNVDTGMLPYINENNIGDKIIADAVE
ALIGCVVSSTGPTSALKLCHKLKIIPSMDESLLNEKIPPRVPFAAQVNIESTFDKLEKII
GYKFNDKLYLCQALTHTSYPIKDAGTYENLEFLGDAVLDFLITSYISEQCPKMSPGKLTD
LRSALVNNVTLACIIVRKEIYKFLKAECRTLYEIIKKFVEFQKAQNNKVTDDVILLTTDE
ETSSAEAVNVPKVLGDIFESIIGAVFCDSNNSLSKTWNVIYNLMKEEIHEFISNVPLQVV
RRLYEYHKGNAEPKFYESRVLPDDEGVAVPLKFKCRGEEKIVIGIGKNRKIAKNAAAKRA
LNYLEKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g9611.t1 CDD cd18034 DEXHc_dicer 17 217 2.60474E-65
29 g9611.t1 CDD cd15903 Dicer_PBD 265 349 4.28838E-11
28 g9611.t1 CDD cd00593 RIBOc 1144 1236 4.79209E-18
27 g9611.t1 CDD cd00593 RIBOc 1389 1552 1.07017E-32
25 g9611.t1 Coils Coil Coil 515 535 -
24 g9611.t1 Coils Coil Coil 1614 1627 -
18 g9611.t1 Gene3D G3DSA:3.40.50.300 - 16 266 1.6E-49
19 g9611.t1 Gene3D G3DSA:3.40.50.300 - 358 536 1.3E-34
21 g9611.t1 Gene3D G3DSA:3.30.160.380 - 571 671 8.0E-20
20 g9611.t1 Gene3D G3DSA:2.170.260.10 paz domain 850 958 3.5E-19
23 g9611.t1 Gene3D G3DSA:1.10.1520.10 - 1367 1559 3.5E-66
22 g9611.t1 Gene3D G3DSA:3.30.160.20 - 1560 1627 1.3E-10
9 g9611.t1 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 14 992 0.0
12 g9611.t1 PANTHER PTHR14950 DICER-RELATED 14 992 0.0
10 g9611.t1 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 1094 1487 0.0
13 g9611.t1 PANTHER PTHR14950 DICER-RELATED 1094 1487 0.0
8 g9611.t1 PANTHER PTHR14950:SF36 DICER-2, ISOFORM A 1492 1626 0.0
11 g9611.t1 PANTHER PTHR14950 DICER-RELATED 1492 1626 0.0
3 g9611.t1 Pfam PF04851 Type III restriction enzyme, res subunit 17 168 3.6E-16
4 g9611.t1 Pfam PF00271 Helicase conserved C-terminal domain 370 499 1.7E-14
6 g9611.t1 Pfam PF03368 Dicer dimerisation domain 575 662 2.2E-18
5 g9611.t1 Pfam PF02170 PAZ domain 855 981 3.5E-17
2 g9611.t1 Pfam PF00636 Ribonuclease III domain 1160 1330 2.6E-20
1 g9611.t1 Pfam PF00636 Ribonuclease III domain 1408 1529 6.0E-22
7 g9611.t1 Pfam PF00035 Double-stranded RNA binding motif 1582 1624 1.2E-4
38 g9611.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 23 184 17.683
37 g9611.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 370 540 13.223
35 g9611.t1 ProSiteProfiles PS51327 Dicer double-stranded RNA-binding fold domain profile. 575 667 22.43
40 g9611.t1 ProSiteProfiles PS50142 Ribonuclease III family domain profile. 1114 1331 19.25
39 g9611.t1 ProSiteProfiles PS50142 Ribonuclease III family domain profile. 1373 1530 34.362
36 g9611.t1 ProSiteProfiles PS50137 Double stranded RNA-binding domain (dsRBD) profile. 1604 1626 10.29
34 g9611.t1 SMART SM00487 ultradead3 12 213 3.0E-14
33 g9611.t1 SMART SM00490 helicmild6 425 502 3.4E-10
32 g9611.t1 SMART SM00949 PAZ_2_a_3 832 985 2.3E-7
30 g9611.t1 SMART SM00535 riboneu5 1128 1353 1.5E-14
31 g9611.t1 SMART SM00535 riboneu5 1388 1553 2.3E-35
17 g9611.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 25 500 5.7E-35
15 g9611.t1 SUPERFAMILY SSF69065 RNase III domain-like 1141 1343 1.22E-23
14 g9611.t1 SUPERFAMILY SSF69065 RNase III domain-like 1372 1552 3.66E-37
16 g9611.t1 SUPERFAMILY SSF54768 dsRNA-binding domain-like 1512 1624 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