General information for g16755.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribonuclease 3.
Parent gene
- The parent gene g16755 is located on chr_4: 10840582..10841808 (+ strand)
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_4 | g16755 | g16755.t1 | TSS | g16755.t1 | 10835886 | 10835886 |
| chr_4 | g16755 | g16755.t1 | isoform | g16755.t1 | 10835906 | 10840582 |
| chr_4 | g16755 | g16755.t1 | exon | g16755.t1.exon1 | 10835906 | 10836432 |
| chr_4 | g16755 | g16755.t1 | cds | g16755.t1.CDS1 | 10835906 | 10836432 |
| chr_4 | g16755 | g16755.t1 | TTS | g16755.t1 | 10836047 | 10836047 |
| chr_4 | g16755 | g16755.t1 | exon | g16755.t1.exon2 | 10836610 | 10836689 |
| chr_4 | g16755 | g16755.t1 | cds | g16755.t1.CDS2 | 10836610 | 10836689 |
| chr_4 | g16755 | g16755.t1 | exon | g16755.t1.exon3 | 10837132 | 10837887 |
| chr_4 | g16755 | g16755.t1 | cds | g16755.t1.CDS3 | 10837132 | 10837887 |
| chr_4 | g16755 | g16755.t1 | exon | g16755.t1.exon4 | 10838278 | 10840008 |
| chr_4 | g16755 | g16755.t1 | cds | g16755.t1.CDS4 | 10838278 | 10840008 |
| chr_4 | g16755 | g16755.t1 | exon | g16755.t1.exon5 | 10840065 | 10840582 |
| chr_4 | g16755 | g16755.t1 | cds | g16755.t1.CDS5 | 10840065 | 10840582 |
Sequences
>g16755.t1 Gene=g16755 Length=3612
ATGGATCAAAAACAAAGCGTATCACAAACAAACAATCCAACAAGAAATTTACAAATTCAA
AATTTTCCATTGCCATCACCAAACTTTTCAAATTCCCATGATACAAAAGAAATTCAAAGT
GAAAGAAAATTTTATGATAGAGAAAAAAGAAGAAGAAGTCGAAGTAGAGAAAAATCAAGG
AAAAGAAGTCGATCGAGATCTAGAGAAAGCAAAACATCACAAAGACGATCAAGATCAAGA
GAATATCGAAGCATGAGTCACAGTTCGAGATATGATAGAGACACAAGAAGTTACAAAAGA
GAAACACGTGAATATAACACATCAAGTAGAAATTATAGAAGTCGTTCAAGAGATAAAAGA
AGTCCTTATAGATCAAGACATTCATCATATAGAAGATCTCCACATCGTTCATCATCATCA
CGTCATCATTCACCACAAAGATCTAAAACAGATGACACAAGACAAAAACCAAAAGAACCA
CGAACAGAAAGATCCAAAATTCTTGAAAAATACAAAAAAAAACTATTAGCTAAAAAAATT
AAAGCCTATTTGCCACCTTATAAACCACCTGAAAGGAAGAGAAAAATTCATGTTTGCAAA
CATAAATCTGAACAATGTTCATCATCATCAGATGAATCAGATGAAGAAATTGAAGAAGAT
AGAACGATGGAAGAACTGTCAAGAAAAACTCAACATCCTTATCGTTTACATTCAGATTTA
TGGCATAATGAACCAGGTGAAATGAACGATGGACCACTTTGTCGTTGTTCAGCACGATCG
AGAAGAAGTGGAATTCGACATGGAATTTATCCTGGTGAATTTGGTTTCCCTAAATGTGCA
CCAAATTCAAATAATGCTGATAAATTGCATCATTATCGAATCACAATAACACCACCAACA
AATTTTCTTACTAAAACACCAACAATCATTAAATATGATGAACATGAATTTCTTTTTGAA
GGTTTTTCACTTTTTACTCATGAAAAAATTGGTGATGAACTTCCAACTTGCAAAGTTATT
CGATTTAATATTGAATACACAATTATTTATGTTGAAGAAAAAATGCCAGAAAATTTTACA
ATTCGTGAACTTGATTTGTTTTTTAATTATCTTTTTATGGAATTGCTTGAACTTGTTGAT
TTTTCACTGACACCATCATTAGCTGGTGATAAAGAAACATGTCAATGTTATCATTTTTAT
CCACGATTTGTTAGAGAATTGCCTGAAAATGGAAAAGAAGTTTTAGCTATGGCTCATGTT
TTGAGATATTTATTGGATAATTCTGGACCTTTAGTTGATGCAACTGTTTTGAAAGAGAAA
GATAAAATGGGACAATTTGAATGGCAAGATTATGTTGATGTTGTCAAAGGAATGATAGTA
ACAAATCCAGCATCTGTGCCATCATCAGTTCGTGTAGATCAATTAGATAGAAAGACAGAC
GACATTCCAGAATGTAAAGACTCAACTGGCATAAATTATCCAGCAATTATTCATTTTGGA
GTTCGTCCACCACAATTATCATATGCTGGCAATCCAGAATATCAAAAAGCATGGAGAGAA
TATGTAAAATTTCGTCATTTATTAGCAAACATGTCAAAGCCATCATTTGATGATAAAAGA
AAACTTGAAGCCAAAGAAAATCGTTTGCAAGAAATGAGAACACAGGGAAGAATGAAAAGA
AATGTGACTGTGGCAATTTCATCAAAGAATTTCTATCGTACTGGAATAATGTGTGACATA
GTTCAACATGCTATGCTTTTGCCTGTTCTTACAACTCATTTACGTTTTCATCGTTCACTT
GGAGTTCTTGAAAAAACAATTAATTATAAATTTAAAAATCGTTATTTACTGCAATTGGCA
TTGACTCATCCAAGTTATAAAGAAAATTTTGGAACAAATCCAGATCATGCTAGAAATTCA
TTGACAAATTGTGGCATAAGACAACCAGAATATGGTGATAAGAAAATTCATTATATGAAC
ACAAGAAAACGTGGAATTAATACATTGATAAATATTATGTCACGATTTGGAAAAGAACAT
GAAGAACAGAGCAATATCACTCACAATGAACGACTTGAATTTCTTGGTGATGCTGTTGTT
GAATTTATAACTTCAATTCATCTTTTTCATCTTTTTCCTGATCTTGAAGAAGGTGGATTA
GCAACATATCGTGCAGCAATTGTTCAAAATCAACATCTTGCAATTTTAGCCAAAAGATTT
GGACTTGAACAATTTATGCTTTTTGCACATGGAAGTGATTTATGTCATGAATTAGAATTA
CGTCATGCAATGGCAAATTGTTTTGAATCTTTAATGGGTTCATTACTTTTAGATGGTGAC
ATAAAAATTGCTGACAAAGTTTTCTCTATTGCACTTATGGATGATTTAGAATTGAAAGAA
ATTTGGGATAATTATCCACCACATCCATTACAATCACAAGAACCTGATGGTGATAGAAAA
TGGATTGAACAATTTGAATTGCTGAAAAGTTTAAGAAATTTTGAAGAACAAATTGGCATT
GAATTTACTCACATTCGTTTACTTGCTAGAGCTTTTACAGATCGTTCAATTGGTTACACA
AATTTAACACTTGGTTCTAATCAGAGACTTGAATTTTTAGGTGATACAGTGCTTCAATTA
ATTTGTTCAGAATTTCTTTATCGTCATTTTCCTGAACATCATGAAGGTCATTTGTCATTA
CTAAGAAGTTCTTTGGTCAATAATAAAACACAAGCTGTTGTTTGTGATGATTTAGGAATG
ACAAAATATGCACTTTATTCTAATCCCAAAGCTGAACTTAAAACTAAAGATCGTGCTGAT
TTACTTGAAGCATTTCTTGGTGCACTTTATGTTGATAAAGATTTAATTTATTGTGAAACT
TTTTGTCAAGTTTGTCTTTTTCCAAGACTTCAAGATTTCATTATGAATCAAGATTGGAAT
GATCCAAAATCAAAATTACAACAGTGTTGTCTTACTTTAAGAACTATGGATGGAAATGAA
CCTGATATTCCTTACTATAAAGTTGTTGAATCAACTGGACCAACAAATACTAGAATTTAT
AAAGTTGCTGTTTATTTCCGTGACAAAAGATTAGCAAGTGCAACTGGACACAGCATTCAA
CAAGCTGAAATGAATGCAGCTAAGAAAGCTCTTGAAAATTCCAAAAATCTTTTCCCTCAA
CTTGATCATCAAAAGCGTGTTATTGCAAATAGTTTGAAGAGACAAAAAGTTCAACATAAA
CCACGTGAATCTGACAGTGAAAAAGAAGAAAAAAGCGATGAAAAAATTGTTAAAATTTCA
AATAATGAAAATCGTTTGCCAAAGCAATATCAAAAAAGAATGAAAATTGTTTCTGATGCT
TCTGATATTAGCAGTTCTTCATTGGAAGAAAATTCATCTGATGATTCTGATTATGAAAGT
AATAATTTGAAATTTAATAAAAATTCAGAAGAAAATGATGAAAATTTTTCAACAAAATCA
GAAAATATTGTTGCATCTTTGGAACATGAAATTGAGCCAATTTCATCATCAGAAACTGAA
CAACAGGAAGTTAAAGAAAATCAACTGGAAGATATTTCAAGTGATTTATCTGATGGTGAA
ATTGATGACTAG
>g16755.t1 Gene=g16755 Length=1203
MDQKQSVSQTNNPTRNLQIQNFPLPSPNFSNSHDTKEIQSERKFYDREKRRRSRSREKSR
KRSRSRSRESKTSQRRSRSREYRSMSHSSRYDRDTRSYKRETREYNTSSRNYRSRSRDKR
SPYRSRHSSYRRSPHRSSSSRHHSPQRSKTDDTRQKPKEPRTERSKILEKYKKKLLAKKI
KAYLPPYKPPERKRKIHVCKHKSEQCSSSSDESDEEIEEDRTMEELSRKTQHPYRLHSDL
WHNEPGEMNDGPLCRCSARSRRSGIRHGIYPGEFGFPKCAPNSNNADKLHHYRITITPPT
NFLTKTPTIIKYDEHEFLFEGFSLFTHEKIGDELPTCKVIRFNIEYTIIYVEEKMPENFT
IRELDLFFNYLFMELLELVDFSLTPSLAGDKETCQCYHFYPRFVRELPENGKEVLAMAHV
LRYLLDNSGPLVDATVLKEKDKMGQFEWQDYVDVVKGMIVTNPASVPSSVRVDQLDRKTD
DIPECKDSTGINYPAIIHFGVRPPQLSYAGNPEYQKAWREYVKFRHLLANMSKPSFDDKR
KLEAKENRLQEMRTQGRMKRNVTVAISSKNFYRTGIMCDIVQHAMLLPVLTTHLRFHRSL
GVLEKTINYKFKNRYLLQLALTHPSYKENFGTNPDHARNSLTNCGIRQPEYGDKKIHYMN
TRKRGINTLINIMSRFGKEHEEQSNITHNERLEFLGDAVVEFITSIHLFHLFPDLEEGGL
ATYRAAIVQNQHLAILAKRFGLEQFMLFAHGSDLCHELELRHAMANCFESLMGSLLLDGD
IKIADKVFSIALMDDLELKEIWDNYPPHPLQSQEPDGDRKWIEQFELLKSLRNFEEQIGI
EFTHIRLLARAFTDRSIGYTNLTLGSNQRLEFLGDTVLQLICSEFLYRHFPEHHEGHLSL
LRSSLVNNKTQAVVCDDLGMTKYALYSNPKAELKTKDRADLLEAFLGALYVDKDLIYCET
FCQVCLFPRLQDFIMNQDWNDPKSKLQQCCLTLRTMDGNEPDIPYYKVVESTGPTNTRIY
KVAVYFRDKRLASATGHSIQQAEMNAAKKALENSKNLFPQLDHQKRVIANSLKRQKVQHK
PRESDSEKEEKSDEKIVKISNNENRLPKQYQKRMKIVSDASDISSSSLEENSSDDSDYES
NNLKFNKNSEENDENFSTKSENIVASLEHEIEPISSSETEQQEVKENQLEDISSDLSDGE
IDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g16755.t1 | CDD | cd00593 | RIBOc | 682 | 788 | 7.03245E-36 |
| 13 | g16755.t1 | CDD | cd00593 | RIBOc | 846 | 975 | 4.89288E-39 |
| 14 | g16755.t1 | CDD | cd19877 | DSRM_RNAse_III_meta_like | 980 | 1054 | 4.97711E-45 |
| 11 | g16755.t1 | Gene3D | G3DSA:1.10.1520.10 | - | 826 | 972 | 2.0E-36 |
| 10 | g16755.t1 | Gene3D | G3DSA:3.30.160.20 | - | 980 | 1066 | 6.2E-23 |
| 6 | g16755.t1 | Hamap | MF_00104 | Ribonuclease 3 [rnc]. | 834 | 1051 | 21.575495 |
| 22 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 34 | - |
| 28 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 168 | - |
| 21 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 35 | 52 | - |
| 20 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 69 | - |
| 25 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 118 | - |
| 23 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 119 | 143 | - |
| 26 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 144 | 168 | - |
| 29 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 194 | 231 | - |
| 24 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1070 | 1203 | - |
| 27 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1076 | 1101 | - |
| 19 | g16755.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1140 | 1157 | - |
| 4 | g16755.t1 | PANTHER | PTHR11207 | RIBONUCLEASE III | 275 | 1086 | 2.5E-248 |
| 5 | g16755.t1 | PANTHER | PTHR11207:SF0 | RIBONUCLEASE 3 | 275 | 1086 | 2.5E-248 |
| 1 | g16755.t1 | Pfam | PF14622 | Ribonuclease-III-like | 684 | 795 | 5.1E-19 |
| 2 | g16755.t1 | Pfam | PF00636 | Ribonuclease III domain | 868 | 953 | 2.6E-18 |
| 3 | g16755.t1 | Pfam | PF00035 | Double-stranded RNA binding motif | 982 | 1053 | 7.8E-14 |
| 18 | g16755.t1 | ProSitePatterns | PS00517 | Ribonuclease III family signature. | 690 | 698 | - |
| 32 | g16755.t1 | ProSiteProfiles | PS50142 | Ribonuclease III family domain profile. | 600 | 780 | 29.47 |
| 31 | g16755.t1 | ProSiteProfiles | PS50142 | Ribonuclease III family domain profile. | 831 | 954 | 32.701 |
| 30 | g16755.t1 | ProSiteProfiles | PS50137 | Double stranded RNA-binding domain (dsRBD) profile. | 981 | 1056 | 12.257 |
| 17 | g16755.t1 | SMART | SM00535 | riboneu5 | 667 | 800 | 1.5E-37 |
| 16 | g16755.t1 | SMART | SM00535 | riboneu5 | 846 | 975 | 1.2E-44 |
| 15 | g16755.t1 | SMART | SM00358 | DRBM_3 | 982 | 1055 | 3.0E-10 |
| 8 | g16755.t1 | SUPERFAMILY | SSF69065 | RNase III domain-like | 593 | 794 | 3.49E-36 |
| 7 | g16755.t1 | SUPERFAMILY | SSF69065 | RNase III domain-like | 830 | 977 | 2.27E-38 |
| 9 | g16755.t1 | SUPERFAMILY | SSF54768 | dsRNA-binding domain-like | 970 | 1056 | 1.09E-14 |
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:0003723 | RNA binding | MF |
| GO:0004525 | ribonuclease III activity | MF |
| GO:0016075 | rRNA catabolic process | BP |
| GO:0031054 | pre-miRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K03685 (ribonuclease III)
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.
