Gene loci information

Transcript annotation

  • This transcript has been annotated as Regulator of nonsense transcripts 1-like protein.

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_3 g3586 g3586.t1 TSS g3586.t1 26557947 26557947
chr_3 g3586 g3586.t1 isoform g3586.t1 26558107 26562256
chr_3 g3586 g3586.t1 exon g3586.t1.exon1 26558107 26558250
chr_3 g3586 g3586.t1 cds g3586.t1.CDS1 26558107 26558250
chr_3 g3586 g3586.t1 exon g3586.t1.exon2 26558597 26559003
chr_3 g3586 g3586.t1 cds g3586.t1.CDS2 26558597 26559003
chr_3 g3586 g3586.t1 exon g3586.t1.exon3 26559071 26559573
chr_3 g3586 g3586.t1 cds g3586.t1.CDS3 26559071 26559573
chr_3 g3586 g3586.t1 exon g3586.t1.exon4 26559633 26559992
chr_3 g3586 g3586.t1 cds g3586.t1.CDS4 26559633 26559992
chr_3 g3586 g3586.t1 exon g3586.t1.exon5 26560063 26560249
chr_3 g3586 g3586.t1 cds g3586.t1.CDS5 26560063 26560249
chr_3 g3586 g3586.t1 exon g3586.t1.exon6 26560313 26560503
chr_3 g3586 g3586.t1 cds g3586.t1.CDS6 26560313 26560503
chr_3 g3586 g3586.t1 exon g3586.t1.exon7 26560567 26560704
chr_3 g3586 g3586.t1 cds g3586.t1.CDS7 26560567 26560704
chr_3 g3586 g3586.t1 exon g3586.t1.exon8 26560764 26561252
chr_3 g3586 g3586.t1 cds g3586.t1.CDS8 26560764 26561252
chr_3 g3586 g3586.t1 exon g3586.t1.exon9 26561364 26562256
chr_3 g3586 g3586.t1 cds g3586.t1.CDS9 26561364 26562256
chr_3 g3586 g3586.t1 TTS g3586.t1 26562742 26562742

Sequences

>g3586.t1 Gene=g3586 Length=3312
ATGTCATTCAGCCAAAGTCTATCTTTTCAAGATGATGATGATTTTATTTCGCAACCTTTC
TCGCAATTTAACTTTCAAGACTTTACACTTCCAAGTCAGACACAACAGTCTCAATTATCT
CAATTAGATCACATTGGAAACCAGCTGAATGGATTCGATGCTAAAGTAGATTCATCGCCA
GTTGCTTCTAGCAGCAAAATTAATGCAATCACCTCTGGTCTCAATGACCTGCAATTTGAA
GAAGAAGATGATGAACAGATAACATCAAAAGAGTTGGCTGCACATAGCTGTCGCTATTGT
GGTATTAGTGAACCATCGACAGTTGTCATGTGCAATATATGTAAAAAATGGTTTTGTAAT
GCCCGTGGTAATACATCTGGTTCTCATATATTGCATCATCTCGTTCGTGCTAAACATCGT
GAAGTAACTTTGCATGAAGATGGACCACTTGGCAGCACTGTTCTTGAATGCTATTCATGT
GGTATTCGAAATGTTTTCGTTTTAGGATTTATTCCAGCTAAGGCAGATTCTGTCGTTGTT
CTTCTTTGTCGTCAACCATGTGCTTCACAAAATTCATTAAAAGATATGAATTGGGATCAA
GATCAATGGAAACCTTTAATTTCTGATCGCTGTTTCTTGCCATGGCTTGTGAAAATTCCA
ACTGAACAGGAACAACTGCGTGCTCGTCAAATAACAGCTACAACTATCAATAAACTTGAA
GAACTTTGGAAAGAAAATGTAGAGGCATCTATATCTGATTTAGAAAAACCGGGAATTGAT
AAGGAACCCTCACAAGTTCAACTACGTTATGACGATGGTTATCAATATCAAAACATATTT
GGCCCACTTGTAAAGTTAGAGGCCGATTATGATAAACGCTTAAAAGAGTCTCAGACTCAA
GAAAATATAGAAGTTCGTTGGGATACTGGTTTAAATAAGAAAATAATTGCATATTTCACT
TTACCTAAAATTGATTCAGATATGAAGTTAATGGCTGGCGATGAATTGCGGTTACGATAT
GTTGGCGAGCTTCATGATTCATGGTCTGCAATAGGTCACGTCATAAAAGTACCAGACAAT
TATGGTGAAGATGTTGGACTTGAAATGAAGAAGCATAGTTCAAATCCACCCGTCAAATGC
TCTAGTAATTTTGTTGTTGATTTTATATGGAAAGGAACTTCGTTCGATAGAATGCAACAA
GCATTAAGGAAATTTGCAGTTGATGACAATTCAGTTTCAAATTTTATATATTCTCGATTG
TTAGGTCATTCAAGTGCTGATGATGTAACTTTTAGAATTAGCAATGCACCGAAACATTTT
TCAGCTCCAAACTTACCAGACCTTAATCGTTCTCAAGTTTATGCTGTAAAACATGCAATT
CAACGTCCTTTGAGTTTGATTCAAGGACCTCCAGGAACTGGAAAAACTGTTACATCAGCC
ACAATTGTGTATCAACTTGTAAAAATTAATGGTGGTCCAGTTTTGGTTTGTGCTCCAAGT
AATACAGCAGTTGATCAACTTACTGAAAAAATCCATCGAACTAATTTAAAAGTAATTCGT
GTTTGTGCTAAATCACGTGAAGCAATCGATTCACCTGTCAGCTTTTTGGCATTACATAAT
CAAATTCGTAACATGGAGACAAATAATGAATATAAAAAGCTTCAACAATTAAAAGACGAA
ACTGGTGAATTATCATCGGGTGACGAGAAAAGATATCGTATTCTAAAAAAGCAAGCAGAA
AAGGAATTATTAGATGCTGCTGATGTCATTTGTTGTACATGTGTTGGAGCAGGAGATCCA
CGTCTATCTCGCATAAAGTTCAATTCAATTTTAATTGATGAGTCAATGCAGAGCACTGAG
CCTGAAGCCATGGTTCCAGTCGTTTTGGGCGCACGTCAATTGATTCTTGTTGGAGATCAT
TGTCAACTTGGGCCAGTCGTAATGTGTAAAAAAGCAGCCAAGGCAGGACTCTCTCAATCA
CTTTTTGAACGTTTAGTTGTTTTGGGCATTCGTCCTTTCCGCTTGGAAGTTCAATATCGT
ATGCATCCCGAATTGTCACAATTTCCTTCAAATTTCTTCTATGAAGGTTCATTACAAAAT
GGTGTTTGTGCTGAAGAAAGAAAATTACGTATTGATTTTCCATGGCCATCTCCTGAATGT
CCGATGTTCTTTCTAGTAACACAAGGTGCTGAAGAAATTGCTGGAAGTGGTACTTCATAT
TTGAATCGAACTGAAGCTGCAAATGTCGAAAAAATTACAACTAGATTTTTGAAATCGGGT
TTGAAGCCAGAACAGATTGGAATCATAACTCCTTATGAAGGTCAACGAGCATATTTGGTT
CAGTACATGCAGTATCAAGGAAGTTTACATAGCAAATTGTATCAAGAAATTGAAATTGCA
TCTGTTGATGCTTTTCAAGGTCGGGAGAAAGACATAATAATTATGTCTTGTGTTCGATCA
AATGAACATCAAGGAATTGGTTTTCTTAATGATCCAAGACGTTTAAATGTGGCTTTGACT
CGTGCGAAATACGGAATTATTATTGTTGGAAATCCTAAAGTACTTTCGAAGCAACAATTA
TGGAATAATTTGTTGAATTTCTATAAAGAAAAGAAAGTTTTGGTTGAGGGATCGTTGAAT
AATCTAAAAGAGTCGATGATTCAATTCGCAAAGCCTAAGAAAATTGTTAATACTTTCAAT
CCCGGTCAACATTTCATGTCATCTACAACATTTGATGCAAAAGAAGCAATGCAACGTCCT
CCTTTTTATGGAGTAGGTGGTAGTAACAACAATAATAATGATCGCATGATGCATAATAAT
ATGGGAATTGGTAATCAATGGAATAATAATCATACAATGGATGGAATGTTCAGAGCTCAT
GATTCAATTTCGTACATCTCACCAGAACGTGCGCAAGCTGCAATGAATGGTCTTTCTGTT
CCAGTAGGCATGTTCATGAATATGTCATCAAATAATATGCCTCCTCGATATTTCCAACAG
CAACAAGCTGCTATTCAACAAGCAGCTAAGCAAAGTCGTATGAAGAAAAATATGAGTTCT
GGAGGATCTAGCAGTAGCAACAATAATATGAATGCTGGAAATTCTCAAAGTAAATTGCGT
GGTAGAAACAGTCAAGCTGGACCATTAACTCAAGGAATGAGTCAAATGATGAGTCAACCT
GGATTCAATGTTGATTTTTCACAAGGCGACTACACTGGCGAATCTCAAATTGATGGATTA
TTATCACAAGATTTCGCTAACAGTCAAGGTCCAGACAAATTTTATAGTAATTTCCAATCG
CAAAATTTTTGA

>g3586.t1 Gene=g3586 Length=1103
MSFSQSLSFQDDDDFISQPFSQFNFQDFTLPSQTQQSQLSQLDHIGNQLNGFDAKVDSSP
VASSSKINAITSGLNDLQFEEEDDEQITSKELAAHSCRYCGISEPSTVVMCNICKKWFCN
ARGNTSGSHILHHLVRAKHREVTLHEDGPLGSTVLECYSCGIRNVFVLGFIPAKADSVVV
LLCRQPCASQNSLKDMNWDQDQWKPLISDRCFLPWLVKIPTEQEQLRARQITATTINKLE
ELWKENVEASISDLEKPGIDKEPSQVQLRYDDGYQYQNIFGPLVKLEADYDKRLKESQTQ
ENIEVRWDTGLNKKIIAYFTLPKIDSDMKLMAGDELRLRYVGELHDSWSAIGHVIKVPDN
YGEDVGLEMKKHSSNPPVKCSSNFVVDFIWKGTSFDRMQQALRKFAVDDNSVSNFIYSRL
LGHSSADDVTFRISNAPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSA
TIVYQLVKINGGPVLVCAPSNTAVDQLTEKIHRTNLKVIRVCAKSREAIDSPVSFLALHN
QIRNMETNNEYKKLQQLKDETGELSSGDEKRYRILKKQAEKELLDAADVICCTCVGAGDP
RLSRIKFNSILIDESMQSTEPEAMVPVVLGARQLILVGDHCQLGPVVMCKKAAKAGLSQS
LFERLVVLGIRPFRLEVQYRMHPELSQFPSNFFYEGSLQNGVCAEERKLRIDFPWPSPEC
PMFFLVTQGAEEIAGSGTSYLNRTEAANVEKITTRFLKSGLKPEQIGIITPYEGQRAYLV
QYMQYQGSLHSKLYQEIEIASVDAFQGREKDIIIMSCVRSNEHQGIGFLNDPRRLNVALT
RAKYGIIIVGNPKVLSKQQLWNNLLNFYKEKKVLVEGSLNNLKESMIQFAKPKKIVNTFN
PGQHFMSSTTFDAKEAMQRPPFYGVGGSNNNNNDRMMHNNMGIGNQWNNNHTMDGMFRAH
DSISYISPERAQAAMNGLSVPVGMFMNMSSNNMPPRYFQQQQAAIQQAAKQSRMKKNMSS
GGSSSSNNNMNAGNSQSKLRGRNSQAGPLTQGMSQMMSQPGFNVDFSQGDYTGESQIDGL
LSQDFANSQGPDKFYSNFQSQNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g3586.t1 CDD cd21400 ZBD_UPF1-like 96 216 4.6724E-80
13 g3586.t1 CDD cd21407 1B_UPF1-like 299 388 4.90646E-48
12 g3586.t1 CDD cd18039 DEXXQc_UPF1 447 680 1.14934E-165
15 g3586.t1 CDD cd18808 SF1_C_Upf1 681 869 3.99723E-79
11 g3586.t1 Gene3D G3DSA:2.40.30.230 - 298 389 1.3E-35
10 g3586.t1 Gene3D G3DSA:3.40.50.300 - 680 890 1.7E-75
9 g3586.t1 MobiDBLite mobidb-lite consensus disorder prediction 999 1045 -
6 g3586.t1 PANTHER PTHR10887 DNA2/NAM7 HELICASE FAMILY 135 898 0.0
7 g3586.t1 PANTHER PTHR10887:SF486 REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN 135 898 0.0
2 g3586.t1 Pfam PF09416 RNA helicase (UPF2 interacting domain) 95 246 2.0E-74
4 g3586.t1 Pfam PF18141 Domain of unknown function (DUF5599) 298 389 7.8E-33
3 g3586.t1 Pfam PF04851 Type III restriction enzyme, res subunit 464 543 5.8E-5
1 g3586.t1 Pfam PF13086 AAA domain 548 648 4.8E-25
5 g3586.t1 Pfam PF13087 AAA domain 657 852 1.3E-59
8 g3586.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 444 872 3.8E-73

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:0003723 RNA binding MF
GO:0003677 DNA binding MF
GO:0005524 ATP binding MF
GO:0003724 RNA helicase activity MF
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay BP
GO:0004386 helicase activity MF
GO:0005737 cytoplasm CC
GO:0016787 hydrolase activity MF
GO:0008270 zinc ion 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