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.t10 isoform g3586.t10 26560067 26562755
chr_3 g3586 g3586.t10 exon g3586.t10.exon1 26560067 26560249
chr_3 g3586 g3586.t10 exon g3586.t10.exon2 26560313 26560503
chr_3 g3586 g3586.t10 cds g3586.t10.CDS1 26560344 26560503
chr_3 g3586 g3586.t10 exon g3586.t10.exon3 26560567 26560704
chr_3 g3586 g3586.t10 cds g3586.t10.CDS2 26560567 26560704
chr_3 g3586 g3586.t10 exon g3586.t10.exon4 26560764 26561252
chr_3 g3586 g3586.t10 cds g3586.t10.CDS3 26560764 26561252
chr_3 g3586 g3586.t10 exon g3586.t10.exon5 26561364 26562755
chr_3 g3586 g3586.t10 cds g3586.t10.CDS4 26561364 26562256
chr_3 g3586 g3586.t10 TTS g3586.t10 26562742 26562742
chr_3 g3586 g3586.t10 TSS g3586.t10 NA NA

Sequences

>g3586.t10 Gene=g3586 Length=2393
TGGAAAAACTGTTACATCAGCCACAATTGTGTATCAACTTGTAAAAATTAATGGTGGTCC
AGTTTTGGTTTGTGCTCCAAGTAATACAGCAGTTGATCAACTTACTGAAAAAATCCATCG
AACTAATTTAAAAGTAATTCGTGTTTGTGCTAAATCACGTGAAGCAATCGATTCACCTGT
CAGCTTTTTGGCATTACATAATCAAATTCGTAACATGGAGACAAATAATGAATATAAAAA
GCTTCAACAATTAAAAGACGAAACTGGTGAATTATCATCGGGTGACGAGAAAAGATATCG
TATTCTAAAAAAGCAAGCAGAAAAGGAATTATTAGATGCTGCTGATGTCATTTGTTGTAC
ATGTGTTGGAGCAGGAGATCCACGTCTATCTCGCATAAAGTTCAATTCAATTTTAATTGA
TGAGTCAATGCAGAGCACTGAGCCTGAAGCCATGGTTCCAGTCGTTTTGGGCGCACGTCA
ATTGATTCTTGTTGGAGATCATTGTCAACTTGGGCCAGTCGTAATGTGTAAAAAAGCAGC
CAAGGCAGGACTCTCTCAATCACTTTTTGAACGTTTAGTTGTTTTGGGCATTCGTCCTTT
CCGCTTGGAAGTTCAATATCGTATGCATCCCGAATTGTCACAATTTCCTTCAAATTTCTT
CTATGAAGGTTCATTACAAAATGGTGTTTGTGCTGAAGAAAGAAAATTACGTATTGATTT
TCCATGGCCATCTCCTGAATGTCCGATGTTCTTTCTAGTAACACAAGGTGCTGAAGAAAT
TGCTGGAAGTGGTACTTCATATTTGAATCGAACTGAAGCTGCAAATGTCGAAAAAATTAC
AACTAGATTTTTGAAATCGGGTTTGAAGCCAGAACAGATTGGAATCATAACTCCTTATGA
AGGTCAACGAGCATATTTGGTTCAGTACATGCAGTATCAAGGAAGTTTACATAGCAAATT
GTATCAAGAAATTGAAATTGCATCTGTTGATGCTTTTCAAGGTCGGGAGAAAGACATAAT
AATTATGTCTTGTGTTCGATCAAATGAACATCAAGGAATTGGTTTTCTTAATGATCCAAG
ACGTTTAAATGTGGCTTTGACTCGTGCGAAATACGGAATTATTATTGTTGGAAATCCTAA
AGTACTTTCGAAGCAACAATTATGGAATAATTTGTTGAATTTCTATAAAGAAAAGAAAGT
TTTGGTTGAGGGATCGTTGAATAATCTAAAAGAGTCGATGATTCAATTCGCAAAGCCTAA
GAAAATTGTTAATACTTTCAATCCCGGTCAACATTTCATGTCATCTACAACATTTGATGC
AAAAGAAGCAATGCAACGTCCTCCTTTTTATGGAGTAGGTGGTAGTAACAACAATAATAA
TGATCGCATGATGCATAATAATATGGGAATTGGTAATCAATGGAATAATAATCATACAAT
GGATGGAATGTTCAGAGCTCATGATTCAATTTCGTACATCTCACCAGAACGTGCGCAAGC
TGCAATGAATGGTCTTTCTGTTCCAGTAGGCATGTTCATGAATATGTCATCAAATAATAT
GCCTCCTCGATATTTCCAACAGCAACAAGCTGCTATTCAACAAGCAGCTAAGCAAAGTCG
TATGAAGAAAAATATGAGTTCTGGAGGATCTAGCAGTAGCAACAATAATATGAATGCTGG
AAATTCTCAAAGTAAATTGCGTGGTAGAAACAGTCAAGCTGGACCATTAACTCAAGGAAT
GAGTCAAATGATGAGTCAACCTGGATTCAATGTTGATTTTTCACAAGGCGACTACACTGG
CGAATCTCAAATTGATGGATTATTATCACAAGATTTCGCTAACAGTCAAGGTCCAGACAA
ATTTTATAGTAATTTCCAATCGCAAAATTTTTGATGAACGATTCACATTAATTGTTATTT
GAAAACAATAATGTAAAATCTAAATGACATGGAGTCAGAAATCACTAAAGTAATTTTGAG
TGAAGGCATTGATTTGGAAGAACCGTTCATAAGACTCATAATATAAATGACTTCAATACT
ATAATATACGAATATGGCAAGGCTCTCTCATCTGGAGCGGAAGTATTGAGTAGCCGGGTT
GGTTTAGATTAAATACACACATACGACAATTATGATGCAAAAGTCATGCAACAAAATGTG
CTTTGTGGAAAAAACAATAAAGAGCAAAATTGTCATCATCGCTCATCATTCATACCCAAC
AAAATGTGCTTTTCAACTGAGAGACTCGAGTTAAAATTTTAAAAGAAAGCAAAAAATATA
ATTTCTAAATAATCCTTTTCACTTTTATTTTATTATTTTACAAAATTGTTGCAAATATTA
TTCCAAAATTTTCAAAACCTTAATAAATTCGACAATTTGAAATCAAAGATTTG

>g3586.t10 Gene=g3586 Length=559
METNNEYKKLQQLKDETGELSSGDEKRYRILKKQAEKELLDAADVICCTCVGAGDPRLSR
IKFNSILIDESMQSTEPEAMVPVVLGARQLILVGDHCQLGPVVMCKKAAKAGLSQSLFER
LVVLGIRPFRLEVQYRMHPELSQFPSNFFYEGSLQNGVCAEERKLRIDFPWPSPECPMFF
LVTQGAEEIAGSGTSYLNRTEAANVEKITTRFLKSGLKPEQIGIITPYEGQRAYLVQYMQ
YQGSLHSKLYQEIEIASVDAFQGREKDIIIMSCVRSNEHQGIGFLNDPRRLNVALTRAKY
GIIIVGNPKVLSKQQLWNNLLNFYKEKKVLVEGSLNNLKESMIQFAKPKKIVNTFNPGQH
FMSSTTFDAKEAMQRPPFYGVGGSNNNNNDRMMHNNMGIGNQWNNNHTMDGMFRAHDSIS
YISPERAQAAMNGLSVPVGMFMNMSSNNMPPRYFQQQQAAIQQAAKQSRMKKNMSSGGSS
SSNNNMNAGNSQSKLRGRNSQAGPLTQGMSQMMSQPGFNVDFSQGDYTGESQIDGLLSQD
FANSQGPDKFYSNFQSQNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3586.t10 CDD cd18808 SF1_C_Upf1 137 325 3.98947E-83
8 g3586.t10 Gene3D G3DSA:3.40.50.300 - 7 134 1.7E-34
9 g3586.t10 Gene3D G3DSA:3.40.50.300 - 136 346 4.7E-76
6 g3586.t10 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
7 g3586.t10 MobiDBLite mobidb-lite consensus disorder prediction 455 501 -
3 g3586.t10 PANTHER PTHR10887 DNA2/NAM7 HELICASE FAMILY 5 354 9.1E-177
4 g3586.t10 PANTHER PTHR10887:SF486 REGULATOR OF NONSENSE TRANSCRIPTS 1-LIKE PROTEIN 5 354 9.1E-177
1 g3586.t10 Pfam PF13086 AAA domain 4 104 1.6E-25
2 g3586.t10 Pfam PF13087 AAA domain 113 308 3.7E-60
5 g3586.t10 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 30 329 9.3E-51

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:0004386 helicase 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