Gene loci information

Transcript annotation

  • This transcript has been annotated as rRNA 2’-O-methyltransferase fibrillarin.

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 g2045 g2045.t17 TTS g2045.t17 14816239 14816239
chr_3 g2045 g2045.t17 isoform g2045.t17 14816687 14818149
chr_3 g2045 g2045.t17 exon g2045.t17.exon1 14816687 14817049
chr_3 g2045 g2045.t17 cds g2045.t17.CDS1 14816687 14817049
chr_3 g2045 g2045.t17 exon g2045.t17.exon2 14817320 14817462
chr_3 g2045 g2045.t17 cds g2045.t17.CDS2 14817320 14817439
chr_3 g2045 g2045.t17 exon g2045.t17.exon3 14817526 14817586
chr_3 g2045 g2045.t17 exon g2045.t17.exon4 14817654 14817704
chr_3 g2045 g2045.t17 exon g2045.t17.exon5 14817780 14817856
chr_3 g2045 g2045.t17 exon g2045.t17.exon6 14818133 14818149
chr_3 g2045 g2045.t17 TSS g2045.t17 14818268 14818268

Sequences

>g2045.t17 Gene=g2045 Length=712
ATGGGAAGACCGCGTAACATTCACTCCAAGAGGTGGTGGAGGACGCGGAGGAAATAGAGG
AGGCGGTGGCAGAGGTGGTGGATTCAAGCCAAGAGGTGGTGGTGGAAGAGGTGGATTCAA
AGGTGCTGATCGTGGCGGTGGACGCGGAAGAGGAGGACCAAGAGGAGGAGGAAGAGGCGG
CCGTGGTGGTGGTGGAGCAAAAGGCGGTTTTAAAGGTGGCAAAACTGTTATGGTTGAGCC
TCATCGACATGCAGGAATTTTTGTTGCTCGTGGAAAAGAGGATGCACTTGTTACATTAAA
TCTTGTACCTGGCTCAGAAGTATATGGAGAAAAACGTATTTCTGTAGAAACTGATGGTGA
GAAAAAAGAATATCGTGTTTGGAATCCATTCAGATCAAAGTTAGCAGCAGCTATTCTCGG
TGGAGTTGAAGAAATCTATATAGCACCAGGTTCAAAGGTTTTATATCTTGGTGCAGCTTC
AGGAACCACTGTTAGTCATGTGAGTGATGTTGTTGGTCCTGAAGGTCTCGTTTATGCAGT
AGAATTCTCTCATCGTTCCGGTCGTGATCTTATAAATGTTGCCAAGAAACGAACCAACAT
TATTCCAATCATTGAAGATGCTCGACATCCACACAAATATCGAATGTTAGTAGGAATGGT
TGATACCATTTTTGCGGATGTTGCTCAACCCGATCAGGCTCGTATTGTGATA

>g2045.t17 Gene=g2045 Length=161
MVEPHRHAGIFVARGKEDALVTLNLVPGSEVYGEKRISVETDGEKKEYRVWNPFRSKLAA
AILGGVEEIYIAPGSKVLYLGAASGTTVSHVSDVVGPEGLVYAVEFSHRSGRDLINVAKK
RTNIIPIIEDARHPHKYRMLVGMVDTIFADVAQPDQARIVI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2045.t17 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 1 51 2.2E-26
12 g2045.t17 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39 52 161 2.7E-59
2 g2045.t17 PANTHER PTHR10335:SF21 BNAA03G47570D PROTEIN 1 160 5.0E-92
3 g2045.t17 PANTHER PTHR10335 RRNA 2-O-METHYLTRANSFERASE FIBRILLARIN 1 160 5.0E-92
13 g2045.t17 PIRSF PIRSF006540 Nop17p 1 161 1.7E-84
8 g2045.t17 PRINTS PR00052 Fibrillarin signature 20 39 5.0E-67
5 g2045.t17 PRINTS PR00052 Fibrillarin signature 47 66 5.0E-67
4 g2045.t17 PRINTS PR00052 Fibrillarin signature 74 95 5.0E-67
7 g2045.t17 PRINTS PR00052 Fibrillarin signature 99 116 5.0E-67
6 g2045.t17 PRINTS PR00052 Fibrillarin signature 124 153 5.0E-67
9 g2045.t17 PRINTS PR00052 Fibrillarin signature 154 161 5.0E-67
1 g2045.t17 Pfam PF01269 Fibrillarin 2 161 2.0E-78
14 g2045.t17 ProSitePatterns PS00566 Fibrillarin signature. 99 113 -
15 g2045.t17 SMART SM01206 Fibrillarin_2 2 161 6.0E-96
10 g2045.t17 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases 2 159 1.06E-34

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:0008168 methyltransferase activity MF
GO:0006364 rRNA processing BP

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