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.t5 TTS g2045.t5 14816239 14816239
chr_3 g2045 g2045.t5 isoform g2045.t5 14816462 14817538
chr_3 g2045 g2045.t5 exon g2045.t5.exon1 14816462 14817049
chr_3 g2045 g2045.t5 cds g2045.t5.CDS1 14816462 14817049
chr_3 g2045 g2045.t5 exon g2045.t5.exon2 14817326 14817462
chr_3 g2045 g2045.t5 cds g2045.t5.CDS2 14817326 14817439
chr_3 g2045 g2045.t5 exon g2045.t5.exon3 14817526 14817538
chr_3 g2045 g2045.t5 TSS g2045.t5 14818268 14818268

Sequences

>g2045.t5 Gene=g2045 Length=738
GGAGCAAAAGGCGGTTTTAAAGGTGGCAAAACTGTTATGGTTGAGCCTCATCGACATGCA
GGAATTTTTGTTGCTCGTGGAAAAGAGGATGCACTTGTTACATTAAATCTTGTACCTGGC
TCAGAAGTATATGGAGAAAAACGTATTTCTACTGATGGTGAGAAAAAAGAATATCGTGTT
TGGAATCCATTCAGATCAAAGTTAGCAGCAGCTATTCTCGGTGGAGTTGAAGAAATCTAT
ATAGCACCAGGTTCAAAGGTTTTATATCTTGGTGCAGCTTCAGGAACCACTGTTAGTCAT
GTGAGTGATGTTGTTGGTCCTGAAGGTCTCGTTTATGCAGTAGAATTCTCTCATCGTTCC
GGTCGTGATCTTATAAATGTTGCCAAGAAACGAACCAACATTATTCCAATCATTGAAGAT
GCTCGACATCCACACAAATATCGAATGTTAGTAGGAATGGTTGATACCATTTTTGCGGAT
GTTGCTCAACCCGATCAGGCTCGTATTGTGATACTTAATGCACAAAACTTTCTCAAAACG
GGCGGGCATTTTGTTATTTCCATCAAAGCATCTTGTATTGATTCAACAGCCAAACCTGAA
GCTGTATTCGCATCAGAAGTTGATAAACTCAAAGCTGAAAAATTGAAACCTCTAGAACAA
GTGACATTAGAACCTTATGAAAGAGATCACGCAGTTGTTTGTGGAGTTTTTAGACCACCA
GAAAAGAAAAAGAACTAA

>g2045.t5 Gene=g2045 Length=233
MVEPHRHAGIFVARGKEDALVTLNLVPGSEVYGEKRISTDGEKKEYRVWNPFRSKLAAAI
LGGVEEIYIAPGSKVLYLGAASGTTVSHVSDVVGPEGLVYAVEFSHRSGRDLINVAKKRT
NIIPIIEDARHPHKYRMLVGMVDTIFADVAQPDQARIVILNAQNFLKTGGHFVISIKASC
IDSTAKPEAVFASEVDKLKAEKLKPLEQVTLEPYERDHAVVCGVFRPPEKKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2045.t5 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 1 49 4.8E-24
14 g2045.t5 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39 50 227 6.5E-90
4 g2045.t5 Hamap MF_00351 Fibrillarin-like rRNA/tRNA 2’-O-methyltransferase [flpA]. 16 226 38.685284
2 g2045.t5 PANTHER PTHR10335:SF6 RRNA/TRNA 2’-O-METHYLTRANSFERASE FIBRILLARIN-LIKE PROTEIN 1 2 231 2.2E-129
3 g2045.t5 PANTHER PTHR10335 RRNA 2-O-METHYLTRANSFERASE FIBRILLARIN 2 231 2.2E-129
15 g2045.t5 PIRSF PIRSF006540 Nop17p 1 229 1.6E-117
11 g2045.t5 PRINTS PR00052 Fibrillarin signature 20 39 1.5E-89
6 g2045.t5 PRINTS PR00052 Fibrillarin signature 45 64 1.5E-89
10 g2045.t5 PRINTS PR00052 Fibrillarin signature 72 93 1.5E-89
5 g2045.t5 PRINTS PR00052 Fibrillarin signature 97 114 1.5E-89
8 g2045.t5 PRINTS PR00052 Fibrillarin signature 122 151 1.5E-89
9 g2045.t5 PRINTS PR00052 Fibrillarin signature 152 181 1.5E-89
7 g2045.t5 PRINTS PR00052 Fibrillarin signature 204 225 1.5E-89
1 g2045.t5 Pfam PF01269 Fibrillarin 2 226 5.4E-109
16 g2045.t5 ProSitePatterns PS00566 Fibrillarin signature. 97 111 -
17 g2045.t5 SMART SM01206 Fibrillarin_2 2 227 1.7E-171
12 g2045.t5 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases 2 225 3.56E-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:0003723 RNA binding MF
GO:0008168 methyltransferase activity MF
GO:0006364 rRNA processing BP

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