General information for g304.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribosomal RNA small subunit methyltransferase NEP1.
Parent gene
- The parent gene g304 is located on chr_3: 2633774..2634776 (+ 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_3 | g304 | g304.t1 | TSS | g304.t1 | 2633505 | 2633505 |
| chr_3 | g304 | g304.t1 | isoform | g304.t1 | 2633583 | 2634366 |
| chr_3 | g304 | g304.t1 | exon | g304.t1.exon1 | 2633583 | 2633723 |
| chr_3 | g304 | g304.t1 | cds | g304.t1.CDS1 | 2633583 | 2633723 |
| chr_3 | g304 | g304.t1 | exon | g304.t1.exon2 | 2633779 | 2634366 |
| chr_3 | g304 | g304.t1 | cds | g304.t1.CDS2 | 2633779 | 2634366 |
| chr_3 | g304 | g304.t1 | TTS | g304.t1 | 2634380 | 2634380 |
Sequences
>g304.t1 Gene=g304 Length=729
ATGGGCAAAAGAAAAGCACAAAATATTAAAACAGAAGGTGAATTCGATCTAAACTTCAAA
AATCCTAAAACAGTTCATCTACAAGGAAATCAGAGAAAATTGATTGTTGTATTAAGTGGC
GCTCAATTGGAAACTGTTAAAGTAGGAAATACTTTTGAATTATTAAATTGCGATGATCAT
TTGCAAATATTGAAGAAATTTAATCGTGAACCAGGGTCTTGTAGACCAGATATAACTCAT
CAATCGCTTTTAATGCTTATGGACTCTCCTCTAAATCGTGCTGGTCTTTTACAAGTTTTC
ATACATACAGAAAAGAATGTATTGATTGAAGTAAATCCTCAAACGAGAATACCAAGAACA
TTTAAACGATTTGCTGGACTTATGGTTCAATTGCTGCATAAATTTGCTGTTAAAGCAAAT
GAAAGTTCAACAAAGTTACTTCATGTAATTAAGAATCCAATCACGGATCATTTGCCTGTT
GGTTCAAAAAAAATTGCAATGACATTTAGCTCAAAAGTTGTGAAAAATTGTCGAGAACTT
GTGCCAACTGGCAAAGAGGAAGCCATAGTATTGGTAATTGGTGCATTTGCTCATGGTCAT
TTAAATTTAGACTATACTGAAGACTCAATATCGATAAGTAATTATCCATTATCAGCAGCT
CTCACATGTGCAAAATTATGTAGTGCATTTGAAGAGGTTTGGAAAGTTGAAGAAATAAAA
GTTGAGTAA
>g304.t1 Gene=g304 Length=242
MGKRKAQNIKTEGEFDLNFKNPKTVHLQGNQRKLIVVLSGAQLETVKVGNTFELLNCDDH
LQILKKFNREPGSCRPDITHQSLLMLMDSPLNRAGLLQVFIHTEKNVLIEVNPQTRIPRT
FKRFAGLMVQLLHKFAVKANESSTKLLHVIKNPITDHLPVGSKKIAMTFSSKVVKNCREL
VPTGKEEAIVLVIGAFAHGHLNLDYTEDSISISNYPLSAALTCAKLCSAFEEVWKVEEIK
VE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g304.t1 | CDD | cd18088 | Nep1-like | 34 | 231 | 0 |
| 5 | g304.t1 | Gene3D | G3DSA:3.40.1280.10 | - | 34 | 236 | 0 |
| 2 | g304.t1 | PANTHER | PTHR12636 | NEP1/MRA1 | 21 | 236 | 0 |
| 3 | g304.t1 | PANTHER | PTHR12636:SF5 | RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE NEP1 | 21 | 236 | 0 |
| 1 | g304.t1 | Pfam | PF03587 | EMG1/NEP1 methyltransferase | 36 | 231 | 0 |
| 4 | g304.t1 | SUPERFAMILY | SSF75217 | alpha/beta knot | 23 | 236 | 0 |
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:0070037 | rRNA (pseudouridine) methyltransferase activity | MF |
| GO:0070475 | rRNA base methylation | BP |
KEGG
Orthology
- This transcript has been annotated with K14568 (rRNA small subunit pseudouridine methyltransferase Nep1)
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.
