General information for g8094.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal export protein NMD3.
Parent gene
- The parent gene g8094 is located on chr_2: 28553029..28555036 (+ 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_2 | g8094 | g8094.t4 | TSS | g8094.t4 | 28551279 | 28551279 |
| chr_2 | g8094 | g8094.t4 | isoform | g8094.t4 | 28551522 | 28552100 |
| chr_2 | g8094 | g8094.t4 | exon | g8094.t4.exon1 | 28551522 | 28552100 |
| chr_2 | g8094 | g8094.t4 | cds | g8094.t4.CDS1 | 28551878 | 28552099 |
| chr_2 | g8094 | g8094.t4 | TTS | g8094.t4 | 28553112 | 28553112 |
Sequences
>g8094.t4 Gene=g8094 Length=579
GTGGATCATTGATTGATCCAAATCCATTAAATCAATGTGCAGCATGTTTACGAACTCACA
TTGATATAACAGAGAACATTCCTAAACAAGGAACTCTCTTCTTTTGCCGTAACTGTGAAA
GATATTTGAATCCACCAAGTGAGTGGGTACATGCATCTCTGGAATCGCGTGAATTGCTCT
CAATTTGTCTTAAAAGAATCAAAGGATTAAAAGATGTGAAACTTATTGATGCAGGATTTA
TTTGGACAGAGCCCCATTCAAAGAGAATCAAAGTTAAACTCACTGTTCATGCTGAAGTGT
CTAATGGCATCGTATTGCAACAAGTTTTTGTGGTTGAGTTCACTGTAACTAATCAAATGT
GTGATGATTGTCATCGTCATGAAGCAAAAGATTACTGGAAATGTATGGTTCAAGTAAGAC
AAAAGGCTTCTAACAAAAAGACACTTTATTATATGGAACAAATGATTCTGAAGCATAAAG
CTCACGAAAACTCTTTAGGAATTAAAAACAATTCAAGTGGATTAGACTTCTTTTATTCTG
GTGAAAACCATGCTCGTAAAATGGTAGATTTTCTACAGA
>g8094.t4 Gene=g8094 Length=74
MCDDCHRHEAKDYWKCMVQVRQKASNKKTLYYMEQMILKHKAHENSLGIKNNSSGLDFFY
SGENHARKMVDFLQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g8094.t4 | PANTHER | PTHR12746:SF2 | 60S RIBOSOMAL EXPORT PROTEIN NMD3 | 1 | 74 | 0 |
| 3 | g8094.t4 | PANTHER | PTHR12746 | NONSENSE-MEDIATED MRNA DECAY PROTEIN 3 | 1 | 74 | 0 |
| 1 | g8094.t4 | Pfam | PF04981 | NMD3 family | 1 | 74 | 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:0043023 | ribosomal large subunit binding | 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.
