General information for g2574.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Eukaryotic translation initiation factor 4E type 2.
Parent gene
- The parent gene g2574 is located on chr_3: 18816651..18817577 (+ 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 | g2574 | g2574.t1 | TSS | g2574.t1 | 18816527 | 18816527 |
| chr_3 | g2574 | g2574.t1 | isoform | g2574.t1 | 18816651 | 18817577 |
| chr_3 | g2574 | g2574.t1 | exon | g2574.t1.exon1 | 18816651 | 18816670 |
| chr_3 | g2574 | g2574.t1 | cds | g2574.t1.CDS1 | 18816651 | 18816670 |
| chr_3 | g2574 | g2574.t1 | exon | g2574.t1.exon2 | 18816768 | 18816873 |
| chr_3 | g2574 | g2574.t1 | cds | g2574.t1.CDS2 | 18816768 | 18816873 |
| chr_3 | g2574 | g2574.t1 | exon | g2574.t1.exon3 | 18816978 | 18817462 |
| chr_3 | g2574 | g2574.t1 | cds | g2574.t1.CDS3 | 18816978 | 18817462 |
| chr_3 | g2574 | g2574.t1 | exon | g2574.t1.exon4 | 18817529 | 18817577 |
| chr_3 | g2574 | g2574.t1 | cds | g2574.t1.CDS4 | 18817529 | 18817577 |
| chr_3 | g2574 | g2574.t1 | TTS | g2574.t1 | 18817795 | 18817795 |
Sequences
>g2574.t1 Gene=g2574 Length=660
ATGTCCACAAAGTACGATGCATTGAAACCATATGAAAGTGACTCGGACGATGAGGACTAC
AATATTGACTTTGATGAGTCTAAATTGCCTCCAATTGAGATTCCTCCAGGAGATCACAAA
TTACAACATTGCTATAATCTCTGGTATGCGAGGAAAGGTAGCCATCGGGCATCTGAATAT
TCTAAATCACTTCATTTTATTGGAAGATGTGCAACTGTTGAGCAATGGTGGGCTCTATAC
TGCCATTTATTACGACCAACAGAATTGAAGCCTTATCGAAAACTGCATCTTTTCAAAGCC
GGGATTAAACCAATGTGGGAAGATCCGGAAAATATCAAAGGAGGAAAATGGATTTTACGT
TTGAGAAAAAATAAAGTTAACCGAGCTTGGGAAAATGTCTGCATGGCGATGTTAGGTGAA
CAATTTCTTGTTGGGCCTGAAATTTGCGGAATTGTACTATCAACTCAATATCCTGAAGAT
TTATTATCTGTTTGGAACCGAACTGCCACCGATGTGGGATGTACAAATCGAATAAGAGAT
GTTCTCAAACGCATATTAAATCTTCCTGCCAATTTCCCAATTGAGTACAAGCCACATTCA
GATTCTTTAAAGGCAACTAAAGTATTGATGAGCAAATCTCAAAATCCTAAGGAGGAATAA
>g2574.t1 Gene=g2574 Length=219
MSTKYDALKPYESDSDDEDYNIDFDESKLPPIEIPPGDHKLQHCYNLWYARKGSHRASEY
SKSLHFIGRCATVEQWWALYCHLLRPTELKPYRKLHLFKAGIKPMWEDPENIKGGKWILR
LRKNKVNRAWENVCMAMLGEQFLVGPEICGIVLSTQYPEDLLSVWNRTATDVGCTNRIRD
VLKRILNLPANFPIEYKPHSDSLKATKVLMSKSQNPKEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2574.t1 | Gene3D | G3DSA:3.30.760.10 | RNA Cap | 38 | 207 | 0 |
| 2 | g2574.t1 | PANTHER | PTHR11960 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4E RELATED | 25 | 209 | 0 |
| 3 | g2574.t1 | PANTHER | PTHR11960:SF17 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TYPE 2 | 25 | 209 | 0 |
| 1 | g2574.t1 | Pfam | PF01652 | Eukaryotic initiation factor 4E | 40 | 196 | 0 |
| 4 | g2574.t1 | SUPERFAMILY | SSF55418 | eIF4e-like | 13 | 206 | 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:0006413 | translational initiation | BP |
| GO:0003743 | translation initiation factor activity | MF |
| GO:0003723 | RNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03259 (translation initiation factor 4E)
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.
