General information for g8392.t21
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Eukaryotic initiation factor 4A.
Parent gene
- The parent gene g8392 is located on chr_2: 30142558..30143950 (- 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 | g8392 | g8392.t21 | TTS | g8392.t21 | 30141837 | 30141837 |
| chr_2 | g8392 | g8392.t21 | isoform | g8392.t21 | 30142558 | 30143410 |
| chr_2 | g8392 | g8392.t21 | exon | g8392.t21.exon1 | 30142558 | 30142964 |
| chr_2 | g8392 | g8392.t21 | cds | g8392.t21.CDS1 | 30142558 | 30142911 |
| chr_2 | g8392 | g8392.t21 | exon | g8392.t21.exon2 | 30143027 | 30143410 |
| chr_2 | g8392 | g8392.t21 | TSS | g8392.t21 | 30143947 | 30143947 |
Sequences
>g8392.t21 Gene=g8392 Length=791
ATGGATGATAACCGTCAACAAGAAACTTATGATGGACCAGCTGGTATGGAAGTCGGTGGC
ATCATTGAATCTAACTGGGACGAAGTTGTTGATAACTTCGATAATATGAATTTAAAAGAG
AAACTCTTACGCGGAATCTACGCTTATGGTTTCGAAAAGCCTTCAGCTATCCAGCAACGG
GCCATCATTCCTTGTATTCGTGGTCGTGATGTTATTGCTCAGGCTCAATCAGGTAAACAA
GCTATAAATTTATTTCATATCATTTTTGTTCATTAAATTTTTCTTTTCATTTAGGTACCG
GAAAAACCGCTACTTTCTCTATTGCTATCCTGCAAACTATTGATACTGATGTTCGCGGTT
GTCAAGCTTTAGTCCTTGCACCAACTCGTGAGTTGGCCACTCAAATTCAGAAGGTTGTTG
TTGCATTGGGTGACTTTATGAATGCTCAATCGCATGCATGTATCGGAGGAACGAATGTTC
GTGAAGATATGAGAAATCTTGAGCAAGGCGTTCACGTAGTAGTTGGAACACCAGGAAGAG
TGCAAGATATGATTCAACGCAAATTTTTGCGTACATCTGATATTAAGCTGTTTGTTCTTG
ACGAGGCCGATGAAATGTTATCGCGTGGATTCAAAGATCAAATTCAAGAGGTCTTTAAAA
AGCTTCCTAATGACGTTCAAGTCATTTTACTTTCTGCTACCATGCCACCAGAAGTTTTGG
AAGTCAGCAAGTATTTCATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGAGTTGA
CTTTGGAAGGT
>g8392.t21 Gene=g8392 Length=118
MNAQSHACIGGTNVREDMRNLEQGVHVVVGTPGRVQDMIQRKFLRTSDIKLFVLDEADEM
LSRGFKDQIQEVFKKLPNDVQVILLSATMPPEVLEVSKYFMRDPVRILVKKEELTLEG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8392.t21 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 118 | 4.6E-38 |
| 2 | g8392.t21 | PANTHER | PTHR24031:SF698 | EUKARYOTIC INITIATION FACTOR 4A-1 | 3 | 118 | 6.2E-51 |
| 3 | g8392.t21 | PANTHER | PTHR24031 | RNA HELICASE | 3 | 118 | 6.2E-51 |
| 1 | g8392.t21 | Pfam | PF00270 | DEAD/DEAH box helicase | 4 | 93 | 4.7E-24 |
| 5 | g8392.t21 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 53 | 61 | - |
| 7 | g8392.t21 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 107 | 20.462 |
| 4 | g8392.t21 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 109 | 1.25E-33 |
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:0005524 | ATP binding | MF |
| GO:0003676 | nucleic acid 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.
