General information for g8392.t20
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.t20 | TTS | g8392.t20 | 30141837 | 30141837 |
| chr_2 | g8392 | g8392.t20 | isoform | g8392.t20 | 30142218 | 30142733 |
| chr_2 | g8392 | g8392.t20 | exon | g8392.t20.exon1 | 30142218 | 30142733 |
| chr_2 | g8392 | g8392.t20 | cds | g8392.t20.CDS1 | 30142219 | 30142647 |
| chr_2 | g8392 | g8392.t20 | TSS | g8392.t20 | 30143414 | 30143414 |
Sequences
>g8392.t20 Gene=g8392 Length=516
TGTTATCGCGTGGATTCAAAGATCAAATTCAAGAGGTCTTTAAAAAGCTTCCTAATGACG
TTCAAGTCATTTTACTTTCTGCTACCATGCCACCAGAAGTTTTGGAAGTCAGCAAGTATT
TCATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGAGTTGACTTTGGAAGGTATTC
GCCAATTTTATGTTAATGTTAAACAAGAACAGTGGAAATTGGGAACATTGTGTGATTTGT
ATGACACATTGAGTATCACCCAAGCTGTCATTTTCTGTAATACTCGTCGTAAGGTAGATC
AGTTGACTGAAGAAATGACTGCTAAGAATTTCACTGTGTCTGCTATGCATGGAGAAATGG
ATCAACGTGAAAGAGATATGATTATGAAACAATTCAGAAGCGGATCTTCACGTGTACTCA
TTACTACTGATTTGCTTGCTCGTGGTATTGATGTGCAGCAAGTCTCATTGGTTATCAACT
ATGATTTGCCTAGTATTAGGGAAAACTATATTCACA
>g8392.t20 Gene=g8392 Length=143
MPPEVLEVSKYFMRDPVRILVKKEELTLEGIRQFYVNVKQEQWKLGTLCDLYDTLSITQA
VIFCNTRRKVDQLTEEMTAKNFTVSAMHGEMDQRERDMIMKQFRSGSSRVLITTDLLARG
IDVQQVSLVINYDLPSIRENYIH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8392.t20 | CDD | cd18787 | SF2_C_DEAD | 31 | 143 | 0.000 |
| 6 | g8392.t20 | Gene3D | G3DSA:3.40.50.300 | - | 23 | 143 | 0.000 |
| 2 | g8392.t20 | PANTHER | PTHR24031:SF625 | - | 1 | 138 | 0.000 |
| 3 | g8392.t20 | PANTHER | PTHR24031 | RNA HELICASE | 1 | 138 | 0.000 |
| 1 | g8392.t20 | Pfam | PF00271 | Helicase conserved C-terminal domain | 44 | 143 | 0.000 |
| 7 | g8392.t20 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 30 | 143 | 18.342 |
| 5 | g8392.t20 | SMART | SM00490 | helicmild6 | 71 | 143 | 0.000 |
| 4 | g8392.t20 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 25 | 143 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
