General information for g8392.t10
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.t10 | TTS | g8392.t10 | 30141045 | 30141045 |
| chr_2 | g8392 | g8392.t10 | isoform | g8392.t10 | 30141680 | 30143410 |
| chr_2 | g8392 | g8392.t10 | exon | g8392.t10.exon1 | 30141680 | 30141994 |
| chr_2 | g8392 | g8392.t10 | cds | g8392.t10.CDS1 | 30141877 | 30141994 |
| chr_2 | g8392 | g8392.t10 | exon | g8392.t10.exon2 | 30142733 | 30142964 |
| chr_2 | g8392 | g8392.t10 | cds | g8392.t10.CDS2 | 30142733 | 30142964 |
| chr_2 | g8392 | g8392.t10 | exon | g8392.t10.exon3 | 30143027 | 30143116 |
| chr_2 | g8392 | g8392.t10 | cds | g8392.t10.CDS3 | 30143027 | 30143116 |
| chr_2 | g8392 | g8392.t10 | exon | g8392.t10.exon4 | 30143179 | 30143410 |
| chr_2 | g8392 | g8392.t10 | cds | g8392.t10.CDS4 | 30143179 | 30143410 |
| chr_2 | g8392 | g8392.t10 | TSS | g8392.t10 | 30143947 | 30143947 |
Sequences
>g8392.t10 Gene=g8392 Length=869
ATGGATGATAACCGTCAACAAGAAACTTATGATGGACCAGCTGGTATGGAAGTCGGTGGC
ATCATTGAATCTAACTGGGACGAAGTTGTTGATAACTTCGATAATATGAATTTAAAAGAG
AAACTCTTACGCGGAATCTACGCTTATGGTTTCGAAAAGCCTTCAGCTATCCAGCAACGG
GCCATCATTCCTTGTATTCGTGGTCGTGATGTTATTGCTCAGGCTCAATCAGGTACCGGA
AAAACCGCTACTTTCTCTATTGCTATCCTGCAAACTATTGATACTGATGTTCGCGGTTGT
CAAGCTTTAGTCCTTGCACCAACTCGTGAGTTGGCCACTCAAATTCAGAAGGTTGTTGTT
GCATTGGGTGACTTTATGAATGCTCAATCGCATGCATGTATCGGAGGAACGAATGTTCGT
GAAGATATGAGAAATCTTGAGCAAGGCGTTCACGTAGTAGTTGGAACACCAGGAAGAGTG
CAAGATATGATTCAACGCAAATTTTTGCGTACATCTGATATTAAGCTGTTTGTTCTTGAC
GAGGCCGATGAAATTTACTTTTTCTGCAAAACTTTTCCTCTTCCTCCTTTTCACCGCTAC
TACACAAAAATATTTTTTTTCTTTTTAATTTGTTGGTGTTTACAGAAGTTTACTATAAAA
ATTATTATATAGTAACATTACGTTTCTCTTCTTAAATAAAAATAATAATGATAAACTGCT
GCTTCTTTCTAAGAACCATTCAAATTTATGTTAGGATTAGAGACATTATACACTTAAATA
AGAATTTTTCCTACAAAAAAAAACTTTCTTGCAAAATCTTCTTGGAAAAAATTATAAAGT
TAAATATTATAATTACTATTATAAAATGC
>g8392.t10 Gene=g8392 Length=223
MDDNRQQETYDGPAGMEVGGIIESNWDEVVDNFDNMNLKEKLLRGIYAYGFEKPSAIQQR
AIIPCIRGRDVIAQAQSGTGKTATFSIAILQTIDTDVRGCQALVLAPTRELATQIQKVVV
ALGDFMNAQSHACIGGTNVREDMRNLEQGVHVVVGTPGRVQDMIQRKFLRTSDIKLFVLD
EADEIYFFCKTFPLPPFHRYYTKIFFFFLICWCLQKFTIKIII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8392.t10 | Gene3D | G3DSA:3.40.50.300 | - | 31 | 190 | 5.1E-53 |
| 2 | g8392.t10 | PANTHER | PTHR24031:SF732 | EUKARYOTIC INITIATION FACTOR 4A-9 | 18 | 185 | 1.1E-72 |
| 3 | g8392.t10 | PANTHER | PTHR24031 | RNA HELICASE | 18 | 185 | 1.1E-72 |
| 1 | g8392.t10 | Pfam | PF00270 | DEAD/DEAH box helicase | 56 | 185 | 2.8E-35 |
| 10 | g8392.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 199 | - |
| 11 | g8392.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 219 | - |
| 9 | g8392.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 220 | 223 | - |
| 7 | g8392.t10 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 31 | 59 | 10.225 |
| 8 | g8392.t10 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 62 | 212 | 21.066 |
| 5 | g8392.t10 | SMART | SM00487 | ultradead3 | 50 | 222 | 1.4E-36 |
| 4 | g8392.t10 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 23 | 185 | 4.87E-51 |
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:0004386 | helicase activity | 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. There were no conditions that were differentially expressed