General information for g3848.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Eukaryotic initiation factor 4A-III.
Parent gene
- The parent gene g3848 is located on chr_3: 28351021..28352284 (- 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 | g3848 | g3848.t2 | TTS | g3848.t2 | 28350123 | 28350123 |
| chr_3 | g3848 | g3848.t2 | isoform | g3848.t2 | 28350234 | 28351036 |
| chr_3 | g3848 | g3848.t2 | exon | g3848.t2.exon1 | 28350234 | 28350378 |
| chr_3 | g3848 | g3848.t2 | cds | g3848.t2.CDS1 | 28350234 | 28350378 |
| chr_3 | g3848 | g3848.t2 | exon | g3848.t2.exon2 | 28350440 | 28350588 |
| chr_3 | g3848 | g3848.t2 | cds | g3848.t2.CDS2 | 28350440 | 28350588 |
| chr_3 | g3848 | g3848.t2 | exon | g3848.t2.exon3 | 28350647 | 28351036 |
| chr_3 | g3848 | g3848.t2 | cds | g3848.t2.CDS3 | 28350647 | 28351015 |
| chr_3 | g3848 | g3848.t2 | TSS | g3848.t2 | 28351876 | 28351876 |
Sequences
>g3848.t2 Gene=g3848 Length=684
GTTTTGGATGAAGCTGATGAAATGTTAAACAAAGGTTTTAAAGAACAAATTTATGATGTA
TATCGTTATTTGCCACCAGCTACACAAGTATGTTTAATTTCTGCTACATTACCACACGAA
ATTCTGGAAATGACTAGCAAATTCATGACGGATCCCATTCGTATTCTTGTAAAACGTGAT
GAATTAACACTTGAAGGTATCAAACAGTTTTTTGTTGCTGTCGAAAGAGAAGAATGGAAG
TTTGATACACTGTGTGATTTATACGATACACTGACAATCACACAAGCAGTCATTTTTTGT
AATACAAAGAGAAAAGTCGATTGGTTGACTGAAAAAATGCGTGAAGCAAATTTCACTGTC
AGTTCTATGCATGGTGACATGCCACAAAAAGAACGTGATGAGATTATGAAAGAATTCCGA
TCTGGACAAACAAGAGTTTTAATCACAACTGACGTTTGGGCAAGAGGTATTGATGTTCAA
CAAGTTTCTCTCGTTATCAATTATGATCTACCAAACAACAGAGAATTGTATATTCACAGA
ATCGGTCGCTCAGGTCGTTTCGGTCGCAAAGGTGTTGGCATTAATTTTGTAAAATCAGAC
GACATAAGGATTCTTAGAGATATTGAACAATACTATTCAACGCAGATCGATGAGATGCCT
ATGAATGTAGCAGATTTGGTTTAA
>g3848.t2 Gene=g3848 Length=220
MLNKGFKEQIYDVYRYLPPATQVCLISATLPHEILEMTSKFMTDPIRILVKRDELTLEGI
KQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDM
PQKERDEIMKEFRSGQTRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRF
GRKGVGINFVKSDDIRILRDIEQYYSTQIDEMPMNVADLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3848.t2 | CDD | cd18787 | SF2_C_DEAD | 60 | 190 | 0.000 |
| 7 | g3848.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 55 | 0.000 |
| 6 | g3848.t2 | Gene3D | G3DSA:3.40.50.300 | - | 56 | 220 | 0.000 |
| 2 | g3848.t2 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 213 | 0.000 |
| 3 | g3848.t2 | PANTHER | PTHR47958:SF49 | EUKARYOTIC INITIATION FACTOR 4A-III | 1 | 213 | 0.000 |
| 1 | g3848.t2 | Pfam | PF00271 | Helicase conserved C-terminal domain | 73 | 181 | 0.000 |
| 9 | g3848.t2 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 48 | 8.371 |
| 8 | g3848.t2 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 59 | 220 | 27.080 |
| 5 | g3848.t2 | SMART | SM00490 | helicmild6 | 100 | 181 | 0.000 |
| 4 | g3848.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 213 | 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.
