General information for g3848.t4
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.t4 | TTS | g3848.t4 | 28350123 | 28350123 |
| chr_3 | g3848 | g3848.t4 | isoform | g3848.t4 | 28350234 | 28351678 |
| chr_3 | g3848 | g3848.t4 | exon | g3848.t4.exon1 | 28350234 | 28350378 |
| chr_3 | g3848 | g3848.t4 | cds | g3848.t4.CDS1 | 28350234 | 28350378 |
| chr_3 | g3848 | g3848.t4 | exon | g3848.t4.exon2 | 28350440 | 28350588 |
| chr_3 | g3848 | g3848.t4 | cds | g3848.t4.CDS2 | 28350440 | 28350588 |
| chr_3 | g3848 | g3848.t4 | exon | g3848.t4.exon3 | 28350647 | 28351036 |
| chr_3 | g3848 | g3848.t4 | cds | g3848.t4.CDS3 | 28350647 | 28351036 |
| chr_3 | g3848 | g3848.t4 | exon | g3848.t4.exon4 | 28351101 | 28351483 |
| chr_3 | g3848 | g3848.t4 | cds | g3848.t4.CDS4 | 28351101 | 28351256 |
| chr_3 | g3848 | g3848.t4 | exon | g3848.t4.exon5 | 28351550 | 28351678 |
| chr_3 | g3848 | g3848.t4 | TSS | g3848.t4 | 28351876 | 28351876 |
Sequences
>g3848.t4 Gene=g3848 Length=1196
ATGGCATCAACTTCGAAAAAATCAGTGACGGAAGATTTATCAAATGTTGAATTTGAGACA
AGTGAAGATGTTGAAGTTGTTCCAACATTTCAATCGATGAAATTACGTGAAGAACTCTTA
AGAGGAATAGATTTGAGAAACCATCAGCCATTCAGCAGAGAAGTATTTTACCGATTGTAA
AGGGACGCGATGTAATAGCACAAGCTCAATCCGGTACTGGTAAAACCGCAACTTTTTCAA
TCGCAATTTTAGAGAAATTAGACACGGCTCTTCGTGAAACTCAAGTTCTTTGCTTATCTC
CTACTCGCGAATTGGCCGTACAGATTCAAAAAGTCATTCTCGCTCTTGGAGATTTTATGA
ACGTTCAATGCCATGCTTGTATTGGAGGTACAAATTTGGGAGAAGATATTCGCAAATTAG
ATTATGGTCAACATGTTGTAAGTGGAACTCCAGGTCGAGTTTTTGACATGATAAAACGTC
GAGTGCTGAGAACTCGTGCAATTAAAATGCTGGTTTTGGATGAAGCTGATGAAATGTTAA
ACAAAGGTTTTAAAGAACAAATTTATGATGTATATCGTTATTTGCCACCAGCTACACAAG
TATGTTTAATTTCTGCTACATTACCACACGAAATTCTGGAAATGACTAGCAAATTCATGA
CGGATCCCATTCGTATTCTTGTAAAACGTGATGAATTAACACTTGAAGGTATCAAACAGT
TTTTTGTTGCTGTCGAAAGAGAAGAATGGAAGTTTGATACACTGTGTGATTTATACGATA
CACTGACAATCACACAAGCAGTCATTTTTTGTAATACAAAGAGAAAAGTCGATTGGTTGA
CTGAAAAAATGCGTGAAGCAAATTTCACTGTCAGTTCTATGCATGGTGACATGCCACAAA
AAGAACGTGATGAGATTATGAAAGAATTCCGATCTGGACAAACAAGAGTTTTAATCACAA
CTGACGTTTGGGCAAGAGGTATTGATGTTCAACAAGTTTCTCTCGTTATCAATTATGATC
TACCAAACAACAGAGAATTGTATATTCACAGAATCGGTCGCTCAGGTCGTTTCGGTCGCA
AAGGTGTTGGCATTAATTTTGTAAAATCAGACGACATAAGGATTCTTAGAGATATTGAAC
AATACTATTCAACGCAGATCGATGAGATGCCTATGAATGTAGCAGATTTGGTTTAA
>g3848.t4 Gene=g3848 Length=279
MNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIKRRVLRTRAIKMLVLDEADEM
LNKGFKEQIYDVYRYLPPATQVCLISATLPHEILEMTSKFMTDPIRILVKRDELTLEGIK
QFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMP
QKERDEIMKEFRSGQTRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG
RKGVGINFVKSDDIRILRDIEQYYSTQIDEMPMNVADLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3848.t4 | CDD | cd18787 | SF2_C_DEAD | 119 | 249 | 1.40918E-64 |
| 6 | g3848.t4 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 114 | 1.6E-32 |
| 7 | g3848.t4 | Gene3D | G3DSA:3.40.50.300 | - | 115 | 279 | 3.3E-62 |
| 3 | g3848.t4 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 1 | 272 | 4.7E-175 |
| 4 | g3848.t4 | PANTHER | PTHR47958:SF49 | EUKARYOTIC INITIATION FACTOR 4A-III | 1 | 272 | 4.7E-175 |
| 1 | g3848.t4 | Pfam | PF00270 | DEAD/DEAH box helicase | 3 | 93 | 2.4E-18 |
| 2 | g3848.t4 | Pfam | PF00271 | Helicase conserved C-terminal domain | 132 | 240 | 8.3E-33 |
| 9 | g3848.t4 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 53 | 61 | - |
| 12 | g3848.t4 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 107 | 16.608 |
| 11 | g3848.t4 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 118 | 279 | 27.08 |
| 10 | g3848.t4 | SMART | SM00490 | helicmild6 | 159 | 240 | 7.1E-36 |
| 5 | g3848.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 262 | 9.15E-65 |
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. There were no conditions that were differentially expressed