General information for g3848.t1
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.t1 | TTS | g3848.t1 | 28350123 | 28350123 |
| chr_3 | g3848 | g3848.t1 | isoform | g3848.t1 | 28350234 | 28351678 |
| chr_3 | g3848 | g3848.t1 | exon | g3848.t1.exon1 | 28350234 | 28350378 |
| chr_3 | g3848 | g3848.t1 | cds | g3848.t1.CDS1 | 28350234 | 28350378 |
| chr_3 | g3848 | g3848.t1 | exon | g3848.t1.exon2 | 28350440 | 28350588 |
| chr_3 | g3848 | g3848.t1 | cds | g3848.t1.CDS2 | 28350440 | 28350588 |
| chr_3 | g3848 | g3848.t1 | exon | g3848.t1.exon3 | 28350647 | 28351036 |
| chr_3 | g3848 | g3848.t1 | cds | g3848.t1.CDS3 | 28350647 | 28351036 |
| chr_3 | g3848 | g3848.t1 | exon | g3848.t1.exon4 | 28351101 | 28351483 |
| chr_3 | g3848 | g3848.t1 | cds | g3848.t1.CDS4 | 28351101 | 28351483 |
| chr_3 | g3848 | g3848.t1 | exon | g3848.t1.exon5 | 28351540 | 28351678 |
| chr_3 | g3848 | g3848.t1 | cds | g3848.t1.CDS5 | 28351540 | 28351678 |
| chr_3 | g3848 | g3848.t1 | TSS | g3848.t1 | 28351876 | 28351876 |
Sequences
>g3848.t1 Gene=g3848 Length=1206
ATGGCATCAACTTCGAAAAAATCAGTGACGGAAGATTTATCAAATGTTGAATTTGAGACA
AGTGAAGATGTTGAAGTTGTTCCAACATTTCAATCGATGAAATTACGTGAAGAACTCTTA
AGAGGAATATATGCTTATGGATTTGAGAAACCATCAGCCATTCAGCAGAGAAGTATTTTA
CCGATTGTAAAGGGACGCGATGTAATAGCACAAGCTCAATCCGGTACTGGTAAAACCGCA
ACTTTTTCAATCGCAATTTTAGAGAAATTAGACACGGCTCTTCGTGAAACTCAAGTTCTT
TGCTTATCTCCTACTCGCGAATTGGCCGTACAGATTCAAAAAGTCATTCTCGCTCTTGGA
GATTTTATGAACGTTCAATGCCATGCTTGTATTGGAGGTACAAATTTGGGAGAAGATATT
CGCAAATTAGATTATGGTCAACATGTTGTAAGTGGAACTCCAGGTCGAGTTTTTGACATG
ATAAAACGTCGAGTGCTGAGAACTCGTGCAATTAAAATGCTGGTTTTGGATGAAGCTGAT
GAAATGTTAAACAAAGGTTTTAAAGAACAAATTTATGATGTATATCGTTATTTGCCACCA
GCTACACAAGTATGTTTAATTTCTGCTACATTACCACACGAAATTCTGGAAATGACTAGC
AAATTCATGACGGATCCCATTCGTATTCTTGTAAAACGTGATGAATTAACACTTGAAGGT
ATCAAACAGTTTTTTGTTGCTGTCGAAAGAGAAGAATGGAAGTTTGATACACTGTGTGAT
TTATACGATACACTGACAATCACACAAGCAGTCATTTTTTGTAATACAAAGAGAAAAGTC
GATTGGTTGACTGAAAAAATGCGTGAAGCAAATTTCACTGTCAGTTCTATGCATGGTGAC
ATGCCACAAAAAGAACGTGATGAGATTATGAAAGAATTCCGATCTGGACAAACAAGAGTT
TTAATCACAACTGACGTTTGGGCAAGAGGTATTGATGTTCAACAAGTTTCTCTCGTTATC
AATTATGATCTACCAAACAACAGAGAATTGTATATTCACAGAATCGGTCGCTCAGGTCGT
TTCGGTCGCAAAGGTGTTGGCATTAATTTTGTAAAATCAGACGACATAAGGATTCTTAGA
GATATTGAACAATACTATTCAACGCAGATCGATGAGATGCCTATGAATGTAGCAGATTTG
GTTTAA
>g3848.t1 Gene=g3848 Length=401
MASTSKKSVTEDLSNVEFETSEDVEVVPTFQSMKLREELLRGIYAYGFEKPSAIQQRSIL
PIVKGRDVIAQAQSGTGKTATFSIAILEKLDTALRETQVLCLSPTRELAVQIQKVILALG
DFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIKRRVLRTRAIKMLVLDEAD
EMLNKGFKEQIYDVYRYLPPATQVCLISATLPHEILEMTSKFMTDPIRILVKRDELTLEG
IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD
MPQKERDEIMKEFRSGQTRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR
FGRKGVGINFVKSDDIRILRDIEQYYSTQIDEMPMNVADLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3848.t1 | CDD | cd18045 | DEADc_EIF4AIII_DDX48 | 30 | 230 | 9.57166E-134 |
| 9 | g3848.t1 | CDD | cd18787 | SF2_C_DEAD | 241 | 371 | 1.23251E-63 |
| 7 | g3848.t1 | Gene3D | G3DSA:3.40.50.300 | - | 29 | 233 | 4.3E-67 |
| 6 | g3848.t1 | Gene3D | G3DSA:3.40.50.300 | - | 234 | 401 | 8.2E-62 |
| 3 | g3848.t1 | PANTHER | PTHR47958 | ATP-DEPENDENT RNA HELICASE DBP3 | 6 | 394 | 1.9E-229 |
| 4 | g3848.t1 | PANTHER | PTHR47958:SF49 | EUKARYOTIC INITIATION FACTOR 4A-III | 6 | 394 | 1.9E-229 |
| 1 | g3848.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 53 | 215 | 2.7E-40 |
| 2 | g3848.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 254 | 362 | 1.7E-32 |
| 10 | g3848.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 175 | 183 | - |
| 13 | g3848.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 28 | 56 | 10.009 |
| 15 | g3848.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 59 | 229 | 28.919 |
| 14 | g3848.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 240 | 401 | 27.08 |
| 12 | g3848.t1 | SMART | SM00487 | ultradead3 | 47 | 244 | 1.6E-58 |
| 11 | g3848.t1 | SMART | SM00490 | helicmild6 | 281 | 362 | 7.1E-36 |
| 5 | g3848.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 96 | 384 | 2.36E-73 |
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 transcript has been annotated with K13025 (ATP-dependent RNA helicase)
Pathway
- This transcript belongs to the following pathways
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.
