General information for g8393.t1
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 g8393 is located on chr_2: 30144892..30146029 (+ 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 | g8393 | g8393.t1 | TSS | g8393.t1 | 30144189 | 30144189 |
| chr_2 | g8393 | g8393.t1 | isoform | g8393.t1 | 30144258 | 30145844 |
| chr_2 | g8393 | g8393.t1 | exon | g8393.t1.exon1 | 30144258 | 30144265 |
| chr_2 | g8393 | g8393.t1 | cds | g8393.t1.CDS1 | 30144258 | 30144265 |
| chr_2 | g8393 | g8393.t1 | exon | g8393.t1.exon2 | 30144480 | 30144688 |
| chr_2 | g8393 | g8393.t1 | cds | g8393.t1.CDS2 | 30144480 | 30144688 |
| chr_2 | g8393 | g8393.t1 | exon | g8393.t1.exon3 | 30144748 | 30144837 |
| chr_2 | g8393 | g8393.t1 | cds | g8393.t1.CDS3 | 30144748 | 30144837 |
| chr_2 | g8393 | g8393.t1 | exon | g8393.t1.exon4 | 30144892 | 30145639 |
| chr_2 | g8393 | g8393.t1 | cds | g8393.t1.CDS4 | 30144892 | 30145639 |
| chr_2 | g8393 | g8393.t1 | exon | g8393.t1.exon5 | 30145700 | 30145844 |
| chr_2 | g8393 | g8393.t1 | cds | g8393.t1.CDS5 | 30145700 | 30145844 |
| chr_2 | g8393 | g8393.t1 | TTS | g8393.t1 | 30146418 | 30146418 |
Sequences
>g8393.t1 Gene=g8393 Length=1200
ATGAGCAGATATGATGAAAATGGCTCTTCAACAATCGATGGATTCGTCATTGAGTCAAAT
TGGCATGAGATTGTCGATAATTTTGATAATATGAATTTAAAAGATAAGCTGCTTCGCGGA
ATCTATGCTTATGGTTTTGAAAAGCCTTCAGCTATCCAGCAACGAGCCATCATTCCTTGT
ATTCGTGGGTTAGATGTCATTGCTCAAGCTCAATCTGGCACTGGAAAAACCGCTACTTTT
TCTATCGCTATTTTACAAAGAATTGATACAACAATCCGTGATTGTCAAGCTTTAATTTTA
GCTCCAACTCGAGAATTAGCTATTCAAATTCAAAAAGTTGTTCTTGCATTGGGTGACTTT
ATGCAGACTGAGTGTCATGCATGTATTGGTGGAACTAACGTTCGTGAAGATATGCGAACG
CTTGAACAAGGCGTAAATGTAGTAGTTGGAACACCAGGTCGTGTATTTGACATGATTCAA
AGAAAAGTACTGAGAACTAACAATATTAAGCTGTTTGTTCTTGATGAAGCCGATGAGATG
CTATCGCGTGGATTCAAAGATCAAATTCATGATGTATTTAAGACTCTTCCTAATGATGTA
CAAGTAATCTTACTTTCTGCTACTATGCCAGTTGATGTTTTGGAAGTCAGCAAGTATTTT
ATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGAGTTGACATTAGAAGGAATTCGA
CAATTTTATGTTAATGTTGAGAAAGAAGAATGGAAATTAGGAACATTGTGTGATTTGTAT
GACACATTGAGTATTGCTCAAGCTGTCATTTTCTGTAATACTCGTCGTAAAGTTGAATTT
TTAACTGAAGAAATGACAAGACAAAACTTTACTGTTTCTGCTATGCATGGAGAAATGGAT
CAGTCTGAAAGAGATATGATTATGAAACAATTCAGAAGCGGATCTTCACGTGTACTCATT
ACTACTGATTTGCTTGCTCGTGGTATTGATGTGCAGCAAGTCTCATTGGTTATCAACTAT
GATTTACCAAATAATCGAGAAAATTATATTCACAGAATTGGTCGAGGTGGCCGCTTTGGA
CGTAAAGGTGTTGCTATAAATTTTGTTACAGAAGAAGATAAGCGCACCTTACTCGATATT
GAACAATTCTGTAATACAAAAATCGAAGAGATGCCTGTGAACGTTGCTGATTTAATCTAA
>g8393.t1 Gene=g8393 Length=399
MSRYDENGSSTIDGFVIESNWHEIVDNFDNMNLKDKLLRGIYAYGFEKPSAIQQRAIIPC
IRGLDVIAQAQSGTGKTATFSIAILQRIDTTIRDCQALILAPTRELAIQIQKVVLALGDF
MQTECHACIGGTNVREDMRTLEQGVNVVVGTPGRVFDMIQRKVLRTNNIKLFVLDEADEM
LSRGFKDQIHDVFKTLPNDVQVILLSATMPVDVLEVSKYFMRDPVRILVKKEELTLEGIR
QFYVNVEKEEWKLGTLCDLYDTLSIAQAVIFCNTRRKVEFLTEEMTRQNFTVSAMHGEMD
QSERDMIMKQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPNNRENYIHRIGRGGRFG
RKGVAINFVTEEDKRTLLDIEQFCNTKIEEMPVNVADLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8393.t1 | CDD | cd18046 | DEADc_EIF4AII_EIF4AI_DDX2 | 28 | 228 | 4.72294E-138 |
| 8 | g8393.t1 | CDD | cd18787 | SF2_C_DEAD | 239 | 354 | 7.3108E-46 |
| 6 | g8393.t1 | Gene3D | G3DSA:3.40.50.300 | - | 14 | 234 | 9.5E-69 |
| 7 | g8393.t1 | Gene3D | G3DSA:3.40.50.300 | - | 235 | 399 | 1.4E-60 |
| 3 | g8393.t1 | PANTHER | PTHR24031:SF720 | EUKARYOTIC INITIATION FACTOR 4A-II | 13 | 399 | 1.1E-200 |
| 4 | g8393.t1 | PANTHER | PTHR24031 | RNA HELICASE | 13 | 399 | 1.1E-200 |
| 1 | g8393.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 51 | 213 | 1.6E-43 |
| 2 | g8393.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 253 | 360 | 1.2E-31 |
| 10 | g8393.t1 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 173 | 181 | - |
| 13 | g8393.t1 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 26 | 54 | 10.169 |
| 15 | g8393.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 57 | 227 | 31.069 |
| 14 | g8393.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 238 | 399 | 26.871 |
| 12 | g8393.t1 | SMART | SM00487 | ultradead3 | 45 | 242 | 2.6E-59 |
| 11 | g8393.t1 | SMART | SM00490 | helicmild6 | 279 | 360 | 2.5E-33 |
| 5 | g8393.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 94 | 382 | 1.58E-75 |
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 K03257 (translation initiation factor 4A)
Pathway
This gene does not belong to any 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.
