General information for g8392.t17
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.t17 | TTS | g8392.t17 | 30141837 | 30141837 |
| chr_2 | g8392 | g8392.t17 | isoform | g8392.t17 | 30142007 | 30143950 |
| chr_2 | g8392 | g8392.t17 | exon | g8392.t17.exon1 | 30142007 | 30142154 |
| chr_2 | g8392 | g8392.t17 | cds | g8392.t17.CDS1 | 30142007 | 30142154 |
| chr_2 | g8392 | g8392.t17 | exon | g8392.t17.exon2 | 30142217 | 30142964 |
| chr_2 | g8392 | g8392.t17 | cds | g8392.t17.CDS2 | 30142217 | 30142964 |
| chr_2 | g8392 | g8392.t17 | exon | g8392.t17.exon3 | 30143027 | 30143116 |
| chr_2 | g8392 | g8392.t17 | cds | g8392.t17.CDS3 | 30143027 | 30143116 |
| chr_2 | g8392 | g8392.t17 | exon | g8392.t17.exon4 | 30143179 | 30143410 |
| chr_2 | g8392 | g8392.t17 | cds | g8392.t17.CDS4 | 30143179 | 30143410 |
| chr_2 | g8392 | g8392.t17 | exon | g8392.t17.exon5 | 30143884 | 30143950 |
| chr_2 | g8392 | g8392.t17 | TSS | g8392.t17 | 30143947 | 30143947 |
Sequences
>g8392.t17 Gene=g8392 Length=1285
CTTTTTCCACAAGGACTTATTAAAAGTTACACTTCTCAACGAGATAGAACAAAAAAAATT
AAAAAATATGGATGATAACCGTCAACAAGAAACTTATGATGGACCAGCTGGTATGGAAGT
CGGTGGCATCATTGAATCTAACTGGGACGAAGTTGTTGATAACTTCGATAATATGAATTT
AAAAGAGAAACTCTTACGCGGAATCTACGCTTATGGTTTCGAAAAGCCTTCAGCTATCCA
GCAACGGGCCATCATTCCTTGTATTCGTGGTCGTGATGTTATTGCTCAGGCTCAATCAGG
TACCGGAAAAACCGCTACTTTCTCTATTGCTATCCTGCAAACTATTGATACTGATGTTCG
CGGTTGTCAAGCTTTAGTCCTTGCACCAACTCGTGAGTTGGCCACTCAAATTCAGAAGGT
TGTTGTTGCATTGGGTGACTTTATGAATGCTCAATCGCATGCATGTATCGGAGGAACGAA
TGTTCGTGAAGATATGAGAAATCTTGAGCAAGGCGTTCACGTAGTAGTTGGAACACCAGG
AAGAGTGCAAGATATGATTCAACGCAAATTTTTGCGTACATCTGATATTAAGCTGTTTGT
TCTTGACGAGGCCGATGAAATGTTATCGCGTGGATTCAAAGATCAAATTCAAGAGGTCTT
TAAAAAGCTTCCTAATGACGTTCAAGTCATTTTACTTTCTGCTACCATGCCACCAGAAGT
TTTGGAAGTCAGCAAGTATTTCATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGA
GTTGACTTTGGAAGGTATTCGCCAATTTTATGTTAATGTTAAACAAGAACAGTGGAAATT
GGGAACATTGTGTGATTTGTATGACACATTGAGTATCACCCAAGCTGTCATTTTCTGTAA
TACTCGTCGTAAGGTAGATCAGTTGACTGAAGAAATGACTGCTAAGAATTTCACTGTGTC
TGCTATGCATGGAGAAATGGATCAACGTGAAAGAGATATGATTATGAAACAATTCAGAAG
CGGATCTTCACGTGTACTCATTACTACTGATTTGCTTGCTCGTGGTATTGATGTGCAGCA
AGTCTCATTGGTTATCAACTATGATTTGCCTAGTATTAGGGAAAACTATATTCACAGAAG
AATCGGTCGTGGTGGTCGTTTCGGACGTAAAGGTGTTGCTATTAATTTCATAACGGATGC
TGATCGTCGTGCATTACAAGAATTGGAACAACATTATCATACAACTATCGAAGAAATGCC
CTGCAACGTTGCTGATTTAATTTAA
>g8392.t17 Gene=g8392 Length=405
MDDNRQQETYDGPAGMEVGGIIESNWDEVVDNFDNMNLKEKLLRGIYAYGFEKPSAIQQR
AIIPCIRGRDVIAQAQSGTGKTATFSIAILQTIDTDVRGCQALVLAPTRELATQIQKVVV
ALGDFMNAQSHACIGGTNVREDMRNLEQGVHVVVGTPGRVQDMIQRKFLRTSDIKLFVLD
EADEMLSRGFKDQIQEVFKKLPNDVQVILLSATMPPEVLEVSKYFMRDPVRILVKKEELT
LEGIRQFYVNVKQEQWKLGTLCDLYDTLSITQAVIFCNTRRKVDQLTEEMTAKNFTVSAM
HGEMDQRERDMIMKQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSIRENYIHRRIG
RGGRFGRKGVAINFITDADRRALQELEQHYHTTIEEMPCNVADLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8392.t17 | CDD | cd18046 | DEADc_EIF4AII_EIF4AI_DDX2 | 33 | 233 | 1.72967E-137 |
| 8 | g8392.t17 | CDD | cd18787 | SF2_C_DEAD | 244 | 356 | 1.60746E-46 |
| 6 | g8392.t17 | Gene3D | G3DSA:3.40.50.300 | - | 20 | 239 | 2.1E-72 |
| 7 | g8392.t17 | Gene3D | G3DSA:3.40.50.300 | - | 240 | 405 | 9.1E-57 |
| 3 | g8392.t17 | PANTHER | PTHR24031:SF720 | EUKARYOTIC INITIATION FACTOR 4A-II | 16 | 405 | 3.1E-194 |
| 4 | g8392.t17 | PANTHER | PTHR24031 | RNA HELICASE | 16 | 405 | 3.1E-194 |
| 1 | g8392.t17 | Pfam | PF00270 | DEAD/DEAH box helicase | 56 | 218 | 9.7E-46 |
| 2 | g8392.t17 | Pfam | PF00271 | Helicase conserved C-terminal domain | 258 | 366 | 3.6E-28 |
| 10 | g8392.t17 | ProSitePatterns | PS00039 | DEAD-box subfamily ATP-dependent helicases signature. | 178 | 186 | - |
| 13 | g8392.t17 | ProSiteProfiles | PS51195 | DEAD-box RNA helicase Q motif profile. | 31 | 59 | 10.225 |
| 15 | g8392.t17 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 62 | 232 | 31.805 |
| 14 | g8392.t17 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 243 | 405 | 25.706 |
| 12 | g8392.t17 | SMART | SM00487 | ultradead3 | 50 | 247 | 4.4E-62 |
| 11 | g8392.t17 | SMART | SM00490 | helicmild6 | 284 | 366 | 1.7E-27 |
| 5 | g8392.t17 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 98 | 387 | 4.68E-72 |
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.
