Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic initiation factor 4A-III.

Parent gene

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.t10 TTS g3848.t10 28350123 28350123
chr_3 g3848 g3848.t10 isoform g3848.t10 28351021 28351678
chr_3 g3848 g3848.t10 exon g3848.t10.exon1 28351021 28351483
chr_3 g3848 g3848.t10 cds g3848.t10.CDS1 28351065 28351483
chr_3 g3848 g3848.t10 exon g3848.t10.exon2 28351540 28351678
chr_3 g3848 g3848.t10 cds g3848.t10.CDS2 28351540 28351678
chr_3 g3848 g3848.t10 TSS g3848.t10 28351876 28351876

Sequences

>g3848.t10 Gene=g3848 Length=602
ATGGCATCAACTTCGAAAAAATCAGTGACGGAAGATTTATCAAATGTTGAATTTGAGACA
AGTGAAGATGTTGAAGTTGTTCCAACATTTCAATCGATGAAATTACGTGAAGAACTCTTA
AGAGGAATATATGCTTATGGATTTGAGAAACCATCAGCCATTCAGCAGAGAAGTATTTTA
CCGATTGTAAAGGGACGCGATGTAATAGCACAAGCTCAATCCGGTACTGGTAAAACCGCA
ACTTTTTCAATCGCAATTTTAGAGAAATTAGACACGGCTCTTCGTGAAACTCAAGTTCTT
TGCTTATCTCCTACTCGCGAATTGGCCGTACAGATTCAAAAAGTCATTCTCGCTCTTGGA
GATTTTATGAACGTTCAATGCCATGCTTGTATTGGAGGTACAAATTTGGGAGAAGATATT
CGCAAATTAGATTATGGTCAACATGTTGTAAGTGGAACTCCAGGTCGAGTTTTTGACATG
ATAAAACGTCGAGTGCTGAGAACTCGTGCAATTAAAATGCTGGTAAGTATTAATTTTTAT
TATTTCTATTTAAGTTAAATTGATATATATATCGTATTGTTAATAGGTTTTGGATGAAGC
TG

>g3848.t10 Gene=g3848 Length=185
MASTSKKSVTEDLSNVEFETSEDVEVVPTFQSMKLREELLRGIYAYGFEKPSAIQQRSIL
PIVKGRDVIAQAQSGTGKTATFSIAILEKLDTALRETQVLCLSPTRELAVQIQKVILALG
DFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIKRRVLRTRAIKMLVSINFY
YFYLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g3848.t10 Gene3D G3DSA:3.40.50.300 - 28 176 1.1E-45
2 g3848.t10 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 6 175 1.9E-81
3 g3848.t10 PANTHER PTHR47958:SF49 EUKARYOTIC INITIATION FACTOR 4A-III 6 175 1.9E-81
1 g3848.t10 Pfam PF00270 DEAD/DEAH box helicase 53 175 2.7E-27
6 g3848.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 165 -
8 g3848.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 166 183 -
7 g3848.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 184 185 -
11 g3848.t10 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 28 56 10.009
12 g3848.t10 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 59 185 18.28
10 g3848.t10 SMART SM00487 ultradead3 47 185 1.5E-16
4 g3848.t10 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 16 175 7.59E-43
9 g3848.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 165 184 -

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 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.

Raw TPM values