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.t9 TTS g3848.t9 28350123 28350123
chr_3 g3848 g3848.t9 isoform g3848.t9 28350662 28351678
chr_3 g3848 g3848.t9 exon g3848.t9.exon1 28350662 28351036
chr_3 g3848 g3848.t9 cds g3848.t9.CDS1 28350662 28351036
chr_3 g3848 g3848.t9 exon g3848.t9.exon2 28351101 28351483
chr_3 g3848 g3848.t9 cds g3848.t9.CDS2 28351101 28351483
chr_3 g3848 g3848.t9 exon g3848.t9.exon3 28351540 28351678
chr_3 g3848 g3848.t9 cds g3848.t9.CDS3 28351540 28351678
chr_3 g3848 g3848.t9 TSS g3848.t9 28351876 28351876

Sequences

>g3848.t9 Gene=g3848 Length=897
ATGGCATCAACTTCGAAAAAATCAGTGACGGAAGATTTATCAAATGTTGAATTTGAGACA
AGTGAAGATGTTGAAGTTGTTCCAACATTTCAATCGATGAAATTACGTGAAGAACTCTTA
AGAGGAATATATGCTTATGGATTTGAGAAACCATCAGCCATTCAGCAGAGAAGTATTTTA
CCGATTGTAAAGGGACGCGATGTAATAGCACAAGCTCAATCCGGTACTGGTAAAACCGCA
ACTTTTTCAATCGCAATTTTAGAGAAATTAGACACGGCTCTTCGTGAAACTCAAGTTCTT
TGCTTATCTCCTACTCGCGAATTGGCCGTACAGATTCAAAAAGTCATTCTCGCTCTTGGA
GATTTTATGAACGTTCAATGCCATGCTTGTATTGGAGGTACAAATTTGGGAGAAGATATT
CGCAAATTAGATTATGGTCAACATGTTGTAAGTGGAACTCCAGGTCGAGTTTTTGACATG
ATAAAACGTCGAGTGCTGAGAACTCGTGCAATTAAAATGCTGGTTTTGGATGAAGCTGAT
GAAATGTTAAACAAAGGTTTTAAAGAACAAATTTATGATGTATATCGTTATTTGCCACCA
GCTACACAAGTATGTTTAATTTCTGCTACATTACCACACGAAATTCTGGAAATGACTAGC
AAATTCATGACGGATCCCATTCGTATTCTTGTAAAACGTGATGAATTAACACTTGAAGGT
ATCAAACAGTTTTTTGTTGCTGTCGAAAGAGAAGAATGGAAGTTTGATACACTGTGTGAT
TTATACGATACACTGACAATCACACAAGCAGTCATTTTTTGTAATACAAAGAGAAAAGTC
GATTGGTTGACTGAAAAAATGCGTGAAGCAAATTTCACTGTCAGTTCTATGCATGGT

>g3848.t9 Gene=g3848 Length=299
MASTSKKSVTEDLSNVEFETSEDVEVVPTFQSMKLREELLRGIYAYGFEKPSAIQQRSIL
PIVKGRDVIAQAQSGTGKTATFSIAILEKLDTALRETQVLCLSPTRELAVQIQKVILALG
DFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIKRRVLRTRAIKMLVLDEAD
EMLNKGFKEQIYDVYRYLPPATQVCLISATLPHEILEMTSKFMTDPIRILVKRDELTLEG
IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3848.t9 CDD cd18045 DEADc_EIF4AIII_DDX48 30 230 4.64433E-136
6 g3848.t9 Gene3D G3DSA:3.40.50.300 - 29 233 1.9E-67
7 g3848.t9 Gene3D G3DSA:3.40.50.300 - 234 299 5.8E-16
2 g3848.t9 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 6 299 1.7E-166
3 g3848.t9 PANTHER PTHR47958:SF49 EUKARYOTIC INITIATION FACTOR 4A-III 6 299 1.7E-166
1 g3848.t9 Pfam PF00270 DEAD/DEAH box helicase 53 215 1.3E-40
9 g3848.t9 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 175 183 -
11 g3848.t9 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 28 56 10.009
13 g3848.t9 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 59 229 28.919
12 g3848.t9 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 240 299 6.954
10 g3848.t9 SMART SM00487 ultradead3 47 244 1.6E-58
4 g3848.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 16 232 2.07E-63
5 g3848.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 206 299 3.09E-10

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