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.t7 TTS g3848.t7 28350123 28350123
chr_3 g3848 g3848.t7 isoform g3848.t7 28350234 28351678
chr_3 g3848 g3848.t7 exon g3848.t7.exon1 28350234 28350588
chr_3 g3848 g3848.t7 cds g3848.t7.CDS1 28350436 28350588
chr_3 g3848 g3848.t7 exon g3848.t7.exon2 28350647 28351036
chr_3 g3848 g3848.t7 cds g3848.t7.CDS2 28350647 28351036
chr_3 g3848 g3848.t7 exon g3848.t7.exon3 28351101 28351483
chr_3 g3848 g3848.t7 cds g3848.t7.CDS3 28351101 28351483
chr_3 g3848 g3848.t7 exon g3848.t7.exon4 28351540 28351678
chr_3 g3848 g3848.t7 cds g3848.t7.CDS4 28351540 28351678
chr_3 g3848 g3848.t7 TSS g3848.t7 28351876 28351876

Sequences

>g3848.t7 Gene=g3848 Length=1267
ATGGCATCAACTTCGAAAAAATCAGTGACGGAAGATTTATCAAATGTTGAATTTGAGACA
AGTGAAGATGTTGAAGTTGTTCCAACATTTCAATCGATGAAATTACGTGAAGAACTCTTA
AGAGGAATATATGCTTATGGATTTGAGAAACCATCAGCCATTCAGCAGAGAAGTATTTTA
CCGATTGTAAAGGGACGCGATGTAATAGCACAAGCTCAATCCGGTACTGGTAAAACCGCA
ACTTTTTCAATCGCAATTTTAGAGAAATTAGACACGGCTCTTCGTGAAACTCAAGTTCTT
TGCTTATCTCCTACTCGCGAATTGGCCGTACAGATTCAAAAAGTCATTCTCGCTCTTGGA
GATTTTATGAACGTTCAATGCCATGCTTGTATTGGAGGTACAAATTTGGGAGAAGATATT
CGCAAATTAGATTATGGTCAACATGTTGTAAGTGGAACTCCAGGTCGAGTTTTTGACATG
ATAAAACGTCGAGTGCTGAGAACTCGTGCAATTAAAATGCTGGTTTTGGATGAAGCTGAT
GAAATGTTAAACAAAGGTTTTAAAGAACAAATTTATGATGTATATCGTTATTTGCCACCA
GCTACACAAGTATGTTTAATTTCTGCTACATTACCACACGAAATTCTGGAAATGACTAGC
AAATTCATGACGGATCCCATTCGTATTCTTGTAAAACGTGATGAATTAACACTTGAAGGT
ATCAAACAGTTTTTTGTTGCTGTCGAAAGAGAAGAATGGAAGTTTGATACACTGTGTGAT
TTATACGATACACTGACAATCACACAAGCAGTCATTTTTTGTAATACAAAGAGAAAAGTC
GATTGGTTGACTGAAAAAATGCGTGAAGCAAATTTCACTGTCAGTTCTATGCATGGTGAC
ATGCCACAAAAAGAACGTGATGAGATTATGAAAGAATTCCGATCTGGACAAACAAGAGTT
TTAATCACAACTGACGTTTGGGCAAGAGGTATTGATGTTCAACAAGTTTCTCTCGTTATC
AATTATGATCTACCAAACAACAGAGAATTGTATATTCACAGGTAGATAAATTTAACTTCT
ATTAATATGCGCCTGTTACAATTAAACTTTAACGAATTTTAGAATCGGTCGCTCAGGTCG
TTTCGGTCGCAAAGGTGTTGGCATTAATTTTGTAAAATCAGACGACATAAGGATTCTTAG
AGATATTGAACAATACTATTCAACGCAGATCGATGAGATGCCTATGAATGTAGCAGATTT
GGTTTAA

>g3848.t7 Gene=g3848 Length=354
MASTSKKSVTEDLSNVEFETSEDVEVVPTFQSMKLREELLRGIYAYGFEKPSAIQQRSIL
PIVKGRDVIAQAQSGTGKTATFSIAILEKLDTALRETQVLCLSPTRELAVQIQKVILALG
DFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIKRRVLRTRAIKMLVLDEAD
EMLNKGFKEQIYDVYRYLPPATQVCLISATLPHEILEMTSKFMTDPIRILVKRDELTLEG
IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD
MPQKERDEIMKEFRSGQTRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3848.t7 CDD cd18045 DEADc_EIF4AIII_DDX48 30 230 7.8102E-135
9 g3848.t7 CDD cd18787 SF2_C_DEAD 241 354 1.32356E-52
7 g3848.t7 Gene3D G3DSA:3.40.50.300 - 29 233 3.1E-67
6 g3848.t7 Gene3D G3DSA:3.40.50.300 - 234 354 3.0E-45
3 g3848.t7 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 6 354 3.6E-204
4 g3848.t7 PANTHER PTHR47958:SF49 EUKARYOTIC INITIATION FACTOR 4A-III 6 354 3.6E-204
1 g3848.t7 Pfam PF00270 DEAD/DEAH box helicase 53 215 2.0E-40
2 g3848.t7 Pfam PF00271 Helicase conserved C-terminal domain 254 354 1.8E-27
10 g3848.t7 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 175 183 -
13 g3848.t7 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 28 56 10.009
15 g3848.t7 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 59 229 28.919
14 g3848.t7 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 240 354 20.129
12 g3848.t7 SMART SM00487 ultradead3 47 244 1.6E-58
11 g3848.t7 SMART SM00490 helicmild6 281 354 3.5E-22
5 g3848.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 96 354 7.46E-64

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