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.t5 TTS g3848.t5 28350123 28350123
chr_3 g3848 g3848.t5 isoform g3848.t5 28350234 28351678
chr_3 g3848 g3848.t5 exon g3848.t5.exon1 28350234 28350378
chr_3 g3848 g3848.t5 cds g3848.t5.CDS1 28350234 28350378
chr_3 g3848 g3848.t5 exon g3848.t5.exon2 28350440 28350588
chr_3 g3848 g3848.t5 cds g3848.t5.CDS2 28350440 28350588
chr_3 g3848 g3848.t5 exon g3848.t5.exon3 28350647 28351036
chr_3 g3848 g3848.t5 cds g3848.t5.CDS3 28350647 28351036
chr_3 g3848 g3848.t5 exon g3848.t5.exon4 28351101 28351327
chr_3 g3848 g3848.t5 cds g3848.t5.CDS4 28351101 28351256
chr_3 g3848 g3848.t5 exon g3848.t5.exon5 28351499 28351678
chr_3 g3848 g3848.t5 TSS g3848.t5 28351876 28351876

Sequences

>g3848.t5 Gene=g3848 Length=1091
ATGGCATCAACTTCGAAAAAATCAGTGACGGAAGATTTATCAAATGTTGAATTTGAGACA
AGTGAAGATGTTGAAGTTGTTCCAACATTTCAATCGATGAAATTACGTGAAGAACTCTTA
AGAGGAATATATGCTTATGGTAAAAATTAAATTCATTTAAAAATATCAAAACAATAACCT
TTCTTTGCTTATCTCCTACTCGCGAATTGGCCGTACAGATTCAAAAAGTCATTCTCGCTC
TTGGAGATTTTATGAACGTTCAATGCCATGCTTGTATTGGAGGTACAAATTTGGGAGAAG
ATATTCGCAAATTAGATTATGGTCAACATGTTGTAAGTGGAACTCCAGGTCGAGTTTTTG
ACATGATAAAACGTCGAGTGCTGAGAACTCGTGCAATTAAAATGCTGGTTTTGGATGAAG
CTGATGAAATGTTAAACAAAGGTTTTAAAGAACAAATTTATGATGTATATCGTTATTTGC
CACCAGCTACACAAGTATGTTTAATTTCTGCTACATTACCACACGAAATTCTGGAAATGA
CTAGCAAATTCATGACGGATCCCATTCGTATTCTTGTAAAACGTGATGAATTAACACTTG
AAGGTATCAAACAGTTTTTTGTTGCTGTCGAAAGAGAAGAATGGAAGTTTGATACACTGT
GTGATTTATACGATACACTGACAATCACACAAGCAGTCATTTTTTGTAATACAAAGAGAA
AAGTCGATTGGTTGACTGAAAAAATGCGTGAAGCAAATTTCACTGTCAGTTCTATGCATG
GTGACATGCCACAAAAAGAACGTGATGAGATTATGAAAGAATTCCGATCTGGACAAACAA
GAGTTTTAATCACAACTGACGTTTGGGCAAGAGGTATTGATGTTCAACAAGTTTCTCTCG
TTATCAATTATGATCTACCAAACAACAGAGAATTGTATATTCACAGAATCGGTCGCTCAG
GTCGTTTCGGTCGCAAAGGTGTTGGCATTAATTTTGTAAAATCAGACGACATAAGGATTC
TTAGAGATATTGAACAATACTATTCAACGCAGATCGATGAGATGCCTATGAATGTAGCAG
ATTTGGTTTAA

>g3848.t5 Gene=g3848 Length=279
MNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIKRRVLRTRAIKMLVLDEADEM
LNKGFKEQIYDVYRYLPPATQVCLISATLPHEILEMTSKFMTDPIRILVKRDELTLEGIK
QFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMP
QKERDEIMKEFRSGQTRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFG
RKGVGINFVKSDDIRILRDIEQYYSTQIDEMPMNVADLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3848.t5 CDD cd18787 SF2_C_DEAD 119 249 1.40918E-64
6 g3848.t5 Gene3D G3DSA:3.40.50.300 - 1 114 1.6E-32
7 g3848.t5 Gene3D G3DSA:3.40.50.300 - 115 279 3.3E-62
3 g3848.t5 PANTHER PTHR47958 ATP-DEPENDENT RNA HELICASE DBP3 1 272 4.7E-175
4 g3848.t5 PANTHER PTHR47958:SF49 EUKARYOTIC INITIATION FACTOR 4A-III 1 272 4.7E-175
1 g3848.t5 Pfam PF00270 DEAD/DEAH box helicase 3 93 2.4E-18
2 g3848.t5 Pfam PF00271 Helicase conserved C-terminal domain 132 240 8.3E-33
9 g3848.t5 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 53 61 -
12 g3848.t5 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 107 16.608
11 g3848.t5 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 118 279 27.08
10 g3848.t5 SMART SM00490 helicmild6 159 240 7.1E-36
5 g3848.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 262 9.15E-65

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: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