Gene loci information

Transcript annotation

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

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_2 g8392 g8392.t9 isoform g8392.t9 30141680 30143410
chr_2 g8392 g8392.t9 exon g8392.t9.exon1 30141680 30142151
chr_2 g8392 g8392.t9 TTS g8392.t9 30141837 30141837
chr_2 g8392 g8392.t9 cds g8392.t9.CDS1 30142007 30142151
chr_2 g8392 g8392.t9 exon g8392.t9.exon2 30142217 30142964
chr_2 g8392 g8392.t9 cds g8392.t9.CDS2 30142217 30142911
chr_2 g8392 g8392.t9 exon g8392.t9.exon3 30143027 30143410
chr_2 g8392 g8392.t9 TSS g8392.t9 30143947 30143947

Sequences

>g8392.t9 Gene=g8392 Length=1604
ATGGATGATAACCGTCAACAAGAAACTTATGATGGACCAGCTGGTATGGAAGTCGGTGGC
ATCATTGAATCTAACTGGGACGAAGTTGTTGATAACTTCGATAATATGAATTTAAAAGAG
AAACTCTTACGCGGAATCTACGCTTATGGTTTCGAAAAGCCTTCAGCTATCCAGCAACGG
GCCATCATTCCTTGTATTCGTGGTCGTGATGTTATTGCTCAGGCTCAATCAGGTAAACAA
GCTATAAATTTATTTCATATCATTTTTGTTCATTAAATTTTTCTTTTCATTTAGGTACCG
GAAAAACCGCTACTTTCTCTATTGCTATCCTGCAAACTATTGATACTGATGTTCGCGGTT
GTCAAGCTTTAGTCCTTGCACCAACTCGTGAGTTGGCCACTCAAATTCAGAAGGTTGTTG
TTGCATTGGGTGACTTTATGAATGCTCAATCGCATGCATGTATCGGAGGAACGAATGTTC
GTGAAGATATGAGAAATCTTGAGCAAGGCGTTCACGTAGTAGTTGGAACACCAGGAAGAG
TGCAAGATATGATTCAACGCAAATTTTTGCGTACATCTGATATTAAGCTGTTTGTTCTTG
ACGAGGCCGATGAAATGTTATCGCGTGGATTCAAAGATCAAATTCAAGAGGTCTTTAAAA
AGCTTCCTAATGACGTTCAAGTCATTTTACTTTCTGCTACCATGCCACCAGAAGTTTTGG
AAGTCAGCAAGTATTTCATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGAGTTGA
CTTTGGAAGGTATTCGCCAATTTTATGTTAATGTTAAACAAGAACAGTGGAAATTGGGAA
CATTGTGTGATTTGTATGACACATTGAGTATCACCCAAGCTGTCATTTTCTGTAATACTC
GTCGTAAGGTAGATCAGTTGACTGAAGAAATGACTGCTAAGAATTTCACTGTGTCTGCTA
TGCATGGAGAAATGGATCAACGTGAAAGAGATATGATTATGAAACAATTCAGAAGCGGAT
CTTCACGTGTACTCATTACTACTGATTTGCTTGCTCGTGGTATTGATGTGCAGCAAGTCT
CATTGGTTATCAACTATGATTTGCCTAGTATTAGGGAAAACTATATTCACAGAATCGGTC
GTGGTGGTCGTTTCGGACGTAAAGGTGTTGCTATTAATTTCATAACGGATGCTGATCGTC
GTGCATTACAAGAATTGGAACAACATTATCATACAACTATCGAAGAAATGCCCTGCAACG
TTGCTGATTTAATTTAAACAATTATTAATTTACTTTTTCTGCAAAACTTTTCCTCTTCCT
CCTTTTCACCGCTACTACACAAAAATATTTTTTTTCTTTTTAATTTGTTGGTGTTTACAG
AAGTTTACTATAAAAATTATTATATAGTAACATTACGTTTCTCTTCTTAAATAAAAATAA
TAATGATAAACTGCTGCTTCTTTCTAAGAACCATTCAAATTTATGTTAGGATTAGAGACA
TTATACACTTAAATAAGAATTTTTCCTACAAAAAAAAACTTTCTTGCAAAATCTTCTTGG
AAAAAATTATAAAGTTAAATATTATAATTACTATTATAAAATGC

>g8392.t9 Gene=g8392 Length=279
MNAQSHACIGGTNVREDMRNLEQGVHVVVGTPGRVQDMIQRKFLRTSDIKLFVLDEADEM
LSRGFKDQIQEVFKKLPNDVQVILLSATMPPEVLEVSKYFMRDPVRILVKKEELTLEGIR
QFYVNVKQEQWKLGTLCDLYDTLSITQAVIFCNTRRKVDQLTEEMTAKNFTVSAMHGEMD
QRERDMIMKQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPSIRENYIHRIGRGGRFG
RKGVAINFITDADRRALQELEQHYHTTIEEMPCNVADLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8392.t9 CDD cd18787 SF2_C_DEAD 119 234 6.96711E-45
6 g8392.t9 Gene3D G3DSA:3.40.50.300 - 1 114 6.1E-37
7 g8392.t9 Gene3D G3DSA:3.40.50.300 - 115 279 2.3E-59
3 g8392.t9 PANTHER PTHR24031:SF720 EUKARYOTIC INITIATION FACTOR 4A-II 4 279 1.7E-138
4 g8392.t9 PANTHER PTHR24031 RNA HELICASE 4 279 1.7E-138
1 g8392.t9 Pfam PF00270 DEAD/DEAH box helicase 5 93 4.4E-23
2 g8392.t9 Pfam PF00271 Helicase conserved C-terminal domain 133 240 7.8E-31
9 g8392.t9 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 53 61 -
12 g8392.t9 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 107 20.462
11 g8392.t9 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 118 279 25.791
10 g8392.t9 SMART SM00490 helicmild6 159 240 6.5E-32
5 g8392.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 261 1.27E-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