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.t12 TTS g8392.t12 30141045 30141045
chr_2 g8392 g8392.t12 isoform g8392.t12 30142007 30143410
chr_2 g8392 g8392.t12 exon g8392.t12.exon1 30142007 30142151
chr_2 g8392 g8392.t12 cds g8392.t12.CDS1 30142099 30142151
chr_2 g8392 g8392.t12 exon g8392.t12.exon2 30142242 30142964
chr_2 g8392 g8392.t12 cds g8392.t12.CDS2 30142242 30142964
chr_2 g8392 g8392.t12 exon g8392.t12.exon3 30143027 30143116
chr_2 g8392 g8392.t12 cds g8392.t12.CDS3 30143027 30143116
chr_2 g8392 g8392.t12 exon g8392.t12.exon4 30143179 30143410
chr_2 g8392 g8392.t12 cds g8392.t12.CDS4 30143179 30143410
chr_2 g8392 g8392.t12 TSS g8392.t12 30143947 30143947

Sequences

>g8392.t12 Gene=g8392 Length=1190
ATGGATGATAACCGTCAACAAGAAACTTATGATGGACCAGCTGGTATGGAAGTCGGTGGC
ATCATTGAATCTAACTGGGACGAAGTTGTTGATAACTTCGATAATATGAATTTAAAAGAG
AAACTCTTACGCGGAATCTACGCTTATGGTTTCGAAAAGCCTTCAGCTATCCAGCAACGG
GCCATCATTCCTTGTATTCGTGGTCGTGATGTTATTGCTCAGGCTCAATCAGGTACCGGA
AAAACCGCTACTTTCTCTATTGCTATCCTGCAAACTATTGATACTGATGTTCGCGGTTGT
CAAGCTTTAGTCCTTGCACCAACTCGTGAGTTGGCCACTCAAATTCAGAAGGTTGTTGTT
GCATTGGGTGACTTTATGAATGCTCAATCGCATGCATGTATCGGAGGAACGAATGTTCGT
GAAGATATGAGAAATCTTGAGCAAGGCGTTCACGTAGTAGTTGGAACACCAGGAAGAGTG
CAAGATATGATTCAACGCAAATTTTTGCGTACATCTGATATTAAGCTGTTTGTTCTTGAC
GAGGCCGATGAAATGTTATCGCGTGGATTCAAAGATCAAATTCAAGAGGTCTTTAAAAAG
CTTCCTAATGACGTTCAAGTCATTTTACTTTCTGCTACCATGCCACCAGAAGTTTTGGAA
GTCAGCAAGTATTTCATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGAGTTGACT
TTGGAAGGTATTCGCCAATTTTATGTTAATGTTAAACAAGAACAGTGGAAATTGGGAACA
TTGTGTGATTTGTATGACACATTGAGTATCACCCAAGCTGTCATTTTCTGTAATACTCGT
CGTAAGGTAGATCAGTTGACTGAAGAAATGACTGCTAAGAATTTCACTGTGTCTGCTATG
CATGGAGAAATGGATCAACGTGAAAGAGATATGATTATGAAACAATTCAGAAGCGGATCT
TCACGTGTACTCATTACTACTGATTTGCTTGCTCGTGGTATTGATGTGCAGCAAGTCTCA
TTGGTTATCAACTATGATTTGCCTAAATCGGTCGTGGTGGTCGTTTCGGACGTAAAGGTG
TTGCTATTAATTTCATAACGGATGCTGATCGTCGTGCATTACAAGAATTGGAACAACATT
ATCATACAACTATCGAAGAAATGCCCTGCAACGTTGCTGATTTAATTTAA

>g8392.t12 Gene=g8392 Length=365
MDDNRQQETYDGPAGMEVGGIIESNWDEVVDNFDNMNLKEKLLRGIYAYGFEKPSAIQQR
AIIPCIRGRDVIAQAQSGTGKTATFSIAILQTIDTDVRGCQALVLAPTRELATQIQKVVV
ALGDFMNAQSHACIGGTNVREDMRNLEQGVHVVVGTPGRVQDMIQRKFLRTSDIKLFVLD
EADEMLSRGFKDQIQEVFKKLPNDVQVILLSATMPPEVLEVSKYFMRDPVRILVKKEELT
LEGIRQFYVNVKQEQWKLGTLCDLYDTLSITQAVIFCNTRRKVDQLTEEMTAKNFTVSAM
HGEMDQRERDMIMKQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPKSVVVVVSDVKV
LLLIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g8392.t12 CDD cd18046 DEADc_EIF4AII_EIF4AI_DDX2 33 233 1.42184E-137
9 g8392.t12 CDD cd18787 SF2_C_DEAD 244 348 3.71169E-43
8 g8392.t12 Gene3D G3DSA:3.40.50.300 - 20 239 1.6E-72
7 g8392.t12 Gene3D G3DSA:3.40.50.300 - 240 358 8.3E-41
3 g8392.t12 PANTHER PTHR24031:SF625 - 18 350 2.5E-167
4 g8392.t12 PANTHER PTHR24031 RNA HELICASE 18 350 2.5E-167
1 g8392.t12 Pfam PF00270 DEAD/DEAH box helicase 56 218 7.6E-46
2 g8392.t12 Pfam PF00271 Helicase conserved C-terminal domain 258 351 2.1E-24
11 g8392.t12 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 178 186 -
14 g8392.t12 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 31 59 10.225
16 g8392.t12 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 62 232 31.805
15 g8392.t12 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 243 365 17.55
13 g8392.t12 SMART SM00487 ultradead3 50 247 4.4E-62
12 g8392.t12 SMART SM00490 helicmild6 284 357 7.1E-16
6 g8392.t12 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 23 235 1.24E-68
5 g8392.t12 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 171 353 7.17E-42

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