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.t18 TTS g8392.t18 30141045 30141045
chr_2 g8392 g8392.t18 isoform g8392.t18 30142007 30143950
chr_2 g8392 g8392.t18 exon g8392.t18.exon1 30142007 30142119
chr_2 g8392 g8392.t18 cds g8392.t18.CDS1 30142007 30142119
chr_2 g8392 g8392.t18 exon g8392.t18.exon2 30142323 30142964
chr_2 g8392 g8392.t18 cds g8392.t18.CDS2 30142323 30142964
chr_2 g8392 g8392.t18 exon g8392.t18.exon3 30143027 30143116
chr_2 g8392 g8392.t18 cds g8392.t18.CDS3 30143027 30143116
chr_2 g8392 g8392.t18 exon g8392.t18.exon4 30143179 30143410
chr_2 g8392 g8392.t18 cds g8392.t18.CDS4 30143179 30143410
chr_2 g8392 g8392.t18 exon g8392.t18.exon5 30143884 30143950
chr_2 g8392 g8392.t18 TSS g8392.t18 30143947 30143947

Sequences

>g8392.t18 Gene=g8392 Length=1144
CTTTTTCCACAAGGACTTATTAAAAGTTACACTTCTCAACGAGATAGAACAAAAAAAATT
AAAAAATATGGATGATAACCGTCAACAAGAAACTTATGATGGACCAGCTGGTATGGAAGT
CGGTGGCATCATTGAATCTAACTGGGACGAAGTTGTTGATAACTTCGATAATATGAATTT
AAAAGAGAAACTCTTACGCGGAATCTACGCTTATGGTTTCGAAAAGCCTTCAGCTATCCA
GCAACGGGCCATCATTCCTTGTATTCGTGGTCGTGATGTTATTGCTCAGGCTCAATCAGG
TACCGGAAAAACCGCTACTTTCTCTATTGCTATCCTGCAAACTATTGATACTGATGTTCG
CGGTTGTCAAGCTTTAGTCCTTGCACCAACTCGTGAGTTGGCCACTCAAATTCAGAAGGT
TGTTGTTGCATTGGGTGACTTTATGAATGCTCAATCGCATGCATGTATCGGAGGAACGAA
TGTTCGTGAAGATATGAGAAATCTTGAGCAAGGCGTTCACGTAGTAGTTGGAACACCAGG
AAGAGTGCAAGATATGATTCAACGCAAATTTTTGCGTACATCTGATATTAAGCTGTTTGT
TCTTGACGAGGCCGATGAAATGTTATCGCGTGGATTCAAAGATCAAATTCAAGAGGTCTT
TAAAAAGCTTCCTAATGACGTTCAAGTCATTTTACTTTCTGCTACCATGCCACCAGAAGT
TTTGGAAGTCAGCAAGTATTTCATGCGTGATCCAGTGAGAATATTGGTCAAAAAAGAAGA
GTTGACTTTGGAAGGTATTCGCCAATTTTATGTTAATGTTAAACAAGAACAGTGGAAATT
GGGAACATTGTGTGATTTGTATGACACATTGAGTATCACCCAAGCTGTCATTTTCTGTAA
TACTCGTCGTAAGGTAGATCAGTTGACTGAAGAAATGACTGCTAAGAATTTCACTGTGTC
TGCTATGCATGGAGAAATGGATCAACGTGAAAGAGATATGATTATGAAACAATTCAGAAG
CGGATCTTCACGTGTTGCTATTAATTTCATAACGGATGCTGATCGTCGTGCATTACAAGA
ATTGGAACAACATTATCATACAACTATCGAAGAAATGCCCTGCAACGTTGCTGATTTAAT
TTAA

>g8392.t18 Gene=g8392 Length=358
MDDNRQQETYDGPAGMEVGGIIESNWDEVVDNFDNMNLKEKLLRGIYAYGFEKPSAIQQR
AIIPCIRGRDVIAQAQSGTGKTATFSIAILQTIDTDVRGCQALVLAPTRELATQIQKVVV
ALGDFMNAQSHACIGGTNVREDMRNLEQGVHVVVGTPGRVQDMIQRKFLRTSDIKLFVLD
EADEMLSRGFKDQIQEVFKKLPNDVQVILLSATMPPEVLEVSKYFMRDPVRILVKKEELT
LEGIRQFYVNVKQEQWKLGTLCDLYDTLSITQAVIFCNTRRKVDQLTEEMTAKNFTVSAM
HGEMDQRERDMIMKQFRSGSSRVAINFITDADRRALQELEQHYHTTIEEMPCNVADLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g8392.t18 CDD cd18046 DEADc_EIF4AII_EIF4AI_DDX2 33 233 3.12031E-138
9 g8392.t18 Gene3D G3DSA:3.40.50.300 - 20 239 1.5E-72
10 g8392.t18 Gene3D G3DSA:3.40.50.300 - 240 325 1.8E-24
4 g8392.t18 PANTHER PTHR24031:SF720 EUKARYOTIC INITIATION FACTOR 4A-II 16 325 1.7E-156
6 g8392.t18 PANTHER PTHR24031 RNA HELICASE 16 325 1.7E-156
3 g8392.t18 PANTHER PTHR24031:SF720 EUKARYOTIC INITIATION FACTOR 4A-II 323 358 1.7E-156
5 g8392.t18 PANTHER PTHR24031 RNA HELICASE 323 358 1.7E-156
1 g8392.t18 Pfam PF00270 DEAD/DEAH box helicase 56 218 7.3E-46
2 g8392.t18 Pfam PF00271 Helicase conserved C-terminal domain 258 325 5.7E-10
12 g8392.t18 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 178 186 -
14 g8392.t18 ProSiteProfiles PS51195 DEAD-box RNA helicase Q motif profile. 31 59 10.225
16 g8392.t18 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 62 232 31.805
15 g8392.t18 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 243 358 10.24
13 g8392.t18 SMART SM00487 ultradead3 50 247 4.4E-62
7 g8392.t18 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 23 235 1.16E-68
8 g8392.t18 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 238 352 4.5E-18

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