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 g8393 g8393.t3 TSS g8393.t3 30144189 30144189
chr_2 g8393 g8393.t3 isoform g8393.t3 30144892 30145844
chr_2 g8393 g8393.t3 exon g8393.t3.exon1 30144892 30145639
chr_2 g8393 g8393.t3 cds g8393.t3.CDS1 30144945 30145639
chr_2 g8393 g8393.t3 exon g8393.t3.exon2 30145700 30145844
chr_2 g8393 g8393.t3 cds g8393.t3.CDS2 30145700 30145844
chr_2 g8393 g8393.t3 TTS g8393.t3 30146418 30146418

Sequences

>g8393.t3 Gene=g8393 Length=893
CTCGAGAATTAGCTATTCAAATTCAAAAAGTTGTTCTTGCATTGGGTGACTTTATGCAGA
CTGAGTGTCATGCATGTATTGGTGGAACTAACGTTCGTGAAGATATGCGAACGCTTGAAC
AAGGCGTAAATGTAGTAGTTGGAACACCAGGTCGTGTATTTGACATGATTCAAAGAAAAG
TACTGAGAACTAACAATATTAAGCTGTTTGTTCTTGATGAAGCCGATGAGATGCTATCGC
GTGGATTCAAAGATCAAATTCATGATGTATTTAAGACTCTTCCTAATGATGTACAAGTAA
TCTTACTTTCTGCTACTATGCCAGTTGATGTTTTGGAAGTCAGCAAGTATTTTATGCGTG
ATCCAGTGAGAATATTGGTCAAAAAAGAAGAGTTGACATTAGAAGGAATTCGACAATTTT
ATGTTAATGTTGAGAAAGAAGAATGGAAATTAGGAACATTGTGTGATTTGTATGACACAT
TGAGTATTGCTCAAGCTGTCATTTTCTGTAATACTCGTCGTAAAGTTGAATTTTTAACTG
AAGAAATGACAAGACAAAACTTTACTGTTTCTGCTATGCATGGAGAAATGGATCAGTCTG
AAAGAGATATGATTATGAAACAATTCAGAAGCGGATCTTCACGTGTACTCATTACTACTG
ATTTGCTTGCTCGTGGTATTGATGTGCAGCAAGTCTCATTGGTTATCAACTATGATTTAC
CAAATAATCGAGAAAATTATATTCACAGAATTGGTCGAGGTGGCCGCTTTGGACGTAAAG
GTGTTGCTATAAATTTTGTTACAGAAGAAGATAAGCGCACCTTACTCGATATTGAACAAT
TCTGTAATACAAAAATCGAAGAGATGCCTGTGAACGTTGCTGATTTAATCTAA

>g8393.t3 Gene=g8393 Length=279
MQTECHACIGGTNVREDMRTLEQGVNVVVGTPGRVFDMIQRKVLRTNNIKLFVLDEADEM
LSRGFKDQIHDVFKTLPNDVQVILLSATMPVDVLEVSKYFMRDPVRILVKKEELTLEGIR
QFYVNVEKEEWKLGTLCDLYDTLSIAQAVIFCNTRRKVEFLTEEMTRQNFTVSAMHGEMD
QSERDMIMKQFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPNNRENYIHRIGRGGRFG
RKGVAINFVTEEDKRTLLDIEQFCNTKIEEMPVNVADLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8393.t3 CDD cd18787 SF2_C_DEAD 119 234 4.61572E-47
6 g8393.t3 Gene3D G3DSA:3.40.50.300 - 1 114 2.1E-35
7 g8393.t3 Gene3D G3DSA:3.40.50.300 - 115 279 5.5E-61
3 g8393.t3 PANTHER PTHR24031:SF720 EUKARYOTIC INITIATION FACTOR 4A-II 3 279 6.6E-143
4 g8393.t3 PANTHER PTHR24031 RNA HELICASE 3 279 6.6E-143
1 g8393.t3 Pfam PF00270 DEAD/DEAH box helicase 4 93 1.4E-22
2 g8393.t3 Pfam PF00271 Helicase conserved C-terminal domain 133 240 5.8E-32
9 g8393.t3 ProSitePatterns PS00039 DEAD-box subfamily ATP-dependent helicases signature. 53 61 -
12 g8393.t3 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 1 107 20.097
11 g8393.t3 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 118 279 26.871
10 g8393.t3 SMART SM00490 helicmild6 159 240 2.5E-33
5 g8393.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 262 7.28E-67

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