Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha.

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_1 g10339 g10339.t39 isoform g10339.t39 8940653 8941891
chr_1 g10339 g10339.t39 exon g10339.t39.exon1 8940653 8940944
chr_1 g10339 g10339.t39 cds g10339.t39.CDS1 8940722 8940944
chr_1 g10339 g10339.t39 exon g10339.t39.exon2 8941009 8941530
chr_1 g10339 g10339.t39 cds g10339.t39.CDS2 8941009 8941530
chr_1 g10339 g10339.t39 exon g10339.t39.exon3 8941710 8941891
chr_1 g10339 g10339.t39 cds g10339.t39.CDS3 8941710 8941726
chr_1 g10339 g10339.t39 TTS g10339.t39 8941863 8941863
chr_1 g10339 g10339.t39 TSS g10339.t39 NA NA

Sequences

>g10339.t39 Gene=g10339 Length=996
ATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCAT
GGTGATAACATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAA
CGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCA
CCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGT
GGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAACCAGGTATGGTC
GTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAA
GCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTC
AAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCT
GCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTTCAAACGGTTAC
ACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTGAAATCAAAGAA
AAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAATCAGGA
GATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAATCATTCCAAGAA
TTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTCGGTGTC
ATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGAAATGTATTTTCTTTAACATTCTTTA
TTATTATTAAATTCATTCCGAATACATACATTCACATACGCCAACTATAACATGCATTTT
TCTATTAAACAATGATTTTATGTTTGTCAAATTATGATTTTTTGCTGGATTAAAAAGAAT
TCAATAACAAAAAATATTTTCTTCTTTTTTATATTT

>g10339.t39 Gene=g10339 Length=253
MLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIG
TVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKEL
RRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKEKVD
RRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKA
VSFKDASGEMYFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10339.t39 CDD cd03693 EF1_alpha_II 42 132 0
10 g10339.t39 CDD cd03705 EF1_alpha_III 135 238 0
7 g10339.t39 Gene3D G3DSA:2.40.30.10 Translation factors 40 132 0
8 g10339.t39 Gene3D G3DSA:2.40.30.10 Translation factors 135 242 0
3 g10339.t39 PANTHER PTHR23115 TRANSLATION FACTOR 1 247 0
4 g10339.t39 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 247 0
2 g10339.t39 Pfam PF03144 Elongation factor Tu domain 2 60 125 0
1 g10339.t39 Pfam PF03143 Elongation factor Tu C-terminal domain 136 241 0
6 g10339.t39 SUPERFAMILY SSF50447 Translation proteins 43 172 0
5 g10339.t39 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 138 241 0

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:0005525 GTP 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. There were no conditions that were differentially expressed