Gene loci information

Transcript annotation

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

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.t38 isoform g10339.t38 8940572 8941577
chr_1 g10339 g10339.t38 exon g10339.t38.exon1 8940572 8940713
chr_1 g10339 g10339.t38 cds g10339.t38.CDS1 8940584 8940713
chr_1 g10339 g10339.t38 exon g10339.t38.exon2 8940789 8940944
chr_1 g10339 g10339.t38 cds g10339.t38.CDS2 8940789 8940944
chr_1 g10339 g10339.t38 exon g10339.t38.exon3 8941009 8941577
chr_1 g10339 g10339.t38 cds g10339.t38.CDS3 8941009 8941577
chr_1 g10339 g10339.t38 TTS g10339.t38 8941863 8941863
chr_1 g10339 g10339.t38 TSS g10339.t38 NA NA

Sequences

>g10339.t38 Gene=g10339 Length=867
GGTGTCAACAAAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATT
AAGAAGGAAGTCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTC
GTTCCAATCTCAGGCTGGCATGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATT
TTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAA
ATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAACCAGGT
ATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCAT
CACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTC
TCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGT
GGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTTCAAAC
GGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTGAAATC
AAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAA
TCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAATCATTC
CAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTC
GGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCT
GAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t38 Gene=g10339 Length=284
MDSTEPPYSEARFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHADGKCLIDALDAILPPQ
RPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHEAL
QEAVPGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQISNGYTP
VLDCHTAHIACKFSEIKEKVDRRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFP
PLGRFAVRDMRQTVAVGVIKAVSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10339.t38 CDD cd03693 EF1_alpha_II 63 153 0
14 g10339.t38 CDD cd03705 EF1_alpha_III 156 259 0
10 g10339.t38 Gene3D G3DSA:3.40.50.300 - 1 59 0
11 g10339.t38 Gene3D G3DSA:2.40.30.10 Translation factors 61 153 0
12 g10339.t38 Gene3D G3DSA:2.40.30.10 Translation factors 156 263 0
3 g10339.t38 PANTHER PTHR23115 TRANSLATION FACTOR 1 45 0
5 g10339.t38 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 45 0
4 g10339.t38 PANTHER PTHR23115 TRANSLATION FACTOR 46 280 0
6 g10339.t38 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 46 280 0
2 g10339.t38 Pfam PF03144 Elongation factor Tu domain 2 81 146 0
1 g10339.t38 Pfam PF03143 Elongation factor Tu C-terminal domain 157 262 0
8 g10339.t38 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 6 82 0
9 g10339.t38 SUPERFAMILY SSF50447 Translation proteins 64 193 0
7 g10339.t38 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 159 262 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.

Raw TPM values