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.t35 TSS g10339.t35 8939297 8939297
chr_1 g10339 g10339.t35 isoform g10339.t35 8940321 8941577
chr_1 g10339 g10339.t35 exon g10339.t35.exon1 8940321 8940860
chr_1 g10339 g10339.t35 cds g10339.t35.CDS1 8940425 8940860
chr_1 g10339 g10339.t35 exon g10339.t35.exon2 8941033 8941577
chr_1 g10339 g10339.t35 cds g10339.t35.CDS2 8941033 8941577
chr_1 g10339 g10339.t35 TTS g10339.t35 8941863 8941863

Sequences

>g10339.t35 Gene=g10339 Length=1085
GTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTCGAAACATCAAAATACTACG
TTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAAAACATGATCACAGGAACAT
CTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGGTA
TTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAAAC
AATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTT
TCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTG
CAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAACATGCTTGAACCATCAACCA
AGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGT
GCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGTCCAACTGACAAACCATTGC
TCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAAGAAGCTG
TACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTG
GTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTC
AAGTAATTGTCTTGAATCATCCAGGTCAAATTTCAAACGGTTACACACCAGTTTTGGATT
GCCACACTGCTCACATTGCCTGCAAGTTCTCTGAAATCAAAGAAAAAGTTGATCGTCGTT
CAGGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAATCAGGAGATGCTGCTATCGTCA
TTTTGGTCCCAACAAAACCATTGTGCGTTGAATCATTCCAAGAATTCCCACCATTGGGAC
GTTTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTCGGTGTCATCAAGGCAGTTTCAT
TCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAGA
AATAG

>g10339.t35 Gene=g10339 Length=326
MITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPP
YSEARFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEG
KADGKCLIDALDAILPPQRPTDKPLLNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSV
KELRRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKE
KVDRRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGV
IKAVSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g10339.t35 CDD cd03705 EF1_alpha_III 198 301 0.0000000
13 g10339.t35 Gene3D G3DSA:3.40.50.300 - 1 137 0.0000000
15 g10339.t35 Gene3D G3DSA:2.40.30.10 Translation factors 139 195 0.0000000
14 g10339.t35 Gene3D G3DSA:2.40.30.10 Translation factors 198 305 0.0000000
4 g10339.t35 PANTHER PTHR23115 TRANSLATION FACTOR 1 145 0.0000000
6 g10339.t35 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 145 0.0000000
5 g10339.t35 PANTHER PTHR23115 TRANSLATION FACTOR 147 322 0.0000000
7 g10339.t35 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 147 322 0.0000000
9 g10339.t35 PRINTS PR00315 GTP-binding elongation factor signature 3 14 0.0000330
8 g10339.t35 PRINTS PR00315 GTP-binding elongation factor signature 47 56 0.0000330
3 g10339.t35 Pfam PF00009 Elongation factor Tu GTP binding domain 1 135 0.0000000
2 g10339.t35 Pfam PF03144 Elongation factor Tu domain 2 144 188 0.0000003
1 g10339.t35 Pfam PF03143 Elongation factor Tu C-terminal domain 199 304 0.0000000
16 g10339.t35 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 141 26.0720000
11 g10339.t35 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 153 0.0000000
12 g10339.t35 SUPERFAMILY SSF50447 Translation proteins 145 197 0.0000000
10 g10339.t35 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 201 304 0.0000000

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
GO:0003924 GTPase activity 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