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.t8 TSS g10339.t8 8939297 8939297
chr_1 g10339 g10339.t8 isoform g10339.t8 8939304 8941577
chr_1 g10339 g10339.t8 exon g10339.t8.exon1 8939304 8939370
chr_1 g10339 g10339.t8 exon g10339.t8.exon2 8940109 8940230
chr_1 g10339 g10339.t8 cds g10339.t8.CDS1 8940211 8940230
chr_1 g10339 g10339.t8 exon g10339.t8.exon3 8940409 8940944
chr_1 g10339 g10339.t8 cds g10339.t8.CDS2 8940409 8940944
chr_1 g10339 g10339.t8 exon g10339.t8.exon4 8941009 8941577
chr_1 g10339 g10339.t8 cds g10339.t8.CDS3 8941009 8941577
chr_1 g10339 g10339.t8 TTS g10339.t8 8941863 8941863

Sequences

>g10339.t8 Gene=g10339 Length=1294
CGTTTTAGCTCTCAAACAGTTCGAACGTTTTCGTTTACTCTTCTCTTGTGTTTAATAATT
TTTGATTAAAGCAAAGCAACATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTG
GACACGTCGACTCTGGCAAGTCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTA
TCGACAAGCTGATTTCATCAAAAACATGATCACAGGAACATCTCAAGCTGATTGCGCTGT
ATTGATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAAC
TCGTGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAA
CAAAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGA
AGTCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAAT
CTCAGGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGG
ATGGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGA
CGCCATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGT
CTACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAA
ACCAGGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGA
AATGCATCACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAA
GAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCC
ACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAAT
TTCAAACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTC
TGAAATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGC
TATCAAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGA
ATCATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGT
TGCTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAA
AGCAGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t8 Gene=g10339 Length=374
MRRYRQADFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLI
VGVNKMDSTEPPYSEARFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEPSTKMP
WFKGWAIERKEGKADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIGTVPVGRVET
GVLKPGMVVVFAPVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDT
KSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKEKVDRRSGKSVED
NPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKAVSFKDASGG
KTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10339.t8 CDD cd03693 EF1_alpha_II 153 243 0.000000
15 g10339.t8 CDD cd03705 EF1_alpha_III 246 349 0.000000
11 g10339.t8 Gene3D G3DSA:3.40.50.300 - 6 149 0.000000
12 g10339.t8 Gene3D G3DSA:2.40.30.10 Translation factors 151 243 0.000000
13 g10339.t8 Gene3D G3DSA:2.40.30.10 Translation factors 246 353 0.000000
4 g10339.t8 PANTHER PTHR23115 TRANSLATION FACTOR 8 370 0.000000
5 g10339.t8 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 8 370 0.000000
6 g10339.t8 PRINTS PR00315 GTP-binding elongation factor signature 15 26 0.000041
7 g10339.t8 PRINTS PR00315 GTP-binding elongation factor signature 59 68 0.000041
3 g10339.t8 Pfam PF00009 Elongation factor Tu GTP binding domain 7 147 0.000000
2 g10339.t8 Pfam PF03144 Elongation factor Tu domain 2 171 236 0.000000
1 g10339.t8 Pfam PF03143 Elongation factor Tu C-terminal domain 247 352 0.000000
16 g10339.t8 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 153 25.940000
9 g10339.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 7 172 0.000000
10 g10339.t8 SUPERFAMILY SSF50447 Translation proteins 149 245 0.000000
8 g10339.t8 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 249 352 0.000000
17 g10339.t8 TIGRFAM TIGR00483 EF-1_alpha: translation elongation factor EF-1, subunit alpha 7 354 0.000000

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:0003746 translation elongation factor activity MF
GO:0006414 translational elongation BP
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