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.t2 isoform g10339.t2 8935468 8941577
chr_1 g10339 g10339.t2 exon g10339.t2.exon1 8935468 8935519
chr_1 g10339 g10339.t2 exon g10339.t2.exon2 8940363 8940944
chr_1 g10339 g10339.t2 cds g10339.t2.CDS1 8940425 8940944
chr_1 g10339 g10339.t2 exon g10339.t2.exon3 8941009 8941577
chr_1 g10339 g10339.t2 cds g10339.t2.CDS2 8941009 8941577
chr_1 g10339 g10339.t2 TTS g10339.t2 8941863 8941863
chr_1 g10339 g10339.t2 TSS g10339.t2 NA NA

Sequences

>g10339.t2 Gene=g10339 Length=1203
CACTGTTGGATATTCTTTGATTGTAGTTTCAAAATCAGAATCAGTCAATTCAAAACATCA
AAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAAAACATGATC
ACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACTGGTGAATTC
GAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCTTTCACATTG
GGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCACCATACTCA
GAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAGATCGGTTAC
AATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAACATGCTTGAA
CCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAGGGTAAAGCT
GATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGTCCAACTGAC
AAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGGTATTGGAACTGTGCCA
GTCGGACGTGTTGAAACTGGTGTTTTGAAACCAGGTATGGTCGTCGTTTTTGCACCAGTC
AACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAAGAAGCTGTA
CCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGT
TATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAA
GTAATTGTCTTGAATCATCCAGGTCAAATTTCAAACGGTTACACACCAGTTTTGGATTGC
CACACTGCTCACATTGCCTGCAAGTTCTCTGAAATCAAAGAAAAAGTTGATCGTCGTTCA
GGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAATCAGGAGATGCTGCTATCGTCATT
TTGGTCCCAACAAAACCATTGTGCGTTGAATCATTCCAAGAATTCCCACCATTGGGACGT
TTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTCGGTGTCATCAAGGCAGTTTCATTC
AAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAGAAA
TAG

>g10339.t2 Gene=g10339 Length=362
MITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPP
YSEARFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEG
KADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFA
PVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFT
AQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKEKVDRRSGKSVEDNPKAIKSGDAAI
VILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKAVSFKDASGGKTTKAAEKAQKA
KK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g10339.t2 CDD cd03693 EF1_alpha_II 141 231 0.000000
16 g10339.t2 CDD cd03705 EF1_alpha_III 234 337 0.000000
11 g10339.t2 Gene3D G3DSA:3.40.50.300 - 1 137 0.000000
13 g10339.t2 Gene3D G3DSA:2.40.30.10 Translation factors 139 231 0.000000
12 g10339.t2 Gene3D G3DSA:2.40.30.10 Translation factors 234 341 0.000000
4 g10339.t2 PANTHER PTHR23115 TRANSLATION FACTOR 1 358 0.000000
5 g10339.t2 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 358 0.000000
7 g10339.t2 PRINTS PR00315 GTP-binding elongation factor signature 3 14 0.000039
6 g10339.t2 PRINTS PR00315 GTP-binding elongation factor signature 47 56 0.000039
3 g10339.t2 Pfam PF00009 Elongation factor Tu GTP binding domain 1 135 0.000000
2 g10339.t2 Pfam PF03144 Elongation factor Tu domain 2 159 224 0.000000
1 g10339.t2 Pfam PF03143 Elongation factor Tu C-terminal domain 235 340 0.000000
14 g10339.t2 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 141 26.072000
9 g10339.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 160 0.000000
10 g10339.t2 SUPERFAMILY SSF50447 Translation proteins 142 271 0.000000
8 g10339.t2 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 237 340 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: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