Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha 2.

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.t36 isoform g10339.t36 8940325 8941839
chr_1 g10339 g10339.t36 exon g10339.t36.exon1 8940325 8940944
chr_1 g10339 g10339.t36 cds g10339.t36.CDS1 8940425 8940944
chr_1 g10339 g10339.t36 exon g10339.t36.exon2 8941009 8941251
chr_1 g10339 g10339.t36 cds g10339.t36.CDS2 8941009 8941251
chr_1 g10339 g10339.t36 exon g10339.t36.exon3 8941614 8941839
chr_1 g10339 g10339.t36 cds g10339.t36.CDS3 8941614 8941636
chr_1 g10339 g10339.t36 TTS g10339.t36 8941863 8941863
chr_1 g10339 g10339.t36 TSS g10339.t36 NA NA

Sequences

>g10339.t36 Gene=g10339 Length=1089
ACGTGGTATCACCATTGATATCGCCTTGTGGAAATTCGAAACATCAAAATACTACGTTAC
CATCATTGACGCTCCCGGACATCGTGATTTCATCAAAAACATGATCACAGGAACATCTCA
AGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGGTATTTC
AAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAAACAATT
GATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGA
AGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGT
TGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGAT
GCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCT
CATTGATGCCTTGGACGCCATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTT
GCCACTTCAAGACGTCTACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGA
AACTGGTGTTTTGAAACCAGGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGA
AGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGT
TGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGA
CACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAA
TCATCCAGGTCAAATTTCAAACGCAAACAAGAAAAATTATTTCTAATGGTAAAAACTATA
ATTTTCATAGAAAAGAATTTAGAAGGAAAGAAGAGTGTGGATTTAATATGGCACATAAGA
AATGTATTTTCTTTAACATTCTTTATTATTATTAAATTCATTCCGAATACATACATTCAC
ATACGCCAACTATAACATGCATTTTTCTATTAAACAATGATTTTATGTTTGTCAAATTAT
GATTTTTTG

>g10339.t36 Gene=g10339 Length=261
MITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPP
YSEARFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEG
KADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFA
PVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFT
AQVIVLNHPGQISNANKKNYF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10339.t36 CDD cd03693 EF1_alpha_II 141 231 0.000000
9 g10339.t36 Gene3D G3DSA:3.40.50.300 - 1 137 0.000000
10 g10339.t36 Gene3D G3DSA:2.40.30.10 Translation factors 139 231 0.000000
3 g10339.t36 PANTHER PTHR23115 TRANSLATION FACTOR 1 254 0.000000
4 g10339.t36 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 254 0.000000
6 g10339.t36 PRINTS PR00315 GTP-binding elongation factor signature 3 14 0.000023
5 g10339.t36 PRINTS PR00315 GTP-binding elongation factor signature 47 56 0.000023
2 g10339.t36 Pfam PF00009 Elongation factor Tu GTP binding domain 1 136 0.000000
1 g10339.t36 Pfam PF03144 Elongation factor Tu domain 2 159 224 0.000000
11 g10339.t36 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 141 26.072000
7 g10339.t36 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 160 0.000000
8 g10339.t36 SUPERFAMILY SSF50447 Translation proteins 137 233 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