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.t20 TSS g10339.t20 8939297 8939297
chr_1 g10339 g10339.t20 isoform g10339.t20 8940109 8940635
chr_1 g10339 g10339.t20 exon g10339.t20.exon1 8940109 8940635
chr_1 g10339 g10339.t20 cds g10339.t20.CDS1 8940122 8940634
chr_1 g10339 g10339.t20 TTS g10339.t20 NA NA

Sequences

>g10339.t20 Gene=g10339 Length=527
AAAGCAAAGCAACATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGT
CGACTCTGGCAAGTCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAA
GCGTACAATCGAGAAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATA
CGCATGGGTTTTGGACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGC
CTTGTGGAAATTCGAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCG
TGATTTCATCAAAAACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGT
CGCTGCCGGTACTGGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACA
CGCTTTGTTGGCTTTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGA
CTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATTAAGA

>g10339.t20 Gene=g10339 Length=171
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10339.t20 CDD cd01883 EF1_alpha 9 171 1.69149E-127
10 g10339.t20 Gene3D G3DSA:3.40.50.300 - 1 171 2.4E-74
2 g10339.t20 PANTHER PTHR23115 TRANSLATION FACTOR 1 171 5.1E-151
3 g10339.t20 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 171 5.1E-151
6 g10339.t20 PRINTS PR00315 GTP-binding elongation factor signature 9 22 3.9E-26
8 g10339.t20 PRINTS PR00315 GTP-binding elongation factor signature 68 76 3.9E-26
7 g10339.t20 PRINTS PR00315 GTP-binding elongation factor signature 88 98 3.9E-26
4 g10339.t20 PRINTS PR00315 GTP-binding elongation factor signature 104 115 3.9E-26
5 g10339.t20 PRINTS PR00315 GTP-binding elongation factor signature 148 157 3.9E-26
1 g10339.t20 Pfam PF00009 Elongation factor Tu GTP binding domain 5 169 2.6E-49
12 g10339.t20 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
13 g10339.t20 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 171 55.845
9 g10339.t20 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 170 4.23E-63

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