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.t19 TSS g10339.t19 8939297 8939297
chr_1 g10339 g10339.t19 isoform g10339.t19 8939431 8940677
chr_1 g10339 g10339.t19 exon g10339.t19.exon1 8939431 8939700
chr_1 g10339 g10339.t19 exon g10339.t19.exon2 8940109 8940677
chr_1 g10339 g10339.t19 cds g10339.t19.CDS1 8940122 8940676
chr_1 g10339 g10339.t19 TTS g10339.t19 NA NA

Sequences

>g10339.t19 Gene=g10339 Length=839
GGTTGTTACTATTGTAAAATTCATAGTGAGATATTATTTAATTATCGCGTAAAAAGTTCT
TTTTCTAATGGTGACCGCGTGGCATATGCGGCATATTAGTTTTACATTTTGAGGCTAATT
TAGTCATCATAATCATTATAATCATTTTTAAATATTATTTATAAGTATCTTTCAAAAATT
AAATTGAATTATTTATCTACAATTTTTTTAAAAATTCACCGGTGAAAGTTGAATGGAAAA
ATTTCATAACCACATGTTTTTCATGTTTTCAAAGCAAAGCAACATGGCTAAAGAAAAGAC
TCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAGTCAACCACTACTGGTCA
TTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAGAAATTCGAAAAGGAAGC
ACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTGGACAAATTGAAGGCCGA
ACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTCGAAACATCAAAATACTA
CGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAAAACATGATCACAGGAAC
ATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGG
TATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAA
ACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCACCATACTCAGAAGCTCG
TTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAGATCGGTTACAATCCAG

>g10339.t19 Gene=g10339 Length=185
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10339.t19 CDD cd01883 EF1_alpha 9 185 3.66934E-136
10 g10339.t19 Gene3D G3DSA:3.40.50.300 - 1 185 1.7E-78
2 g10339.t19 PANTHER PTHR23115 TRANSLATION FACTOR 1 185 3.0E-164
3 g10339.t19 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 185 3.0E-164
6 g10339.t19 PRINTS PR00315 GTP-binding elongation factor signature 9 22 5.2E-26
8 g10339.t19 PRINTS PR00315 GTP-binding elongation factor signature 68 76 5.2E-26
7 g10339.t19 PRINTS PR00315 GTP-binding elongation factor signature 88 98 5.2E-26
4 g10339.t19 PRINTS PR00315 GTP-binding elongation factor signature 104 115 5.2E-26
5 g10339.t19 PRINTS PR00315 GTP-binding elongation factor signature 148 157 5.2E-26
1 g10339.t19 Pfam PF00009 Elongation factor Tu GTP binding domain 5 178 5.4E-51
12 g10339.t19 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
13 g10339.t19 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 185 57.575
9 g10339.t19 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 185 3.13E-67

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