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 g11500 g11500.t4 TSS g11500.t4 16650082 16650082
chr_1 g11500 g11500.t4 isoform g11500.t4 16650214 16650639
chr_1 g11500 g11500.t4 exon g11500.t4.exon1 16650214 16650639
chr_1 g11500 g11500.t4 cds g11500.t4.CDS1 16650214 16650639
chr_1 g11500 g11500.t4 TTS g11500.t4 NA NA

Sequences

>g11500.t4 Gene=g11500 Length=426
ATGGGTAAAGAGAAGACTCATATTAATATTGTTGTCATTGGACATGTCGATTCTGGCAAG
TCAACTACAACCGGTCACTTGATCTACAAATGTGGCGGTATTGACAAACGTACCATCGAG
AAGTTCGAGAAGGAAGCTCAAGAAATGGGCAAAGGTTCATTCAAATACGCATGGGTATTG
GATAAGTTGAAGGCTGAACGTGAGCGTGGTATCACCATTGATATCGCCTTATGGAAGTTT
GAAACTGCCAAGTACTACGTTACCATCATTGACGCTCCTGGACATCGTGATTTCATCAAG
AACATGATTACAGGAACATCTCAAGCCGATTGCGCTGTATTGATTGTCGCTGCTGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAGCATGCATTGTTGGCT
TTCACA

>g11500.t4 Gene=g11500 Length=142
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11500.t4 Gene3D G3DSA:3.40.50.300 - 1 142 1.4E-62
2 g11500.t4 PANTHER PTHR23115 TRANSLATION FACTOR 1 142 7.6E-124
3 g11500.t4 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 142 7.6E-124
5 g11500.t4 PRINTS PR00315 GTP-binding elongation factor signature 9 22 6.5E-22
7 g11500.t4 PRINTS PR00315 GTP-binding elongation factor signature 68 76 6.5E-22
6 g11500.t4 PRINTS PR00315 GTP-binding elongation factor signature 88 98 6.5E-22
4 g11500.t4 PRINTS PR00315 GTP-binding elongation factor signature 104 115 6.5E-22
1 g11500.t4 Pfam PF00009 Elongation factor Tu GTP binding domain 5 141 7.7E-42
9 g11500.t4 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
11 g11500.t4 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 142 49.04
8 g11500.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 141 6.31E-54

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