Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Elongation factor Tu.

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_3 g3703 g3703.t2 TSS g3703.t2 27559298 27559298
chr_3 g3703 g3703.t2 isoform g3703.t2 27559446 27560015
chr_3 g3703 g3703.t2 exon g3703.t2.exon1 27559446 27559485
chr_3 g3703 g3703.t2 cds g3703.t2.CDS1 27559446 27559485
chr_3 g3703 g3703.t2 exon g3703.t2.exon2 27559554 27559676
chr_3 g3703 g3703.t2 cds g3703.t2.CDS2 27559554 27559676
chr_3 g3703 g3703.t2 exon g3703.t2.exon3 27559735 27559779
chr_3 g3703 g3703.t2 cds g3703.t2.CDS3 27559735 27559779
chr_3 g3703 g3703.t2 exon g3703.t2.exon4 27559835 27560015
chr_3 g3703 g3703.t2 cds g3703.t2.CDS4 27559835 27560013
chr_3 g3703 g3703.t2 TTS g3703.t2 NA NA

Sequences

>g3703.t2 Gene=g3703 Length=389
ATGTCGGCTTTAGTAGCTGTTAAACAAGCATTATCGCCAGCTCTTCGCTCCACATTCAGA
CAATTTCTGTTAAATACCAATGTTAAGTCATCAGGTTGCATTTCTGTATCGCCATTTATC
ATTTCAAAAAGATATTTTGCAGAGAAAAAAGTTTTCCAAAGAACTAAACCTCATTGCAAT
ATTGGCACAATTGGGCATGTAGATCACGGCAAAACGACATTGACAGCTGCTATAACAAAA
GTATTGGCTGAAAAAGATTTAGCTGAAAGTAAAGCATATTCTGATATAGATAATGCACCA
GAAGAAAAAGCTCGTGGAATCACAATCAATGTAGCTCATATTGAATATCAAACAGATAAT
CGTCATTATGGACATACAGATTGCCCTGG

>g3703.t2 Gene=g3703 Length=129
MSALVAVKQALSPALRSTFRQFLLNTNVKSSGCISVSPFIISKRYFAEKKVFQRTKPHCN
IGTIGHVDHGKTTLTAAITKVLAEKDLAESKAYSDIDNAPEEKARGITINVAHIEYQTDN
RHYGHTDCP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3703.t2 Gene3D G3DSA:3.40.50.300 - 47 129 5.9E-23
2 g3703.t2 PANTHER PTHR43721:SF22 ELONGATION FACTOR TU, MITOCHONDRIAL 47 129 9.5E-40
3 g3703.t2 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED 47 129 9.5E-40
6 g3703.t2 PRINTS PR00315 GTP-binding elongation factor signature 60 73 2.3E-9
4 g3703.t2 PRINTS PR00315 GTP-binding elongation factor signature 104 112 2.3E-9
5 g3703.t2 PRINTS PR00315 GTP-binding elongation factor signature 124 129 2.3E-9
1 g3703.t2 Pfam PF00009 Elongation factor Tu GTP binding domain 56 129 3.2E-20
10 g3703.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
11 g3703.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g3703.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
13 g3703.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
9 g3703.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 129 -
14 g3703.t2 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 97 112 -
15 g3703.t2 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 56 129 22.537
7 g3703.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 46 129 1.83E-19

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