Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor Tu, mitochondrial.

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.t15 TSS g3703.t15 27559298 27559298
chr_3 g3703 g3703.t15 isoform g3703.t15 27560103 27561217
chr_3 g3703 g3703.t15 exon g3703.t15.exon1 27560103 27560596
chr_3 g3703 g3703.t15 cds g3703.t15.CDS1 27560116 27560596
chr_3 g3703 g3703.t15 exon g3703.t15.exon2 27560672 27560767
chr_3 g3703 g3703.t15 cds g3703.t15.CDS2 27560672 27560767
chr_3 g3703 g3703.t15 exon g3703.t15.exon3 27560820 27561217
chr_3 g3703 g3703.t15 cds g3703.t15.CDS3 27560820 27561217
chr_3 g3703 g3703.t15 TTS g3703.t15 27561360 27561360

Sequences

>g3703.t15 Gene=g3703 Length=988
GGGTACTGCACAAATGGATGGAGCTATTTTAGTCGTCGCTGCAACGGATGGAGCTATGCC
TCAAACTAGAGAACATCTCTTATTGGCTAAACAAATTGGAGTTAATGATATTGTTGTATT
TATTAATAAAGTAGACGCTGCTGATGCTGAAATGGTTGAACTTGTTGAGATGGAAATTCG
TGAACTCATGACAGAAATGGGCTATGATGGCGATAAAGTTCCTATTATTAAAGGTTCAGC
ATTGTGCGCATTAGAAGAGAAAAATCCAGATATCGGTCAAAAAGCAATTTTGGAACTTCT
TGATACTGTTGATAAGACAATTCCTACTCCAGTTAGAGAGTTAGATAAACCATTCCTATT
ACCTGTTGAAAATGTCTATAGCATTCAAGGTCGCGGTACAGTTGTGTCGGGAAGATTAGA
ACGAGGTGTTTTAAAGAAGGGAGCTGAATGTGAATTTGTTGGATATAACAAAGTATTGAA
ATCAACTGTTACAGGAGTTGAAATGTTCCATCAAATTCTCGAAGAAGCTCAAGCAGGTGA
TCAACTTGGTGCATTAGTCAGAGGAGTGAAGCGTGACGATATTAAAAGAGGTATGGTAAT
GTGTAAACCTGGATCATGCAAAGCAATTGATCAAGTTGAAGCCCAAGTTTACATTTTAAG
CAAAGAAGAAGGCGGTCGAACAAAACCTTTTACAAGCTTCTTCCAATTACAAATGTTCTC
ACGTACATGGGACTGTGCTGCTGTTTGTATAATACCTGGAAAAGAAATGTGTATGCCAGG
TGAAGATACAAGTCTTCAATTGAAACTTTTTAGACCAATGGTTCTTGAACAAGGACAGAG
ATTCACACTTAGAGATGGCAAAATTACACTTGGAACTGGCGTTGTAACTAAAATTTTACC
ACCATTATCTGAAATAGAACGACAAGAATTGACAGAAGGTAAGAAAGGACGTGAAAAGAA
AGAGAAAAAGAACAAGAAAACAGTTTAA

>g3703.t15 Gene=g3703 Length=324
MDGAILVVAATDGAMPQTREHLLLAKQIGVNDIVVFINKVDAADAEMVELVEMEIRELMT
EMGYDGDKVPIIKGSALCALEEKNPDIGQKAILELLDTVDKTIPTPVRELDKPFLLPVEN
VYSIQGRGTVVSGRLERGVLKKGAECEFVGYNKVLKSTVTGVEMFHQILEEAQAGDQLGA
LVRGVKRDDIKRGMVMCKPGSCKAIDQVEAQVYILSKEEGGRTKPFTSFFQLQMFSRTWD
CAAVCIIPGKEMCMPGEDTSLQLKLFRPMVLEQGQRFTLRDGKITLGTGVVTKILPPLSE
IERQELTEGKKGREKKEKKNKKTV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3703.t15 CDD cd03697 EFTU_II 114 200 9.27955E-49
14 g3703.t15 CDD cd03706 mtEFTU_III 203 294 8.73066E-52
10 g3703.t15 Gene3D G3DSA:3.40.50.300 - 1 106 5.1E-28
11 g3703.t15 Gene3D G3DSA:2.40.30.10 Translation factors 109 203 2.7E-34
12 g3703.t15 Gene3D G3DSA:2.40.30.10 Translation factors 206 304 1.3E-31
9 g3703.t15 MobiDBLite mobidb-lite consensus disorder prediction 303 324 -
4 g3703.t15 PANTHER PTHR43721:SF22 ELONGATION FACTOR TU, MITOCHONDRIAL 1 295 3.4E-135
5 g3703.t15 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED 1 295 3.4E-135
3 g3703.t15 Pfam PF00009 Elongation factor Tu GTP binding domain 1 104 4.8E-20
2 g3703.t15 Pfam PF03144 Elongation factor Tu domain 2 128 197 1.1E-15
1 g3703.t15 Pfam PF03143 Elongation factor Tu C-terminal domain 202 294 1.1E-23
13 g3703.t15 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 107 30.505
7 g3703.t15 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 122 2.67E-25
8 g3703.t15 SUPERFAMILY SSF50447 Translation proteins 108 201 2.75E-27
6 g3703.t15 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 206 299 2.3E-31

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