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.t13 TSS g3703.t13 27559298 27559298
chr_3 g3703 g3703.t13 isoform g3703.t13 27559446 27561217
chr_3 g3703 g3703.t13 exon g3703.t13.exon1 27559446 27559676
chr_3 g3703 g3703.t13 exon g3703.t13.exon2 27559735 27559779
chr_3 g3703 g3703.t13 exon g3703.t13.exon3 27559835 27560014
chr_3 g3703 g3703.t13 exon g3703.t13.exon4 27560072 27560596
chr_3 g3703 g3703.t13 cds g3703.t13.CDS1 27560095 27560596
chr_3 g3703 g3703.t13 exon g3703.t13.exon5 27560672 27560767
chr_3 g3703 g3703.t13 cds g3703.t13.CDS2 27560672 27560767
chr_3 g3703 g3703.t13 exon g3703.t13.exon6 27560820 27561217
chr_3 g3703 g3703.t13 cds g3703.t13.CDS3 27560820 27561217
chr_3 g3703 g3703.t13 TTS g3703.t13 27561360 27561360

Sequences

>g3703.t13 Gene=g3703 Length=1475
ATGTCGGCTTTAGTAGCTGTTAAACAAGCATTATCGCCAGGTGAATAAAATTTGGTTATA
TTTTCTCTATTGTTATTCAATATATTTATCTAATTGTGAAATTTACAGCTCTTCGCTCCA
CATTCAGACAATTTCTGTTAAATACCAATGTTAAGTCATCAGGTTGCATTTCTGTATCGC
CATTTATCATTTCAAAAAGATATTTTGCAGAGAAAAAAGTTTTCCAAAGAACTAAACCTC
ATTGCAATATTGGCACAATTGGGCATGTAGATCACGGCAAAACGACATTGACAGCTGCTA
TAACAAAAGTATTGGCTGAAAAAGATTTAGCTGAAAGTAAAGCATATTCTGATATAGATA
ATGCACCAGAAGAAAAAGCTCGTGGAATCACAATCAATGTAGCTCATATTGAATATCAAA
CAGATAATCGTCATTATGGACATACAGATTGCCCTGGACATGCTGATTATATTAAAAACA
TGATTACGGGTACTGCACAAATGGATGGAGCTATTTTAGTCGTCGCTGCAACGGATGGAG
CTATGCCTCAAACTAGAGAACATCTCTTATTGGCTAAACAAATTGGAGTTAATGATATTG
TTGTATTTATTAATAAAGTAGACGCTGCTGATGCTGAAATGGTTGAACTTGTTGAGATGG
AAATTCGTGAACTCATGACAGAAATGGGCTATGATGGCGATAAAGTTCCTATTATTAAAG
GTTCAGCATTGTGCGCATTAGAAGAGAAAAATCCAGATATCGGTCAAAAAGCAATTTTGG
AACTTCTTGATACTGTTGATAAGACAATTCCTACTCCAGTTAGAGAGTTAGATAAACCAT
TCCTATTACCTGTTGAAAATGTCTATAGCATTCAAGGTCGCGGTACAGTTGTGTCGGGAA
GATTAGAACGAGGTGTTTTAAAGAAGGGAGCTGAATGTGAATTTGTTGGATATAACAAAG
TATTGAAATCAACTGTTACAGGAGTTGAAATGTTCCATCAAATTCTCGAAGAAGCTCAAG
CAGGTGATCAACTTGGTGCATTAGTCAGAGGAGTGAAGCGTGACGATATTAAAAGAGGTA
TGGTAATGTGTAAACCTGGATCATGCAAAGCAATTGATCAAGTTGAAGCCCAAGTTTACA
TTTTAAGCAAAGAAGAAGGCGGTCGAACAAAACCTTTTACAAGCTTCTTCCAATTACAAA
TGTTCTCACGTACATGGGACTGTGCTGCTGTTTGTATAATACCTGGAAAAGAAATGTGTA
TGCCAGGTGAAGATACAAGTCTTCAATTGAAACTTTTTAGACCAATGGTTCTTGAACAAG
GACAGAGATTCACACTTAGAGATGGCAAAATTACACTTGGAACTGGCGTTGTAACTAAAA
TTTTACCACCATTATCTGAAATAGAACGACAAGAATTGACAGAAGGTAAGAAAGGACGTG
AAAAGAAAGAGAAAAAGAACAAGAAAACAGTTTAA

>g3703.t13 Gene=g3703 Length=331
MITGTAQMDGAILVVAATDGAMPQTREHLLLAKQIGVNDIVVFINKVDAADAEMVELVEM
EIRELMTEMGYDGDKVPIIKGSALCALEEKNPDIGQKAILELLDTVDKTIPTPVRELDKP
FLLPVENVYSIQGRGTVVSGRLERGVLKKGAECEFVGYNKVLKSTVTGVEMFHQILEEAQ
AGDQLGALVRGVKRDDIKRGMVMCKPGSCKAIDQVEAQVYILSKEEGGRTKPFTSFFQLQ
MFSRTWDCAAVCIIPGKEMCMPGEDTSLQLKLFRPMVLEQGQRFTLRDGKITLGTGVVTK
ILPPLSEIERQELTEGKKGREKKEKKNKKTV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3703.t13 CDD cd03697 EFTU_II 121 207 1.43835E-48
14 g3703.t13 CDD cd03706 mtEFTU_III 210 301 2.09745E-51
11 g3703.t13 Gene3D G3DSA:3.40.50.300 - 1 113 7.9E-31
13 g3703.t13 Gene3D G3DSA:2.40.30.10 Translation factors 116 210 2.8E-34
12 g3703.t13 Gene3D G3DSA:2.40.30.10 Translation factors 213 311 1.4E-31
16 g3703.t13 MobiDBLite mobidb-lite consensus disorder prediction 309 331 -
4 g3703.t13 PANTHER PTHR43721:SF22 ELONGATION FACTOR TU, MITOCHONDRIAL 1 302 5.0E-140
5 g3703.t13 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED 1 302 5.0E-140
7 g3703.t13 PRINTS PR00315 GTP-binding elongation factor signature 3 14 5.3E-6
6 g3703.t13 PRINTS PR00315 GTP-binding elongation factor signature 40 49 5.3E-6
3 g3703.t13 Pfam PF00009 Elongation factor Tu GTP binding domain 1 111 8.2E-23
2 g3703.t13 Pfam PF03144 Elongation factor Tu domain 2 135 204 1.1E-15
1 g3703.t13 Pfam PF03143 Elongation factor Tu C-terminal domain 209 301 1.2E-23
17 g3703.t13 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 114 32.965
9 g3703.t13 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 136 1.65E-27
10 g3703.t13 SUPERFAMILY SSF50447 Translation proteins 115 208 2.95E-27
8 g3703.t13 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 213 306 2.4E-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