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.t9 TSS g3703.t9 27559298 27559298
chr_3 g3703 g3703.t9 isoform g3703.t9 27559446 27561217
chr_3 g3703 g3703.t9 exon g3703.t9.exon1 27559446 27559485
chr_3 g3703 g3703.t9 cds g3703.t9.CDS1 27559446 27559485
chr_3 g3703 g3703.t9 exon g3703.t9.exon2 27559554 27559676
chr_3 g3703 g3703.t9 cds g3703.t9.CDS2 27559554 27559676
chr_3 g3703 g3703.t9 exon g3703.t9.exon3 27559735 27559779
chr_3 g3703 g3703.t9 cds g3703.t9.CDS3 27559735 27559779
chr_3 g3703 g3703.t9 exon g3703.t9.exon4 27559835 27560014
chr_3 g3703 g3703.t9 cds g3703.t9.CDS4 27559835 27560014
chr_3 g3703 g3703.t9 exon g3703.t9.exon5 27560072 27560596
chr_3 g3703 g3703.t9 cds g3703.t9.CDS5 27560072 27560596
chr_3 g3703 g3703.t9 exon g3703.t9.exon6 27560672 27561217
chr_3 g3703 g3703.t9 cds g3703.t9.CDS6 27560672 27560781
chr_3 g3703 g3703.t9 TTS g3703.t9 27561360 27561360

Sequences

>g3703.t9 Gene=g3703 Length=1459
ATGTCGGCTTTAGTAGCTGTTAAACAAGCATTATCGCCAGCTCTTCGCTCCACATTCAGA
CAATTTCTGTTAAATACCAATGTTAAGTCATCAGGTTGCATTTCTGTATCGCCATTTATC
ATTTCAAAAAGATATTTTGCAGAGAAAAAAGTTTTCCAAAGAACTAAACCTCATTGCAAT
ATTGGCACAATTGGGCATGTAGATCACGGCAAAACGACATTGACAGCTGCTATAACAAAA
GTATTGGCTGAAAAAGATTTAGCTGAAAGTAAAGCATATTCTGATATAGATAATGCACCA
GAAGAAAAAGCTCGTGGAATCACAATCAATGTAGCTCATATTGAATATCAAACAGATAAT
CGTCATTATGGACATACAGATTGCCCTGGACATGCTGATTATATTAAAAACATGATTACG
GGTACTGCACAAATGGATGGAGCTATTTTAGTCGTCGCTGCAACGGATGGAGCTATGCCT
CAAACTAGAGAACATCTCTTATTGGCTAAACAAATTGGAGTTAATGATATTGTTGTATTT
ATTAATAAAGTAGACGCTGCTGATGCTGAAATGGTTGAACTTGTTGAGATGGAAATTCGT
GAACTCATGACAGAAATGGGCTATGATGGCGATAAAGTTCCTATTATTAAAGGTTCAGCA
TTGTGCGCATTAGAAGAGAAAAATCCAGATATCGGTCAAAAAGCAATTTTGGAACTTCTT
GATACTGTTGATAAGACAATTCCTACTCCAGTTAGAGAGTTAGATAAACCATTCCTATTA
CCTGTTGAAAATGTCTATAGCATTCAAGGTCGCGGTACAGTTGTGTCGGGAAGATTAGAA
CGAGGTGTTTTAAAGAAGGGAGCTGAATGTGAATTTGTTGGATATAACAAAGTATTGAAA
TCAACTGTTACAGGAGTTGAAATGTTCCATCAAATTCTCGAAGAAGCTCAAGCAGGTGAT
CAACTTGGTGCATTAGTCAGAGGAGTGAAGCGTGACGATATTAAAAGAGGTATAAAAATA
TAAGATATTATTATATATTATTATTATAACATTATTTTAAGGTATGGTAATGTGTAAACC
TGGATCATGCAAAGCAATTGATCAAGTTGAAGCCCAAGTTTACATTTTAAGCAAAGAAGA
AGGCGGTCGAACAAAACCTTTTACAAGCTTCTTCCAATTACAAATGTTCTCACGTACATG
GGACTGTGCTGCTGTTTGTATAATACCTGGAAAAGAAATGTGTATGCCAGGTGAAGATAC
AAGTCTTCAATTGAAACTTTTTAGACCAATGGTTCTTGAACAAGGACAGAGATTCACACT
TAGAGATGGCAAAATTACACTTGGAACTGGCGTTGTAACTAAAATTTTACCACCATTATC
TGAAATAGAACGACAAGAATTGACAGAAGGTAAGAAAGGACGTGAAAAGAAAGAGAAAAA
GAACAAGAAAACAGTTTAA

>g3703.t9 Gene=g3703 Length=340
MSALVAVKQALSPALRSTFRQFLLNTNVKSSGCISVSPFIISKRYFAEKKVFQRTKPHCN
IGTIGHVDHGKTTLTAAITKVLAEKDLAESKAYSDIDNAPEEKARGITINVAHIEYQTDN
RHYGHTDCPGHADYIKNMITGTAQMDGAILVVAATDGAMPQTREHLLLAKQIGVNDIVVF
INKVDAADAEMVELVEMEIRELMTEMGYDGDKVPIIKGSALCALEEKNPDIGQKAILELL
DTVDKTIPTPVRELDKPFLLPVENVYSIQGRGTVVSGRLERGVLKKGAECEFVGYNKVLK
STVTGVEMFHQILEEAQAGDQLGALVRGVKRDDIKRGIKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g3703.t9 CDD cd01884 EF_Tu 57 250 7.26029E-142
19 g3703.t9 CDD cd03697 EFTU_II 258 337 3.06679E-44
12 g3703.t9 Gene3D G3DSA:3.40.50.300 - 48 250 3.9E-67
13 g3703.t9 Gene3D G3DSA:2.40.30.10 Translation factors 253 340 1.5E-29
3 g3703.t9 PANTHER PTHR43721:SF22 ELONGATION FACTOR TU, MITOCHONDRIAL 47 338 1.9E-153
4 g3703.t9 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED 47 338 1.9E-153
9 g3703.t9 PRINTS PR00315 GTP-binding elongation factor signature 60 73 1.4E-24
6 g3703.t9 PRINTS PR00315 GTP-binding elongation factor signature 104 112 1.4E-24
5 g3703.t9 PRINTS PR00315 GTP-binding elongation factor signature 124 134 1.4E-24
8 g3703.t9 PRINTS PR00315 GTP-binding elongation factor signature 140 151 1.4E-24
7 g3703.t9 PRINTS PR00315 GTP-binding elongation factor signature 177 186 1.4E-24
2 g3703.t9 Pfam PF00009 Elongation factor Tu GTP binding domain 56 248 3.3E-56
1 g3703.t9 Pfam PF03144 Elongation factor Tu domain 2 272 337 1.1E-13
15 g3703.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 16 -
16 g3703.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
17 g3703.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 11 -
18 g3703.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 16 -
14 g3703.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 17 340 -
21 g3703.t9 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 97 112 -
23 g3703.t9 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 56 251 57.627
10 g3703.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 54 273 3.56E-58
11 g3703.t9 SUPERFAMILY SSF50447 Translation proteins 252 338 1.81E-23
22 g3703.t9 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 60 196 6.4E-12

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