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_1 g10328 g10328.t1 TSS g10328.t1 8925759 8925759
chr_1 g10328 g10328.t1 isoform g10328.t1 8925827 8927229
chr_1 g10328 g10328.t1 exon g10328.t1.exon1 8925827 8926190
chr_1 g10328 g10328.t1 cds g10328.t1.CDS1 8925827 8926190
chr_1 g10328 g10328.t1 exon g10328.t1.exon2 8926247 8927229
chr_1 g10328 g10328.t1 cds g10328.t1.CDS2 8926247 8927229
chr_1 g10328 g10328.t1 TTS g10328.t1 8927236 8927236

Sequences

>g10328.t1 Gene=g10328 Length=1347
ATGTTACTTAGGCATTTTATTTACAGTAAAAGAATATTTAAAAATGAAATATTTAGTAAA
ATAAAGAGTATCAATCATTCATTAAATTCAATAAAATATCTTTCAACAAAACCATCAGAA
AAATCAAACCAAGAAAACCTCAAACCTCACTGTAATATAGGAACGATTGGTCATGTTGAT
CACGGTAAGACAACTTTAACAGCAGCAATAACAAAAGTATTGGAAAAGAGAGGACTTGCA
AATTTTACATCTTACGATGAAATTGATAAAGCGCCAGAAGAGAAAGCAAGAGGAATAACT
ATTAATGCTGCACATATAGGATATGAAACAAGCAAACGAACTTATGCACATACTGATTGT
CCTGGACATGCTGATTATATAAAAAACATGATTTCGGGAGCAAGTCAGATGGATGGAAGT
ATTTTAGTTGTTGGTGCAGATGATGGTCAAATGCCTCAAACTAGAGAACATTTGCTGCTA
GCAAAGCAAGTAGGAATTGATAAAATAGTTGTTTACATAAATAAAGCCGACAAAGTAGAT
AATGAGATACTTGAACTTGTTGAGCTTGAAGTTAGAGAACTACTTTGCGATTTTGGTTTT
GATGGCGGCAATTGTCCGGTAATTTATGGTTCAGCATTGAAAGCACTTACAGGAGATGAA
AGCGAAATCGGTGAACAATCTATTTTAAAACTTCTCGATGCAATTGATAATTATATTCCT
ACACCTCAAAGAGATGTGAATGGACCGCTTTTAATGCCCATAGATAATTTTTTTACTGTA
CCTGGGCGTGGAAGTGTAGTTGTTGGTACAATTAAAAGAGGTACTATGGTAAAGAATAGC
GATATAGAATTACTAGGTTTTGATCAGAAATTCAAATCAACAGTTTCTGATATTCAAATT
TTCAAGAAAAGTTATAATAAAGCATTAGCTGGCGAGAATGTTGGTGTATTATTAAGGAAT
ATTAAAATAAAAAATATTCAACGTGGGATGTTGCTATGTGCTCCAAATACTGAAACACTT
TCAAATCATTTTGAAGCAAATATGTATCTTCTCTCAAAAGCTGAAGGAGGAAGAAAACTT
CCACTCGCATCTAAATATATACAACAAATATACAGTCGAACATGGTGTATACCAGCAAGA
ATAGATTTGGAAAACTCTCAAATTTTGATGCCGGGTGATCATGGAAAAGTTAGAATAACA
CTCTTTAAAAAAATGGTCATGTCAATAGGTCAACCTTTTACATTTAGAGAGCAAGGAACA
ACTGTTGCAACTGGTATTATTACTAAAAGATTTGATCCTATTCAATTACCGCAAAATAAA
TTATCAAAAGTTGTGTTAAACATTTAA

>g10328.t1 Gene=g10328 Length=448
MLLRHFIYSKRIFKNEIFSKIKSINHSLNSIKYLSTKPSEKSNQENLKPHCNIGTIGHVD
HGKTTLTAAITKVLEKRGLANFTSYDEIDKAPEEKARGITINAAHIGYETSKRTYAHTDC
PGHADYIKNMISGASQMDGSILVVGADDGQMPQTREHLLLAKQVGIDKIVVYINKADKVD
NEILELVELEVRELLCDFGFDGGNCPVIYGSALKALTGDESEIGEQSILKLLDAIDNYIP
TPQRDVNGPLLMPIDNFFTVPGRGSVVVGTIKRGTMVKNSDIELLGFDQKFKSTVSDIQI
FKKSYNKALAGENVGVLLRNIKIKNIQRGMLLCAPNTETLSNHFEANMYLLSKAEGGRKL
PLASKYIQQIYSRTWCIPARIDLENSQILMPGDHGKVRITLFKKMVMSIGQPFTFREQGT
TVATGIITKRFDPIQLPQNKLSKVVLNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g10328.t1 CDD cd01884 EF_Tu 49 242 1.30957E-136
18 g10328.t1 CDD cd03697 EFTU_II 251 336 1.55019E-35
17 g10328.t1 CDD cd03706 mtEFTU_III 339 429 1.64047E-42
14 g10328.t1 Gene3D G3DSA:3.40.50.300 - 40 242 1.3E-65
16 g10328.t1 Gene3D G3DSA:2.40.30.10 Translation factors 245 338 2.4E-27
15 g10328.t1 Gene3D G3DSA:2.40.30.10 Translation factors 340 430 4.6E-25
4 g10328.t1 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED 16 438 1.1E-193
5 g10328.t1 PANTHER PTHR43721:SF2 AT01345P 16 438 1.1E-193
10 g10328.t1 PRINTS PR00315 GTP-binding elongation factor signature 52 65 4.2E-22
9 g10328.t1 PRINTS PR00315 GTP-binding elongation factor signature 96 104 4.2E-22
7 g10328.t1 PRINTS PR00315 GTP-binding elongation factor signature 116 126 4.2E-22
6 g10328.t1 PRINTS PR00315 GTP-binding elongation factor signature 132 143 4.2E-22
8 g10328.t1 PRINTS PR00315 GTP-binding elongation factor signature 169 178 4.2E-22
3 g10328.t1 Pfam PF00009 Elongation factor Tu GTP binding domain 48 240 3.5E-52
2 g10328.t1 Pfam PF03144 Elongation factor Tu domain 2 264 333 1.5E-10
1 g10328.t1 Pfam PF03143 Elongation factor Tu C-terminal domain 342 429 4.3E-17
20 g10328.t1 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 89 104 -
22 g10328.t1 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 48 243 53.172
12 g10328.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 38 253 7.95E-57
13 g10328.t1 SUPERFAMILY SSF50447 Translation proteins 243 337 4.99E-22
11 g10328.t1 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 342 432 1.12E-24
21 g10328.t1 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 52 186 6.9E-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

Pathway

  • This transcript belongs to the following pathways

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