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.t2 TSS g10328.t2 8925998 8925998
chr_1 g10328 g10328.t2 isoform g10328.t2 8926250 8927229
chr_1 g10328 g10328.t2 exon g10328.t2.exon1 8926250 8927229
chr_1 g10328 g10328.t2 cds g10328.t2.CDS1 8926270 8927229
chr_1 g10328 g10328.t2 TTS g10328.t2 8927236 8927236

Sequences

>g10328.t2 Gene=g10328 Length=980
ATGCTGATTATATAAAAAACATGATTTCGGGAGCAAGTCAGATGGATGGAAGTATTTTAG
TTGTTGGTGCAGATGATGGTCAAATGCCTCAAACTAGAGAACATTTGCTGCTAGCAAAGC
AAGTAGGAATTGATAAAATAGTTGTTTACATAAATAAAGCCGACAAAGTAGATAATGAGA
TACTTGAACTTGTTGAGCTTGAAGTTAGAGAACTACTTTGCGATTTTGGTTTTGATGGCG
GCAATTGTCCGGTAATTTATGGTTCAGCATTGAAAGCACTTACAGGAGATGAAAGCGAAA
TCGGTGAACAATCTATTTTAAAACTTCTCGATGCAATTGATAATTATATTCCTACACCTC
AAAGAGATGTGAATGGACCGCTTTTAATGCCCATAGATAATTTTTTTACTGTACCTGGGC
GTGGAAGTGTAGTTGTTGGTACAATTAAAAGAGGTACTATGGTAAAGAATAGCGATATAG
AATTACTAGGTTTTGATCAGAAATTCAAATCAACAGTTTCTGATATTCAAATTTTCAAGA
AAAGTTATAATAAAGCATTAGCTGGCGAGAATGTTGGTGTATTATTAAGGAATATTAAAA
TAAAAAATATTCAACGTGGGATGTTGCTATGTGCTCCAAATACTGAAACACTTTCAAATC
ATTTTGAAGCAAATATGTATCTTCTCTCAAAAGCTGAAGGAGGAAGAAAACTTCCACTCG
CATCTAAATATATACAACAAATATACAGTCGAACATGGTGTATACCAGCAAGAATAGATT
TGGAAAACTCTCAAATTTTGATGCCGGGTGATCATGGAAAAGTTAGAATAACACTCTTTA
AAAAAATGGTCATGTCAATAGGTCAACCTTTTACATTTAGAGAGCAAGGAACAACTGTTG
CAACTGGTATTATTACTAAAAGATTTGATCCTATTCAATTACCGCAAAATAAATTATCAA
AAGTTGTGTTAAACATTTAA

>g10328.t2 Gene=g10328 Length=319
MISGASQMDGSILVVGADDGQMPQTREHLLLAKQVGIDKIVVYINKADKVDNEILELVEL
EVRELLCDFGFDGGNCPVIYGSALKALTGDESEIGEQSILKLLDAIDNYIPTPQRDVNGP
LLMPIDNFFTVPGRGSVVVGTIKRGTMVKNSDIELLGFDQKFKSTVSDIQIFKKSYNKAL
AGENVGVLLRNIKIKNIQRGMLLCAPNTETLSNHFEANMYLLSKAEGGRKLPLASKYIQQ
IYSRTWCIPARIDLENSQILMPGDHGKVRITLFKKMVMSIGQPFTFREQGTTVATGIITK
RFDPIQLPQNKLSKVVLNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10328.t2 CDD cd03706 mtEFTU_III 210 300 0.000
9 g10328.t2 Gene3D G3DSA:3.40.50.300 - 1 113 0.000
11 g10328.t2 Gene3D G3DSA:2.40.30.10 Translation factors 116 209 0.000
10 g10328.t2 Gene3D G3DSA:2.40.30.10 Translation factors 211 301 0.000
4 g10328.t2 PANTHER PTHR43721 ELONGATION FACTOR TU-RELATED 1 309 0.000
5 g10328.t2 PANTHER PTHR43721:SF2 AT01345P 1 309 0.000
3 g10328.t2 Pfam PF00009 Elongation factor Tu GTP binding domain 1 111 0.000
2 g10328.t2 Pfam PF03144 Elongation factor Tu domain 2 135 204 0.000
1 g10328.t2 Pfam PF03143 Elongation factor Tu C-terminal domain 213 300 0.000
12 g10328.t2 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 1 114 30.881
7 g10328.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 135 0.000
8 g10328.t2 SUPERFAMILY SSF50447 Translation proteins 114 208 0.000
6 g10328.t2 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 213 303 0.000

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