Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 2.

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 g12287 g12287.t21 TSS g12287.t21 22169829 22169829
chr_1 g12287 g12287.t21 isoform g12287.t21 22170544 22171552
chr_1 g12287 g12287.t21 exon g12287.t21.exon1 22170544 22171552
chr_1 g12287 g12287.t21 cds g12287.t21.CDS1 22170613 22171551
chr_1 g12287 g12287.t21 TTS g12287.t21 NA NA

Sequences

>g12287.t21 Gene=g12287 Length=1009
GGTGTTTGTGTACAAACTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCA
GTTTTGTTCATGAACAAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGAT
TTGTACCAAACATTCCAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGC
GATGACGATGGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTC
GGTTCCGGCTTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCT
AAATTCAAGATCGATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAAT
GCAAAGACCAAGAAATGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCATG
TATGTATTGGATCCAATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGAA
ATTCCTGGCTTATTGGAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGAT
GGTAAACAATTATTGAAAGTTGTCATGCGCTCATGGTTGCCAGCTGGTGAAGCTTTACTT
CAAATGATTGCTATTCACTTGCCTTCACCAGTCGTCGCTCAAAAATACCGTATGGAAATG
TTGTATGAGGGACCACTCGATGACGAGGCTGCCGTTGCTGTCAAGAACTGCGATCCAAAT
GGTCCATTGATGATGTACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCGTTTCTAT
GCTTTCGGACGTGTGTTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTATAATGGGA
CCAAATTACACACCTGGCAAGAAGGAAGACTTGTACGAAAAATCAATTCAACGTACTATT
TTGATGATGGGTCGTTATGTTGAAGCCATTGAAGATGTTCCATGCGGTAACATTTGCGGT
TTGGTTGGTGTTGATCAATTCTTGGTCAAGACTGGAACAATCACAACAT

>g12287.t21 Gene=g12287 Length=313
MNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATYSDDDGPMGEVRVDPSKGSVGFGSG
LHGWAFTLKQFSEMYAAKFKIDVVKLMNRLWGENFFNAKTKKWAKTKDDDNKRSFVMYVL
DPIYKVFDVIMNYKKEEIPGLLEKIGVTLKHEDKDKDGKQLLKVVMRSWLPAGEALLQMI
AIHLPSPVVAQKYRMEMLYEGPLDDEAAVAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFG
RVFSGKVQTGQKCRIMGPNYTPGKKEDLYEKSIQRTILMMGRYVEAIEDVPCGNICGLVG
VDQFLVKTGTITT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12287.t21 CDD cd03700 EF2_snRNP_like_II 220 313 0.0e+00
8 g12287.t21 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 68 170 0.0e+00
7 g12287.t21 Gene3D G3DSA:2.40.30.10 Translation factors 187 313 0.0e+00
3 g12287.t21 PANTHER PTHR42908:SF29 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2A, TANDEM DUPLICATE 1-RELATED 1 313 0.0e+00
4 g12287.t21 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 313 0.0e+00
2 g12287.t21 Pfam PF00009 Elongation factor Tu GTP binding domain 1 185 3.8e-06
1 g12287.t21 Pfam PF03144 Elongation factor Tu domain 2 236 311 0.0e+00
5 g12287.t21 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 185 0.0e+00
6 g12287.t21 SUPERFAMILY SSF50447 Translation proteins 186 313 0.0e+00

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