Gene loci information

Transcript annotation

  • This transcript has been annotated as Translation 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.t4 TSS g12287.t4 22169311 22169311
chr_1 g12287 g12287.t4 isoform g12287.t4 22169380 22170949
chr_1 g12287 g12287.t4 exon g12287.t4.exon1 22169380 22169382
chr_1 g12287 g12287.t4 cds g12287.t4.CDS1 22169380 22169382
chr_1 g12287 g12287.t4 exon g12287.t4.exon2 22169830 22170044
chr_1 g12287 g12287.t4 cds g12287.t4.CDS2 22169830 22170044
chr_1 g12287 g12287.t4 exon g12287.t4.exon3 22170108 22170375
chr_1 g12287 g12287.t4 cds g12287.t4.CDS3 22170108 22170375
chr_1 g12287 g12287.t4 exon g12287.t4.exon4 22170723 22170949
chr_1 g12287 g12287.t4 TTS g12287.t4 NA NA

Sequences

>g12287.t4 Gene=g12287 Length=713
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGC
AAGGATGAACAAGAAAGATGTATCACAATTAAGTCAACTGCTATCTCTATGTTCTTTGAG
TTAGAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAGAAGAAAAA
GGTTTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAGAAGTCACA
GCCGCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTATCAGGTAAATTA
CAAAATTTTTACTTATTTTGCATTTCTTTATCAATCGTTTATGACTTCGTTATCAAATAT
CAATGACGATGACGATGGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGT
CGGTTTCGGTTCCGGCTTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTA
TGCAGCTAAATTCAAGATCGATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTT
CTTCAATGCAAAGACCAAGAAATGGGCAAAGACAAAGGACGATGATAACAAGC

>g12287.t4 Gene=g12287 Length=161
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTR
KDEQERCITIKSTAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVT
AALRVTDGALVVVDCVSGKLQNFYLFCISLSIVYDFVIKYQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12287.t4 Gene3D G3DSA:3.40.50.300 - 3 142 6.9E-51
2 g12287.t4 PANTHER PTHR42908:SF29 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2A, TANDEM DUPLICATE 1-RELATED 1 139 1.4E-70
3 g12287.t4 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 139 1.4E-70
7 g12287.t4 PRINTS PR00315 GTP-binding elongation factor signature 21 34 2.4E-12
6 g12287.t4 PRINTS PR00315 GTP-binding elongation factor signature 65 73 2.4E-12
5 g12287.t4 PRINTS PR00315 GTP-binding elongation factor signature 105 115 2.4E-12
4 g12287.t4 PRINTS PR00315 GTP-binding elongation factor signature 121 132 2.4E-12
1 g12287.t4 Pfam PF00009 Elongation factor Tu GTP binding domain 17 139 2.5E-44
10 g12287.t4 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 58 73 -
11 g12287.t4 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 17 161 37.582
8 g12287.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 139 7.13E-51
12 g12287.t4 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 139 1.8E-13

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