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.t27 isoform g12287.t27 22172260 22173484
chr_1 g12287 g12287.t27 exon g12287.t27.exon1 22172260 22172432
chr_1 g12287 g12287.t27 cds g12287.t27.CDS1 22172426 22172432
chr_1 g12287 g12287.t27 exon g12287.t27.exon2 22172626 22173484
chr_1 g12287 g12287.t27 cds g12287.t27.CDS2 22172626 22173107
chr_1 g12287 g12287.t27 TTS g12287.t27 22173564 22173564
chr_1 g12287 g12287.t27 TSS g12287.t27 NA NA

Sequences

>g12287.t27 Gene=g12287 Length=1032
GGATGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGACGGTACAGGTCCAAATGT
AATTGTTGACGTCACTAAGGGTGTACAATATTTGAATGAAATCAAGGACTCTGTTGTTGC
TGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAGAACATGAGAGCTGTTCG
TTTCAACATTTATGATGTTACACTGCATGCTGACGCTATCCATCGTGGAGGTGGTCAAAT
CATTCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACAGCTTCTCCACGTTTGAT
GGAGCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTCGGTGGTATTTATGG
TGTGCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAAGTTGCCGGTACACCTAT
GTTCGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTTGGATTCACTGCTGATTTGCG
CTCAAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTTGACCATTGGCAGATCTTCCC
AGGTGACCCTAACGAACCATCATCAAAACCATACCAGATTGTGCAAGATACAAGAAAACG
TAAAGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATACTATGATAAAATGTAAAAGTC
TTTCCGAGCTTCTTCAGTTATACTTATTATTTTTTCCCTCTTCATTTTTTGCTTATAATT
TTTTGATTTTTATATTTTTATCATAACATTACGCATAAAAGATAAAACAACATCAAAGCA
AGAAAAAAGCGTTGATTATTTTATATCAATTAATCGTAATATTGTAATCAAACTTAAAAT
ATTTTTTGAGCGTCTTAATATGAGTTAAGTTAAAAGCATTCTCCTATGAAAATTAAAAGC
GTTTATGAGTTCGCCATAAATATGCTGTTACATCTACGCGCGAAAGTGGTTGAAATGAAA
AAGAATTTCATATAAATATTAACAATGATATCCAGCAACATGGAAGAAAAATTAGAACGA
CGGAAACGGAAA

>g12287.t27 Gene=g12287 Length=162
MRAVRFNIYDVTLHADAIHRGGGQIIPTTRRCLYASYITASPRLMEPVYLCEIQCPEVAV
GGIYGVLNRRRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDH
WQIFPGDPNEPSSKPYQIVQDTRKRKGLKEGLPDLNQYYDKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12287.t27 CDD cd04096 eEF2_snRNP_like_C 46 125 0.0e+00
8 g12287.t27 Gene3D G3DSA:3.30.230.10 - 1 41 0.0e+00
9 g12287.t27 Gene3D G3DSA:3.30.70.240 - 42 162 0.0e+00
3 g12287.t27 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 162 0.0e+00
4 g12287.t27 PANTHER PTHR42908:SF28 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2,-LIKE 2-RELATED 1 162 0.0e+00
1 g12287.t27 Pfam PF03764 Elongation factor G, domain IV 2 40 6.3e-06
2 g12287.t27 Pfam PF00679 Elongation factor G C-terminus 43 129 0.0e+00
7 g12287.t27 SMART SM00838 EFG_C_a 43 132 0.0e+00
5 g12287.t27 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 1 45 0.0e+00
6 g12287.t27 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 46 160 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

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