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.t3 TSS g12287.t3 22169311 22169311
chr_1 g12287 g12287.t3 isoform g12287.t3 22169380 22170949
chr_1 g12287 g12287.t3 exon g12287.t3.exon1 22169380 22169382
chr_1 g12287 g12287.t3 cds g12287.t3.CDS1 22169380 22169382
chr_1 g12287 g12287.t3 exon g12287.t3.exon2 22169830 22170044
chr_1 g12287 g12287.t3 cds g12287.t3.CDS2 22169830 22170044
chr_1 g12287 g12287.t3 exon g12287.t3.exon3 22170108 22170294
chr_1 g12287 g12287.t3 cds g12287.t3.CDS3 22170108 22170294
chr_1 g12287 g12287.t3 exon g12287.t3.exon4 22170545 22170949
chr_1 g12287 g12287.t3 cds g12287.t3.CDS4 22170545 22170616
chr_1 g12287 g12287.t3 TTS g12287.t3 NA NA

Sequences

>g12287.t3 Gene=g12287 Length=810
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGC
AAGGATGAACAAGAAAGATGTATCACAATTAAGTCAACTGCTATCTCTATGTTCTTTGAG
TTAGAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAGAAGAAAAA
GGTTTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAGAAGTCACA
GCCGCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTGTTTGTGTACAAA
CTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCAGTTTTGTTCATGAACA
AGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATTTGTACCAAACATTCC
AACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCGATGACGATGGTCCAA
TGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCGGTTCCGGCTTGCACG
GATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTAAATTCAAGATCGATG
TCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAATGCAAAGACCAAGAAAT
GGGCAAAGACAAAGGACGATGATAACAAGC

>g12287.t3 Gene=g12287 Length=158
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTR
KDEQERCITIKSTAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVT
AALRVTDGALVVVDCVFVYKLRLYCVKLLPNVLSQFCS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12287.t3 Gene3D G3DSA:3.40.50.300 - 3 137 4.5E-50
2 g12287.t3 PANTHER PTHR42908:SF27 ELONGATION FACTOR 2 1 137 3.2E-69
3 g12287.t3 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 137 3.2E-69
7 g12287.t3 PRINTS PR00315 GTP-binding elongation factor signature 21 34 2.3E-12
6 g12287.t3 PRINTS PR00315 GTP-binding elongation factor signature 65 73 2.3E-12
5 g12287.t3 PRINTS PR00315 GTP-binding elongation factor signature 105 115 2.3E-12
4 g12287.t3 PRINTS PR00315 GTP-binding elongation factor signature 121 132 2.3E-12
1 g12287.t3 Pfam PF00009 Elongation factor Tu GTP binding domain 17 136 5.8E-43
10 g12287.t3 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 58 73 -
11 g12287.t3 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 17 158 34.46
8 g12287.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 136 1.47E-49
12 g12287.t3 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 134 9.2E-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