Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha 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 g10339 g10339.t4 TSS g10339.t4 8939297 8939297
chr_1 g10339 g10339.t4 isoform g10339.t4 8939304 8941577
chr_1 g10339 g10339.t4 exon g10339.t4.exon1 8939304 8939370
chr_1 g10339 g10339.t4 exon g10339.t4.exon2 8940109 8940962
chr_1 g10339 g10339.t4 cds g10339.t4.CDS1 8940122 8940949
chr_1 g10339 g10339.t4 exon g10339.t4.exon3 8941033 8941577
chr_1 g10339 g10339.t4 TTS g10339.t4 8941863 8941863

Sequences

>g10339.t4 Gene=g10339 Length=1466
CGTTTTAGCTCTCAAACAGTTCGAACGTTTTCGTTTACTCTTCTCTTGTGTTTAATAATT
TTTGATTAAAGCAAAGCAACATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTG
GACACGTCGACTCTGGCAAGTCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTA
TCGACAAGCGTACAATCGAGAAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCAT
TCAAATACGCATGGGTTTTGGACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTG
ATATCGCCTTGTGGAAATTCGAAACATCAAAATACTACGTTACCATCATTGACGCTCCCG
GACATCGTGATTTCATCAAAAACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTAT
TGATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTC
GTGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACA
AAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAG
TCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCT
CAGGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGAT
GGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACG
CCATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCT
ACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAAC
CAGGTTAGTTTTGAAAATAAATCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATC
ACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCT
CAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTG
GTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTTCAAACG
GTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTGAAATCA
AAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAAT
CAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAATCATTCC
AAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTCG
GTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCTG
AGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t4 Gene=g10339 Length=275
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10339.t4 CDD cd01883 EF1_alpha 9 239 1.23805E-161
10 g10339.t4 Gene3D G3DSA:3.40.50.300 - 1 238 1.9E-95
11 g10339.t4 Gene3D G3DSA:2.40.30.10 Translation factors 240 275 8.9E-14
2 g10339.t4 PANTHER PTHR23115 TRANSLATION FACTOR 1 275 3.2E-239
3 g10339.t4 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 275 3.2E-239
6 g10339.t4 PRINTS PR00315 GTP-binding elongation factor signature 9 22 2.4E-25
8 g10339.t4 PRINTS PR00315 GTP-binding elongation factor signature 68 76 2.4E-25
7 g10339.t4 PRINTS PR00315 GTP-binding elongation factor signature 88 98 2.4E-25
4 g10339.t4 PRINTS PR00315 GTP-binding elongation factor signature 104 115 2.4E-25
5 g10339.t4 PRINTS PR00315 GTP-binding elongation factor signature 148 157 2.4E-25
1 g10339.t4 Pfam PF00009 Elongation factor Tu GTP binding domain 5 237 1.6E-54
13 g10339.t4 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
14 g10339.t4 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
9 g10339.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 3.7E-81

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

Pathway

  • This transcript belongs to the following pathways

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