Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha.

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.t24 TSS g10339.t24 8939297 8939297
chr_1 g10339 g10339.t24 isoform g10339.t24 8940122 8941577
chr_1 g10339 g10339.t24 exon g10339.t24.exon1 8940122 8940929
chr_1 g10339 g10339.t24 cds g10339.t24.CDS1 8940122 8940929
chr_1 g10339 g10339.t24 exon g10339.t24.exon2 8941009 8941577
chr_1 g10339 g10339.t24 cds g10339.t24.CDS2 8941009 8941577
chr_1 g10339 g10339.t24 TTS g10339.t24 8941863 8941863

Sequences

>g10339.t24 Gene=g10339 Length=1377
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCA
CCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAG
ATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAG
GGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGGTATTGGA
ACTGTGCCAGTCGGACGTGTTGAAACTGGTATGGTCGTCGTTTTTGCACCAGTCAACTTG
ACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAAGAAGCTGTACCAGGT
GACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTT
GCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATT
GTCTTGAATCATCCAGGTCAAATTTCAAACGGTTACACACCAGTTTTGGATTGCCACACT
GCTCACATTGCCTGCAAGTTCTCTGAAATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAA
TCAGTTGAAGATAACCCCAAGGCTATCAAATCAGGAGATGCTGCTATCGTCATTTTGGTC
CCAACAAAACCATTGTGCGTTGAATCATTCCAAGAATTCCCACCATTGGGACGTTTCGCC
GTTCGTGATATGAGACAAACAGTTGCTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGAT
GCTTCAGGTGGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t24 Gene=g10339 Length=458
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGMVVVFAPVNLTTEVKSVEMHHEALQEAVPG
DNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHT
AHIACKFSEIKEKVDRRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFA
VRDMRQTVAVGVIKAVSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g10339.t24 CDD cd01883 EF1_alpha 9 239 3.27781E-160
17 g10339.t24 CDD cd03693 EF1_alpha_II 242 327 5.04456E-53
19 g10339.t24 CDD cd03705 EF1_alpha_III 330 433 1.67965E-71
14 g10339.t24 Gene3D G3DSA:3.40.50.300 - 1 238 9.0E-95
15 g10339.t24 Gene3D G3DSA:2.40.30.10 Translation factors 240 327 5.7E-36
16 g10339.t24 Gene3D G3DSA:2.40.30.10 Translation factors 330 437 1.9E-51
4 g10339.t24 PANTHER PTHR23115 TRANSLATION FACTOR 1 454 0.0
5 g10339.t24 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 454 0.0
8 g10339.t24 PRINTS PR00315 GTP-binding elongation factor signature 9 22 2.0E-24
10 g10339.t24 PRINTS PR00315 GTP-binding elongation factor signature 68 76 2.0E-24
9 g10339.t24 PRINTS PR00315 GTP-binding elongation factor signature 88 98 2.0E-24
6 g10339.t24 PRINTS PR00315 GTP-binding elongation factor signature 104 115 2.0E-24
7 g10339.t24 PRINTS PR00315 GTP-binding elongation factor signature 148 157 2.0E-24
3 g10339.t24 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 7.4E-54
2 g10339.t24 Pfam PF03144 Elongation factor Tu domain 2 265 320 3.7E-9
1 g10339.t24 Pfam PF03143 Elongation factor Tu C-terminal domain 331 436 1.1E-31
20 g10339.t24 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
22 g10339.t24 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
12 g10339.t24 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 1.51E-80
13 g10339.t24 SUPERFAMILY SSF50447 Translation proteins 238 329 1.72E-24
11 g10339.t24 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 333 436 1.51E-43
21 g10339.t24 TIGRFAM TIGR00483 EF-1_alpha: translation elongation factor EF-1, subunit alpha 1 438 5.9E-216

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:0003746 translation elongation factor activity MF
GO:0006414 translational elongation BP
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