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.t26 TSS g10339.t26 8939297 8939297
chr_1 g10339 g10339.t26 isoform g10339.t26 8940122 8941577
chr_1 g10339 g10339.t26 exon g10339.t26.exon1 8940122 8940890
chr_1 g10339 g10339.t26 cds g10339.t26.CDS1 8940122 8940890
chr_1 g10339 g10339.t26 exon g10339.t26.exon2 8941099 8941577
chr_1 g10339 g10339.t26 cds g10339.t26.CDS2 8941099 8941577
chr_1 g10339 g10339.t26 TTS g10339.t26 8941863 8941863

Sequences

>g10339.t26 Gene=g10339 Length=1248
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCA
CCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAG
ATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAG
GGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGACAATGTT
GGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGAC
ACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAAT
CATCCAGGTCAAATTTCAAACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATT
GCCTGCAAGTTCTCTGAAATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAA
GATAACCCCAAGGCTATCAAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAA
CCATTGTGCGTTGAATCATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGAT
ATGAGACAAACAGTTGCTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGT
GGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t26 Gene=g10339 Length=415
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFTAQVIVLN
HPGQISNGYTPVLDCHTAHIACKFSEIKEKVDRRSGKSVEDNPKAIKSGDAAIVILVPTK
PLCVESFQEFPPLGRFAVRDMRQTVAVGVIKAVSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g10339.t26 CDD cd01883 EF1_alpha 9 239 3.70741E-161
18 g10339.t26 CDD cd03705 EF1_alpha_III 287 390 1.51868E-72
14 g10339.t26 Gene3D G3DSA:3.40.50.300 - 1 238 6.9E-95
15 g10339.t26 Gene3D G3DSA:2.40.30.10 Translation factors 255 284 5.4E-5
16 g10339.t26 Gene3D G3DSA:2.40.30.10 Translation factors 287 394 1.6E-51
4 g10339.t26 PANTHER PTHR23115 TRANSLATION FACTOR 1 257 0.0
6 g10339.t26 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 257 0.0
3 g10339.t26 PANTHER PTHR23115 TRANSLATION FACTOR 257 411 0.0
5 g10339.t26 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 257 411 0.0
9 g10339.t26 PRINTS PR00315 GTP-binding elongation factor signature 9 22 1.3E-24
11 g10339.t26 PRINTS PR00315 GTP-binding elongation factor signature 68 76 1.3E-24
10 g10339.t26 PRINTS PR00315 GTP-binding elongation factor signature 88 98 1.3E-24
7 g10339.t26 PRINTS PR00315 GTP-binding elongation factor signature 104 115 1.3E-24
8 g10339.t26 PRINTS PR00315 GTP-binding elongation factor signature 148 157 1.3E-24
2 g10339.t26 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 5.7E-54
1 g10339.t26 Pfam PF03143 Elongation factor Tu C-terminal domain 288 393 9.5E-32
19 g10339.t26 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
20 g10339.t26 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
13 g10339.t26 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 257 8.92E-79
12 g10339.t26 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 290 393 3.7E-44

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