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.t23 TSS g10339.t23 8939297 8939297
chr_1 g10339 g10339.t23 isoform g10339.t23 8940122 8941577
chr_1 g10339 g10339.t23 exon g10339.t23.exon1 8940122 8940944
chr_1 g10339 g10339.t23 cds g10339.t23.CDS1 8940122 8940944
chr_1 g10339 g10339.t23 exon g10339.t23.exon2 8941009 8941176
chr_1 g10339 g10339.t23 cds g10339.t23.CDS2 8941009 8941176
chr_1 g10339 g10339.t23 exon g10339.t23.exon3 8941237 8941577
chr_1 g10339 g10339.t23 cds g10339.t23.CDS3 8941237 8941577
chr_1 g10339 g10339.t23 TTS g10339.t23 8941863 8941863

Sequences

>g10339.t23 Gene=g10339 Length=1332
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCA
CCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAG
ATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAG
GGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGGTATTGGA
ACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAACCAGGTATGGTCGTCGTTTTT
GCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAA
GAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTG
CGTCGTGGTTATGTTGCTGGTGACACCAAGAGTCAAATTTCAAACGGTTACACACCAGTT
TTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTGAAATCAAAGAAAAAGTTGAT
CGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAATCAGGAGATGCTGCT
ATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAATCATTCCAAGAATTCCCACCA
TTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTCGGTGTCATCAAGGCA
GTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAG
GCCAAGAAATAG

>g10339.t23 Gene=g10339 Length=443
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHEALQ
EAVPGDNVGFNVKNVSVKELRRGYVAGDTKSQISNGYTPVLDCHTAHIACKFSEIKEKVD
RRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKA
VSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g10339.t23 CDD cd01883 EF1_alpha 9 239 7.3165E-160
19 g10339.t23 CDD cd03693 EF1_alpha_II 242 330 1.9672E-59
21 g10339.t23 CDD cd03705 EF1_alpha_III 331 418 5.84286E-58
16 g10339.t23 Gene3D G3DSA:3.40.50.300 - 1 238 8.2E-95
18 g10339.t23 Gene3D G3DSA:2.40.30.10 Translation factors 240 328 1.2E-42
17 g10339.t23 Gene3D G3DSA:2.40.30.10 Translation factors 329 422 9.7E-44
5 g10339.t23 PANTHER PTHR23115 TRANSLATION FACTOR 1 330 0.0
7 g10339.t23 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 330 0.0
4 g10339.t23 PANTHER PTHR23115 TRANSLATION FACTOR 332 439 0.0
6 g10339.t23 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 332 439 0.0
10 g10339.t23 PRINTS PR00315 GTP-binding elongation factor signature 9 22 1.7E-24
12 g10339.t23 PRINTS PR00315 GTP-binding elongation factor signature 68 76 1.7E-24
11 g10339.t23 PRINTS PR00315 GTP-binding elongation factor signature 88 98 1.7E-24
8 g10339.t23 PRINTS PR00315 GTP-binding elongation factor signature 104 115 1.7E-24
9 g10339.t23 PRINTS PR00315 GTP-binding elongation factor signature 148 157 1.7E-24
3 g10339.t23 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 6.8E-54
2 g10339.t23 Pfam PF03144 Elongation factor Tu domain 2 260 325 3.7E-15
1 g10339.t23 Pfam PF03143 Elongation factor Tu C-terminal domain 327 421 3.5E-27
22 g10339.t23 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
24 g10339.t23 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
14 g10339.t23 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 1.37E-80
15 g10339.t23 SUPERFAMILY SSF50447 Translation proteins 238 331 3.98E-29
13 g10339.t23 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 329 421 4.6E-36
23 g10339.t23 TIGRFAM TIGR00483 EF-1_alpha: translation elongation factor EF-1, subunit alpha 1 330 1.3E-163

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