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.t30 TSS g10339.t30 8939297 8939297
chr_1 g10339 g10339.t30 isoform g10339.t30 8940122 8941577
chr_1 g10339 g10339.t30 exon g10339.t30.exon1 8940122 8940944
chr_1 g10339 g10339.t30 cds g10339.t30.CDS1 8940122 8940944
chr_1 g10339 g10339.t30 exon g10339.t30.exon2 8941009 8941214
chr_1 g10339 g10339.t30 cds g10339.t30.CDS2 8941009 8941214
chr_1 g10339 g10339.t30 exon g10339.t30.exon3 8941375 8941577
chr_1 g10339 g10339.t30 cds g10339.t30.CDS3 8941375 8941473
chr_1 g10339 g10339.t30 TTS g10339.t30 8941863 8941863

Sequences

>g10339.t30 Gene=g10339 Length=1232
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCA
CCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAG
ATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAG
GGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGGTATTGGA
ACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAACCAGGTATGGTCGTCGTTTTT
GCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAA
GAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTG
CGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTC
ACCGCTCAAGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAAT
CATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTG
CTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAG
CAGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t30 Gene=g10339 Length=375
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHEALQ
EAVPGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFTAQEMLLSSFWSQQNHCALN
HSKNSHHWDVSPFVI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g10339.t30 CDD cd01883 EF1_alpha 9 239 8.07295E-162
14 g10339.t30 CDD cd03693 EF1_alpha_II 242 332 1.23208E-61
12 g10339.t30 Gene3D G3DSA:3.40.50.300 - 1 238 5.2E-95
13 g10339.t30 Gene3D G3DSA:2.40.30.10 Translation factors 240 332 8.9E-43
3 g10339.t30 PANTHER PTHR23115 TRANSLATION FACTOR 1 347 0.0
4 g10339.t30 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 347 0.0
7 g10339.t30 PRINTS PR00315 GTP-binding elongation factor signature 9 22 8.4E-25
9 g10339.t30 PRINTS PR00315 GTP-binding elongation factor signature 68 76 8.4E-25
8 g10339.t30 PRINTS PR00315 GTP-binding elongation factor signature 88 98 8.4E-25
5 g10339.t30 PRINTS PR00315 GTP-binding elongation factor signature 104 115 8.4E-25
6 g10339.t30 PRINTS PR00315 GTP-binding elongation factor signature 148 157 8.4E-25
2 g10339.t30 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 4.3E-54
1 g10339.t30 Pfam PF03144 Elongation factor Tu domain 2 260 325 2.9E-15
16 g10339.t30 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
18 g10339.t30 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
10 g10339.t30 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 8.3E-81
11 g10339.t30 SUPERFAMILY SSF50447 Translation proteins 238 334 1.02E-29
17 g10339.t30 TIGRFAM TIGR00483 EF-1_alpha: translation elongation factor EF-1, subunit alpha 1 347 3.8E-169

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

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