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.t7 TSS g10339.t7 8939297 8939297
chr_1 g10339 g10339.t7 isoform g10339.t7 8939304 8941577
chr_1 g10339 g10339.t7 exon g10339.t7.exon1 8939304 8939370
chr_1 g10339 g10339.t7 exon g10339.t7.exon2 8940109 8940944
chr_1 g10339 g10339.t7 cds g10339.t7.CDS1 8940122 8940944
chr_1 g10339 g10339.t7 exon g10339.t7.exon3 8941009 8941074
chr_1 g10339 g10339.t7 cds g10339.t7.CDS2 8941009 8941074
chr_1 g10339 g10339.t7 exon g10339.t7.exon4 8941135 8941577
chr_1 g10339 g10339.t7 cds g10339.t7.CDS3 8941135 8941577
chr_1 g10339 g10339.t7 TTS g10339.t7 8941863 8941863

Sequences

>g10339.t7 Gene=g10339 Length=1412
CGTTTTAGCTCTCAAACAGTTCGAACGTTTTCGTTTACTCTTCTCTTGTGTTTAATAATT
TTTGATTAAAGCAAAGCAACATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTG
GACACGTCGACTCTGGCAAGTCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTA
TCGACAAGCGTACAATCGAGAAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCAT
TCAAATACGCATGGGTTTTGGACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTG
ATATCGCCTTGTGGAAATTCGAAACATCAAAATACTACGTTACCATCATTGACGCTCCCG
GACATCGTGATTTCATCAAAAACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTAT
TGATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTC
GTGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACA
AAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAG
TCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCT
CAGGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGAT
GGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACG
CCATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCT
ACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAAC
CAGGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAA
TGCATCACGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCAC
CACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTT
CAAACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTG
AAATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTA
TCAAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAAT
CATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTG
CTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAG
CAGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t7 Gene=g10339 Length=443
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHVKEL
RRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKEKVD
RRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKA
VSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g10339.t7 CDD cd01883 EF1_alpha 9 239 2.42432E-160
18 g10339.t7 CDD cd03693 EF1_alpha_II 242 312 4.84791E-40
20 g10339.t7 CDD cd03705 EF1_alpha_III 315 418 1.79727E-71
15 g10339.t7 Gene3D G3DSA:3.40.50.300 - 1 238 8.2E-95
17 g10339.t7 Gene3D G3DSA:2.40.30.10 Translation factors 240 311 4.5E-26
16 g10339.t7 Gene3D G3DSA:2.40.30.10 Translation factors 315 422 1.8E-51
4 g10339.t7 PANTHER PTHR23115 TRANSLATION FACTOR 1 296 0.0
6 g10339.t7 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 296 0.0
3 g10339.t7 PANTHER PTHR23115 TRANSLATION FACTOR 297 439 0.0
5 g10339.t7 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 297 439 0.0
9 g10339.t7 PRINTS PR00315 GTP-binding elongation factor signature 9 22 1.7E-24
11 g10339.t7 PRINTS PR00315 GTP-binding elongation factor signature 68 76 1.7E-24
10 g10339.t7 PRINTS PR00315 GTP-binding elongation factor signature 88 98 1.7E-24
7 g10339.t7 PRINTS PR00315 GTP-binding elongation factor signature 104 115 1.7E-24
8 g10339.t7 PRINTS PR00315 GTP-binding elongation factor signature 148 157 1.7E-24
2 g10339.t7 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 6.8E-54
1 g10339.t7 Pfam PF03143 Elongation factor Tu C-terminal domain 316 421 1.1E-31
21 g10339.t7 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
22 g10339.t7 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
13 g10339.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 1.36E-80
14 g10339.t7 SUPERFAMILY SSF50447 Translation proteins 237 308 2.87E-18
12 g10339.t7 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 318 421 4.8E-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

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