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.t16 TSS g10339.t16 8939297 8939297
chr_1 g10339 g10339.t16 isoform g10339.t16 8939365 8941577
chr_1 g10339 g10339.t16 exon g10339.t16.exon1 8939365 8939370
chr_1 g10339 g10339.t16 exon g10339.t16.exon2 8940109 8940944
chr_1 g10339 g10339.t16 cds g10339.t16.CDS1 8940122 8940944
chr_1 g10339 g10339.t16 exon g10339.t16.exon3 8941009 8941577
chr_1 g10339 g10339.t16 cds g10339.t16.CDS2 8941009 8941577
chr_1 g10339 g10339.t16 TTS g10339.t16 8941863 8941863

Sequences

>g10339.t16 Gene=g10339 Length=1411
TTGATTAAAGCAAAGCAACATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGG
ACACGTCGACTCTGGCAAGTCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTAT
CGACAAGCGTACAATCGAGAAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATT
CAAATACGCATGGGTTTTGGACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGA
TATCGCCTTGTGGAAATTCGAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGG
ACATCGTGATTTCATCAAAAACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATT
GATTGTCGCTGCCGGTACTGGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCG
TGAACACGCTTTGTTGGCTTTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAA
AATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGT
CTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTC
AGGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATG
GGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGC
CATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTA
CAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAACC
AGGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAAT
GCATCACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAA
CGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACC
ACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTTC
AAACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTGA
AATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTAT
CAAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAATC
ATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTGC
TGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAGC
AGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t16 Gene=g10339 Length=463
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHEALQ
EAVPGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQISNGYTPV
LDCHTAHIACKFSEIKEKVDRRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVESFQEFPP
LGRFAVRDMRQTVAVGVIKAVSFKDASGGKTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g10339.t16 CDD cd01883 EF1_alpha 9 239 3.55557E-160
18 g10339.t16 CDD cd03693 EF1_alpha_II 242 332 2.79849E-59
20 g10339.t16 CDD cd03705 EF1_alpha_III 335 438 2.38124E-71
15 g10339.t16 Gene3D G3DSA:3.40.50.300 - 1 238 9.2E-95
16 g10339.t16 Gene3D G3DSA:2.40.30.10 Translation factors 240 332 1.3E-42
17 g10339.t16 Gene3D G3DSA:2.40.30.10 Translation factors 335 442 1.9E-51
6 g10339.t16 Hamap MF_00118_A Elongation factor Tu [tuf]. 2 444 51.357845
4 g10339.t16 PANTHER PTHR23115 TRANSLATION FACTOR 1 459 0.0
5 g10339.t16 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 459 0.0
9 g10339.t16 PRINTS PR00315 GTP-binding elongation factor signature 9 22 2.1E-24
11 g10339.t16 PRINTS PR00315 GTP-binding elongation factor signature 68 76 2.1E-24
10 g10339.t16 PRINTS PR00315 GTP-binding elongation factor signature 88 98 2.1E-24
7 g10339.t16 PRINTS PR00315 GTP-binding elongation factor signature 104 115 2.1E-24
8 g10339.t16 PRINTS PR00315 GTP-binding elongation factor signature 148 157 2.1E-24
3 g10339.t16 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 7.6E-54
2 g10339.t16 Pfam PF03144 Elongation factor Tu domain 2 260 325 3.9E-15
1 g10339.t16 Pfam PF03143 Elongation factor Tu C-terminal domain 336 441 1.2E-31
21 g10339.t16 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
23 g10339.t16 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.508
13 g10339.t16 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 1.55E-80
14 g10339.t16 SUPERFAMILY SSF50447 Translation proteins 238 334 1.55E-29
12 g10339.t16 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 338 441 1.51E-43
22 g10339.t16 TIGRFAM TIGR00483 EF-1_alpha: translation elongation factor EF-1, subunit alpha 1 443 4.8E-222

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