Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha 2.

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.t3 TSS g10339.t3 8939297 8939297
chr_1 g10339 g10339.t3 isoform g10339.t3 8939304 8941237
chr_1 g10339 g10339.t3 exon g10339.t3.exon1 8939304 8939370
chr_1 g10339 g10339.t3 exon g10339.t3.exon2 8940109 8940295
chr_1 g10339 g10339.t3 cds g10339.t3.CDS1 8940122 8940295
chr_1 g10339 g10339.t3 exon g10339.t3.exon3 8940374 8940948
chr_1 g10339 g10339.t3 cds g10339.t3.CDS2 8940374 8940948
chr_1 g10339 g10339.t3 exon g10339.t3.exon4 8941009 8941237
chr_1 g10339 g10339.t3 cds g10339.t3.CDS3 8941009 8941009
chr_1 g10339 g10339.t3 TTS g10339.t3 8941863 8941863

Sequences

>g10339.t3 Gene=g10339 Length=1058
CGTTTTAGCTCTCAAACAGTTCGAACGTTTTCGTTTACTCTTCTCTTGTGTTTAATAATT
TTTGATTAAAGCAAAGCAACATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTG
GACACGTCGACTCTGGCAAGTCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTA
TCGACAAGCGTACAATCGAGAAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCAT
TCAAATACGCATGGTACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCA
AAAACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTA
CTGGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGG
CTTTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGC
CACCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGA
AGATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATA
ACATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAG
AGGGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAAC
GTCCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGGTATTG
GAACTGTGCCAGTCGGACGTGTTGAAACTGGTGTTTTGAAACCAGGTTAGTATGGTCGTC
GTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCC
TTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAG
GAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCTGCT
GATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGG

>g10339.t3 Gene=g10339 Length=249
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWYY
VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGTGEFEAGISKNGQTREHALLAFTLGVK
QLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKKIGYNPAAVAFVPISGWHGDNMLEPST
KMPWFKGWAIERKEGKADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIGTVPVGR
VETGVLKPG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10339.t3 CDD cd01883 EF1_alpha 9 213 0.000
11 g10339.t3 Gene3D G3DSA:3.40.50.300 - 1 212 0.000
12 g10339.t3 Gene3D G3DSA:2.40.30.10 Translation factors 214 249 0.000
3 g10339.t3 PANTHER PTHR23115 TRANSLATION FACTOR 1 58 0.000
5 g10339.t3 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 58 0.000
2 g10339.t3 PANTHER PTHR23115 TRANSLATION FACTOR 59 249 0.000
4 g10339.t3 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 59 249 0.000
8 g10339.t3 PRINTS PR00315 GTP-binding elongation factor signature 9 22 0.000
7 g10339.t3 PRINTS PR00315 GTP-binding elongation factor signature 62 72 0.000
6 g10339.t3 PRINTS PR00315 GTP-binding elongation factor signature 78 89 0.000
9 g10339.t3 PRINTS PR00315 GTP-binding elongation factor signature 122 131 0.000
1 g10339.t3 Pfam PF00009 Elongation factor Tu GTP binding domain 5 211 0.000
13 g10339.t3 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 216 45.204
10 g10339.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 235 0.000

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