Gene loci information

Transcript annotation

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

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 g11500 g11500.t10 TSS g11500.t10 16650082 16650082
chr_1 g11500 g11500.t10 isoform g11500.t10 16651096 16652523
chr_1 g11500 g11500.t10 exon g11500.t10.exon1 16651096 16651594
chr_1 g11500 g11500.t10 cds g11500.t10.CDS1 16651100 16651594
chr_1 g11500 g11500.t10 exon g11500.t10.exon2 16651670 16652523
chr_1 g11500 g11500.t10 cds g11500.t10.CDS2 16651670 16651738
chr_1 g11500 g11500.t10 TTS g11500.t10 16652519 16652519

Sequences

>g11500.t10 Gene=g11500 Length=1353
AGGTATGGTTGTCGTATTTGCACCAGTCAATTTGACCACTGAAGTAAAATCAGTCGAAAT
GCATCATGAAGCTTTGCAAGAAGCTGTACCTGGTGACAATGTTGGTTTTAACGTCAAGAA
CGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACAGCAAGAGCAGTCCACC
ACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTGC
AAATGGTTATACACCAGTTTTGGATTGTCACACTGCTCACATTGCTTGCAAATTTGCTGA
AATCAAAGAGAAGTGCGATCGTCGTACTGGCAAGACAACAGAAGAGAATCCAAAGGCTAT
CAAATCAGGTGATGCCGCTATTGTGAATTTAGTTCCATCAAAGCCATTGTGTGTTGAATC
ATTCTCCGAATTTCCACCATTGGGACGTTTTGCTGTTCGTGACATGAGACAAACTGTTGC
TGTTGGTGTTATCAAAGCCGTTAACTTCAAAGAAGCGAGCGGTGGAAAAGTAACAAAAGC
CGCTGAGAAGGCAGCAAAGAAAAAATAACTAGATTGTCAACTTGGCAAATTTGCCGTGTT
TCGATTATCGAACGGCAAACTTGAAATTTTTCATTCTATAAGAAATATTCAAACATTTCA
CCATGCTGATGGTGTCAAACATCTTTTTCAATTGATTTCTTCTACTCTTTCTAATAACTT
TTATTTTACACATCCCCATTCGTTTTTAATCTTTCATCATCATCGCAGGAAAAAGCCGAA
TGGATGTCATTTCTTTTTCGATTTATTCTCATTTACGTTGCATAAGATTAATTTAGTTTT
GGCAAATGTTGTCAATATTAAGACAAAACAAATAAACTTATGATAACATCATTTTATAGT
TGCGAGTTTATTTTAATTTTGGCCATACACACACACACAATACACAGGAATGGAAAAGGA
TCGAAGGCTATTTCTTTATTTAAATAATAATGATTAGAAGTACCTACGTGTATAGTCTTC
TTCTTATAATTTGTGATATTTTTTAAGTTGAAGAAATCATTGAGGCGTTACTTTAAATAT
TTACTTACTTACTTATTATTGATAAATTAACTCTTCTCTAATAAACGAGAACGAAATATT
AAATTGGTGAAACTGTAATAGTTTATTACGAATAATTTTTTTGGCTATTAAATTGTTACA
TGCAAGAATAAAAGCGAGACACACAAGAGAAAAAAAAGTTTTGTATTGCACCTGTTTCCG
ATAAATGAAAATCAGCATGGTGAACTATCCAAAAAGAAAGAAAAAATCTTATTATATTCA
AACAAAAATACTCAAAATAAAAGCTTGAGAAAA

>g11500.t10 Gene=g11500 Length=187
MVVVFAPVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDSKSSPPR
GAADFTAQVIVLNHPGQIANGYTPVLDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAIK
SGDAAIVNLVPSKPLCVESFSEFPPLGRFAVRDMRQTVAVGVIKAVNFKEASGGKVTKAA
EKAAKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11500.t10 CDD cd03705 EF1_alpha_III 60 163 0e+00
8 g11500.t10 Gene3D G3DSA:2.40.30.10 Translation factors 1 57 0e+00
7 g11500.t10 Gene3D G3DSA:2.40.30.10 Translation factors 60 167 0e+00
3 g11500.t10 PANTHER PTHR23115 TRANSLATION FACTOR 1 184 0e+00
4 g11500.t10 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 184 0e+00
2 g11500.t10 Pfam PF03144 Elongation factor Tu domain 2 10 50 1e-07
1 g11500.t10 Pfam PF03143 Elongation factor Tu C-terminal domain 61 166 0e+00
6 g11500.t10 SUPERFAMILY SSF50447 Translation proteins 2 97 0e+00
5 g11500.t10 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 63 166 0e+00

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

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