General information for g10339.t40
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor 1-alpha.
Parent gene
- The parent gene g10339 is located on chr_1: 8941394..8942064 (+ strand)
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.t40 | isoform | g10339.t40 | 8940677 | 8941577 |
| chr_1 | g10339 | g10339.t40 | exon | g10339.t40.exon1 | 8940677 | 8940917 |
| chr_1 | g10339 | g10339.t40 | cds | g10339.t40.CDS1 | 8940722 | 8940917 |
| chr_1 | g10339 | g10339.t40 | exon | g10339.t40.exon2 | 8941009 | 8941577 |
| chr_1 | g10339 | g10339.t40 | cds | g10339.t40.CDS2 | 8941009 | 8941577 |
| chr_1 | g10339 | g10339.t40 | TTS | g10339.t40 | 8941863 | 8941863 |
| chr_1 | g10339 | g10339.t40 | TSS | g10339.t40 | NA | NA |
Sequences
>g10339.t40 Gene=g10339 Length=810
GCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAACATGCTTGAACCATCA
ACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGA
AAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGTCCAACTGACAAACCA
TTGCGTTTGCCACTTCAAGACGTCTACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGA
CGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGTCGAAATG
CATCACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGTCAAGAAC
GTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAGTCCACCA
CGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTTCA
AACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTTCTCTGAA
ATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAAGGCTATC
AAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGTTGAATCA
TTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAACAGTTGCT
GTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCA
GCTGAGAAGGCACAAAAGGCCAAGAAATAG
>g10339.t40 Gene=g10339 Length=254
MLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIG
TVPVGRMVVVFAPVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDT
KSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKEKVDRRSGKSVED
NPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKAVSFKDASGG
KTTKAAEKAQKAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10339.t40 | CDD | cd03693 | EF1_alpha_II | 42 | 123 | 0e+00 |
| 10 | g10339.t40 | CDD | cd03705 | EF1_alpha_III | 126 | 229 | 0e+00 |
| 8 | g10339.t40 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 40 | 123 | 0e+00 |
| 7 | g10339.t40 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 126 | 233 | 0e+00 |
| 3 | g10339.t40 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 1 | 250 | 0e+00 |
| 4 | g10339.t40 | PANTHER | PTHR23115:SF236 | ELONGATION FACTOR 1-ALPHA 1 | 1 | 250 | 0e+00 |
| 2 | g10339.t40 | Pfam | PF03144 | Elongation factor Tu domain 2 | 60 | 116 | 1e-07 |
| 1 | g10339.t40 | Pfam | PF03143 | Elongation factor Tu C-terminal domain | 127 | 232 | 0e+00 |
| 6 | g10339.t40 | SUPERFAMILY | SSF50447 | Translation proteins | 43 | 163 | 0e+00 |
| 5 | g10339.t40 | SUPERFAMILY | SSF50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 129 | 232 | 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.
