General information for g10339.t37
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor 1-alpha 1.
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.t37 | isoform | g10339.t37 | 8940572 | 8941577 |
| chr_1 | g10339 | g10339.t37 | exon | g10339.t37.exon1 | 8940572 | 8940929 |
| chr_1 | g10339 | g10339.t37 | exon | g10339.t37.exon2 | 8940999 | 8941577 |
| chr_1 | g10339 | g10339.t37 | cds | g10339.t37.CDS1 | 8941065 | 8941577 |
| chr_1 | g10339 | g10339.t37 | TTS | g10339.t37 | 8941863 | 8941863 |
| chr_1 | g10339 | g10339.t37 | TSS | g10339.t37 | NA | NA |
Sequences
>g10339.t37 Gene=g10339 Length=937
GGTGTCAACAAAATGGACTCAACTGAGCCACCATACTCAGAAGCTCGTTTCGAAGAAATT
AAGAAGGAAGTCTCATCATACATCAAGAAGATCGGTTACAATCCAGCTGCAGTTGCTTTC
GTTCCAATCTCAGGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGATGCCATGG
TTCAAGGGATGGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATTGAT
GCCTTGGACGCCATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCACTT
CAAGACGTCTACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACTGTT
GTACATAGGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTTAAATCAGT
CGAAATGCATCACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGTTTCAACGT
CAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACCAAGAGTAG
TCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCA
AATTTCAAACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCCTGCAAGTT
CTCTGAAATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGATAACCCCAA
GGCTATCAAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCATTGTGCGT
TGAATCATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATGAGACAAAC
AGTTGCTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGTAAGACCAC
AAAAGCAGCTGAGAAGGCACAAAAGGCCAAGAAATAG
>g10339.t37 Gene=g10339 Length=170
MHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDTKSSPPRGAADFTAQVIVLNHPGQI
SNGYTPVLDCHTAHIACKFSEIKEKVDRRSGKSVEDNPKAIKSGDAAIVILVPTKPLCVE
SFQEFPPLGRFAVRDMRQTVAVGVIKAVSFKDASGGKTTKAAEKAQKAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10339.t37 | CDD | cd03705 | EF1_alpha_III | 42 | 145 | 0e+00 |
| 6 | g10339.t37 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 1 | 39 | 0e+00 |
| 7 | g10339.t37 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 42 | 149 | 0e+00 |
| 2 | g10339.t37 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 1 | 166 | 0e+00 |
| 3 | g10339.t37 | PANTHER | PTHR23115:SF236 | ELONGATION FACTOR 1-ALPHA 1 | 1 | 166 | 0e+00 |
| 1 | g10339.t37 | Pfam | PF03143 | Elongation factor Tu C-terminal domain | 43 | 148 | 0e+00 |
| 5 | g10339.t37 | SUPERFAMILY | SSF50447 | Translation proteins | 1 | 41 | 3e-07 |
| 4 | g10339.t37 | SUPERFAMILY | SSF50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 45 | 148 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
