General information for g10339.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor 1-alpha 2.
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.t28 | TSS | g10339.t28 | 8939297 | 8939297 |
| chr_1 | g10339 | g10339.t28 | isoform | g10339.t28 | 8940122 | 8941577 |
| chr_1 | g10339 | g10339.t28 | exon | g10339.t28.exon1 | 8940122 | 8940877 |
| chr_1 | g10339 | g10339.t28 | cds | g10339.t28.CDS1 | 8940122 | 8940877 |
| chr_1 | g10339 | g10339.t28 | exon | g10339.t28.exon2 | 8941009 | 8941577 |
| chr_1 | g10339 | g10339.t28 | cds | g10339.t28.CDS2 | 8941009 | 8941041 |
| chr_1 | g10339 | g10339.t28 | TTS | g10339.t28 | 8941863 | 8941863 |
Sequences
>g10339.t28 Gene=g10339 Length=1325
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCA
CCATACTCAGAAGCTCGTTTCGAAGAAATTAAGAAGGAAGTCTCATCATACATCAAGAAG
ATCGGTTACAATCCAGCTGCAGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAACCAAGATGCCATGGTTCAAGGGATGGGCCATCGAACGTAAAGAG
GGTAAAGCTGATGGAAAGTGCCTCATTGATGCCTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGACGTATGGTCGTCGTTTTTGCACCAG
TCAACTTGACCACTGAAGTTAAATCAGTCGAAATGCATCACGAAGCCTTGCAAGAAGCTG
TACCAGGTGACAATGTTGGTTTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTG
GTTATGTTGCTGGTGACACCAAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTC
AAGTAATTGTCTTGAATCATCCAGGTCAAATTTCAAACGGTTACACACCAGTTTTGGATT
GCCACACTGCTCACATTGCCTGCAAGTTCTCTGAAATCAAAGAAAAAGTTGATCGTCGTT
CAGGTAAATCAGTTGAAGATAACCCCAAGGCTATCAAATCAGGAGATGCTGCTATCGTCA
TTTTGGTCCCAACAAAACCATTGTGCGTTGAATCATTCCAAGAATTCCCACCATTGGGAC
GTTTCGCCGTTCGTGATATGAGACAAACAGTTGCTGTCGGTGTCATCAAGGCAGTTTCAT
TCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAGA
AATAG
>g10339.t28 Gene=g10339 Length=262
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSTKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVWSSFLHQST
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10339.t28 | CDD | cd01883 | EF1_alpha | 9 | 239 | 8.50344E-163 |
| 10 | g10339.t28 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 238 | 1.6E-95 |
| 2 | g10339.t28 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 1 | 254 | 1.2E-219 |
| 3 | g10339.t28 | PANTHER | PTHR23115:SF236 | ELONGATION FACTOR 1-ALPHA 1 | 1 | 254 | 1.2E-219 |
| 6 | g10339.t28 | PRINTS | PR00315 | GTP-binding elongation factor signature | 9 | 22 | 2.0E-25 |
| 8 | g10339.t28 | PRINTS | PR00315 | GTP-binding elongation factor signature | 68 | 76 | 2.0E-25 |
| 7 | g10339.t28 | PRINTS | PR00315 | GTP-binding elongation factor signature | 88 | 98 | 2.0E-25 |
| 4 | g10339.t28 | PRINTS | PR00315 | GTP-binding elongation factor signature | 104 | 115 | 2.0E-25 |
| 5 | g10339.t28 | PRINTS | PR00315 | GTP-binding elongation factor signature | 148 | 157 | 2.0E-25 |
| 1 | g10339.t28 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 5 | 237 | 1.4E-54 |
| 12 | g10339.t28 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 61 | 76 | - |
| 13 | g10339.t28 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 5 | 242 | 61.508 |
| 9 | g10339.t28 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 255 | 9.66E-79 |
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.
