General information for g12287.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Translation elongation factor 2.
Parent gene
- The parent gene g12287 is located on chr_1: 22172800..22173568 (+ 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 | g12287 | g12287.t2 | TSS | g12287.t2 | 22169311 | 22169311 |
| chr_1 | g12287 | g12287.t2 | isoform | g12287.t2 | 22169380 | 22170878 |
| chr_1 | g12287 | g12287.t2 | exon | g12287.t2.exon1 | 22169380 | 22170025 |
| chr_1 | g12287 | g12287.t2 | exon | g12287.t2.exon2 | 22170108 | 22170301 |
| chr_1 | g12287 | g12287.t2 | cds | g12287.t2.CDS1 | 22170118 | 22170301 |
| chr_1 | g12287 | g12287.t2 | exon | g12287.t2.exon3 | 22170545 | 22170878 |
| chr_1 | g12287 | g12287.t2 | cds | g12287.t2.CDS2 | 22170545 | 22170876 |
| chr_1 | g12287 | g12287.t2 | TTS | g12287.t2 | NA | NA |
Sequences
>g12287.t2 Gene=g12287 Length=1174
ATGGTAAGCAGCTTTAATTTATATTCTAATTAATCGTAAATTGAAAGAGATCATCAGGAT
GAACATTTTGGTGTATTAAAGTGTTGTGAAAATAAGAAATTACAGTCAATAATTGCAAAA
ATAAAATGGATCAAGATAATTGCGATCAAATCCAAATTTCGGTTTTCTGTAATGGCGCTT
ATAAGAATGAATGAAAATATATAATTGTTTATTTGTTATACAATAGAATGAATGAGTAAG
GATTTATGCAAAATATATTTAATTTATTTTAATAATGTAATTTTAAGAAAAAAAAATTTC
ACAGCATTTTGAAATCGCCATGATGTTGGATATAAGAAAAGAAAATGTGTGTCACTGTAT
TAAAAATAAAGAGACCTGATGATTTTAAAATGTAGAAAAATTGATTTTCTGAGAAATTAT
TAATTTATGATTATTCGATTTTCTTTACAGGTCAACTTTACTGTCGACGAAATCCGTGCT
ATGATGGACAAGAAGAAGAACATCCGTAATATGTCTGTCATTGCTCATGTCGATCACGGA
AAATCTACTTTAACTGATTCGTTGGTTTCAAAAGCTGGTATTATTGCTGGTGCAAAAGCT
GGTGAAACAAGATTCACAGACACACGCAAGGATGAACAAGAAAGATTGCTATCTCTATGT
TCTTTGAGTTAGAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAG
AAGAAAAAGGTTTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAG
AAGTCACAGCCGCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTATCAG
GTGTTTGTGTACAAACTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCAG
TTTTGTTCATGAACAAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATT
TGTACCAAACATTCCAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCG
ATGACGATGGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCG
GTTCCGGCTTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTA
AATTCAAGATCGATGTCGTTAAACTCATGAATCG
>g12287.t2 Gene=g12287 Length=172
MFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCV
SGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNVIIATY
SDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFKIDVVKLMN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12287.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 167 | 0.0000000 |
| 2 | g12287.t2 | PANTHER | PTHR42908:SF29 | EUKARYOTIC TRANSLATION ELONGATION FACTOR 2A, TANDEM DUPLICATE 1-RELATED | 1 | 165 | 0.0000000 |
| 3 | g12287.t2 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 165 | 0.0000000 |
| 5 | g12287.t2 | PRINTS | PR00315 | GTP-binding elongation factor signature | 29 | 39 | 0.0000071 |
| 6 | g12287.t2 | PRINTS | PR00315 | GTP-binding elongation factor signature | 45 | 56 | 0.0000071 |
| 4 | g12287.t2 | PRINTS | PR00315 | GTP-binding elongation factor signature | 81 | 90 | 0.0000071 |
| 1 | g12287.t2 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 21 | 151 | 0.0000000 |
| 10 | g12287.t2 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 1 | 172 | 33.6720000 |
| 7 | g12287.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 19 | 172 | 0.0000000 |
| 9 | g12287.t2 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 14 | 92 | 0.0000000 |
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.
