General information for g12287.t24
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t24 | TSS | g12287.t24 | 22169829 | 22169829 |
| chr_1 | g12287 | g12287.t24 | isoform | g12287.t24 | 22170723 | 22172062 |
| chr_1 | g12287 | g12287.t24 | exon | g12287.t24.exon1 | 22170723 | 22171129 |
| chr_1 | g12287 | g12287.t24 | cds | g12287.t24.CDS1 | 22170739 | 22171129 |
| chr_1 | g12287 | g12287.t24 | exon | g12287.t24.exon2 | 22171244 | 22171575 |
| chr_1 | g12287 | g12287.t24 | cds | g12287.t24.CDS2 | 22171244 | 22171575 |
| chr_1 | g12287 | g12287.t24 | exon | g12287.t24.exon3 | 22171753 | 22172062 |
| chr_1 | g12287 | g12287.t24 | cds | g12287.t24.CDS3 | 22171753 | 22172061 |
| chr_1 | g12287 | g12287.t24 | TTS | g12287.t24 | NA | NA |
Sequences
>g12287.t24 Gene=g12287 Length=1049
CGATGACGATGGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTT
CGGTTCCGGCTTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGC
TAAATTCAAGATCGATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAA
TGCAAAGACCAAGAAATGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCAT
GTATGTATTGGATCCAATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGA
AATTCCTGGCTTATTGGAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGA
TGGTAAACAATTATTGAAAGTTGTCATGCGCTCATGGTTGCCAGCTGTCAAGAACTGCGA
TCCAAATGGTCCATTGATGATGTACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCG
TTTCTATGCTTTCGGACGTGTGTTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTAT
AATGGGACCAAATTACACACCTGGCAAGAAGGAAGACTTGTACGAAAAATCAATTCAACG
TACTATTTTGATGATGGGTCGTTATGTTGAAGCCATTGAAGATGTTCCATGCGGTAACAT
TTGCGGTTTGGTTGGTGTTGATCAATTCTTGGTCAAGACTGGAACAATCACAACATTCAA
AGATGCCCATAACATGAAGGTCATGAAATTTTCAGTTTCACCTGTCGTGCGTGTTGCTGT
CGAGCCTAAAAATCCAGCTGATTTGCCCAAACTCGTCGAAGGTCTTAAGCGTTTGGCTAA
ATCCGATCCTATGGTACAATGTATCATTGAAGAATCTGGCGAACATATTATTGCTGGTGC
TGGTGAATTGCATTTGGAAATTTGCTTGAAGGACTTGGAAGAAGATCACGCTTGTATCCC
ATTGAAGAAATCCGATCCAGTTGTATCGTATCGTGAAACAGTCTCTGATGAATCATCCAT
GATGTGTTTATCAAAATCACCAAACAAGC
>g12287.t24 Gene=g12287 Length=344
MGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFKIDVVKLMNRLWGENFFNAKTKK
WAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPGLLEKIGVTLKHEDKDKDGKQLL
KVVMRSWLPAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNY
TPGKKEDLYEKSIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITTFKDAHNM
KVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
EICLKDLEEDHACIPLKKSDPVVSYRETVSDESSMMCLSKSPNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g12287.t24 | CDD | cd03700 | EF2_snRNP_like_II | 140 | 234 | 0.0e+00 |
| 13 | g12287.t24 | CDD | cd16261 | EF2_snRNP_III | 249 | 320 | 0.0e+00 |
| 10 | g12287.t24 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 41 | 5.3e-06 |
| 12 | g12287.t24 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 118 | 246 | 0.0e+00 |
| 11 | g12287.t24 | Gene3D | G3DSA:3.30.70.870 | Elongation Factor G (Translational Gtpase) | 247 | 324 | 0.0e+00 |
| 4 | g12287.t24 | PANTHER | PTHR42908:SF24 | EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 | 1 | 130 | 0.0e+00 |
| 6 | g12287.t24 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 130 | 0.0e+00 |
| 3 | g12287.t24 | PANTHER | PTHR42908:SF24 | EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 | 131 | 344 | 0.0e+00 |
| 5 | g12287.t24 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 131 | 344 | 0.0e+00 |
| 2 | g12287.t24 | Pfam | PF03144 | Elongation factor Tu domain 2 | 156 | 231 | 0.0e+00 |
| 1 | g12287.t24 | Pfam | PF14492 | Elongation Factor G, domain III | 249 | 310 | 0.0e+00 |
| 7 | g12287.t24 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 130 | 0.0e+00 |
| 9 | g12287.t24 | SUPERFAMILY | SSF50447 | Translation proteins | 130 | 243 | 0.0e+00 |
| 8 | g12287.t24 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 246 | 321 | 0.0e+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.
