General information for g12287.t26
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.t26 | isoform | g12287.t26 | 22171838 | 22173107 |
| chr_1 | g12287 | g12287.t26 | exon | g12287.t26.exon1 | 22171838 | 22172190 |
| chr_1 | g12287 | g12287.t26 | cds | g12287.t26.CDS1 | 22171864 | 22172190 |
| chr_1 | g12287 | g12287.t26 | exon | g12287.t26.exon2 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t26 | cds | g12287.t26.CDS2 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t26 | exon | g12287.t26.exon3 | 22172626 | 22173107 |
| chr_1 | g12287 | g12287.t26 | cds | g12287.t26.CDS3 | 22172626 | 22173107 |
| chr_1 | g12287 | g12287.t26 | TTS | g12287.t26 | 22173564 | 22173564 |
| chr_1 | g12287 | g12287.t26 | TSS | g12287.t26 | NA | NA |
Sequences
>g12287.t26 Gene=g12287 Length=1007
TTAAGCGTTTGGCTAAATCCGATCCTATGGTACAATGTATCATTGAAGAATCTGGCGAAC
ATATTATTGCTGGTGCTGGTGAATTGCATTTGGAAATTTGCTTGAAGGACTTGGAAGAAG
ATCACGCTTGTATCCCATTGAAGAAATCCGATCCAGTTGTATCGTATCGTGAAACAGTCT
CTGATGAATCATCCATGATGTGTTTATCAAAATCACCAAACAAGCATAATCGTCTTTTCA
TGAAGGCCATGCCTATGCCTGATGGTCTTGCTGAAGATATTGATGGAGGTGCAGTTAATG
CTCGTGACGATTTCAAGATTCGTGCACGTTACTTGGCTGAGAAATACGAATGGGATGTTA
CAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGACGGTACAGGTCCAAATGTAATTGTTG
ACGTCACTAAGGGTGTACAATATTTGAATGAAATCAAGGACTCTGTTGTTGCTGGCTTCC
AATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAGAACATGAGAGCTGTTCGTTTCAACA
TTTATGATGTTACACTGCATGCTGACGCTATCCATCGTGGAGGTGGTCAAATCATTCCAA
CAACTCGTCGTTGCTTGTATGCATCATACATCACAGCTTCTCCACGTTTGATGGAGCCAG
TTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTCGGTGGTATTTATGGTGTGCTTA
ATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAAGTTGCCGGTACACCTATGTTCGTTG
TCAAAGCTTATTTGCCTGTAAATGAATCATTTGGATTCACTGCTGATTTGCGCTCAAATA
CTGGAGGTCAAGCTTTCCCACAATGTGTATTTGACCATTGGCAGATCTTCCCAGGTGACC
CTAACGAACCATCATCAAAACCATACCAGATTGTGCAAGATACAAGAAAACGTAAAGGTC
TCAAAGAAGGTTTACCAGATTTGAACCAATACTATGATAAAATGTAA
>g12287.t26 Gene=g12287 Length=326
MVQCIIEESGEHIIAGAGELHLEICLKDLEEDHACIPLKKSDPVVSYRETVSDESSMMCL
SKSPNKHNRLFMKAMPMPDGLAEDIDGGAVNARDDFKIRARYLAEKYEWDVTEARKIWCF
GPDGTGPNVIVDVTKGVQYLNEIKDSVVAGFQWATKEGVLAEENMRAVRFNIYDVTLHAD
AIHRGGGQIIPTTRRCLYASYITASPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFE
ESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQIFPGDPNEPSSKPY
QIVQDTRKRKGLKEGLPDLNQYYDKM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g12287.t26 | CDD | cd01681 | aeEF2_snRNP_like_IV | 42 | 214 | 0e+00 |
| 13 | g12287.t26 | CDD | cd04096 | eEF2_snRNP_like_C | 210 | 289 | 0e+00 |
| 11 | g12287.t26 | Gene3D | G3DSA:3.30.70.870 | Elongation Factor G (Translational Gtpase) | 1 | 46 | 0e+00 |
| 10 | g12287.t26 | Gene3D | G3DSA:3.30.230.10 | - | 52 | 205 | 0e+00 |
| 12 | g12287.t26 | Gene3D | G3DSA:3.30.70.240 | - | 206 | 326 | 0e+00 |
| 3 | g12287.t26 | PANTHER | PTHR42908:SF27 | ELONGATION FACTOR 2 | 1 | 326 | 0e+00 |
| 4 | g12287.t26 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 326 | 0e+00 |
| 1 | g12287.t26 | Pfam | PF03764 | Elongation factor G, domain IV | 90 | 204 | 0e+00 |
| 2 | g12287.t26 | Pfam | PF00679 | Elongation factor G C-terminus | 207 | 293 | 0e+00 |
| 8 | g12287.t26 | SMART | SM00889 | EFG_IV_2 | 89 | 205 | 0e+00 |
| 9 | g12287.t26 | SMART | SM00838 | EFG_C_a | 207 | 296 | 0e+00 |
| 7 | g12287.t26 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 3 | 43 | 4e-07 |
| 5 | g12287.t26 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 45 | 209 | 0e+00 |
| 6 | g12287.t26 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 210 | 324 | 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.
