General information for g12287.t12
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.t12 | TSS | g12287.t12 | 22169311 | 22169311 |
| chr_1 | g12287 | g12287.t12 | isoform | g12287.t12 | 22169380 | 22173107 |
| chr_1 | g12287 | g12287.t12 | exon | g12287.t12.exon1 | 22169380 | 22169382 |
| chr_1 | g12287 | g12287.t12 | cds | g12287.t12.CDS1 | 22169380 | 22169382 |
| chr_1 | g12287 | g12287.t12 | exon | g12287.t12.exon2 | 22169830 | 22169968 |
| chr_1 | g12287 | g12287.t12 | cds | g12287.t12.CDS2 | 22169830 | 22169968 |
| chr_1 | g12287 | g12287.t12 | exon | g12287.t12.exon3 | 22171910 | 22172190 |
| chr_1 | g12287 | g12287.t12 | cds | g12287.t12.CDS3 | 22171910 | 22172190 |
| chr_1 | g12287 | g12287.t12 | exon | g12287.t12.exon4 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t12 | cds | g12287.t12.CDS4 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t12 | exon | g12287.t12.exon5 | 22172626 | 22173107 |
| chr_1 | g12287 | g12287.t12 | cds | g12287.t12.CDS5 | 22172626 | 22173107 |
| chr_1 | g12287 | g12287.t12 | TTS | g12287.t12 | 22173564 | 22173564 |
Sequences
>g12287.t12 Gene=g12287 Length=1077
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCTGGTGAATTGCATTTGGAAATTTGCTTGAAGGAC
TTGGAAGAAGATCACGCTTGTATCCCATTGAAGAAATCCGATCCAGTTGTATCGTATCGT
GAAACAGTCTCTGATGAATCATCCATGATGTGTTTATCAAAATCACCAAACAAGCATAAT
CGTCTTTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCTGAAGATATTGATGGAGGT
GCAGTTAATGCTCGTGACGATTTCAAGATTCGTGCACGTTACTTGGCTGAGAAATACGAA
TGGGATGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGACGGTACAGGTCCAAAT
GTAATTGTTGACGTCACTAAGGGTGTACAATATTTGAATGAAATCAAGGACTCTGTTGTT
GCTGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAGAACATGAGAGCTGTT
CGTTTCAACATTTATGATGTTACACTGCATGCTGACGCTATCCATCGTGGAGGTGGTCAA
ATCATTCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACAGCTTCTCCACGTTTG
ATGGAGCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTCGGTGGTATTTAT
GGTGTGCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAAGTTGCCGGTACACCT
ATGTTCGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTTGGATTCACTGCTGATTTG
CGCTCAAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTTGACCATTGGCAGATCTTC
CCAGGTGACCCTAACGAACCATCATCAAAACCATACCAGATTGTGCAAGATACAAGAAAA
CGTAAAGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATACTATGATAAAATGTAA
>g12287.t12 Gene=g12287 Length=358
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAGELHLEICLKD
LEEDHACIPLKKSDPVVSYRETVSDESSMMCLSKSPNKHNRLFMKAMPMPDGLAEDIDGG
AVNARDDFKIRARYLAEKYEWDVTEARKIWCFGPDGTGPNVIVDVTKGVQYLNEIKDSVV
AGFQWATKEGVLAEENMRAVRFNIYDVTLHADAIHRGGGQIIPTTRRCLYASYITASPRL
MEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADL
RSNTGGQAFPQCVFDHWQIFPGDPNEPSSKPYQIVQDTRKRKGLKEGLPDLNQYYDKM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g12287.t12 | CDD | cd01681 | aeEF2_snRNP_like_IV | 74 | 246 | 0 |
| 16 | g12287.t12 | CDD | cd04096 | eEF2_snRNP_like_C | 242 | 321 | 0 |
| 14 | g12287.t12 | Gene3D | G3DSA:3.30.70.870 | Elongation Factor G (Translational Gtpase) | 21 | 78 | 0 |
| 15 | g12287.t12 | Gene3D | G3DSA:3.30.70.240 | - | 80 | 344 | 0 |
| 13 | g12287.t12 | Gene3D | G3DSA:3.30.230.10 | - | 86 | 346 | 0 |
| 5 | g12287.t12 | PANTHER | PTHR42908:SF27 | ELONGATION FACTOR 2 | 1 | 49 | 0 |
| 7 | g12287.t12 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 49 | 0 |
| 4 | g12287.t12 | PANTHER | PTHR42908:SF27 | ELONGATION FACTOR 2 | 45 | 358 | 0 |
| 6 | g12287.t12 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 45 | 358 | 0 |
| 2 | g12287.t12 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 17 | 53 | 0 |
| 1 | g12287.t12 | Pfam | PF03764 | Elongation factor G, domain IV | 122 | 236 | 0 |
| 3 | g12287.t12 | Pfam | PF00679 | Elongation factor G C-terminus | 239 | 325 | 0 |
| 11 | g12287.t12 | SMART | SM00889 | EFG_IV_2 | 121 | 237 | 0 |
| 12 | g12287.t12 | SMART | SM00838 | EFG_C_a | 239 | 328 | 0 |
| 9 | g12287.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 57 | 0 |
| 8 | g12287.t12 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 77 | 241 | 0 |
| 10 | g12287.t12 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 242 | 356 | 0 |
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.
