General information for g12287.t10
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.t10 | TSS | g12287.t10 | 22169311 | 22169311 |
| chr_1 | g12287 | g12287.t10 | isoform | g12287.t10 | 22169380 | 22172800 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon1 | 22169380 | 22169382 |
| chr_1 | g12287 | g12287.t10 | cds | g12287.t10.CDS1 | 22169380 | 22169382 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon2 | 22169830 | 22170044 |
| chr_1 | g12287 | g12287.t10 | cds | g12287.t10.CDS2 | 22169830 | 22170044 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon3 | 22170108 | 22170301 |
| chr_1 | g12287 | g12287.t10 | cds | g12287.t10.CDS3 | 22170108 | 22170301 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon4 | 22170545 | 22171372 |
| chr_1 | g12287 | g12287.t10 | cds | g12287.t10.CDS4 | 22170545 | 22171372 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon5 | 22171753 | 22172190 |
| chr_1 | g12287 | g12287.t10 | cds | g12287.t10.CDS5 | 22171753 | 22171802 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon6 | 22172261 | 22172432 |
| chr_1 | g12287 | g12287.t10 | exon | g12287.t10.exon7 | 22172626 | 22172800 |
| chr_1 | g12287 | g12287.t10 | TTS | g12287.t10 | 22173564 | 22173564 |
Sequences
>g12287.t10 Gene=g12287 Length=2025
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGC
AAGGATGAACAAGAAAGATGTATCACAATTAAGTCAACTGCTATCTCTATGTTCTTTGAG
TTAGAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAGAAGAAAAA
GGTTTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAGAAGTCACA
GCCGCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTATCAGGTGTTTGT
GTACAAACTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCAGTTTTGTTC
ATGAACAAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATTTGTACCAA
ACATTCCAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCGATGACGAT
GGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCGGTTCCGGC
TTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTAAATTCAAG
ATCGATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAATGCAAAGACC
AAGAAATGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCATGTATGTATTG
GATCCAATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGAAATTCCTGGC
TTATTGGAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGATGGTAAACAA
TTATTGAAAGTTGTCATGCGCTCATGGTTGCCAGCTGGTGAAGCTTTACTTCAAATGATT
GCTATTCACTTGCCTTCACCAGTCGTCGCTCAAAAATACCGTATGGAAATGTTGTATGAG
GGACCACTCGATGACGAGGCTGCCGTTGCTGTCAAGAACTGCGATCCAAATGGTCCATTG
ATGATGTACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCGTTTCTATGCTTTCGGA
CGTGTGTTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTCATGAAATTTTCAGTTTC
ACCTGTCGTGCGTGTTGCTGTCGAGCCTAAAAATCCAGCTGATTTGCCCAAACTCGTCGA
AGGTCTTAAGCGTTTGGCTAAATCCGATCCTATGGTACAATGTATCATTGAAGAATCTGG
CGAACATATTATTGCTGGTGCTGGTGAATTGCATTTGGAAATTTGCTTGAAGGACTTGGA
AGAAGATCACGCTTGTATCCCATTGAAGAAATCCGATCCAGTTGTATCGTATCGTGAAAC
AGTCTCTGATGAATCATCCATGATGTGTTTATCAAAATCACCAAACAAGCATAATCGTCT
TTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCTGAAGATATTGATGGAGGTGCAGT
TAATGCTCGTGACGATTTCAAGATTCGTGCACGTTACTTGGCTGAGAAATACGAATGGGA
TGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGACGGTACAGGTCCAAATGTAAT
TGTTGACGTCACTAAGGGTGTACAATATTTGAATGAAATCAAGGACTCTGTTGTTGCTGG
CTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAGAACATGAGAGCTGTTCGTTT
CAACATTTATGATGTTACACTGCATGCTGACGCTATCCATCGTGGAGGTGGTCAAATCAT
TCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACAGCTTCTCCACGTTTGATGGA
GCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTCGG
>g12287.t10 Gene=g12287 Length=429
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTR
KDEQERCITIKSTAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVT
AALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQ
TFQRIVENVNVIIATYSDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFK
IDVVKLMNRLWGENFFNAKTKKWAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPG
LLEKIGVTLKHEDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYE
GPLDDEAAVAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRHEIFSF
TCRACCCRA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g12287.t10 | CDD | cd01885 | EF2 | 20 | 236 | 1.83305E-124 |
| 11 | g12287.t10 | Gene3D | G3DSA:3.40.50.300 | - | 13 | 346 | 1.2E-162 |
| 12 | g12287.t10 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 49 | 414 | 1.2E-162 |
| 13 | g12287.t10 | Gene3D | G3DSA:3.90.1430.10 | Yeast translation eEF2 (G’ domain) | 228 | 330 | 1.2E-162 |
| 2 | g12287.t10 | PANTHER | PTHR42908:SF29 | EUKARYOTIC TRANSLATION ELONGATION FACTOR 2A, TANDEM DUPLICATE 1-RELATED | 1 | 415 | 2.4E-212 |
| 3 | g12287.t10 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 415 | 2.4E-212 |
| 8 | g12287.t10 | PRINTS | PR00315 | GTP-binding elongation factor signature | 21 | 34 | 2.2E-14 |
| 7 | g12287.t10 | PRINTS | PR00315 | GTP-binding elongation factor signature | 65 | 73 | 2.2E-14 |
| 6 | g12287.t10 | PRINTS | PR00315 | GTP-binding elongation factor signature | 105 | 115 | 2.2E-14 |
| 5 | g12287.t10 | PRINTS | PR00315 | GTP-binding elongation factor signature | 121 | 132 | 2.2E-14 |
| 4 | g12287.t10 | PRINTS | PR00315 | GTP-binding elongation factor signature | 157 | 166 | 2.2E-14 |
| 1 | g12287.t10 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 17 | 345 | 1.4E-67 |
| 15 | g12287.t10 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 58 | 73 | - |
| 17 | g12287.t10 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 17 | 348 | 54.195 |
| 9 | g12287.t10 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 345 | 2.54E-111 |
| 10 | g12287.t10 | SUPERFAMILY | SSF50447 | Translation proteins | 346 | 415 | 7.07E-21 |
| 16 | g12287.t10 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 19 | 168 | 1.3E-18 |
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.
