General information for g11500.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor 1-alpha 2.
Parent gene
- The parent gene g11500 is located on chr_1: 16651670..16652523 (+ 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 | g11500 | g11500.t5 | TSS | g11500.t5 | 16650082 | 16650082 |
| chr_1 | g11500 | g11500.t5 | isoform | g11500.t5 | 16650214 | 16651147 |
| chr_1 | g11500 | g11500.t5 | exon | g11500.t5.exon1 | 16650214 | 16651036 |
| chr_1 | g11500 | g11500.t5 | cds | g11500.t5.CDS1 | 16650214 | 16651036 |
| chr_1 | g11500 | g11500.t5 | exon | g11500.t5.exon2 | 16651098 | 16651147 |
| chr_1 | g11500 | g11500.t5 | cds | g11500.t5.CDS2 | 16651098 | 16651147 |
| chr_1 | g11500 | g11500.t5 | TTS | g11500.t5 | 16652059 | 16652059 |
Sequences
>g11500.t5 Gene=g11500 Length=873
ATGGGTAAAGAGAAGACTCATATTAATATTGTTGTCATTGGACATGTCGATTCTGGCAAG
TCAACTACAACCGGTCACTTGATCTACAAATGTGGCGGTATTGACAAACGTACCATCGAG
AAGTTCGAGAAGGAAGCTCAAGAAATGGGCAAAGGTTCATTCAAATACGCATGGGTATTG
GATAAGTTGAAGGCTGAACGTGAGCGTGGTATCACCATTGATATCGCCTTATGGAAGTTT
GAAACTGCCAAGTACTACGTTACCATCATTGACGCTCCTGGACATCGTGATTTCATCAAG
AACATGATTACAGGAACATCTCAAGCCGATTGCGCTGTATTGATTGTCGCTGCTGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAGCATGCATTGTTGGCT
TTCACATTGGGTGTTAAGCAATTGATTGTCGGTGTCAACAAGATGGACTCAACTGAGCCA
CCATACTCAGAAGCACGTTTCGAGGAAATTAAAAAGGAAGTCTCGTCATACATCAAGAAG
ATCGGTTATAATCCAGCTGCTGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAGATAAAATGCCATGGTTCAAGGGCTGGGCTATTGAACGCAAAGAA
GGCAAGGCTGATGGCAAATGTCTTATTGATGCTTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGATGTTTACAAAATTGGTGGTATTGGA
ACTGTTCCAGTCGGTCGCGTTGAAACTGGTGTTTTGAAGCCAGGTATGGTTGTCGTATTT
GCACCAGTCAATTTGACCACTGAAGTAAAATCA
>g11500.t5 Gene=g11500 Length=291
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSDKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11500.t5 | CDD | cd01883 | EF1_alpha | 9 | 239 | 1.64033E-161 |
| 10 | g11500.t5 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 238 | 5.0E-95 |
| 11 | g11500.t5 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 240 | 291 | 2.5E-21 |
| 2 | g11500.t5 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 1 | 291 | 2.3E-252 |
| 3 | g11500.t5 | PANTHER | PTHR23115:SF236 | ELONGATION FACTOR 1-ALPHA 1 | 1 | 291 | 2.3E-252 |
| 6 | g11500.t5 | PRINTS | PR00315 | GTP-binding elongation factor signature | 9 | 22 | 3.0E-25 |
| 8 | g11500.t5 | PRINTS | PR00315 | GTP-binding elongation factor signature | 68 | 76 | 3.0E-25 |
| 7 | g11500.t5 | PRINTS | PR00315 | GTP-binding elongation factor signature | 88 | 98 | 3.0E-25 |
| 4 | g11500.t5 | PRINTS | PR00315 | GTP-binding elongation factor signature | 104 | 115 | 3.0E-25 |
| 5 | g11500.t5 | PRINTS | PR00315 | GTP-binding elongation factor signature | 148 | 157 | 3.0E-25 |
| 1 | g11500.t5 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 5 | 236 | 2.1E-54 |
| 13 | g11500.t5 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 61 | 76 | - |
| 14 | g11500.t5 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 5 | 242 | 61.39 |
| 9 | g11500.t5 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 261 | 3.59E-81 |
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 transcript has been annotated with K00956 (sulfate adenylyltransferase subunit 1)
Pathway
- This transcript belongs to the following pathways
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.
