General information for g11500.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation factor 1-alpha.
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.t8 | TSS | g11500.t8 | 16650082 | 16650082 |
| chr_1 | g11500 | g11500.t8 | isoform | g11500.t8 | 16650214 | 16652523 |
| chr_1 | g11500 | g11500.t8 | exon | g11500.t8.exon1 | 16650214 | 16651021 |
| chr_1 | g11500 | g11500.t8 | cds | g11500.t8.CDS1 | 16650214 | 16651021 |
| chr_1 | g11500 | g11500.t8 | exon | g11500.t8.exon2 | 16651098 | 16651594 |
| chr_1 | g11500 | g11500.t8 | cds | g11500.t8.CDS2 | 16651098 | 16651594 |
| chr_1 | g11500 | g11500.t8 | exon | g11500.t8.exon3 | 16651670 | 16652523 |
| chr_1 | g11500 | g11500.t8 | cds | g11500.t8.CDS3 | 16651670 | 16651738 |
| chr_1 | g11500 | g11500.t8 | TTS | g11500.t8 | 16652519 | 16652519 |
Sequences
>g11500.t8 Gene=g11500 Length=2159
ATGGGTAAAGAGAAGACTCATATTAATATTGTTGTCATTGGACATGTCGATTCTGGCAAG
TCAACTACAACCGGTCACTTGATCTACAAATGTGGCGGTATTGACAAACGTACCATCGAG
AAGTTCGAGAAGGAAGCTCAAGAAATGGGCAAAGGTTCATTCAAATACGCATGGGTATTG
GATAAGTTGAAGGCTGAACGTGAGCGTGGTATCACCATTGATATCGCCTTATGGAAGTTT
GAAACTGCCAAGTACTACGTTACCATCATTGACGCTCCTGGACATCGTGATTTCATCAAG
AACATGATTACAGGAACATCTCAAGCCGATTGCGCTGTATTGATTGTCGCTGCTGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAGCATGCATTGTTGGCT
TTCACATTGGGTGTTAAGCAATTGATTGTCGGTGTCAACAAGATGGACTCAACTGAGCCA
CCATACTCAGAAGCACGTTTCGAGGAAATTAAAAAGGAAGTCTCGTCATACATCAAGAAG
ATCGGTTATAATCCAGCTGCTGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAGATAAAATGCCATGGTTCAAGGGCTGGGCTATTGAACGCAAAGAA
GGCAAGGCTGATGGCAAATGTCTTATTGATGCTTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGATGTTTACAAAATTGGTGGTATTGGA
ACTGTTCCAGTCGGTCGCGTTGAAACTGGTATGGTTGTCGTATTTGCACCAGTCAATTTG
ACCACTGAAGTAAAATCAGTCGAAATGCATCATGAAGCTTTGCAAGAAGCTGTACCTGGT
GACAATGTTGGTTTTAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTT
GCTGGTGACAGCAAGAGCAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATT
GTCTTGAATCATCCAGGTCAAATTGCAAATGGTTATACACCAGTTTTGGATTGTCACACT
GCTCACATTGCTTGCAAATTTGCTGAAATCAAAGAGAAGTGCGATCGTCGTACTGGCAAG
ACAACAGAAGAGAATCCAAAGGCTATCAAATCAGGTGATGCCGCTATTGTGAATTTAGTT
CCATCAAAGCCATTGTGTGTTGAATCATTCTCCGAATTTCCACCATTGGGACGTTTTGCT
GTTCGTGACATGAGACAAACTGTTGCTGTTGGTGTTATCAAAGCCGTTAACTTCAAAGAA
GCGAGCGGTGGAAAAGTAACAAAAGCCGCTGAGAAGGCAGCAAAGAAAAAATAACTAGAT
TGTCAACTTGGCAAATTTGCCGTGTTTCGATTATCGAACGGCAAACTTGAAATTTTTCAT
TCTATAAGAAATATTCAAACATTTCACCATGCTGATGGTGTCAAACATCTTTTTCAATTG
ATTTCTTCTACTCTTTCTAATAACTTTTATTTTACACATCCCCATTCGTTTTTAATCTTT
CATCATCATCGCAGGAAAAAGCCGAATGGATGTCATTTCTTTTTCGATTTATTCTCATTT
ACGTTGCATAAGATTAATTTAGTTTTGGCAAATGTTGTCAATATTAAGACAAAACAAATA
AACTTATGATAACATCATTTTATAGTTGCGAGTTTATTTTAATTTTGGCCATACACACAC
ACACAATACACAGGAATGGAAAAGGATCGAAGGCTATTTCTTTATTTAAATAATAATGAT
TAGAAGTACCTACGTGTATAGTCTTCTTCTTATAATTTGTGATATTTTTTAAGTTGAAGA
AATCATTGAGGCGTTACTTTAAATATTTACTTACTTACTTATTATTGATAAATTAACTCT
TCTCTAATAAACGAGAACGAAATATTAAATTGGTGAAACTGTAATAGTTTATTACGAATA
ATTTTTTTGGCTATTAAATTGTTACATGCAAGAATAAAAGCGAGACACACAAGAGAAAAA
AAAGTTTTGTATTGCACCTGTTTCCGATAAATGAAAATCAGCATGGTGAACTATCCAAAA
AGAAAGAAAAAATCTTATTATATTCAAACAAAAATACTCAAAATAAAAGCTTGAGAAAA
>g11500.t8 Gene=g11500 Length=457
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSDKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGMVVVFAPVNLTTEVKSVEMHHEALQEAVPG
DNVGFNVKNVSVKELRRGYVAGDSKSSPPRGAADFTAQVIVLNHPGQIANGYTPVLDCHT
AHIACKFAEIKEKCDRRTGKTTEENPKAIKSGDAAIVNLVPSKPLCVESFSEFPPLGRFA
VRDMRQTVAVGVIKAVNFKEASGGKVTKAAEKAAKKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g11500.t8 | CDD | cd01883 | EF1_alpha | 9 | 239 | 1.13135E-160 |
| 17 | g11500.t8 | CDD | cd03693 | EF1_alpha_II | 242 | 327 | 5.09548E-53 |
| 19 | g11500.t8 | CDD | cd03705 | EF1_alpha_III | 330 | 433 | 1.61088E-72 |
| 14 | g11500.t8 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 238 | 1.9E-94 |
| 15 | g11500.t8 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 240 | 327 | 3.6E-36 |
| 16 | g11500.t8 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 330 | 437 | 1.1E-51 |
| 4 | g11500.t8 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 1 | 454 | 0.0 |
| 5 | g11500.t8 | PANTHER | PTHR23115:SF236 | ELONGATION FACTOR 1-ALPHA 1 | 1 | 454 | 0.0 |
| 8 | g11500.t8 | PRINTS | PR00315 | GTP-binding elongation factor signature | 9 | 22 | 2.0E-24 |
| 10 | g11500.t8 | PRINTS | PR00315 | GTP-binding elongation factor signature | 68 | 76 | 2.0E-24 |
| 9 | g11500.t8 | PRINTS | PR00315 | GTP-binding elongation factor signature | 88 | 98 | 2.0E-24 |
| 6 | g11500.t8 | PRINTS | PR00315 | GTP-binding elongation factor signature | 104 | 115 | 2.0E-24 |
| 7 | g11500.t8 | PRINTS | PR00315 | GTP-binding elongation factor signature | 148 | 157 | 2.0E-24 |
| 3 | g11500.t8 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 5 | 236 | 7.7E-54 |
| 2 | g11500.t8 | Pfam | PF03144 | Elongation factor Tu domain 2 | 265 | 320 | 3.7E-9 |
| 1 | g11500.t8 | Pfam | PF03143 | Elongation factor Tu C-terminal domain | 331 | 436 | 1.3E-32 |
| 20 | g11500.t8 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 61 | 76 | - |
| 22 | g11500.t8 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 5 | 242 | 61.39 |
| 12 | g11500.t8 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 261 | 5.74E-81 |
| 13 | g11500.t8 | SUPERFAMILY | SSF50447 | Translation proteins | 238 | 329 | 1.48E-24 |
| 11 | g11500.t8 | SUPERFAMILY | SSF50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 333 | 436 | 4.6E-44 |
| 21 | g11500.t8 | TIGRFAM | TIGR00483 | EF-1_alpha: translation elongation factor EF-1, subunit alpha | 1 | 439 | 4.3E-216 |
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:0003746 | translation elongation factor activity | MF |
| GO:0006414 | translational elongation | BP |
| GO:0005525 | GTP binding | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03231 (elongation factor 1-alpha)
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.
