Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha.

Parent gene

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 g10339 g10339.t34 TSS g10339.t34 8939297 8939297
chr_1 g10339 g10339.t34 isoform g10339.t34 8940122 8942038
chr_1 g10339 g10339.t34 exon g10339.t34.exon1 8940122 8940572
chr_1 g10339 g10339.t34 cds g10339.t34.CDS1 8940122 8940572
chr_1 g10339 g10339.t34 exon g10339.t34.exon2 8941483 8942038
chr_1 g10339 g10339.t34 cds g10339.t34.CDS2 8941483 8941577
chr_1 g10339 g10339.t34 TTS g10339.t34 NA NA

Sequences

>g10339.t34 Gene=g10339 Length=1007
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGTTGCTGTCGGTGTCATCAAGGCAGTTTCA
TTCAAGGATGCTTCAGGTGGTAAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAG
AAATAGCCATGCATCGATATTATCTTTTATCCGCACAAACAGCAAACAAGAAAAATTATT
TCTAATGGTAAAAACTATAATTTTCATAGAAAAGAATTTAGAAGGAAAGAAGAGTGTGGA
TTTAATATGGCACATAAGAAATGTATTTTCTTTAACATTCTTTATTATTATTAAATTCAT
TCCGAATACATACATTCACATACGCCAACTATAACATGCATTTTTCTATTAAACAATGAT
TTTATGTTTGTCAAATTATGATTTTTTGCTGGATTAAAAAGAATTCAATAACAAAAAATA
TTTTCTTCTTTTTTATATTTCTATCATTTATTAACATTCTTCATTGGCGTTTACAGAGTA
TTAAGATAAAAAATGATCTTATAATGAGCGAAGAAAAGATTGAATAAATATATTTCTGTG
AGATTTATCATCTCGTATTTTTGGAAAAATTTTATACCTAATCTACT

>g10339.t34 Gene=g10339 Length=181
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVVAVGVIKAVSFKDASGGKTTKAAEKAQKAK
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10339.t34 CDD cd01883 EF1_alpha 9 151 3.4937E-111
11 g10339.t34 Gene3D G3DSA:3.40.50.300 - 1 152 3.2E-66
3 g10339.t34 PANTHER PTHR23115 TRANSLATION FACTOR 1 150 1.1E-138
5 g10339.t34 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 150 1.1E-138
2 g10339.t34 PANTHER PTHR23115 TRANSLATION FACTOR 151 177 1.1E-138
4 g10339.t34 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 151 177 1.1E-138
7 g10339.t34 PRINTS PR00315 GTP-binding elongation factor signature 9 22 1.3E-21
9 g10339.t34 PRINTS PR00315 GTP-binding elongation factor signature 68 76 1.3E-21
8 g10339.t34 PRINTS PR00315 GTP-binding elongation factor signature 88 98 1.3E-21
6 g10339.t34 PRINTS PR00315 GTP-binding elongation factor signature 104 115 1.3E-21
1 g10339.t34 Pfam PF00009 Elongation factor Tu GTP binding domain 5 151 3.7E-44
14 g10339.t34 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
15 g10339.t34 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 181 48.429
10 g10339.t34 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 151 2.39E-57
13 g10339.t34 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 137 159 -

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.

Raw TPM values