Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 1-alpha 2.

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 g11500 g11500.t6 TSS g11500.t6 16650082 16650082
chr_1 g11500 g11500.t6 isoform g11500.t6 16650214 16652064
chr_1 g11500 g11500.t6 exon g11500.t6.exon1 16650214 16651011
chr_1 g11500 g11500.t6 cds g11500.t6.CDS1 16650214 16651011
chr_1 g11500 g11500.t6 exon g11500.t6.exon2 16651179 16651594
chr_1 g11500 g11500.t6 cds g11500.t6.CDS2 16651179 16651307
chr_1 g11500 g11500.t6 exon g11500.t6.exon3 16651670 16652064
chr_1 g11500 g11500.t6 TTS g11500.t6 16652519 16652519

Sequences

>g11500.t6 Gene=g11500 Length=1609
ATGGGTAAAGAGAAGACTCATATTAATATTGTTGTCATTGGACATGTCGATTCTGGCAAG
TCAACTACAACCGGTCACTTGATCTACAAATGTGGCGGTATTGACAAACGTACCATCGAG
AAGTTCGAGAAGGAAGCTCAAGAAATGGGCAAAGGTTCATTCAAATACGCATGGGTATTG
GATAAGTTGAAGGCTGAACGTGAGCGTGGTATCACCATTGATATCGCCTTATGGAAGTTT
GAAACTGCCAAGTACTACGTTACCATCATTGACGCTCCTGGACATCGTGATTTCATCAAG
AACATGATTACAGGAACATCTCAAGCCGATTGCGCTGTATTGATTGTCGCTGCTGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAGCATGCATTGTTGGCT
TTCACATTGGGTGTTAAGCAATTGATTGTCGGTGTCAACAAGATGGACTCAACTGAGCCA
CCATACTCAGAAGCACGTTTCGAGGAAATTAAAAAGGAAGTCTCGTCATACATCAAGAAG
ATCGGTTATAATCCAGCTGCTGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAGATAAAATGCCATGGTTCAAGGGCTGGGCTATTGAACGCAAAGAA
GGCAAGGCTGATGGCAAATGTCTTATTGATGCTTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGATGTTTACAAAATTGGTGGTATTGGA
ACTGTTCCAGTCGGTCGCCTGTACCTGGTGACAATGTTGGTTTTAACGTCAAGAACGTCT
CAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACAGCAAGAGCAGTCCACCACGTG
GTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTGCAAATG
GTTATACACCAGTTTTGGATTGTCACACTGCTCACATTGCTTGCAAATTTGCTGAAATCA
AAGAGAAGTGCGATCGTCGTACTGGCAAGACAACAGAAGAGAATCCAAAGGCTATCAAAT
CAGGTGATGCCGCTATTGTGAATTTAGTTCCATCAAAGCCATTGTGTGTTGAATCATTCT
CCGAATTTCCACCATTGGGACGTTTTGCTGTTCGTGACATGAGACAAACTGTTGCTGTTG
GTGTTATCAAAGCCGTTAACTTCAAAGAAGCGAGCGGTGGAAAAGTAACAAAAGCCGCTG
AGAAGGCAGCAAAGAAAAAATAACTAGATTGTCAACTTGGCAAATTTGCCGTGTTTCGAT
TATCGAACGGCAAACTTGAAATTTTTCATTCTATAAGAAATATTCAAACATTTCACCATG
CTGATGGTGTCAAACATCTTTTTCAATTGATTTCTTCTACTCTTTCTAATAACTTTTATT
TTACACATCCCCATTCGTTTTTAATCTTTCATCATCATCGCAGGAAAAAGCCGAATGGAT
GTCATTTCTTTTTCGATTTATTCTCATTTACGTTGCATAAGATTAATTTAGTTTTGGCAA
ATGTTGTCAATATTAAGACAAAACAAATAAACTTATGATAACATCATTT

>g11500.t6 Gene=g11500 Length=308
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSDKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRLYLVTMLVLTSRTSQSRNCVVVMLLVTARAVHHV
VLLISPLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g11500.t6 CDD cd01883 EF1_alpha 9 239 4.06861E-163
10 g11500.t6 Gene3D G3DSA:3.40.50.300 - 1 238 6.1E-95
11 g11500.t6 Gene3D G3DSA:2.40.30.10 Translation factors 240 276 1.3E-8
2 g11500.t6 PANTHER PTHR23115 TRANSLATION FACTOR 1 267 5.8E-231
3 g11500.t6 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 267 5.8E-231
6 g11500.t6 PRINTS PR00315 GTP-binding elongation factor signature 9 22 3.7E-25
8 g11500.t6 PRINTS PR00315 GTP-binding elongation factor signature 68 76 3.7E-25
7 g11500.t6 PRINTS PR00315 GTP-binding elongation factor signature 88 98 3.7E-25
4 g11500.t6 PRINTS PR00315 GTP-binding elongation factor signature 104 115 3.7E-25
5 g11500.t6 PRINTS PR00315 GTP-binding elongation factor signature 148 157 3.7E-25
1 g11500.t6 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 2.1E-54
14 g11500.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 252 -
16 g11500.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 253 275 -
12 g11500.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 276 286 -
15 g11500.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 287 307 -
13 g11500.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 308 308 -
18 g11500.t6 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
19 g11500.t6 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.39
9 g11500.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 1.93E-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 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