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.t32 TSS g10339.t32 8939297 8939297
chr_1 g10339 g10339.t32 isoform g10339.t32 8940122 8941577
chr_1 g10339 g10339.t32 exon g10339.t32.exon1 8940122 8940617
chr_1 g10339 g10339.t32 cds g10339.t32.CDS1 8940122 8940617
chr_1 g10339 g10339.t32 exon g10339.t32.exon2 8940705 8940944
chr_1 g10339 g10339.t32 cds g10339.t32.CDS2 8940705 8940944
chr_1 g10339 g10339.t32 exon g10339.t32.exon3 8941009 8941577
chr_1 g10339 g10339.t32 cds g10339.t32.CDS3 8941009 8941577
chr_1 g10339 g10339.t32 TTS g10339.t32 8941863 8941863

Sequences

>g10339.t32 Gene=g10339 Length=1305
ATGGCTAAAGAAAAGACTCATATTAACATTGTCGTCATTGGACACGTCGACTCTGGCAAG
TCAACCACTACTGGTCATTTGATCTATAAATGCGGCGGTATCGACAAGCGTACAATCGAG
AAATTCGAAAAGGAAGCACAGGAAATGGGTAAAGGTTCATTCAAATACGCATGGGTTTTG
GACAAATTGAAGGCCGAACGTGAACGTGGTATCACCATTGATATCGCCTTGTGGAAATTC
GAAACATCAAAATACTACGTTACCATCATTGACGCTCCCGGACATCGTGATTTCATCAAA
AACATGATCACAGGAACATCTCAAGCTGATTGCGCTGTATTGATTGTCGCTGCCGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAACACGCTTTGTTGGCT
TTCACATTGGGTGTCAAACAATTGATTGTCGGTGTCAACAAAATGGACTCAACTGAGCCA
CCATACTCAGAAGCTCGCTGGCATGGTGATAACATGCTTGAACCATCAACCAAGATGCCA
TGGTTCAAGGGATGGGCCATCGAACGTAAAGAGGGTAAAGCTGATGGAAAGTGCCTCATT
GATGCCTTGGACGCCATTTTACCACCACAACGTCCAACTGACAAACCATTGCGTTTGCCA
CTTCAAGACGTCTACAAAATTGGTGGTATTGGAACTGTGCCAGTCGGACGTGTTGAAACT
GGTGTTTTGAAACCAGGTATGGTCGTCGTTTTTGCACCAGTCAACTTGACCACTGAAGTT
AAATCAGTCGAAATGCATCACGAAGCCTTGCAAGAAGCTGTACCAGGTGACAATGTTGGT
TTCAACGTCAAGAACGTCTCAGTCAAGGAATTGCGTCGTGGTTATGTTGCTGGTGACACC
AAGAGTAGTCCACCACGTGGTGCTGCTGATTTCACCGCTCAAGTAATTGTCTTGAATCAT
CCAGGTCAAATTTCAAACGGTTACACACCAGTTTTGGATTGCCACACTGCTCACATTGCC
TGCAAGTTCTCTGAAATCAAAGAAAAAGTTGATCGTCGTTCAGGTAAATCAGTTGAAGAT
AACCCCAAGGCTATCAAATCAGGAGATGCTGCTATCGTCATTTTGGTCCCAACAAAACCA
TTGTGCGTTGAATCATTCCAAGAATTCCCACCATTGGGACGTTTCGCCGTTCGTGATATG
AGACAAACAGTTGCTGTCGGTGTCATCAAGGCAGTTTCATTCAAGGATGCTTCAGGTGGT
AAGACCACAAAAGCAGCTGAGAAGGCACAAAAGGCCAAGAAATAG

>g10339.t32 Gene=g10339 Length=434
MAKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARWHGDNMLEPSTKMP
WFKGWAIERKEGKADGKCLIDALDAILPPQRPTDKPLRLPLQDVYKIGGIGTVPVGRVET
GVLKPGMVVVFAPVNLTTEVKSVEMHHEALQEAVPGDNVGFNVKNVSVKELRRGYVAGDT
KSSPPRGAADFTAQVIVLNHPGQISNGYTPVLDCHTAHIACKFSEIKEKVDRRSGKSVED
NPKAIKSGDAAIVILVPTKPLCVESFQEFPPLGRFAVRDMRQTVAVGVIKAVSFKDASGG
KTTKAAEKAQKAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g10339.t32 CDD cd01883 EF1_alpha 9 210 3.08965E-135
19 g10339.t32 CDD cd03693 EF1_alpha_II 213 303 1.1051E-59
21 g10339.t32 CDD cd03705 EF1_alpha_III 306 409 5.78366E-72
16 g10339.t32 Gene3D G3DSA:3.40.50.300 - 1 209 1.1E-77
18 g10339.t32 Gene3D G3DSA:2.40.30.10 Translation factors 211 303 1.1E-42
17 g10339.t32 Gene3D G3DSA:2.40.30.10 Translation factors 306 413 1.7E-51
5 g10339.t32 PANTHER PTHR23115 TRANSLATION FACTOR 1 166 0.0
7 g10339.t32 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 166 0.0
4 g10339.t32 PANTHER PTHR23115 TRANSLATION FACTOR 167 430 0.0
6 g10339.t32 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 167 430 0.0
10 g10339.t32 PRINTS PR00315 GTP-binding elongation factor signature 9 22 1.6E-24
12 g10339.t32 PRINTS PR00315 GTP-binding elongation factor signature 68 76 1.6E-24
11 g10339.t32 PRINTS PR00315 GTP-binding elongation factor signature 88 98 1.6E-24
8 g10339.t32 PRINTS PR00315 GTP-binding elongation factor signature 104 115 1.6E-24
9 g10339.t32 PRINTS PR00315 GTP-binding elongation factor signature 148 157 1.6E-24
3 g10339.t32 Pfam PF00009 Elongation factor Tu GTP binding domain 5 164 4.1E-48
2 g10339.t32 Pfam PF03144 Elongation factor Tu domain 2 231 296 3.6E-15
1 g10339.t32 Pfam PF03143 Elongation factor Tu C-terminal domain 307 412 1.0E-31
22 g10339.t32 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
23 g10339.t32 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 213 56.007
14 g10339.t32 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 232 8.15E-69
15 g10339.t32 SUPERFAMILY SSF50447 Translation proteins 209 305 1.39E-29
13 g10339.t32 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 309 412 1.37E-43

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