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 g11500 g11500.t1 TSS g11500.t1 16650082 16650082
chr_1 g11500 g11500.t1 isoform g11500.t1 16650214 16651738
chr_1 g11500 g11500.t1 exon g11500.t1.exon1 16650214 16651036
chr_1 g11500 g11500.t1 cds g11500.t1.CDS1 16650214 16651036
chr_1 g11500 g11500.t1 exon g11500.t1.exon2 16651098 16651594
chr_1 g11500 g11500.t1 cds g11500.t1.CDS2 16651098 16651594
chr_1 g11500 g11500.t1 exon g11500.t1.exon3 16651670 16651738
chr_1 g11500 g11500.t1 cds g11500.t1.CDS3 16651670 16651738
chr_1 g11500 g11500.t1 TTS g11500.t1 16652519 16652519

Sequences

>g11500.t1 Gene=g11500 Length=1389
ATGGGTAAAGAGAAGACTCATATTAATATTGTTGTCATTGGACATGTCGATTCTGGCAAG
TCAACTACAACCGGTCACTTGATCTACAAATGTGGCGGTATTGACAAACGTACCATCGAG
AAGTTCGAGAAGGAAGCTCAAGAAATGGGCAAAGGTTCATTCAAATACGCATGGGTATTG
GATAAGTTGAAGGCTGAACGTGAGCGTGGTATCACCATTGATATCGCCTTATGGAAGTTT
GAAACTGCCAAGTACTACGTTACCATCATTGACGCTCCTGGACATCGTGATTTCATCAAG
AACATGATTACAGGAACATCTCAAGCCGATTGCGCTGTATTGATTGTCGCTGCTGGTACT
GGTGAATTCGAAGCTGGTATTTCAAAGAACGGTCAAACTCGTGAGCATGCATTGTTGGCT
TTCACATTGGGTGTTAAGCAATTGATTGTCGGTGTCAACAAGATGGACTCAACTGAGCCA
CCATACTCAGAAGCACGTTTCGAGGAAATTAAAAAGGAAGTCTCGTCATACATCAAGAAG
ATCGGTTATAATCCAGCTGCTGTTGCTTTCGTTCCAATCTCAGGCTGGCATGGTGATAAC
ATGCTTGAACCATCAGATAAAATGCCATGGTTCAAGGGCTGGGCTATTGAACGCAAAGAA
GGCAAGGCTGATGGCAAATGTCTTATTGATGCTTTGGACGCCATTTTACCACCACAACGT
CCAACTGACAAACCATTGCGTTTGCCACTTCAAGATGTTTACAAAATTGGTGGTATTGGA
ACTGTTCCAGTCGGTCGCGTTGAAACTGGTGTTTTGAAGCCAGGTATGGTTGTCGTATTT
GCACCAGTCAATTTGACCACTGAAGTAAAATCAGTCGAAATGCATCATGAAGCTTTGCAA
GAAGCTGTACCTGGTGACAATGTTGGTTTTAACGTCAAGAACGTCTCAGTCAAGGAATTG
CGTCGTGGTTATGTTGCTGGTGACAGCAAGAGCAGTCCACCACGTGGTGCTGCTGATTTC
ACCGCTCAAGTAATTGTCTTGAATCATCCAGGTCAAATTGCAAATGGTTATACACCAGTT
TTGGATTGTCACACTGCTCACATTGCTTGCAAATTTGCTGAAATCAAAGAGAAGTGCGAT
CGTCGTACTGGCAAGACAACAGAAGAGAATCCAAAGGCTATCAAATCAGGTGATGCCGCT
ATTGTGAATTTAGTTCCATCAAAGCCATTGTGTGTTGAATCATTCTCCGAATTTCCACCA
TTGGGACGTTTTGCTGTTCGTGACATGAGACAAACTGTTGCTGTTGGTGTTATCAAAGCC
GTTAACTTCAAAGAAGCGAGCGGTGGAAAAGTAACAAAAGCCGCTGAGAAGGCAGCAAAG
AAAAAATAA

>g11500.t1 Gene=g11500 Length=462
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAQEMGKGSFKYAWVL
DKLKAERERGITIDIALWKFETAKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGT
GEFEAGISKNGQTREHALLAFTLGVKQLIVGVNKMDSTEPPYSEARFEEIKKEVSSYIKK
IGYNPAAVAFVPISGWHGDNMLEPSDKMPWFKGWAIERKEGKADGKCLIDALDAILPPQR
PTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVVFAPVNLTTEVKSVEMHHEALQ
EAVPGDNVGFNVKNVSVKELRRGYVAGDSKSSPPRGAADFTAQVIVLNHPGQIANGYTPV
LDCHTAHIACKFAEIKEKCDRRTGKTTEENPKAIKSGDAAIVNLVPSKPLCVESFSEFPP
LGRFAVRDMRQTVAVGVIKAVNFKEASGGKVTKAAEKAAKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g11500.t1 CDD cd01883 EF1_alpha 9 239 1.29644E-160
18 g11500.t1 CDD cd03693 EF1_alpha_II 242 332 2.85266E-59
20 g11500.t1 CDD cd03705 EF1_alpha_III 335 438 2.28688E-72
15 g11500.t1 Gene3D G3DSA:3.40.50.300 - 1 238 2.0E-94
16 g11500.t1 Gene3D G3DSA:2.40.30.10 Translation factors 240 332 8.0E-43
17 g11500.t1 Gene3D G3DSA:2.40.30.10 Translation factors 335 442 1.1E-51
6 g11500.t1 Hamap MF_00118_A Elongation factor Tu [tuf]. 2 444 51.351295
4 g11500.t1 PANTHER PTHR23115 TRANSLATION FACTOR 1 459 0.0
5 g11500.t1 PANTHER PTHR23115:SF236 ELONGATION FACTOR 1-ALPHA 1 1 459 0.0
9 g11500.t1 PRINTS PR00315 GTP-binding elongation factor signature 9 22 2.1E-24
11 g11500.t1 PRINTS PR00315 GTP-binding elongation factor signature 68 76 2.1E-24
10 g11500.t1 PRINTS PR00315 GTP-binding elongation factor signature 88 98 2.1E-24
7 g11500.t1 PRINTS PR00315 GTP-binding elongation factor signature 104 115 2.1E-24
8 g11500.t1 PRINTS PR00315 GTP-binding elongation factor signature 148 157 2.1E-24
3 g11500.t1 Pfam PF00009 Elongation factor Tu GTP binding domain 5 236 7.9E-54
2 g11500.t1 Pfam PF03144 Elongation factor Tu domain 2 260 325 3.9E-15
1 g11500.t1 Pfam PF03143 Elongation factor Tu C-terminal domain 336 441 1.3E-32
21 g11500.t1 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 61 76 -
23 g11500.t1 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 5 242 61.39
13 g11500.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 261 5.82E-81
14 g11500.t1 SUPERFAMILY SSF50447 Translation proteins 238 334 1.3E-29
12 g11500.t1 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 338 441 4.75E-44
22 g11500.t1 TIGRFAM TIGR00483 EF-1_alpha: translation elongation factor EF-1, subunit alpha 1 444 3.5E-222

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

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.

Raw TPM values