Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation factor 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 g12287 g12287.t6 TSS g12287.t6 22169311 22169311
chr_1 g12287 g12287.t6 isoform g12287.t6 22169380 22171552
chr_1 g12287 g12287.t6 exon g12287.t6.exon1 22169380 22170044
chr_1 g12287 g12287.t6 cds g12287.t6.CDS1 22169860 22170044
chr_1 g12287 g12287.t6 exon g12287.t6.exon2 22170108 22170301
chr_1 g12287 g12287.t6 cds g12287.t6.CDS2 22170108 22170301
chr_1 g12287 g12287.t6 exon g12287.t6.exon3 22170545 22171552
chr_1 g12287 g12287.t6 cds g12287.t6.CDS3 22170545 22171551
chr_1 g12287 g12287.t6 TTS g12287.t6 NA NA

Sequences

>g12287.t6 Gene=g12287 Length=1867
ATGGTAAGCAGCTTTAATTTATATTCTAATTAATCGTAAATTGAAAGAGATCATCAGGAT
GAACATTTTGGTGTATTAAAGTGTTGTGAAAATAAGAAATTACAGTCAATAATTGCAAAA
ATAAAATGGATCAAGATAATTGCGATCAAATCCAAATTTCGGTTTTCTGTAATGGCGCTT
ATAAGAATGAATGAAAATATATAATTGTTTATTTGTTATACAATAGAATGAATGAGTAAG
GATTTATGCAAAATATATTTAATTTATTTTAATAATGTAATTTTAAGAAAAAAAAATTTC
ACAGCATTTTGAAATCGCCATGATGTTGGATATAAGAAAAGAAAATGTGTGTCACTGTAT
TAAAAATAAAGAGACCTGATGATTTTAAAATGTAGAAAAATTGATTTTCTGAGAAATTAT
TAATTTATGATTATTCGATTTTCTTTACAGGTCAACTTTACTGTCGACGAAATCCGTGCT
ATGATGGACAAGAAGAAGAACATCCGTAATATGTCTGTCATTGCTCATGTCGATCACGGA
AAATCTACTTTAACTGATTCGTTGGTTTCAAAAGCTGGTATTATTGCTGGTGCAAAAGCT
GGTGAAACAAGATTCACAGACACACGCAAGGATGAACAAGAAAGATGTATCACAATTAAG
TCAACTGCTATCTCTATGTTCTTTGAGTTAGAAGACAAAGATTTGGTTTTCATTACAAAT
CCTGATCAACGTGACAAAGAAGAAAAAGGTTTCTTGATTAATTTGATTGACTCACCCGGT
CACGTTGATTTCTCATCAGAAGTCACAGCCGCTCTTCGTGTTACTGATGGTGCTCTTGTT
GTTGTCGATTGCGTATCAGGTGTTTGTGTACAAACTGAGACTGTATTGCGTCAAGCTATT
GCCGAACGTATTAAGCCAGTTTTGTTCATGAACAAGATGGACCGTGCTTTGTTGGAATTG
CAATTGGATGCTGAAGATTTGTACCAAACATTCCAACGTATCGTCGAAAACGTCAACGTT
ATCATCGCCACTTACAGCGATGACGATGGTCCAATGGGAGAAGTTCGTGTTGATCCATCA
AAGGGTTCAGTCGGTTTCGGTTCCGGCTTGCACGGATGGGCTTTCACTCTCAAACAATTT
TCGGAAATGTATGCAGCTAAATTCAAGATCGATGTCGTTAAACTCATGAATCGCTTATGG
GGTGAAAATTTCTTCAATGCAAAGACCAAGAAATGGGCAAAGACAAAGGACGATGATAAC
AAGCGTTCATTTGTCATGTATGTATTGGATCCAATTTATAAGGTATTCGATGTCATTATG
AATTACAAGAAAGAAGAAATTCCTGGCTTATTGGAGAAAATCGGAGTCACACTCAAGCAC
GAAGACAAAGATAAGGATGGTAAACAATTATTGAAAGTTGTCATGCGCTCATGGTTGCCA
GCTGGTGAAGCTTTACTTCAAATGATTGCTATTCACTTGCCTTCACCAGTCGTCGCTCAA
AAATACCGTATGGAAATGTTGTATGAGGGACCACTCGATGACGAGGCTGCCGTTGCTGTC
AAGAACTGCGATCCAAATGGTCCATTGATGATGTACGTCTCAAAAATGGTACCAACCAGT
GACAAGGGTCGTTTCTATGCTTTCGGACGTGTGTTCTCCGGAAAAGTTCAAACTGGTCAA
AAATGCCGTATAATGGGACCAAATTACACACCTGGCAAGAAGGAAGACTTGTACGAAAAA
TCAATTCAACGTACTATTTTGATGATGGGTCGTTATGTTGAAGCCATTGAAGATGTTCCA
TGCGGTAACATTTGCGGTTTGGTTGGTGTTGATCAATTCTTGGTCAAGACTGGAACAATC
ACAACAT

>g12287.t6 Gene=g12287 Length=462
MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK
STAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV
VVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNV
IIATYSDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFKIDVVKLMNRLW
GENFFNAKTKKWAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPGLLEKIGVTLKH
EDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYEGPLDDEAAVAV
KNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNYTPGKKEDLYEK
SIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12287.t6 CDD cd01885 EF2 9 225 3.13303E-124
15 g12287.t6 CDD cd03700 EF2_snRNP_like_II 369 462 6.48996E-55
12 g12287.t6 Gene3D G3DSA:3.40.50.300 - 2 335 3.9E-190
13 g12287.t6 Gene3D G3DSA:2.40.30.10 Translation factors 38 462 3.9E-190
14 g12287.t6 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 217 319 3.9E-190
3 g12287.t6 PANTHER PTHR42908:SF29 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2A, TANDEM DUPLICATE 1-RELATED 1 462 6.4E-246
4 g12287.t6 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 462 6.4E-246
8 g12287.t6 PRINTS PR00315 GTP-binding elongation factor signature 10 23 3.0E-14
7 g12287.t6 PRINTS PR00315 GTP-binding elongation factor signature 54 62 3.0E-14
9 g12287.t6 PRINTS PR00315 GTP-binding elongation factor signature 94 104 3.0E-14
6 g12287.t6 PRINTS PR00315 GTP-binding elongation factor signature 110 121 3.0E-14
5 g12287.t6 PRINTS PR00315 GTP-binding elongation factor signature 146 155 3.0E-14
2 g12287.t6 Pfam PF00009 Elongation factor Tu GTP binding domain 6 334 1.8E-67
1 g12287.t6 Pfam PF03144 Elongation factor Tu domain 2 386 460 1.6E-13
17 g12287.t6 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 47 62 -
19 g12287.t6 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 6 337 54.195
10 g12287.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 334 2.9E-109
11 g12287.t6 SUPERFAMILY SSF50447 Translation proteins 335 462 1.81E-43
18 g12287.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 8 157 1.5E-18

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