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.t17 TSS g12287.t17 22169311 22169311
chr_1 g12287 g12287.t17 isoform g12287.t17 22169830 22173484
chr_1 g12287 g12287.t17 exon g12287.t17.exon1 22169830 22170044
chr_1 g12287 g12287.t17 cds g12287.t17.CDS1 22169860 22170044
chr_1 g12287 g12287.t17 exon g12287.t17.exon2 22170108 22170301
chr_1 g12287 g12287.t17 cds g12287.t17.CDS2 22170108 22170301
chr_1 g12287 g12287.t17 exon g12287.t17.exon3 22170545 22171575
chr_1 g12287 g12287.t17 cds g12287.t17.CDS3 22170545 22171575
chr_1 g12287 g12287.t17 exon g12287.t17.exon4 22171753 22172190
chr_1 g12287 g12287.t17 cds g12287.t17.CDS4 22171753 22172190
chr_1 g12287 g12287.t17 exon g12287.t17.exon5 22172261 22172432
chr_1 g12287 g12287.t17 cds g12287.t17.CDS5 22172261 22172432
chr_1 g12287 g12287.t17 exon g12287.t17.exon6 22172626 22173484
chr_1 g12287 g12287.t17 cds g12287.t17.CDS6 22172626 22173107
chr_1 g12287 g12287.t17 TTS g12287.t17 22173564 22173564

Sequences

>g12287.t17 Gene=g12287 Length=2909
GTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGTAAT
ATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTTTCA
AAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGCAAG
GATGAACAAGAAAGATGTATCACAATTAAGTCAACTGCTATCTCTATGTTCTTTGAGTTA
GAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAGAAGAAAAAGGT
TTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAGAAGTCACAGCC
GCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTATCAGGTGTTTGTGTA
CAAACTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCAGTTTTGTTCATG
AACAAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATTTGTACCAAACA
TTCCAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCGATGACGATGGT
CCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCGGTTCCGGCTTG
CACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTAAATTCAAGATC
GATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAATGCAAAGACCAAG
AAATGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCATGTATGTATTGGAT
CCAATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGAAATTCCTGGCTTA
TTGGAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGATGGTAAACAATTA
TTGAAAGTTGTCATGCGCTCATGGTTGCCAGCTGGTGAAGCTTTACTTCAAATGATTGCT
ATTCACTTGCCTTCACCAGTCGTCGCTCAAAAATACCGTATGGAAATGTTGTATGAGGGA
CCACTCGATGACGAGGCTGCCGTTGCTGTCAAGAACTGCGATCCAAATGGTCCATTGATG
ATGTACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCGTTTCTATGCTTTCGGACGT
GTGTTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTATAATGGGACCAAATTACACA
CCTGGCAAGAAGGAAGACTTGTACGAAAAATCAATTCAACGTACTATTTTGATGATGGGT
CGTTATGTTGAAGCCATTGAAGATGTTCCATGCGGTAACATTTGCGGTTTGGTTGGTGTT
GATCAATTCTTGGTCAAGACTGGAACAATCACAACATTCAAAGATGCCCATAACATGAAG
GTCATGAAATTTTCAGTTTCACCTGTCGTGCGTGTTGCTGTCGAGCCTAAAAATCCAGCT
GATTTGCCCAAACTCGTCGAAGGTCTTAAGCGTTTGGCTAAATCCGATCCTATGGTACAA
TGTATCATTGAAGAATCTGGCGAACATATTATTGCTGGTGCTGGTGAATTGCATTTGGAA
ATTTGCTTGAAGGACTTGGAAGAAGATCACGCTTGTATCCCATTGAAGAAATCCGATCCA
GTTGTATCGTATCGTGAAACAGTCTCTGATGAATCATCCATGATGTGTTTATCAAAATCA
CCAAACAAGCATAATCGTCTTTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCTGAA
GATATTGATGGAGGTGCAGTTAATGCTCGTGACGATTTCAAGATTCGTGCACGTTACTTG
GCTGAGAAATACGAATGGGATGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGAC
GGTACAGGTCCAAATGTAATTGTTGACGTCACTAAGGGTGTACAATATTTGAATGAAATC
AAGGACTCTGTTGTTGCTGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAG
AACATGAGAGCTGTTCGTTTCAACATTTATGATGTTACACTGCATGCTGACGCTATCCAT
CGTGGAGGTGGTCAAATCATTCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACA
GCTTCTCCACGTTTGATGGAGCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCT
GTCGGTGGTATTTATGGTGTGCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAA
GTTGCCGGTACACCTATGTTCGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTTGGA
TTCACTGCTGATTTGCGCTCAAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTTGAC
CATTGGCAGATCTTCCCAGGTGACCCTAACGAACCATCATCAAAACCATACCAGATTGTG
CAAGATACAAGAAAACGTAAAGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATACTAT
GATAAAATGTAAAAGTCTTTCCGAGCTTCTTCAGTTATACTTATTATTTTTTCCCTCTTC
ATTTTTTGCTTATAATTTTTTGATTTTTATATTTTTATCATAACATTACGCATAAAAGAT
AAAACAACATCAAAGCAAGAAAAAAGCGTTGATTATTTTATATCAATTAATCGTAATATT
GTAATCAAACTTAAAATATTTTTTGAGCGTCTTAATATGAGTTAAGTTAAAAGCATTCTC
CTATGAAAATTAAAAGCGTTTATGAGTTCGCCATAAATATGCTGTTACATCTACGCGCGA
AAGTGGTTGAAATGAAAAAGAATTTCATATAAATATTAACAATGATATCCAGCAACATGG
AAGAAAAATTAGAACGACGGAAACGGAAA

>g12287.t17 Gene=g12287 Length=833
MMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTRKDEQERCITIK
STAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVTAALRVTDGALV
VVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQTFQRIVENVNV
IIATYSDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFKIDVVKLMNRLW
GENFFNAKTKKWAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPGLLEKIGVTLKH
EDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYEGPLDDEAAVAV
KNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNYTPGKKEDLYEK
SIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITTFKDAHNMKVMKFSVSPVV
RVAVEPKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLEEDH
ACIPLKKSDPVVSYRETVSDESSMMCLSKSPNKHNRLFMKAMPMPDGLAEDIDGGAVNAR
DDFKIRARYLAEKYEWDVTEARKIWCFGPDGTGPNVIVDVTKGVQYLNEIKDSVVAGFQW
ATKEGVLAEENMRAVRFNIYDVTLHADAIHRGGGQIIPTTRRCLYASYITASPRLMEPVY
LCEIQCPEVAVGGIYGVLNRRRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTG
GQAFPQCVFDHWQIFPGDPNEPSSKPYQIVQDTRKRKGLKEGLPDLNQYYDKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
28 g12287.t17 CDD cd01885 EF2 9 225 1.02233E-120
27 g12287.t17 CDD cd03700 EF2_snRNP_like_II 369 463 4.03134E-54
26 g12287.t17 CDD cd16261 EF2_snRNP_III 478 549 7.66546E-43
25 g12287.t17 CDD cd01681 aeEF2_snRNP_like_IV 549 721 7.3059E-106
24 g12287.t17 CDD cd04096 eEF2_snRNP_like_C 717 796 1.19677E-49
18 g12287.t17 Gene3D G3DSA:3.40.50.300 - 2 335 2.1E-189
22 g12287.t17 Gene3D G3DSA:2.40.30.10 Translation factors 38 462 2.1E-189
23 g12287.t17 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 217 319 2.1E-189
20 g12287.t17 Gene3D G3DSA:3.30.70.870 Elongation Factor G (Translational Gtpase) 476 553 1.4E-38
21 g12287.t17 Gene3D G3DSA:3.30.70.240 - 555 819 5.4E-127
19 g12287.t17 Gene3D G3DSA:3.30.230.10 - 561 821 5.4E-127
6 g12287.t17 PANTHER PTHR42908:SF24 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 1 833 0.0
7 g12287.t17 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 833 0.0
11 g12287.t17 PRINTS PR00315 GTP-binding elongation factor signature 10 23 4.2E-13
10 g12287.t17 PRINTS PR00315 GTP-binding elongation factor signature 54 62 4.2E-13
12 g12287.t17 PRINTS PR00315 GTP-binding elongation factor signature 94 104 4.2E-13
9 g12287.t17 PRINTS PR00315 GTP-binding elongation factor signature 110 121 4.2E-13
8 g12287.t17 PRINTS PR00315 GTP-binding elongation factor signature 146 155 4.2E-13
4 g12287.t17 Pfam PF00009 Elongation factor Tu GTP binding domain 6 334 8.2E-67
3 g12287.t17 Pfam PF03144 Elongation factor Tu domain 2 386 460 3.6E-13
1 g12287.t17 Pfam PF14492 Elongation Factor G, domain III 478 539 1.6E-13
2 g12287.t17 Pfam PF03764 Elongation factor G, domain IV 597 711 1.5E-31
5 g12287.t17 Pfam PF00679 Elongation factor G C-terminus 714 800 4.9E-22
29 g12287.t17 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 47 62 -
33 g12287.t17 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 6 337 54.195
30 g12287.t17 SMART SM00889 EFG_IV_2 596 712 1.3E-27
31 g12287.t17 SMART SM00838 EFG_C_a 714 803 2.6E-19
14 g12287.t17 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 334 1.41E-108
17 g12287.t17 SUPERFAMILY SSF50447 Translation proteins 335 472 6.19E-45
16 g12287.t17 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 475 550 9.71E-21
13 g12287.t17 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 552 716 2.48E-70
15 g12287.t17 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 717 831 6.23E-34
32 g12287.t17 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 8 157 4.3E-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

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