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.t23 TSS g12287.t23 22169829 22169829
chr_1 g12287 g12287.t23 isoform g12287.t23 22170619 22173484
chr_1 g12287 g12287.t23 exon g12287.t23.exon1 22170619 22171575
chr_1 g12287 g12287.t23 cds g12287.t23.CDS1 22170622 22171575
chr_1 g12287 g12287.t23 exon g12287.t23.exon2 22171753 22172190
chr_1 g12287 g12287.t23 cds g12287.t23.CDS2 22171753 22172190
chr_1 g12287 g12287.t23 exon g12287.t23.exon3 22172261 22172432
chr_1 g12287 g12287.t23 cds g12287.t23.CDS3 22172261 22172432
chr_1 g12287 g12287.t23 exon g12287.t23.exon4 22172626 22173484
chr_1 g12287 g12287.t23 cds g12287.t23.CDS4 22172626 22173107
chr_1 g12287 g12287.t23 TTS g12287.t23 22173564 22173564

Sequences

>g12287.t23 Gene=g12287 Length=2426
AAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATTTGTACCAAACATTC
CAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCGATGACGATGGTCCA
ATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCGGTTCCGGCTTGCAC
GGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTAAATTCAAGATCGAT
GTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAATGCAAAGACCAAGAAA
TGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCATGTATGTATTGGATCCA
ATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGAAATTCCTGGCTTATTG
GAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGATGGTAAACAATTATTG
AAAGTTGTCATGCGCTCATGGTTGCCAGCTGGTGAAGCTTTACTTCAAATGATTGCTATT
CACTTGCCTTCACCAGTCGTCGCTCAAAAATACCGTATGGAAATGTTGTATGAGGGACCA
CTCGATGACGAGGCTGCCGTTGCTGTCAAGAACTGCGATCCAAATGGTCCATTGATGATG
TACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCGTTTCTATGCTTTCGGACGTGTG
TTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTATAATGGGACCAAATTACACACCT
GGCAAGAAGGAAGACTTGTACGAAAAATCAATTCAACGTACTATTTTGATGATGGGTCGT
TATGTTGAAGCCATTGAAGATGTTCCATGCGGTAACATTTGCGGTTTGGTTGGTGTTGAT
CAATTCTTGGTCAAGACTGGAACAATCACAACATTCAAAGATGCCCATAACATGAAGGTC
ATGAAATTTTCAGTTTCACCTGTCGTGCGTGTTGCTGTCGAGCCTAAAAATCCAGCTGAT
TTGCCCAAACTCGTCGAAGGTCTTAAGCGTTTGGCTAAATCCGATCCTATGGTACAATGT
ATCATTGAAGAATCTGGCGAACATATTATTGCTGGTGCTGGTGAATTGCATTTGGAAATT
TGCTTGAAGGACTTGGAAGAAGATCACGCTTGTATCCCATTGAAGAAATCCGATCCAGTT
GTATCGTATCGTGAAACAGTCTCTGATGAATCATCCATGATGTGTTTATCAAAATCACCA
AACAAGCATAATCGTCTTTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCTGAAGAT
ATTGATGGAGGTGCAGTTAATGCTCGTGACGATTTCAAGATTCGTGCACGTTACTTGGCT
GAGAAATACGAATGGGATGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGACGGT
ACAGGTCCAAATGTAATTGTTGACGTCACTAAGGGTGTACAATATTTGAATGAAATCAAG
GACTCTGTTGTTGCTGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAGAAC
ATGAGAGCTGTTCGTTTCAACATTTATGATGTTACACTGCATGCTGACGCTATCCATCGT
GGAGGTGGTCAAATCATTCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACAGCT
TCTCCACGTTTGATGGAGCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTC
GGTGGTATTTATGGTGTGCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAAGTT
GCCGGTACACCTATGTTCGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTTGGATTC
ACTGCTGATTTGCGCTCAAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTTGACCAT
TGGCAGATCTTCCCAGGTGACCCTAACGAACCATCATCAAAACCATACCAGATTGTGCAA
GATACAAGAAAACGTAAAGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATACTATGAT
AAAATGTAAAAGTCTTTCCGAGCTTCTTCAGTTATACTTATTATTTTTTCCCTCTTCATT
TTTTGCTTATAATTTTTTGATTTTTATATTTTTATCATAACATTACGCATAAAAGATAAA
ACAACATCAAAGCAAGAAAAAAGCGTTGATTATTTTATATCAATTAATCGTAATATTGTA
ATCAAACTTAAAATATTTTTTGAGCGTCTTAATATGAGTTAAGTTAAAAGCATTCTCCTA
TGAAAATTAAAAGCGTTTATGAGTTCGCCATAAATATGCTGTTACATCTACGCGCGAAAG
TGGTTGAAATGAAAAAGAATTTCATATAAATATTAACAATGATATCCAGCAACATGGAAG
AAAAATTAGAACGACGGAAACGGAAA

>g12287.t23 Gene=g12287 Length=681
MDRALLELQLDAEDLYQTFQRIVENVNVIIATYSDDDGPMGEVRVDPSKGSVGFGSGLHG
WAFTLKQFSEMYAAKFKIDVVKLMNRLWGENFFNAKTKKWAKTKDDDNKRSFVMYVLDPI
YKVFDVIMNYKKEEIPGLLEKIGVTLKHEDKDKDGKQLLKVVMRSWLPAGEALLQMIAIH
LPSPVVAQKYRMEMLYEGPLDDEAAVAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVF
SGKVQTGQKCRIMGPNYTPGKKEDLYEKSIQRTILMMGRYVEAIEDVPCGNICGLVGVDQ
FLVKTGTITTFKDAHNMKVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLAKSDPMVQCI
IEESGEHIIAGAGELHLEICLKDLEEDHACIPLKKSDPVVSYRETVSDESSMMCLSKSPN
KHNRLFMKAMPMPDGLAEDIDGGAVNARDDFKIRARYLAEKYEWDVTEARKIWCFGPDGT
GPNVIVDVTKGVQYLNEIKDSVVAGFQWATKEGVLAEENMRAVRFNIYDVTLHADAIHRG
GGQIIPTTRRCLYASYITASPRLMEPVYLCEIQCPEVAVGGIYGVLNRRRGHVFEESQVA
GTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQIFPGDPNEPSSKPYQIVQD
TRKRKGLKEGLPDLNQYYDKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g12287.t23 CDD cd03700 EF2_snRNP_like_II 217 311 8.5567E-55
22 g12287.t23 CDD cd16261 EF2_snRNP_III 326 397 2.16736E-43
21 g12287.t23 CDD cd01681 aeEF2_snRNP_like_IV 397 569 1.04182E-107
20 g12287.t23 CDD cd04096 eEF2_snRNP_like_C 565 644 3.87015E-50
19 g12287.t23 Coils Coil Coil 674 681 -
18 g12287.t23 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 65 167 5.7E-34
17 g12287.t23 Gene3D G3DSA:2.40.30.10 Translation factors 184 323 1.7E-55
15 g12287.t23 Gene3D G3DSA:3.30.70.870 Elongation Factor G (Translational Gtpase) 324 401 1.1E-38
16 g12287.t23 Gene3D G3DSA:3.30.70.240 - 403 667 3.6E-127
14 g12287.t23 Gene3D G3DSA:3.30.230.10 - 409 669 3.6E-127
5 g12287.t23 PANTHER PTHR42908:SF24 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 1 681 0.0
6 g12287.t23 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 681 0.0
3 g12287.t23 Pfam PF03144 Elongation factor Tu domain 2 234 308 2.7E-13
1 g12287.t23 Pfam PF14492 Elongation Factor G, domain III 326 387 1.2E-13
2 g12287.t23 Pfam PF03764 Elongation factor G, domain IV 445 559 1.1E-31
4 g12287.t23 Pfam PF00679 Elongation factor G C-terminus 562 648 3.7E-22
12 g12287.t23 SMART SM00889 EFG_IV_2 444 560 1.3E-27
13 g12287.t23 SMART SM00838 EFG_C_a 562 651 2.6E-19
8 g12287.t23 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 182 1.7E-38
11 g12287.t23 SUPERFAMILY SSF50447 Translation proteins 183 320 4.42E-45
10 g12287.t23 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 323 398 7.19E-21
7 g12287.t23 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 400 564 1.74E-70
9 g12287.t23 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 565 679 4.6E-34

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

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