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.t11 TSS g12287.t11 22169311 22169311
chr_1 g12287 g12287.t11 isoform g12287.t11 22169380 22173107
chr_1 g12287 g12287.t11 exon g12287.t11.exon1 22169380 22169382
chr_1 g12287 g12287.t11 exon g12287.t11.exon2 22169830 22170079
chr_1 g12287 g12287.t11 cds g12287.t11.CDS1 22170011 22170079
chr_1 g12287 g12287.t11 exon g12287.t11.exon3 22170949 22171575
chr_1 g12287 g12287.t11 cds g12287.t11.CDS2 22170949 22171575
chr_1 g12287 g12287.t11 exon g12287.t11.exon4 22171753 22172190
chr_1 g12287 g12287.t11 cds g12287.t11.CDS3 22171753 22172190
chr_1 g12287 g12287.t11 exon g12287.t11.exon5 22172261 22172432
chr_1 g12287 g12287.t11 cds g12287.t11.CDS4 22172261 22172432
chr_1 g12287 g12287.t11 exon g12287.t11.exon6 22172626 22173107
chr_1 g12287 g12287.t11 cds g12287.t11.CDS5 22172626 22173107
chr_1 g12287 g12287.t11 TTS g12287.t11 22173564 22173564

Sequences

>g12287.t11 Gene=g12287 Length=1972
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGC
AAGGATGAACAAGAAAGATGTATCACAATTAAGTCAACGTAAGGACTATTTTATTAATTT
CTATCATTATCATCGTTCATTTGTCATGTATGTATTGGATCCAATTTATAAGGTATTCGA
TGTCATTATGAATTACAAGAAAGAAGAAATTCCTGGCTTATTGGAGAAAATCGGAGTCAC
ACTCAAGCACGAAGACAAAGATAAGGATGGTAAACAATTATTGAAAGTTGTCATGCGCTC
ATGGTTGCCAGCTGGTGAAGCTTTACTTCAAATGATTGCTATTCACTTGCCTTCACCAGT
CGTCGCTCAAAAATACCGTATGGAAATGTTGTATGAGGGACCACTCGATGACGAGGCTGC
CGTTGCTGTCAAGAACTGCGATCCAAATGGTCCATTGATGATGTACGTCTCAAAAATGGT
ACCAACCAGTGACAAGGGTCGTTTCTATGCTTTCGGACGTGTGTTCTCCGGAAAAGTTCA
AACTGGTCAAAAATGCCGTATAATGGGACCAAATTACACACCTGGCAAGAAGGAAGACTT
GTACGAAAAATCAATTCAACGTACTATTTTGATGATGGGTCGTTATGTTGAAGCCATTGA
AGATGTTCCATGCGGTAACATTTGCGGTTTGGTTGGTGTTGATCAATTCTTGGTCAAGAC
TGGAACAATCACAACATTCAAAGATGCCCATAACATGAAGGTCATGAAATTTTCAGTTTC
ACCTGTCGTGCGTGTTGCTGTCGAGCCTAAAAATCCAGCTGATTTGCCCAAACTCGTCGA
AGGTCTTAAGCGTTTGGCTAAATCCGATCCTATGGTACAATGTATCATTGAAGAATCTGG
CGAACATATTATTGCTGGTGCTGGTGAATTGCATTTGGAAATTTGCTTGAAGGACTTGGA
AGAAGATCACGCTTGTATCCCATTGAAGAAATCCGATCCAGTTGTATCGTATCGTGAAAC
AGTCTCTGATGAATCATCCATGATGTGTTTATCAAAATCACCAAACAAGCATAATCGTCT
TTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCTGAAGATATTGATGGAGGTGCAGT
TAATGCTCGTGACGATTTCAAGATTCGTGCACGTTACTTGGCTGAGAAATACGAATGGGA
TGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCAGACGGTACAGGTCCAAATGTAAT
TGTTGACGTCACTAAGGGTGTACAATATTTGAATGAAATCAAGGACTCTGTTGTTGCTGG
CTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAAGAGAACATGAGAGCTGTTCGTTT
CAACATTTATGATGTTACACTGCATGCTGACGCTATCCATCGTGGAGGTGGTCAAATCAT
TCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACAGCTTCTCCACGTTTGATGGA
GCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTCGGTGGTATTTATGGTGT
GCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAAGTTGCCGGTACACCTATGTT
CGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTTGGATTCACTGCTGATTTGCGCTC
AAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTTGACCATTGGCAGATCTTCCCAGG
TGACCCTAACGAACCATCATCAAAACCATACCAGATTGTGCAAGATACAAGAAAACGTAA
AGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATACTATGATAAAATGTAA

>g12287.t11 Gene=g12287 Length=595
MNKKDVSQLSQRKDYFINFYHYHRSFVMYVLDPIYKVFDVIMNYKKEEIPGLLEKIGVTL
KHEDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYEGPLDDEAAV
AVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNYTPGKKEDLY
EKSIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITTFKDAHNMKVMKFSVSP
VVRVAVEPKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLEE
DHACIPLKKSDPVVSYRETVSDESSMMCLSKSPNKHNRLFMKAMPMPDGLAEDIDGGAVN
ARDDFKIRARYLAEKYEWDVTEARKIWCFGPDGTGPNVIVDVTKGVQYLNEIKDSVVAGF
QWATKEGVLAEENMRAVRFNIYDVTLHADAIHRGGGQIIPTTRRCLYASYITASPRLMEP
VYLCEIQCPEVAVGGIYGVLNRRRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSN
TGGQAFPQCVFDHWQIFPGDPNEPSSKPYQIVQDTRKRKGLKEGLPDLNQYYDKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g12287.t11 CDD cd03700 EF2_snRNP_like_II 131 225 0
21 g12287.t11 CDD cd16261 EF2_snRNP_III 240 311 0
20 g12287.t11 CDD cd01681 aeEF2_snRNP_like_IV 311 483 0
19 g12287.t11 CDD cd04096 eEF2_snRNP_like_C 479 558 0
18 g12287.t11 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 3 81 0
17 g12287.t11 Gene3D G3DSA:2.40.30.10 Translation factors 98 237 0
15 g12287.t11 Gene3D G3DSA:3.30.70.870 Elongation Factor G (Translational Gtpase) 238 315 0
16 g12287.t11 Gene3D G3DSA:3.30.70.240 - 317 581 0
14 g12287.t11 Gene3D G3DSA:3.30.230.10 - 323 583 0
5 g12287.t11 PANTHER PTHR42908:SF24 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 23 595 0
6 g12287.t11 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 23 595 0
3 g12287.t11 Pfam PF03144 Elongation factor Tu domain 2 148 222 0
1 g12287.t11 Pfam PF14492 Elongation Factor G, domain III 240 301 0
2 g12287.t11 Pfam PF03764 Elongation factor G, domain IV 359 473 0
4 g12287.t11 Pfam PF00679 Elongation factor G C-terminus 476 562 0
12 g12287.t11 SMART SM00889 EFG_IV_2 358 474 0
13 g12287.t11 SMART SM00838 EFG_C_a 476 565 0
8 g12287.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 12 96 0
11 g12287.t11 SUPERFAMILY SSF50447 Translation proteins 97 234 0
10 g12287.t11 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 237 312 0
7 g12287.t11 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 314 478 0
9 g12287.t11 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 479 593 0

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