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.t14 TSS g12287.t14 22169311 22169311
chr_1 g12287 g12287.t14 isoform g12287.t14 22169380 22173484
chr_1 g12287 g12287.t14 exon g12287.t14.exon1 22169380 22169382
chr_1 g12287 g12287.t14 cds g12287.t14.CDS1 22169380 22169382
chr_1 g12287 g12287.t14 exon g12287.t14.exon2 22169830 22170044
chr_1 g12287 g12287.t14 cds g12287.t14.CDS2 22169830 22170044
chr_1 g12287 g12287.t14 exon g12287.t14.exon3 22170108 22170301
chr_1 g12287 g12287.t14 cds g12287.t14.CDS3 22170108 22170301
chr_1 g12287 g12287.t14 exon g12287.t14.exon4 22170545 22171575
chr_1 g12287 g12287.t14 cds g12287.t14.CDS4 22170545 22171575
chr_1 g12287 g12287.t14 exon g12287.t14.exon5 22171753 22172190
chr_1 g12287 g12287.t14 cds g12287.t14.CDS5 22171753 22172190
chr_1 g12287 g12287.t14 exon g12287.t14.exon6 22172261 22172432
chr_1 g12287 g12287.t14 cds g12287.t14.CDS6 22172261 22172432
chr_1 g12287 g12287.t14 exon g12287.t14.exon7 22172639 22173484
chr_1 g12287 g12287.t14 cds g12287.t14.CDS7 22172639 22172751
chr_1 g12287 g12287.t14 TTS g12287.t14 22173564 22173564

Sequences

>g12287.t14 Gene=g12287 Length=2899
ATGGTCAACTTTACTGTCGACGAAATCCGTGCTATGATGGACAAGAAGAAGAACATCCGT
AATATGTCTGTCATTGCTCATGTCGATCACGGAAAATCTACTTTAACTGATTCGTTGGTT
TCAAAAGCTGGTATTATTGCTGGTGCAAAAGCTGGTGAAACAAGATTCACAGACACACGC
AAGGATGAACAAGAAAGATGTATCACAATTAAGTCAACTGCTATCTCTATGTTCTTTGAG
TTAGAAGACAAAGATTTGGTTTTCATTACAAATCCTGATCAACGTGACAAAGAAGAAAAA
GGTTTCTTGATTAATTTGATTGACTCACCCGGTCACGTTGATTTCTCATCAGAAGTCACA
GCCGCTCTTCGTGTTACTGATGGTGCTCTTGTTGTTGTCGATTGCGTATCAGGTGTTTGT
GTACAAACTGAGACTGTATTGCGTCAAGCTATTGCCGAACGTATTAAGCCAGTTTTGTTC
ATGAACAAGATGGACCGTGCTTTGTTGGAATTGCAATTGGATGCTGAAGATTTGTACCAA
ACATTCCAACGTATCGTCGAAAACGTCAACGTTATCATCGCCACTTACAGCGATGACGAT
GGTCCAATGGGAGAAGTTCGTGTTGATCCATCAAAGGGTTCAGTCGGTTTCGGTTCCGGC
TTGCACGGATGGGCTTTCACTCTCAAACAATTTTCGGAAATGTATGCAGCTAAATTCAAG
ATCGATGTCGTTAAACTCATGAATCGCTTATGGGGTGAAAATTTCTTCAATGCAAAGACC
AAGAAATGGGCAAAGACAAAGGACGATGATAACAAGCGTTCATTTGTCATGTATGTATTG
GATCCAATTTATAAGGTATTCGATGTCATTATGAATTACAAGAAAGAAGAAATTCCTGGC
TTATTGGAGAAAATCGGAGTCACACTCAAGCACGAAGACAAAGATAAGGATGGTAAACAA
TTATTGAAAGTTGTCATGCGCTCATGGTTGCCAGCTGGTGAAGCTTTACTTCAAATGATT
GCTATTCACTTGCCTTCACCAGTCGTCGCTCAAAAATACCGTATGGAAATGTTGTATGAG
GGACCACTCGATGACGAGGCTGCCGTTGCTGTCAAGAACTGCGATCCAAATGGTCCATTG
ATGATGTACGTCTCAAAAATGGTACCAACCAGTGACAAGGGTCGTTTCTATGCTTTCGGA
CGTGTGTTCTCCGGAAAAGTTCAAACTGGTCAAAAATGCCGTATAATGGGACCAAATTAC
ACACCTGGCAAGAAGGAAGACTTGTACGAAAAATCAATTCAACGTACTATTTTGATGATG
GGTCGTTATGTTGAAGCCATTGAAGATGTTCCATGCGGTAACATTTGCGGTTTGGTTGGT
GTTGATCAATTCTTGGTCAAGACTGGAACAATCACAACATTCAAAGATGCCCATAACATG
AAGGTCATGAAATTTTCAGTTTCACCTGTCGTGCGTGTTGCTGTCGAGCCTAAAAATCCA
GCTGATTTGCCCAAACTCGTCGAAGGTCTTAAGCGTTTGGCTAAATCCGATCCTATGGTA
CAATGTATCATTGAAGAATCTGGCGAACATATTATTGCTGGTGCTGGTGAATTGCATTTG
GAAATTTGCTTGAAGGACTTGGAAGAAGATCACGCTTGTATCCCATTGAAGAAATCCGAT
CCAGTTGTATCGTATCGTGAAACAGTCTCTGATGAATCATCCATGATGTGTTTATCAAAA
TCACCAAACAAGCATAATCGTCTTTTCATGAAGGCCATGCCTATGCCTGATGGTCTTGCT
GAAGATATTGATGGAGGTGCAGTTAATGCTCGTGACGATTTCAAGATTCGTGCACGTTAC
TTGGCTGAGAAATACGAATGGGATGTTACAGAAGCTCGTAAGATTTGGTGTTTCGGTCCA
GACGGTACAGGTCCAAATGTAATTGTTGACGTCACTAAGGGTGTACAATATTTGAATGAA
ATCAAGGACTCTGTTGTTGCTGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGGCTGAA
GAGAACATGAGAGCATTTATGATGTTACACTGCATGCTGACGCTATCCATCGTGGAGGTG
GTCAAATCATTCCAACAACTCGTCGTTGCTTGTATGCATCATACATCACAGCTTCTCCAC
GTTTGATGGAGCCAGTTTATTTGTGTGAAATTCAATGTCCAGAAGTTGCTGTCGGTGGTA
TTTATGGTGTGCTTAATCGTCGTCGTGGTCATGTCTTTGAAGAATCACAAGTTGCCGGTA
CACCTATGTTCGTTGTCAAAGCTTATTTGCCTGTAAATGAATCATTTGGATTCACTGCTG
ATTTGCGCTCAAATACTGGAGGTCAAGCTTTCCCACAATGTGTATTTGACCATTGGCAGA
TCTTCCCAGGTGACCCTAACGAACCATCATCAAAACCATACCAGATTGTGCAAGATACAA
GAAAACGTAAAGGTCTCAAAGAAGGTTTACCAGATTTGAACCAATACTATGATAAAATGT
AAAAGTCTTTCCGAGCTTCTTCAGTTATACTTATTATTTTTTCCCTCTTCATTTTTTGCT
TATAATTTTTTGATTTTTATATTTTTATCATAACATTACGCATAAAAGATAAAACAACAT
CAAAGCAAGAAAAAAGCGTTGATTATTTTATATCAATTAATCGTAATATTGTAATCAAAC
TTAAAATATTTTTTGAGCGTCTTAATATGAGTTAAGTTAAAAGCATTCTCCTATGAAAAT
TAAAAGCGTTTATGAGTTCGCCATAAATATGCTGTTACATCTACGCGCGAAAGTGGTTGA
AATGAAAAAGAATTTCATATAAATATTAACAATGATATCCAGCAACATGGAAGAAAAATT
AGAACGACGGAAACGGAAA

>g12287.t14 Gene=g12287 Length=721
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTR
KDEQERCITIKSTAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVT
AALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQ
TFQRIVENVNVIIATYSDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFK
IDVVKLMNRLWGENFFNAKTKKWAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPG
LLEKIGVTLKHEDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYE
GPLDDEAAVAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNY
TPGKKEDLYEKSIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITTFKDAHNM
KVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
EICLKDLEEDHACIPLKKSDPVVSYRETVSDESSMMCLSKSPNKHNRLFMKAMPMPDGLA
EDIDGGAVNARDDFKIRARYLAEKYEWDVTEARKIWCFGPDGTGPNVIVDVTKGVQYLNE
IKDSVVAGFQWATKEGVLAEENMRAFMMLHCMLTLSIVEVVKSFQQLVVACMHHTSQLLH
V

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g12287.t14 CDD cd01885 EF2 20 236 1.59649E-120
23 g12287.t14 CDD cd03700 EF2_snRNP_like_II 380 474 1.77795E-54
22 g12287.t14 CDD cd16261 EF2_snRNP_III 489 560 2.68825E-42
21 g12287.t14 CDD cd01681 aeEF2_snRNP_like_IV 560 684 2.57718E-71
16 g12287.t14 Gene3D G3DSA:3.40.50.300 - 13 346 1.4E-189
19 g12287.t14 Gene3D G3DSA:2.40.30.10 Translation factors 49 473 1.4E-189
20 g12287.t14 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 228 330 1.4E-189
18 g12287.t14 Gene3D G3DSA:3.30.70.870 Elongation Factor G (Translational Gtpase) 487 564 1.2E-38
17 g12287.t14 Gene3D G3DSA:3.30.230.10 - 570 706 1.7E-49
5 g12287.t14 PANTHER PTHR42908:SF24 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 1 688 0.0
6 g12287.t14 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 688 0.0
11 g12287.t14 PRINTS PR00315 GTP-binding elongation factor signature 21 34 2.2E-13
10 g12287.t14 PRINTS PR00315 GTP-binding elongation factor signature 65 73 2.2E-13
9 g12287.t14 PRINTS PR00315 GTP-binding elongation factor signature 105 115 2.2E-13
8 g12287.t14 PRINTS PR00315 GTP-binding elongation factor signature 121 132 2.2E-13
7 g12287.t14 PRINTS PR00315 GTP-binding elongation factor signature 157 166 2.2E-13
4 g12287.t14 Pfam PF00009 Elongation factor Tu GTP binding domain 17 345 5.9E-67
3 g12287.t14 Pfam PF03144 Elongation factor Tu domain 2 397 471 3.0E-13
1 g12287.t14 Pfam PF14492 Elongation Factor G, domain III 489 550 1.3E-13
2 g12287.t14 Pfam PF03764 Elongation factor G, domain IV 608 684 4.9E-19
25 g12287.t14 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 58 73 -
28 g12287.t14 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 17 348 54.195
26 g12287.t14 SMART SM00889 EFG_IV_2 607 720 1.4E-4
13 g12287.t14 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 345 1.18E-110
15 g12287.t14 SUPERFAMILY SSF50447 Translation proteins 346 483 4.86E-45
14 g12287.t14 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 486 561 7.91E-21
12 g12287.t14 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 563 687 7.84E-51
27 g12287.t14 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 168 3.5E-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