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.t9 TSS g12287.t9 22169311 22169311
chr_1 g12287 g12287.t9 isoform g12287.t9 22169380 22172414
chr_1 g12287 g12287.t9 exon g12287.t9.exon1 22169380 22169382
chr_1 g12287 g12287.t9 cds g12287.t9.CDS1 22169380 22169382
chr_1 g12287 g12287.t9 exon g12287.t9.exon2 22169830 22170044
chr_1 g12287 g12287.t9 cds g12287.t9.CDS2 22169830 22170044
chr_1 g12287 g12287.t9 exon g12287.t9.exon3 22170108 22170301
chr_1 g12287 g12287.t9 cds g12287.t9.CDS3 22170108 22170301
chr_1 g12287 g12287.t9 exon g12287.t9.exon4 22170545 22171575
chr_1 g12287 g12287.t9 cds g12287.t9.CDS4 22170545 22171575
chr_1 g12287 g12287.t9 exon g12287.t9.exon5 22171753 22172190
chr_1 g12287 g12287.t9 cds g12287.t9.CDS5 22171753 22172190
chr_1 g12287 g12287.t9 exon g12287.t9.exon6 22172261 22172414
chr_1 g12287 g12287.t9 cds g12287.t9.CDS6 22172261 22172413
chr_1 g12287 g12287.t9 TTS g12287.t9 NA NA

Sequences

>g12287.t9 Gene=g12287 Length=2035
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
ATCAAGGACTCTGTTGTTGCTGGCTTCCAATGGGCTACAAAAGAAGGTGTCTTGG

>g12287.t9 Gene=g12287 Length=678
MVNFTVDEIRAMMDKKKNIRNMSVIAHVDHGKSTLTDSLVSKAGIIAGAKAGETRFTDTR
KDEQERCITIKSTAISMFFELEDKDLVFITNPDQRDKEEKGFLINLIDSPGHVDFSSEVT
AALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLFMNKMDRALLELQLDAEDLYQ
TFQRIVENVNVIIATYSDDDGPMGEVRVDPSKGSVGFGSGLHGWAFTLKQFSEMYAAKFK
IDVVKLMNRLWGENFFNAKTKKWAKTKDDDNKRSFVMYVLDPIYKVFDVIMNYKKEEIPG
LLEKIGVTLKHEDKDKDGKQLLKVVMRSWLPAGEALLQMIAIHLPSPVVAQKYRMEMLYE
GPLDDEAAVAVKNCDPNGPLMMYVSKMVPTSDKGRFYAFGRVFSGKVQTGQKCRIMGPNY
TPGKKEDLYEKSIQRTILMMGRYVEAIEDVPCGNICGLVGVDQFLVKTGTITTFKDAHNM
KVMKFSVSPVVRVAVEPKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHL
EICLKDLEEDHACIPLKKSDPVVSYRETVSDESSMMCLSKSPNKHNRLFMKAMPMPDGLA
EDIDGGAVNARDDFKIRARYLAEKYEWDVTEARKIWCFGPDGTGPNVIVDVTKGVQYLNE
IKDSVVAGFQWATKEGVL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g12287.t9 CDD cd01885 EF2 20 236 2.41467E-121
23 g12287.t9 CDD cd03700 EF2_snRNP_like_II 380 474 1.3235E-54
22 g12287.t9 CDD cd16261 EF2_snRNP_III 489 560 1.62975E-42
21 g12287.t9 CDD cd01681 aeEF2_snRNP_like_IV 560 678 1.07497E-66
16 g12287.t9 Gene3D G3DSA:3.40.50.300 - 13 346 1.2E-189
19 g12287.t9 Gene3D G3DSA:2.40.30.10 Translation factors 49 473 1.2E-189
20 g12287.t9 Gene3D G3DSA:3.90.1430.10 Yeast translation eEF2 (G’ domain) 228 330 1.2E-189
18 g12287.t9 Gene3D G3DSA:3.30.70.870 Elongation Factor G (Translational Gtpase) 487 564 1.1E-38
17 g12287.t9 Gene3D G3DSA:3.30.230.10 - 572 678 6.5E-47
5 g12287.t9 PANTHER PTHR42908:SF24 EUKARYOTIC TRANSLATION ELONGATION FACTOR 2, GENE 2 1 678 0.0
6 g12287.t9 PANTHER PTHR42908 TRANSLATION ELONGATION FACTOR-RELATED 1 678 0.0
11 g12287.t9 PRINTS PR00315 GTP-binding elongation factor signature 21 34 1.7E-13
10 g12287.t9 PRINTS PR00315 GTP-binding elongation factor signature 65 73 1.7E-13
9 g12287.t9 PRINTS PR00315 GTP-binding elongation factor signature 105 115 1.7E-13
8 g12287.t9 PRINTS PR00315 GTP-binding elongation factor signature 121 132 1.7E-13
7 g12287.t9 PRINTS PR00315 GTP-binding elongation factor signature 157 166 1.7E-13
4 g12287.t9 Pfam PF00009 Elongation factor Tu GTP binding domain 17 345 5.1E-67
3 g12287.t9 Pfam PF03144 Elongation factor Tu domain 2 397 471 2.7E-13
1 g12287.t9 Pfam PF14492 Elongation Factor G, domain III 489 550 1.2E-13
2 g12287.t9 Pfam PF03764 Elongation factor G, domain IV 608 678 1.7E-16
25 g12287.t9 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 58 73 -
27 g12287.t9 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 17 348 54.195
13 g12287.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 345 9.81E-111
15 g12287.t9 SUPERFAMILY SSF50447 Translation proteins 346 483 4.42E-45
14 g12287.t9 SUPERFAMILY SSF54980 EF-G C-terminal domain-like 486 561 7.19E-21
12 g12287.t9 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 563 678 4.8E-47
26 g12287.t9 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 19 168 3.0E-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. There were no conditions that were differentially expressed