Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic translation initiation factor 3 subunit E.

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_2 g6822 g6822.t4 TSS g6822.t4 18952047 18952047
chr_2 g6822 g6822.t4 isoform g6822.t4 18952097 18953608
chr_2 g6822 g6822.t4 exon g6822.t4.exon1 18952097 18952186
chr_2 g6822 g6822.t4 cds g6822.t4.CDS1 18952097 18952186
chr_2 g6822 g6822.t4 exon g6822.t4.exon2 18952267 18952536
chr_2 g6822 g6822.t4 cds g6822.t4.CDS2 18952267 18952536
chr_2 g6822 g6822.t4 exon g6822.t4.exon3 18952595 18952652
chr_2 g6822 g6822.t4 cds g6822.t4.CDS3 18952595 18952652
chr_2 g6822 g6822.t4 exon g6822.t4.exon4 18953136 18953277
chr_2 g6822 g6822.t4 cds g6822.t4.CDS4 18953136 18953277
chr_2 g6822 g6822.t4 exon g6822.t4.exon5 18953341 18953608
chr_2 g6822 g6822.t4 cds g6822.t4.CDS5 18953341 18953608
chr_2 g6822 g6822.t4 TTS g6822.t4 18953755 18953755

Sequences

>g6822.t4 Gene=g6822 Length=828
ATGGCAAAATTCGATTTAACAACACGAAATCTTCAGTTTTTGGATCGTCATTTGACTTTT
CCATTATTAGAGTTTCTACTGAGTAAGGATATTTATGACAAAAATGTTCTCCTCAACTTT
ATACTGGAAACAGTCAATAAGACTAACATGATTGATTACACGACCGATATTCGTCAACGT
CTTAATCTTCCAGAAAAGATGCCCGAAGAGTTGCAACTGAAAAGGCAGACGGTTTTAGCA
AAGCTAAAGGAACTTCAATTGGAAGTTGAACCTTTAATGAAATGTATGGAAGAAATCAAG
ACAAGAGACACAATGAAGGATTCAAAAACTTTAATTAGTGTACTACAAACCGAATATAAT
ATCAAAATTGACATTATACAGAGTGTTTACAAGTTGGCAAAATACCTCTATGAGTGTGGT
GCTCGTATGAAATTACATGAGTGTCAAACAGTCATTTTAAATGATTTCTTCATTATTGGC
TGCTTGGATGAATTCGTAGAAAATGCCCGTTTAATGATTTTCGAAACATTCTGTCGCATT
CATCAATGTATTACAAGCCAATTGCTGGCTGACAAGTTAAATATGGAACCAGAGGAAGCA
GAATGTTGGATTGTTAATCTCATTCGTAATGCACGACTTGATGCAAAAATTGATTCAAAA
TTAGGATATGTTGTTATGGGAGGACAGCCTCTCAGTCCATATCAGCAATTTGTTGAGAAA
ATTGATTCACTTTCTGTTCGATCAGAGGCACTCACTGAATTAGTAGAACGTAAAAATCGT
GTTAAAAACCAAGAAGGAGAAAGCAACTGGAAATATTACACAAATTAA

>g6822.t4 Gene=g6822 Length=275
MAKFDLTTRNLQFLDRHLTFPLLEFLLSKDIYDKNVLLNFILETVNKTNMIDYTTDIRQR
LNLPEKMPEELQLKRQTVLAKLKELQLEVEPLMKCMEEIKTRDTMKDSKTLISVLQTEYN
IKIDIIQSVYKLAKYLYECGARMKLHECQTVILNDFFIIGCLDEFVENARLMIFETFCRI
HQCITSQLLADKLNMEPEEAECWIVNLIRNARLDAKIDSKLGYVVMGGQPLSPYQQFVEK
IDSLSVRSEALTELVERKNRVKNQEGESNWKYYTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g6822.t4 PANTHER PTHR10317 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E 1 141 0.000
4 g6822.t4 PANTHER PTHR10317 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT E 140 264 0.000
1 g6822.t4 Pfam PF09440 eIF3 subunit 6 N terminal domain 5 135 0.000
2 g6822.t4 Pfam PF01399 PCI domain 144 227 0.000
9 g6822.t4 ProSiteProfiles PS50250 PCI domain profile. 49 231 16.251
8 g6822.t4 SMART SM01186 eIF3_N_2 5 136 0.000
6 g6822.t4 SMART SM00088 PINT_4 160 244 0.000
7 g6822.t4 SMART SM00753 motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 160 244 0.000
5 g6822.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 154 228 0.000

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:0003743 translation initiation factor activity MF
GO:0005852 eukaryotic translation initiation factor 3 complex CC
GO:0005737 cytoplasm CC

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