Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic translation initiation factor 5.

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_3 g2176 g2176.t9 isoform g2176.t9 15791563 15793163
chr_3 g2176 g2176.t9 exon g2176.t9.exon1 15791563 15792313
chr_3 g2176 g2176.t9 cds g2176.t9.CDS1 15791564 15792070
chr_3 g2176 g2176.t9 exon g2176.t9.exon2 15792418 15792500
chr_3 g2176 g2176.t9 exon g2176.t9.exon3 15792947 15793163
chr_3 g2176 g2176.t9 TSS g2176.t9 15793180 15793180
chr_3 g2176 g2176.t9 TTS g2176.t9 NA NA

Sequences

>g2176.t9 Gene=g2176 Length=1051
TGAGAAAATTTTATTCGTAAAATGTTTTCATCTTATTCTTGTCGTGTGAAAGTTTTATAT
CGTCAAAATAATACCAAACGATAGATAAATAACACCAATATTCTATGTAATTGGAGTTTA
AAAGTCACTTTTTGAGGCAATCGAGAAAAATATAAATCATCAAGTTTTTAAGCTTATCGG
GGGATTTTATGAATTTAAAAAACACATTTGAAGGTCAATCGAACAGCCGATATTTTTAAA
TTTATCACATCAGAATCCTTTAAAGTGCATGTCAGCGAATTTAAATCAGTTGAGTCATAG
GACTTCAAAATTTTCAAGCAATCGACATCGGAAATTGCAACCATTTAGAAAAACATCGTG
AATTAGTCATAAACATTGAGTAAAGTGAACAAGAGTTCTATTATTATCATCATCATCACC
ATCATCAAAGAATATAATACATAATCAAAAAAATAAGGGAACGTAATTCAAATTTAATTT
GATAGAAGGATGGGGACTTTGAATGTCAATCGTAATGTTACGGACTTGTATTATCGCTAC
AAGATGCCACGTATTTGTGCCAAAGTAGAAGGCAAGGGCAATGGCATTAAGACCGTTATT
GTCAATATGGCTGAAGTAGCTAAAGCACTCAATCGTCCTGCTACTTATCCAACTAAATAC
TTTGGTTGCGAGCTTGGCGCTCAGACTCAATTCGATCATAAGAATGAACGTTTTATTGTC
AATGGCTCGCATGATGCATCAAAATTGCAAGATCTTCTTGATGGATTTATTCGCAAATAT
GTCTTGTGTCCAGAATGCGACAATCCTGAGACCGATTTAATCATTGTTGCAAAGAAAGAG
CAAATTTCGCAAACTTGTAAAGCATGCGGTTTTCATGGATTGCTAAAAGTTCAGCATAAG
GTGAATACTTTTATCTTGAAAAATCCACCAACAATGAATCCAGCTGCACCAGGTGCATCT
TTGACTGAGGGAAAACGTTCTAAGCGCTCCAAGAAAGCTGAAGGTGATTCAAATCATGCT
ACAAATGGCGATAGCTCAAAAGATTCCGATG

>g2176.t9 Gene=g2176 Length=169
MPRICAKVEGKGNGIKTVIVNMAEVAKALNRPATYPTKYFGCELGAQTQFDHKNERFIVN
GSHDASKLQDLLDGFIRKYVLCPECDNPETDLIIVAKKEQISQTCKACGFHGLLKVQHKV
NTFILKNPPTMNPAAPGASLTEGKRSKRSKKAEGDSNHATNGDSSKDSD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2176.t9 Gene3D G3DSA:3.30.30.50 Translation initiation factor 2 beta 5 81 5.3E-37
9 g2176.t9 Gene3D G3DSA:2.20.25.350 - 82 127 2.7E-21
7 g2176.t9 MobiDBLite mobidb-lite consensus disorder prediction 127 169 -
8 g2176.t9 MobiDBLite mobidb-lite consensus disorder prediction 143 169 -
2 g2176.t9 PANTHER PTHR23001:SF7 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 1 166 2.5E-69
3 g2176.t9 PANTHER PTHR23001 EUKARYOTIC TRANSLATION INITIATION FACTOR 1 166 2.5E-69
1 g2176.t9 Pfam PF01873 Domain found in IF2B/IF5 1 110 1.7E-37
6 g2176.t9 SMART SM00653 eIF2Bneu4 1 111 2.8E-55
4 g2176.t9 SUPERFAMILY SSF100966 Translation initiation factor 2 beta, aIF2beta, N-terminal domain 1 82 8.11E-22
5 g2176.t9 SUPERFAMILY SSF75689 Zinc-binding domain of translation initiation factor 2 beta 79 112 1.29E-6

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:0006413 translational initiation BP
GO:0003743 translation initiation factor 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