Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic translation initiation factor 2 subunit 1.

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 g7321 g7321.t9 TTS g7321.t9 22940445 22940445
chr_2 g7321 g7321.t9 isoform g7321.t9 22941257 22941978
chr_2 g7321 g7321.t9 exon g7321.t9.exon1 22941257 22941617
chr_2 g7321 g7321.t9 cds g7321.t9.CDS1 22941259 22941617
chr_2 g7321 g7321.t9 exon g7321.t9.exon2 22941676 22941871
chr_2 g7321 g7321.t9 cds g7321.t9.CDS2 22941676 22941871
chr_2 g7321 g7321.t9 exon g7321.t9.exon3 22941937 22941978
chr_2 g7321 g7321.t9 cds g7321.t9.CDS3 22941937 22941978
chr_2 g7321 g7321.t9 TSS g7321.t9 22942380 22942380

Sequences

>g7321.t9 Gene=g7321 Length=599
ATGGTTTTAACGTGTCGCTTTTATAAGCAAAAATACCCGGAAGTGGAAGATGTTGTGATG
GTAAATGTGAGATCAATAGCTGAAATGGGTGCCTACGTTCATTTATTAGAATACAATAAT
ATTGAGGGTATGATTCTACTATCAGAATTATCAAGAAGACGTATTCGTTCCATCAATAAG
CTCATTCGAGTTGGAAAAACTGAACCAGTTGTTGTTATTCGTGTTGATAAAGAAAAGGGG
TATATTGATTTATCAAAACGTCGTGTGTCGCCTGAGGATGTAGAAAAATGTACAGAACGT
TTTAGTAAAGCTAAAGCAGTGAGCTCAATTTTGCGGCATGTCGCAGAACTTCTCAAATAC
GATACTGATGAGCAGTTAGAAGATTTATATCAAAAGACTGCATGGCATTTCGAGGAGAAG
CATAAAAATAAAACAGCGTCCTATGACATTTTTAAGCAAGCAGTTACGGAACCATCGCTA
TTGGATGAATGCAATCTAGACGAAAATACAAAGAATGTGCTTTTGACGAATATCAAAAGG
AAATTAACTTCACAAGCAATGAAAATTCGTGCAGACATTGAATGTGCATGTTACGGATA

>g7321.t9 Gene=g7321 Length=199
MVLTCRFYKQKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
LIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDVEKCTERFSKAKAVSSILRHVAELLKY
DTDEQLEDLYQKTAWHFEEKHKNKTASYDIFKQAVTEPSLLDECNLDENTKNVLLTNIKR
KLTSQAMKIRADIECACYG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7321.t9 CDD cd04452 S1_IF2_alpha 13 88 0.000
8 g7321.t9 Gene3D G3DSA:2.40.50.140 - 2 89 0.000
9 g7321.t9 Gene3D G3DSA:1.10.150.190 Translation initiation factor 2; subunit 1; domain 2 90 180 0.000
3 g7321.t9 PANTHER PTHR10602:SF0 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 2 198 0.000
4 g7321.t9 PANTHER PTHR10602 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 2 198 0.000
1 g7321.t9 Pfam PF00575 S1 RNA binding domain 13 87 0.000
2 g7321.t9 Pfam PF07541 Eukaryotic translation initiation factor 2 alpha subunit 129 198 0.000
10 g7321.t9 ProSiteProfiles PS50126 S1 domain profile. 16 87 17.569
7 g7321.t9 SMART SM00316 S1_6 14 87 0.000
6 g7321.t9 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 11 92 0.000
5 g7321.t9 SUPERFAMILY SSF116742 eIF2alpha middle domain-like 89 181 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:0003723 RNA binding MF
GO:0003676 nucleic acid binding 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