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.t1 TTS g7321.t1 22940445 22940445
chr_2 g7321 g7321.t1 isoform g7321.t1 22940724 22941978
chr_2 g7321 g7321.t1 exon g7321.t1.exon1 22940724 22940909
chr_2 g7321 g7321.t1 cds g7321.t1.CDS1 22940724 22940909
chr_2 g7321 g7321.t1 exon g7321.t1.exon2 22940971 22941086
chr_2 g7321 g7321.t1 cds g7321.t1.CDS2 22940971 22941086
chr_2 g7321 g7321.t1 exon g7321.t1.exon3 22941156 22941617
chr_2 g7321 g7321.t1 cds g7321.t1.CDS3 22941156 22941617
chr_2 g7321 g7321.t1 exon g7321.t1.exon4 22941676 22941871
chr_2 g7321 g7321.t1 cds g7321.t1.CDS4 22941676 22941871
chr_2 g7321 g7321.t1 exon g7321.t1.exon5 22941937 22941978
chr_2 g7321 g7321.t1 cds g7321.t1.CDS5 22941937 22941978
chr_2 g7321 g7321.t1 TSS g7321.t1 22942380 22942380

Sequences

>g7321.t1 Gene=g7321 Length=1002
ATGGTTTTAACGTGTCGCTTTTATAAGCAAAAATACCCGGAAGTGGAAGATGTTGTGATG
GTAAATGTGAGATCAATAGCTGAAATGGGTGCCTACGTTCATTTATTAGAATACAATAAT
ATTGAGGGTATGATTCTACTATCAGAATTATCAAGAAGACGTATTCGTTCCATCAATAAG
CTCATTCGAGTTGGAAAAACTGAACCAGTTGTTGTTATTCGTGTTGATAAAGAAAAGGGG
TATATTGATTTATCAAAACGTCGTGTGTCGCCTGAGGATGTAGAAAAATGTACAGAACGT
TTTAGTAAAGCTAAAGCAGTGAGCTCAATTTTGCGGCATGTCGCAGAACTTCTCAAATAC
GATACTGATGAGCAGTTAGAAGATTTATATCAAAAGACTGCATGGCATTTCGAGGAGAAG
CATAAAAATAAAACAGCGTCCTATGACATTTTTAAGCAAGCAGTTACGGAACCATCGCTA
TTGGATGAATGCAATCTAGACGAAAATACAAAGAATGTGCTTTTGACGAATATCAAAAGG
AAATTAACTTCACAAGCAATGAAAATTCGTGCAGACATTGAATGTGCATGTTACGGATAT
GAGGGCATTGATGCTGTTAAACAAGCTTTGCGTGCTGGTCTTGAAACATCAACTGAAGAT
ATTCCAATTAAAATCAATTTGATTGCGCCGCCCATTTATGTCATAACGACATCGACTCCT
GAAAAAAATGATGGTCTTAAGGCTCTTGAAAATGCCATAGATAAAATCAAGTCTACAATT
GAGAAGCTTGACGGACATTTTGCTATTCAAATGGCGCCTAAAGTTGTTACTGCAATTGAT
GAAGCTGATTTAGCAAGACGAATGGAACGCGCTGAAATGGAAAATGCAGAAGTTTCAGGA
GATGAAGATGAAAGTGAAGAGGAAGAAGGTATGAAATTCGATGCTGATGAGAATGATACA
GGTGACAAAAATTCAGACAAATCAGGTTCTGACGATGAATAA

>g7321.t1 Gene=g7321 Length=333
MVLTCRFYKQKYPEVEDVVMVNVRSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK
LIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDVEKCTERFSKAKAVSSILRHVAELLKY
DTDEQLEDLYQKTAWHFEEKHKNKTASYDIFKQAVTEPSLLDECNLDENTKNVLLTNIKR
KLTSQAMKIRADIECACYGYEGIDAVKQALRAGLETSTEDIPIKINLIAPPIYVITTSTP
EKNDGLKALENAIDKIKSTIEKLDGHFAIQMAPKVVTAIDEADLARRMERAEMENAEVSG
DEDESEEEEGMKFDADENDTGDKNSDKSGSDDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g7321.t1 CDD cd04452 S1_IF2_alpha 13 88 2.57685E-43
10 g7321.t1 Coils Coil Coil 246 266 -
11 g7321.t1 Coils Coil Coil 288 308 -
8 g7321.t1 Gene3D G3DSA:2.40.50.140 - 2 89 1.3E-39
9 g7321.t1 Gene3D G3DSA:1.10.150.190 Translation initiation factor 2; subunit 1; domain 2 90 180 1.1E-35
7 g7321.t1 Gene3D G3DSA:3.30.70.1130 EIF_2_alpha 186 331 3.1E-44
14 g7321.t1 MobiDBLite mobidb-lite consensus disorder prediction 289 333 -
15 g7321.t1 MobiDBLite mobidb-lite consensus disorder prediction 296 315 -
16 g7321.t1 MobiDBLite mobidb-lite consensus disorder prediction 316 333 -
3 g7321.t1 PANTHER PTHR10602 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 2 311 2.1E-136
1 g7321.t1 Pfam PF00575 S1 RNA binding domain 13 87 3.9E-18
2 g7321.t1 Pfam PF07541 Eukaryotic translation initiation factor 2 alpha subunit 129 242 7.7E-36
17 g7321.t1 ProSiteProfiles PS50126 S1 domain profile. 16 87 17.569
13 g7321.t1 SMART SM00316 S1_6 14 87 1.1E-14
6 g7321.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 11 91 1.86E-18
5 g7321.t1 SUPERFAMILY SSF116742 eIF2alpha middle domain-like 89 181 7.85E-33
4 g7321.t1 SUPERFAMILY SSF110993 eIF-2-alpha, C-terminal domain 185 301 1.06E-40

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

Pathway

  • This transcript belongs to the following pathways

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