General information for g12246.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Translation initiation factor eIF-2B subunit beta.
Parent gene
- The parent gene g12246 is located on chr_1: 21982834..21984384 (- strand)
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 | g12246 | g12246.t1 | TTS | g12246.t1 | 21981559 | 21981559 |
| chr_1 | g12246 | g12246.t1 | isoform | g12246.t1 | 21981622 | 21982834 |
| chr_1 | g12246 | g12246.t1 | exon | g12246.t1.exon1 | 21981622 | 21981700 |
| chr_1 | g12246 | g12246.t1 | cds | g12246.t1.CDS1 | 21981622 | 21981700 |
| chr_1 | g12246 | g12246.t1 | exon | g12246.t1.exon2 | 21981763 | 21982698 |
| chr_1 | g12246 | g12246.t1 | cds | g12246.t1.CDS2 | 21981763 | 21982698 |
| chr_1 | g12246 | g12246.t1 | exon | g12246.t1.exon3 | 21982770 | 21982834 |
| chr_1 | g12246 | g12246.t1 | cds | g12246.t1.CDS3 | 21982770 | 21982834 |
| chr_1 | g12246 | g12246.t1 | TSS | g12246.t1 | 21982903 | 21982903 |
Sequences
>g12246.t1 Gene=g12246 Length=1080
ATGGTTGAAAGTAATGTTTATTTTACTGCCTCATTAGCTTCATTGATACATGATATTAAA
GTCGGTAAAATTGTCGGATCATATTCAATTTCTCAAGCAATGCTCAATCATTTTCTTAGT
ACTCTAAATGAAAGTCAATGGTCAACAGCTGATGAACTTATGACTATTGTGCGTGAAACA
GGGAGAATTTGTGAAAATGCACTTCCAACAGAGGCAATTTTGGGAAATATTGTTCGAAGA
ATGCTTAAAATAATTAGAGAAGAGTATGATGAATTGAATATGCCACAAGAACAAATAAAA
CAAACGGATGATTCTCAAGCTGCCTCTTTACAAAAATTAGTAACACAAAACAGTGAGAAG
TCTGTTGAAAAATCCGACTATAAAGCTCTTTATACAGATTTGAGAGAAAATCTTATTACA
CATTTAACTGAGATAGAAAATGAATTGCATCTTAGTCATGACAATCTTGCACAACAAGCA
TCACAACATGTTCATTCAGCTGAGTTAATTTTAACATTGGGATACTCAAAGAGTGTAGAG
AAATTTCTAAAATCAGTTCCTAAGGAACGAAAATTTGAAGTAGTTATTGCTGAATGTGCT
CCTGCATGCAGAGGACATTTGCTTGCTACCTCTTTAGCTTCCTCGAAAATAGACTCAACA
ATCATTCCAGATTCTGCAATTTATGGCTATATGAATAGAGTCAATAAAGTTATATTGGGG
ACACATAGTGTCTTAGCAAATGGTGGATTAAGAGCCGCAAGCGGAGCATTCACTGTAGCA
TTAGCAGCAAAGCACTTTTCTGTACCCGTTATTGTACTTGTACCTATGTTTAAAATGTCT
CCAGTTTTTCTATTCAATTATGAACAAGAAGCGTTCAATCTCGTAGGCAGCACACAAAGT
GTTTTACCTTACAATACACCAGTTTCACAGCAAGTTAAGGCTTATAGTCCTGCTTTTGAT
TATGTGCCGCCAAAATTAATAACACTCTTCATATCAAGCGCTGGCGGGTTTACTCCAGAT
TATGTTTATCGATTACTTGCTGAAATGTATCATCCTGATGACTATAATTTAACGAAATGA
>g12246.t1 Gene=g12246 Length=359
MVESNVYFTASLASLIHDIKVGKIVGSYSISQAMLNHFLSTLNESQWSTADELMTIVRET
GRICENALPTEAILGNIVRRMLKIIREEYDELNMPQEQIKQTDDSQAASLQKLVTQNSEK
SVEKSDYKALYTDLRENLITHLTEIENELHLSHDNLAQQASQHVHSAELILTLGYSKSVE
KFLKSVPKERKFEVVIAECAPACRGHLLATSLASSKIDSTIIPDSAIYGYMNRVNKVILG
THSVLANGGLRAASGAFTVALAAKHFSVPVIVLVPMFKMSPVFLFNYEQEAFNLVGSTQS
VLPYNTPVSQQVKAYSPAFDYVPPKLITLFISSAGGFTPDYVYRLLAEMYHPDDYNLTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12246.t1 | Gene3D | G3DSA:3.40.50.10470 | - | 159 | 350 | 0 |
| 2 | g12246.t1 | PANTHER | PTHR45859:SF1 | TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT BETA | 12 | 357 | 0 |
| 3 | g12246.t1 | PANTHER | PTHR45859 | TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT BETA | 12 | 357 | 0 |
| 1 | g12246.t1 | Pfam | PF01008 | Initiation factor 2 subunit family | 23 | 339 | 0 |
| 4 | g12246.t1 | SUPERFAMILY | SSF100950 | NagB/RpiA/CoA transferase-like | 4 | 351 | 0 |
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:0044237 | cellular metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K03754 (translation initiation factor eIF-2B subunit beta)
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.
