General information for g6457.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Eukaryotic peptide chain release factor subunit 1.
Parent gene
- The parent gene g6457 is located on chr_2: 17135554..17138935 (- 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_2 | g6457 | g6457.t2 | isoform | g6457.t2 | 17134579 | 17136720 |
| chr_2 | g6457 | g6457.t2 | exon | g6457.t2.exon1 | 17134579 | 17134673 |
| chr_2 | g6457 | g6457.t2 | cds | g6457.t2.CDS1 | 17134579 | 17134673 |
| chr_2 | g6457 | g6457.t2 | exon | g6457.t2.exon2 | 17135108 | 17135255 |
| chr_2 | g6457 | g6457.t2 | cds | g6457.t2.CDS2 | 17135108 | 17135255 |
| chr_2 | g6457 | g6457.t2 | exon | g6457.t2.exon3 | 17135413 | 17136233 |
| chr_2 | g6457 | g6457.t2 | cds | g6457.t2.CDS3 | 17135413 | 17136233 |
| chr_2 | g6457 | g6457.t2 | exon | g6457.t2.exon4 | 17136465 | 17136720 |
| chr_2 | g6457 | g6457.t2 | cds | g6457.t2.CDS4 | 17136465 | 17136720 |
| chr_2 | g6457 | g6457.t2 | TSS | g6457.t2 | 17137500 | 17137500 |
| chr_2 | g6457 | g6457.t2 | TTS | g6457.t2 | NA | NA |
Sequences
>g6457.t2 Gene=g6457 Length=1320
ATGGATGATACGAGTGCAGATAGAAATGTTGAAATTTGGAAGATTAAAAAGCTTATTAAA
AGCTTAGAATTAGCAAGAGGAAATGGAACGAGCATGATTTCATTAATTATTCCACCTAAA
GATCAAATATCGAGAGTTAGCAAAATGTTGGCTGATGAATTTGGAACTGCGTCTAACATC
AAATCAAGAGTTAATCGTCTTTCGGTTTTAGGTGCCATCACATCAGTACAACATAGATTA
AAACTCTATACCAAAGTGCCTCCGAATGGGTTGGTGATTTACTGTGGAACAATTGTGACC
GAAGAGGGAAAAGAAAAGAAAGTCAACATTGATTTTGAACCATTTAAACCTATAAATACC
TCACTATATCTTTGCGATAATAAATTTCATACGGAAGCATTAACTGCACTTCTTGCTGAT
GACAACAAATTCGGGTTTATTGTCATGGATGGTAATGGAGCACTTTTCGGAACACTTCAG
GGTAATACGCGTGAAGTTCTTCACAAATTTACTGTCGACCTTCCGAAAAAGCACGGTCGT
GGTGGTCAATCTGCTCTTCGTTTTGCTCGTCTTCGTATGGAAAAACGTCACAATTATGTG
AGAAAAGTTGCTGAAGTTGCCACTCAATTATTCATTAGCAATGACAAGCCTAATATAGCA
GGACTTATTCTTGCTGGTAGTGCTGATTTCAAAACTGAATTGAGTCAATCAGATATGTTT
GATCCAAGATTACAATCAAAAGTTATAAAACTTGTAGATATTTCTTACAGTGGTGAAAAT
GGTTTCAATCAAGCAATTGAATTGGCAGCTGAATCATTACAAAACGTCAAATTCATTCAA
GAGAAGAAACTCATTGGACGATACTTTGATGAAATTTCTCAAGACACTGGCAAATATTGT
TTCGGTGTTGAAGATACACTAAAGGCCTTAGAGCTCGGATCTGTTGAAATTTTAATCTGC
TGGGAAAACTTGGACATTCAACGCTATGTACTAAAAAATACAACAACAAACACAACGACT
GTTTTACATTTAACTCCAGAACAAGAAAAAGACAAAACACATTTTACGGACAAAGAAAGT
GGAGTTGAAATGGAATTAGTCGAATCACAGCAATTACTAGAATGGCTTGCAAATAATTAC
AAAAGTTTTGGAGCCACATTAGAAATCATCACAGACAAGTCTCAAGAAGGAAGTCAGTTT
GTGAGAGGATTTGGTGGAATTGGCGGAATTTTGCGTTATAAAGTTGATTTCCAATCGATT
CAGTTAGATGATGGATATTATGATGATGATGACATAGAATATGATTTAGATGAATACTAA
>g6457.t2 Gene=g6457 Length=439
MDDTSADRNVEIWKIKKLIKSLELARGNGTSMISLIIPPKDQISRVSKMLADEFGTASNI
KSRVNRLSVLGAITSVQHRLKLYTKVPPNGLVIYCGTIVTEEGKEKKVNIDFEPFKPINT
SLYLCDNKFHTEALTALLADDNKFGFIVMDGNGALFGTLQGNTREVLHKFTVDLPKKHGR
GGQSALRFARLRMEKRHNYVRKVAEVATQLFISNDKPNIAGLILAGSADFKTELSQSDMF
DPRLQSKVIKLVDISYSGENGFNQAIELAAESLQNVKFIQEKKLIGRYFDEISQDTGKYC
FGVEDTLKALELGSVEILICWENLDIQRYVLKNTTTNTTTVLHLTPEQEKDKTHFTDKES
GVEMELVESQQLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIGGILRYKVDFQSI
QLDDGYYDDDDIEYDLDEY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g6457.t2 | Gene3D | G3DSA:3.30.960.10 | Translation | 1 | 134 | 0 |
| 10 | g6457.t2 | Gene3D | G3DSA:3.30.420.60 | - | 135 | 274 | 0 |
| 9 | g6457.t2 | Gene3D | G3DSA:3.30.1330.30 | - | 276 | 439 | 0 |
| 4 | g6457.t2 | PANTHER | PTHR10113 | PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 | 3 | 424 | 0 |
| 3 | g6457.t2 | Pfam | PF03463 | eRF1 domain 1 | 16 | 136 | 0 |
| 2 | g6457.t2 | Pfam | PF03464 | eRF1 domain 2 | 143 | 275 | 0 |
| 1 | g6457.t2 | Pfam | PF03465 | eRF1 domain 3 | 278 | 415 | 0 |
| 8 | g6457.t2 | SMART | SM01194 | eRF1_1_2 | 4 | 139 | 0 |
| 5 | g6457.t2 | SUPERFAMILY | SSF55481 | N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | 6 | 140 | 0 |
| 6 | g6457.t2 | SUPERFAMILY | SSF53137 | Translational machinery components | 141 | 273 | 0 |
| 7 | g6457.t2 | SUPERFAMILY | SSF55315 | L30e-like | 275 | 418 | 0 |
| 12 | g6457.t2 | TIGRFAM | TIGR03676 | aRF1/eRF1: peptide chain release factor 1, archaeal and eukaryotic forms | 11 | 415 | 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:0006415 | translational termination | BP |
| GO:0003747 | translation release factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03265 (peptide chain release factor subunit 1)
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.
