General information for g6458.t1
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 g6458 is located on chr_2: 17140152..17141669 (+ 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 | g6458 | g6458.t1 | TSS | g6458.t1 | 17137331 | 17137331 |
| chr_2 | g6458 | g6458.t1 | isoform | g6458.t1 | 17137515 | 17140240 |
| chr_2 | g6458 | g6458.t1 | exon | g6458.t1.exon1 | 17137515 | 17137600 |
| chr_2 | g6458 | g6458.t1 | cds | g6458.t1.CDS1 | 17137515 | 17137600 |
| chr_2 | g6458 | g6458.t1 | exon | g6458.t1.exon2 | 17137851 | 17138026 |
| chr_2 | g6458 | g6458.t1 | cds | g6458.t1.CDS2 | 17137851 | 17138026 |
| chr_2 | g6458 | g6458.t1 | exon | g6458.t1.exon3 | 17138112 | 17138935 |
| chr_2 | g6458 | g6458.t1 | cds | g6458.t1.CDS3 | 17138112 | 17138935 |
| chr_2 | g6458 | g6458.t1 | exon | g6458.t1.exon4 | 17139000 | 17139147 |
| chr_2 | g6458 | g6458.t1 | cds | g6458.t1.CDS4 | 17139000 | 17139147 |
| chr_2 | g6458 | g6458.t1 | exon | g6458.t1.exon5 | 17140152 | 17140240 |
| chr_2 | g6458 | g6458.t1 | cds | g6458.t1.CDS5 | 17140152 | 17140240 |
| chr_2 | g6458 | g6458.t1 | TTS | g6458.t1 | 17140954 | 17140954 |
Sequences
>g6458.t1 Gene=g6458 Length=1323
ATGAGTTTCGACGATACGAGTGCAGATAGAAATGTCGAGATTTGGAAAATCAAAAAACTC
ATCAAAAGTCTCGAACTTGCGAGAGGAAATGGAACGAGCATGATTTCATTGATTATTCCG
CCCAAAGATCAGATTGCACGTATCAGCAAAATGTTGGCTGATGAATTTGGAACAGCATCT
AACATCAAATCAAGAGTTAATCGTCTTTCAGTTTTAGGAGCCATCACCTCAGTTCAACAT
AGATTAAAACTCTATACCAAAGTGCCTCCGAATGGGTTGGTGATTTACTGTGGAACTATT
GTGACGGAAGAAAATAAAGAAAAGAAAGTCAACATTGATTTTGAACCATTTAAACCTATA
AATACCTCACTATATCTTTGCGATAATAAATTTCATACGGAAGCATTAACTGCACTTCTT
GCTGATGACAACAAATTCGGGTTTATTGTCATGGATGGTAATGGAGCACTTTTCGGAACA
CTTCAGGGTAATACGCGTGAAGTTCTTCACAAATTTACTGTCGACCTTCCGAAAAAGCAC
GGTCGTGGTGGTCAATCTGCTCTTCGTTTTGCTCGTCTTCGTATGGAAAAACGTCACAAT
TATGTGAGAAAAGTTGCTGAAGTTGCCACTCAATTATTCATTAGCAATGACAAGCCTAAT
ATAGCAGGACTTATTCTTGCTGGTAGTGCTGATTTCAAAACTGAATTGAGTCAGTCAGAT
ATGTTTGATCCAAGATTGCAATCAAAAGTCATAAAACTTGTGGACGTTTCGTATGGAGGT
GAAAATGGTTTCAACCAAGCAATTGAATTGGCAGCTGAATCATTACAAAATGTCAAATTC
ATTCAAGAGAAGAAACTCATTGGACGATACTTTGATGAAATTTCTCAAGACACTGGCAAA
TATTGTTTCGGTGTTGAAGATACACTAAAGGCCTTAGAGCTCGGATCTGTTGAAATTTTA
ATCTGCTGGGAAAACTTGGACATTCAACGTTATGTGCTAAAAAATACTTCGAATGCTGCA
CAAACTACAATCCTGCATCTAACTCCAGAGCAAGAAAAGGATAAGTCACACTTTACGGAC
AAAGAAAGTGGAGCTGAATTAGAATTGTTAGAATCACAGCCGCTTCTTGAATGGCTCGCA
AATAATTATAAAAGTTTTGGTGCCACATTAGAAATCATCACAGACAAGTCTCAAGAAGGA
AGTCAGTTTGTGAGAGGATTTGGTGGAATTGGCGGAATTTTACGTTACAAAGTTGATTTC
CAATCAATGCAATTAGAGGATGGACTTTATGATGATTTAGATATTGACTTTGATGACTAC
TAA
>g6458.t1 Gene=g6458 Length=440
MSFDDTSADRNVEIWKIKKLIKSLELARGNGTSMISLIIPPKDQIARISKMLADEFGTAS
NIKSRVNRLSVLGAITSVQHRLKLYTKVPPNGLVIYCGTIVTEENKEKKVNIDFEPFKPI
NTSLYLCDNKFHTEALTALLADDNKFGFIVMDGNGALFGTLQGNTREVLHKFTVDLPKKH
GRGGQSALRFARLRMEKRHNYVRKVAEVATQLFISNDKPNIAGLILAGSADFKTELSQSD
MFDPRLQSKVIKLVDVSYGGENGFNQAIELAAESLQNVKFIQEKKLIGRYFDEISQDTGK
YCFGVEDTLKALELGSVEILICWENLDIQRYVLKNTSNAAQTTILHLTPEQEKDKSHFTD
KESGAELELLESQPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIGGILRYKVDF
QSMQLEDGLYDDLDIDFDDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g6458.t1 | Gene3D | G3DSA:3.30.960.10 | Translation | 2 | 136 | 0 |
| 10 | g6458.t1 | Gene3D | G3DSA:3.30.420.60 | - | 137 | 276 | 0 |
| 9 | g6458.t1 | Gene3D | G3DSA:3.30.1330.30 | - | 278 | 440 | 0 |
| 4 | g6458.t1 | PANTHER | PTHR10113 | PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 | 2 | 427 | 0 |
| 3 | g6458.t1 | Pfam | PF03463 | eRF1 domain 1 | 18 | 138 | 0 |
| 2 | g6458.t1 | Pfam | PF03464 | eRF1 domain 2 | 145 | 277 | 0 |
| 1 | g6458.t1 | Pfam | PF03465 | eRF1 domain 3 | 280 | 418 | 0 |
| 8 | g6458.t1 | SMART | SM01194 | eRF1_1_2 | 6 | 141 | 0 |
| 5 | g6458.t1 | SUPERFAMILY | SSF55481 | N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | 8 | 142 | 0 |
| 6 | g6458.t1 | SUPERFAMILY | SSF53137 | Translational machinery components | 143 | 275 | 0 |
| 7 | g6458.t1 | SUPERFAMILY | SSF55315 | L30e-like | 277 | 421 | 0 |
| 12 | g6458.t1 | TIGRFAM | TIGR03676 | aRF1/eRF1: peptide chain release factor 1, archaeal and eukaryotic forms | 13 | 418 | 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.
