Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic peptide chain release factor 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 g6458 g6458.t9 TSS g6458.t9 17137331 17137331
chr_2 g6458 g6458.t9 isoform g6458.t9 17138122 17139141
chr_2 g6458 g6458.t9 exon g6458.t9.exon1 17138122 17138935
chr_2 g6458 g6458.t9 cds g6458.t9.CDS1 17138300 17138935
chr_2 g6458 g6458.t9 exon g6458.t9.exon2 17139000 17139141
chr_2 g6458 g6458.t9 cds g6458.t9.CDS2 17139000 17139140
chr_2 g6458 g6458.t9 TTS g6458.t9 NA NA

Sequences

>g6458.t9 Gene=g6458 Length=956
TGGGTTGGTGATTTACTGTGGAACTATTGTGACGGAAGAAAATAAAGAAAAGAAAGTCAA
CATTGATTTTGAACCATTTAAACCTATAAATACCTCACTATATCTTTGCGATAATAAATT
TCATACGGAAGCATTAACTGCACTTCTTGCTGATGACAACAAATTCGGGTTTATTGTCAT
GGATGGTAATGGAGCACTTTTCGGAACACTTCAGGGTAATACGCGTGAAGTTCTTCACAA
ATTTACTGTCGACCTTCCGAAAAAGCACGGTCGTGGTGGTCAATCTGCTCTTCGTTTTGC
TCGTCTTCGTATGGAAAAACGTCACAATTATGTGAGAAAAGTTGCTGAAGTTGCCACTCA
ATTATTCATTAGCAATGACAAGCCTAATATAGCAGGACTTATTCTTGCTGGTAGTGCTGA
TTTCAAAACTGAATTGAGTCAGTCAGATATGTTTGATCCAAGATTGCAATCAAAAGTCAT
AAAACTTGTGGACGTTTCGTATGGAGGTGAAAATGGTTTCAACCAAGCAATTGAATTGGC
AGCTGAATCATTACAAAATGTCAAATTCATTCAAGAGAAGAAACTCATTGGACGATACTT
TGATGAAATTTCTCAAGACACTGGCAAATATTGTTTCGGTGTTGAAGATACACTAAAGGC
CTTAGAGCTCGGATCTGTTGAAATTTTAATCTGCTGGGAAAACTTGGACATTCAACGTTA
TGTGCTAAAAAATACTTCGAATGCTGCACAAACTACAATCCTGCATCTAACTCCAGAGCA
AGAAAAGGATAAGTCACACTTTACGGACAAAGAAAGTGGAGCTGAATTAGAATTGTTAGA
ATCACAGCCGCTTCTTGAATGGCTCGCAAATAATTATAAAAGTTTTGGTGCCACATTAGA
AATCATCACAGACAAGTCTCAAGAAGGAAGTCAGTTTGTGAGAGGATTTGGTGGAA

>g6458.t9 Gene=g6458 Length=259
MDGNGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAEVAT
QLFISNDKPNIAGLILAGSADFKTELSQSDMFDPRLQSKVIKLVDVSYGGENGFNQAIEL
AAESLQNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALELGSVEILICWENLDIQR
YVLKNTSNAAQTTILHLTPEQEKDKSHFTDKESGAELELLESQPLLEWLANNYKSFGATL
EIITDKSQEGSQFVRGFGG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6458.t9 Gene3D G3DSA:3.30.420.60 - 1 126 0
7 g6458.t9 Gene3D G3DSA:3.30.1330.30 - 128 259 0
3 g6458.t9 PANTHER PTHR10113:SF21 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 1 259 0
4 g6458.t9 PANTHER PTHR10113 PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 1 259 0
2 g6458.t9 Pfam PF03464 eRF1 domain 2 1 127 0
1 g6458.t9 Pfam PF03465 eRF1 domain 3 130 259 0
5 g6458.t9 SUPERFAMILY SSF53137 Translational machinery components 1 125 0
6 g6458.t9 SUPERFAMILY SSF55315 L30e-like 127 259 0
9 g6458.t9 TIGRFAM TIGR03676 aRF1/eRF1: peptide chain release factor 1, archaeal and eukaryotic forms 1 259 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 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