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 g6457 g6457.t5 isoform g6457.t5 17134952 17136207
chr_2 g6457 g6457.t5 exon g6457.t5.exon1 17134952 17135255
chr_2 g6457 g6457.t5 cds g6457.t5.CDS1 17135100 17135255
chr_2 g6457 g6457.t5 exon g6457.t5.exon2 17135413 17136207
chr_2 g6457 g6457.t5 cds g6457.t5.CDS2 17135413 17136045
chr_2 g6457 g6457.t5 TSS g6457.t5 17136941 17136941
chr_2 g6457 g6457.t5 TTS g6457.t5 NA NA

Sequences

>g6457.t5 Gene=g6457 Length=1099
TGTGGAACAATTGTGACCGAAGAGGGAAAAGAAAAGAAAGTCAACATTGATTTTGAACCA
TTTAAACCTATAAATACCTCACTATATCTTTGCGATAATAAATTTCATACGGAAGCATTA
ACTGCACTTCTTGCTGATGACAACAAATTCGGGTTTATTGTCATGGATGGTAATGGAGCA
CTTTTCGGAACACTTCAGGGTAATACGCGTGAAGTTCTTCACAAATTTACTGTCGACCTT
CCGAAAAAGCACGGTCGTGGTGGTCAATCTGCTCTTCGTTTTGCTCGTCTTCGTATGGAA
AAACGTCACAATTATGTGAGAAAAGTTGCTGAAGTTGCCACTCAATTATTCATTAGCAAT
GACAAGCCTAATATAGCAGGACTTATTCTTGCTGGTAGTGCTGATTTCAAAACTGAATTG
AGTCAATCAGATATGTTTGATCCAAGATTACAATCAAAAGTTATAAAACTTGTAGATATT
TCTTACAGTGGTGAAAATGGTTTCAATCAAGCAATTGAATTGGCAGCTGAATCATTACAA
AACGTCAAATTCATTCAAGAGAAGAAACTCATTGGACGATACTTTGATGAAATTTCTCAA
GACACTGGCAAATATTGTTTCGGTGTTGAAGATACACTAAAGGCCTTAGAGCTCGGATCT
GTTGAAATTTTAATCTGCTGGGAAAACTTGGACATTCAACGCTATGTACTAAAAAATACA
ACAACAAACACAACGACTGTTTTACATTTAACTCCAGAACAAGAAAAAGACAAAACACAT
TTTACGGACAAAGAAAGTGGAGTTGAAATGGAATTAGTCGAATCACAGCAATTACTAGAA
TGGCTTGCAAATAATTACAAAAGTTTTGGAGCCACATTAGAAATCATCACAGACAAGTCT
CAAGAAGGAAGTCAGTTTGTGAGAGGATTTGGTGGAATTGGCGGTGAGTAATTTTAAGGA
ATTTTTTCATATAAAGCTATTTTTCATTTTTCACATTTTCTGCTATTTCACTAAAGGTAT
TTTGCGCTATAAAGTTGATTTTCAATCTATGGCAGCGGAAGAAGAGCCGCTTGATGATGT
CGATCTTGACGAATACTAA

>g6457.t5 Gene=g6457 Length=262
MDGNGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAEVAT
QLFISNDKPNIAGLILAGSADFKTELSQSDMFDPRLQSKVIKLVDISYSGENGFNQAIEL
AAESLQNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALELGSVEILICWENLDIQR
YVLKNTTTNTTTVLHLTPEQEKDKTHFTDKESGVEMELVESQQLLEWLANNYKSFGATLE
IITDKSQEGSQFVRGFGGIGGE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6457.t5 Gene3D G3DSA:3.30.420.60 - 1 126 0
7 g6457.t5 Gene3D G3DSA:3.30.1330.30 - 128 262 0
3 g6457.t5 PANTHER PTHR10113:SF21 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 1 261 0
4 g6457.t5 PANTHER PTHR10113 PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 1 261 0
2 g6457.t5 Pfam PF03464 eRF1 domain 2 1 127 0
1 g6457.t5 Pfam PF03465 eRF1 domain 3 130 261 0
5 g6457.t5 SUPERFAMILY SSF53137 Translational machinery components 1 125 0
6 g6457.t5 SUPERFAMILY SSF55315 L30e-like 127 261 0
9 g6457.t5 TIGRFAM TIGR03676 aRF1/eRF1: peptide chain release factor 1, archaeal and eukaryotic forms 1 261 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