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.t6 isoform g6457.t6 17135413 17136720
chr_2 g6457 g6457.t6 exon g6457.t6.exon1 17135413 17136233
chr_2 g6457 g6457.t6 cds g6457.t6.CDS1 17135413 17136233
chr_2 g6457 g6457.t6 exon g6457.t6.exon2 17136465 17136720
chr_2 g6457 g6457.t6 cds g6457.t6.CDS2 17136465 17136720
chr_2 g6457 g6457.t6 TSS g6457.t6 17137500 17137500
chr_2 g6457 g6457.t6 TTS g6457.t6 NA NA

Sequences

>g6457.t6 Gene=g6457 Length=1077
ATGGATGATACGAGTGCAGATAGAAATGTTGAAATTTGGAAGATTAAAAAGCTTATTAAA
AGCTTAGAATTAGCAAGAGGAAATGGAACGAGCATGATTTCATTAATTATTCCACCTAAA
GATCAAATATCGAGAGTTAGCAAAATGTTGGCTGATGAATTTGGAACTGCGTCTAACATC
AAATCAAGAGTTAATCGTCTTTCGGTTTTAGGTGCCATCACATCAGTACAACATAGATTA
AAACTCTATACCAAAGTGCCTCCGAATGGGTTGGTGATTTACTGTGGAACAATTGTGACC
GAAGAGGGAAAAGAAAAGAAAGTCAACATTGATTTTGAACCATTTAAACCTATAAATACC
TCACTATATCTTTGCGATAATAAATTTCATACGGAAGCATTAACTGCACTTCTTGCTGAT
GACAACAAATTCGGGTTTATTGTCATGGATGGTAATGGAGCACTTTTCGGAACACTTCAG
GGTAATACGCGTGAAGTTCTTCACAAATTTACTGTCGACCTTCCGAAAAAGCACGGTCGT
GGTGGTCAATCTGCTCTTCGTTTTGCTCGTCTTCGTATGGAAAAACGTCACAATTATGTG
AGAAAAGTTGCTGAAGTTGCCACTCAATTATTCATTAGCAATGACAAGCCTAATATAGCA
GGACTTATTCTTGCTGGTAGTGCTGATTTCAAAACTGAATTGAGTCAATCAGATATGTTT
GATCCAAGATTACAATCAAAAGTTATAAAACTTGTAGATATTTCTTACAGTGGTGAAAAT
GGTTTCAATCAAGCAATTGAATTGGCAGCTGAATCATTACAAAACGTCAAATTCATTCAA
GAGAAGAAACTCATTGGACGATACTTTGATGAAATTTCTCAAGACACTGGCAAATATTGT
TTCGGTGTTGAAGATACACTAAAGGCCTTAGAGCTCGGATCTGTTGAAATTTTAATCTGC
TGGGAAAACTTGGACATTCAACGCTATGTACTAAAAAATACAACAACAAACACAACGACT
GTTTTACATTTAACTCCAGAACAAGAAAAAGACAAAACACATTTTACGGACAAAGAA

>g6457.t6 Gene=g6457 Length=359
MDDTSADRNVEIWKIKKLIKSLELARGNGTSMISLIIPPKDQISRVSKMLADEFGTASNI
KSRVNRLSVLGAITSVQHRLKLYTKVPPNGLVIYCGTIVTEEGKEKKVNIDFEPFKPINT
SLYLCDNKFHTEALTALLADDNKFGFIVMDGNGALFGTLQGNTREVLHKFTVDLPKKHGR
GGQSALRFARLRMEKRHNYVRKVAEVATQLFISNDKPNIAGLILAGSADFKTELSQSDMF
DPRLQSKVIKLVDISYSGENGFNQAIELAAESLQNVKFIQEKKLIGRYFDEISQDTGKYC
FGVEDTLKALELGSVEILICWENLDIQRYVLKNTTTNTTTVLHLTPEQEKDKTHFTDKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6457.t6 Gene3D G3DSA:3.30.960.10 Translation 1 134 0
10 g6457.t6 Gene3D G3DSA:3.30.420.60 - 135 274 0
9 g6457.t6 Gene3D G3DSA:3.30.1330.30 - 276 359 0
4 g6457.t6 PANTHER PTHR10113 PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1 3 359 0
3 g6457.t6 Pfam PF03463 eRF1 domain 1 16 136 0
2 g6457.t6 Pfam PF03464 eRF1 domain 2 143 275 0
1 g6457.t6 Pfam PF03465 eRF1 domain 3 278 338 0
8 g6457.t6 SMART SM01194 eRF1_1_2 4 139 0
5 g6457.t6 SUPERFAMILY SSF55481 N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 6 140 0
6 g6457.t6 SUPERFAMILY SSF53137 Translational machinery components 141 273 0
7 g6457.t6 SUPERFAMILY SSF55315 L30e-like 275 358 0
12 g6457.t6 TIGRFAM TIGR03676 aRF1/eRF1: peptide chain release factor 1, archaeal and eukaryotic forms 11 353 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

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.

Raw TPM values