Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic peptide chain release factor GTP-binding subunit ERF3A.

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 g5235 g5235.t5 TTS g5235.t5 7947867 7947867
chr_2 g5235 g5235.t5 isoform g5235.t5 7947936 7949290
chr_2 g5235 g5235.t5 exon g5235.t5.exon1 7947936 7947979
chr_2 g5235 g5235.t5 cds g5235.t5.CDS1 7947936 7947979
chr_2 g5235 g5235.t5 exon g5235.t5.exon2 7948046 7948214
chr_2 g5235 g5235.t5 cds g5235.t5.CDS2 7948046 7948214
chr_2 g5235 g5235.t5 exon g5235.t5.exon3 7948272 7948448
chr_2 g5235 g5235.t5 cds g5235.t5.CDS3 7948272 7948448
chr_2 g5235 g5235.t5 exon g5235.t5.exon4 7948517 7948603
chr_2 g5235 g5235.t5 cds g5235.t5.CDS4 7948517 7948603
chr_2 g5235 g5235.t5 exon g5235.t5.exon5 7948682 7948952
chr_2 g5235 g5235.t5 cds g5235.t5.CDS5 7948682 7948952
chr_2 g5235 g5235.t5 exon g5235.t5.exon6 7949020 7949222
chr_2 g5235 g5235.t5 cds g5235.t5.CDS6 7949020 7949153
chr_2 g5235 g5235.t5 exon g5235.t5.exon7 7949287 7949290
chr_2 g5235 g5235.t5 TSS g5235.t5 NA NA

Sequences

>g5235.t5 Gene=g5235 Length=955
TCTGGTAATTTCCGCACGTAAAGGAGAATTTGAAACTGGATTTGATCGAGGAGGTCAAAC
GAGAGAGCATGCAATGTTAGCAAAGACAGCTGGCGTCAAGCACTTGGTAGTTTTAGTCAA
TAAAATGGACGATCCGACAGTTAACTGGGAGGAAGTTCGCTACAACGAATGTAAAGATAA
AATTTTACCATATCTCAAAAAACTCGGTTTTAAAGCAAAGGACTTGACATTTATGCCAGT
ATCAGGAATCACGGGAATGGGACTTAAAGAACCAATTGATAAAAATTTATGCCCCTGGTA
TGATGGACCAGGTTTCATTCCATTCATCGACGACTTACCATCACTAAATCGCAAAACAGA
CGGCCCATTTATTATGCCAATTGTCGATAAATACAAAGATATGGGAACGGTGGTCATGGG
AAAAGTTGAAAGTGGAATGGCCAAGAAGGGACAAAATTTACTCGTAATGCCTAATAGAAC
ACAAGTAGCAGTTGATCAATTGTGGTCTGATGAAGAGGAAGTAACAAGTGTTGGTCCAGG
TGAAAATGTAAAAATTAAACTCAAAGGCATCGAAGAAGAAGATGTTTCACCCGGATTTGT
CCTATGCGATGCTTCCAATCCAATCAAAACAGGAAAGATCTTCGACGCCCAAGTAGTTAT
ATTAGAGCATAAATCAATTATCTGTGCGGGATATTCTGCTGTAATGCATATTCATTGTGC
AGCTGAAGAAGTCACTGTTAAAGCCCTTATTTGTTTAGTAGATAAAAAGAGCGGAGACAA
ATCGAAAACTCGTCCAAGATTTGTTAAACAAGACCAAGTCGCAATAATGCGAATTGAATG
CTCTGGTATGATTTGCTTAGAACAATTTAAGCTCTTCCCTCAGATGGGTCGATTCACGTT
GCGTGATGAGAATAAAACAATTGCCATCGGAAAAGTGTTAAAAGTTATTGAATAA

>g5235.t5 Gene=g5235 Length=293
MLAKTAGVKHLVVLVNKMDDPTVNWEEVRYNECKDKILPYLKKLGFKAKDLTFMPVSGIT
GMGLKEPIDKNLCPWYDGPGFIPFIDDLPSLNRKTDGPFIMPIVDKYKDMGTVVMGKVES
GMAKKGQNLLVMPNRTQVAVDQLWSDEEEVTSVGPGENVKIKLKGIEEEDVSPGFVLCDA
SNPIKTGKIFDAQVVILEHKSIICAGYSAVMHIHCAAEEVTVKALICLVDKKSGDKSKTR
PRFVKQDQVAIMRIECSGMICLEQFKLFPQMGRFTLRDENKTIAIGKVLKVIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5235.t5 CDD cd04089 eRF3_II 98 179 0
12 g5235.t5 CDD cd03704 eRF3_C_III 185 291 0
8 g5235.t5 Gene3D G3DSA:3.40.50.300 - 1 93 0
9 g5235.t5 Gene3D G3DSA:2.40.30.10 Translation factors 94 181 0
10 g5235.t5 Gene3D G3DSA:2.40.30.10 Translation factors 183 291 0
3 g5235.t5 PANTHER PTHR23115:SF125 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A 1 292 0
4 g5235.t5 PANTHER PTHR23115 TRANSLATION FACTOR 1 292 0
2 g5235.t5 Pfam PF03144 Elongation factor Tu domain 2 111 178 0
1 g5235.t5 Pfam PF03143 Elongation factor Tu C-terminal domain 183 291 0
6 g5235.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 111 0
7 g5235.t5 SUPERFAMILY SSF50447 Translation proteins 93 183 0
5 g5235.t5 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 189 292 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5235/g5235.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t5.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005525 GTP binding 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