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.t8 isoform g5235.t8 7948936 7950336
chr_2 g5235 g5235.t8 exon g5235.t8.exon1 7948936 7948952
chr_2 g5235 g5235.t8 cds g5235.t8.CDS1 7948937 7948952
chr_2 g5235 g5235.t8 exon g5235.t8.exon2 7949020 7949222
chr_2 g5235 g5235.t8 cds g5235.t8.CDS2 7949020 7949222
chr_2 g5235 g5235.t8 exon g5235.t8.exon3 7949287 7949432
chr_2 g5235 g5235.t8 cds g5235.t8.CDS3 7949287 7949432
chr_2 g5235 g5235.t8 exon g5235.t8.exon4 7949501 7949647
chr_2 g5235 g5235.t8 cds g5235.t8.CDS4 7949501 7949647
chr_2 g5235 g5235.t8 exon g5235.t8.exon5 7949707 7949830
chr_2 g5235 g5235.t8 cds g5235.t8.CDS5 7949707 7949830
chr_2 g5235 g5235.t8 exon g5235.t8.exon6 7949888 7949970
chr_2 g5235 g5235.t8 cds g5235.t8.CDS6 7949888 7949970
chr_2 g5235 g5235.t8 exon g5235.t8.exon7 7950150 7950336
chr_2 g5235 g5235.t8 cds g5235.t8.CDS7 7950150 7950336
chr_2 g5235 g5235.t8 TSS g5235.t8 7950481 7950481
chr_2 g5235 g5235.t8 TTS g5235.t8 NA NA

Sequences

>g5235.t8 Gene=g5235 Length=907
ATGGAAAACGATCAGGAAATTCATAAAATTGGTTCACAATTTTCAACGCTAAATGTTAAT
GCAGTTGAATTTGTTCCGAGCTTCGTTGTGTCTCATCAACCACAGAAAGATATTGAAAAT
AGCATCGAAGATCCTCCGCCTACAGCACCTTCAAAGCCAATTGAAACTCCTGAAAACAAT
GGAAATGTGGTCGAAAATGAACCTCTTGATACATGGGACGAAGAAGAAACAATTCTAACT
CCAGATGGAGACAATGAAAATGAAGAGGAGGAAATGGAAGTTGAAGATGGCAGCGATGCA
CTACCAAAACCATCAACTAAAAGGAAACCTCCAAAAGTTGAAGAAAATTGTAGCAAAAAG
GAGCATGTGAATGTTGTTTTTATCGGTCATGTTGATGCCGGAAAGTCTACTATTGGCGGT
CAAATTATGTCTTTGACTGGAATGGTTGATAAGCGTACATTGGAAAAATACGAACGTGAA
GCTCGTGAAAAATCAAGAGAAAGCTGGTATCTTTCGTGGGCCTTGGATACAAATCAGGAA
GAACGTGATAAAGGTAAAACTGTTGAAGTTGGCAGAGCCTATTTTGAGACTGAGAAAAAG
CATTTCACCATACTCGATGCTCCTGGACATAAGAGCTTTGTACCAAACATGATTGGAGGA
GCAGCACAAGCCGATTTAGCAGTTCTGGTAATTTCCGCACGTAAAGGAGAATTTGAAACT
GGATTTGATCGAGGAGGTCAAACGAGAGAGCATGCAATGTTAGCAAAGACAGCTGGCGTC
AAGCACTTGGTAGTTTTAGTCAATAAAATGGACGATCCGACAGTTAACTGGGAGGAAGTT
CGCTACAACGAATGTAAAGATAAAATTTTACCATATCTCAAAAAACTCGGTTTTAAAGCA
AAGGACT

>g5235.t8 Gene=g5235 Length=302
MENDQEIHKIGSQFSTLNVNAVEFVPSFVVSHQPQKDIENSIEDPPPTAPSKPIETPENN
GNVVENEPLDTWDEEETILTPDGDNENEEEEMEVEDGSDALPKPSTKRKPPKVEENCSKK
EHVNVVFIGHVDAGKSTIGGQIMSLTGMVDKRTLEKYEREAREKSRESWYLSWALDTNQE
ERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGAAQADLAVLVISARKGEFET
GFDRGGQTREHAMLAKTAGVKHLVVLVNKMDDPTVNWEEVRYNECKDKILPYLKKLGFKA
KD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5235.t8 CDD cd01883 EF1_alpha 124 302 3.84222E-123
11 g5235.t8 Gene3D G3DSA:3.40.50.300 - 98 302 1.5E-71
15 g5235.t8 MobiDBLite mobidb-lite consensus disorder prediction 32 116 -
14 g5235.t8 MobiDBLite mobidb-lite consensus disorder prediction 68 96 -
16 g5235.t8 MobiDBLite mobidb-lite consensus disorder prediction 97 116 -
3 g5235.t8 PANTHER PTHR23115:SF125 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A 53 301 1.2E-122
4 g5235.t8 PANTHER PTHR23115 TRANSLATION FACTOR 53 301 1.2E-122
7 g5235.t8 PRINTS PR00315 GTP-binding elongation factor signature 124 137 8.7E-17
6 g5235.t8 PRINTS PR00315 GTP-binding elongation factor signature 183 191 8.7E-17
9 g5235.t8 PRINTS PR00315 GTP-binding elongation factor signature 203 213 8.7E-17
8 g5235.t8 PRINTS PR00315 GTP-binding elongation factor signature 219 230 8.7E-17
5 g5235.t8 PRINTS PR00315 GTP-binding elongation factor signature 263 272 8.7E-17
2 g5235.t8 Pfam PF07145 Ataxin-2 C-terminal region 13 28 1.4E-5
1 g5235.t8 Pfam PF00009 Elongation factor Tu GTP binding domain 120 287 1.4E-40
13 g5235.t8 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 176 191 -
17 g5235.t8 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 120 302 52.06
10 g5235.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 114 299 2.85E-55

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5235/g5235.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t8.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005525 GTP binding MF
GO:0003924 GTPase 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