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.t6 TTS g5235.t6 7947867 7947867
chr_2 g5235 g5235.t6 isoform g5235.t6 7947936 7949829
chr_2 g5235 g5235.t6 exon g5235.t6.exon1 7947936 7947979
chr_2 g5235 g5235.t6 cds g5235.t6.CDS1 7947936 7947979
chr_2 g5235 g5235.t6 exon g5235.t6.exon2 7948046 7948214
chr_2 g5235 g5235.t6 cds g5235.t6.CDS2 7948046 7948214
chr_2 g5235 g5235.t6 exon g5235.t6.exon3 7948272 7948448
chr_2 g5235 g5235.t6 cds g5235.t6.CDS3 7948272 7948448
chr_2 g5235 g5235.t6 exon g5235.t6.exon4 7948517 7948603
chr_2 g5235 g5235.t6 cds g5235.t6.CDS4 7948517 7948603
chr_2 g5235 g5235.t6 exon g5235.t6.exon5 7948682 7948952
chr_2 g5235 g5235.t6 cds g5235.t6.CDS5 7948682 7948952
chr_2 g5235 g5235.t6 exon g5235.t6.exon6 7949020 7949222
chr_2 g5235 g5235.t6 cds g5235.t6.CDS6 7949020 7949222
chr_2 g5235 g5235.t6 exon g5235.t6.exon7 7949287 7949432
chr_2 g5235 g5235.t6 cds g5235.t6.CDS7 7949287 7949432
chr_2 g5235 g5235.t6 exon g5235.t6.exon8 7949501 7949647
chr_2 g5235 g5235.t6 cds g5235.t6.CDS8 7949501 7949647
chr_2 g5235 g5235.t6 exon g5235.t6.exon9 7949707 7949829
chr_2 g5235 g5235.t6 cds g5235.t6.CDS9 7949707 7949827
chr_2 g5235 g5235.t6 TSS g5235.t6 7950481 7950481

Sequences

>g5235.t6 Gene=g5235 Length=1367
AAATGGAAGTTGAAGATGGCAGCGATGCACTACCAAAACCATCAACTAAAAGGAAACCTC
CAAAAGTTGAAGAAAATTGTAGCAAAAAGGAGCATGTGAATGTTGTTTTTATCGGTCATG
TTGATGCCGGAAAGTCTACTATTGGCGGTCAAATTATGTCTTTGACTGGAATGGTTGATA
AGCGTACATTGGAAAAATACGAACGTGAAGCTCGTGAAAAATCAAGAGAAAGCTGGTATC
TTTCGTGGGCCTTGGATACAAATCAGGAAGAACGTGATAAAGGTAAAACTGTTGAAGTTG
GCAGAGCCTATTTTGAGACTGAGAAAAAGCATTTCACCATACTCGATGCTCCTGGACATA
AGAGCTTTGTACCAAACATGATTGGAGGAGCAGCACAAGCCGATTTAGCAGTTCTGGTAA
TTTCCGCACGTAAAGGAGAATTTGAAACTGGATTTGATCGAGGAGGTCAAACGAGAGAGC
ATGCAATGTTAGCAAAGACAGCTGGCGTCAAGCACTTGGTAGTTTTAGTCAATAAAATGG
ACGATCCGACAGTTAACTGGGAGGAAGTTCGCTACAACGAATGTAAAGATAAAATTTTAC
CATATCTCAAAAAACTCGGTTTTAAAGCAAAGGACTTGACATTTATGCCAGTATCAGGAA
TCACGGGAATGGGACTTAAAGAACCAATTGATAAAAATTTATGCCCCTGGTATGATGGAC
CAGGTTTCATTCCATTCATCGACGACTTACCATCACTAAATCGCAAAACAGACGGCCCAT
TTATTATGCCAATTGTCGATAAATACAAAGATATGGGAACGGTGGTCATGGGAAAAGTTG
AAAGTGGAATGGCCAAGAAGGGACAAAATTTACTCGTAATGCCTAATAGAACACAAGTAG
CAGTTGATCAATTGTGGTCTGATGAAGAGGAAGTAACAAGTGTTGGTCCAGGTGAAAATG
TAAAAATTAAACTCAAAGGCATCGAAGAAGAAGATGTTTCACCCGGATTTGTCCTATGCG
ATGCTTCCAATCCAATCAAAACAGGAAAGATCTTCGACGCCCAAGTAGTTATATTAGAGC
ATAAATCAATTATCTGTGCGGGATATTCTGCTGTAATGCATATTCATTGTGCAGCTGAAG
AAGTCACTGTTAAAGCCCTTATTTGTTTAGTAGATAAAAAGAGCGGAGACAAATCGAAAA
CTCGTCCAAGATTTGTTAAACAAGACCAAGTCGCAATAATGCGAATTGAATGCTCTGGTA
TGATTTGCTTAGAACAATTTAAGCTCTTCCCTCAGATGGGTCGATTCACGTTGCGTGATG
AGAATAAAACAATTGCCATCGGAAAAGTGTTAAAAGTTATTGAATAA

>g5235.t6 Gene=g5235 Length=454
MEVEDGSDALPKPSTKRKPPKVEENCSKKEHVNVVFIGHVDAGKSTIGGQIMSLTGMVDK
RTLEKYEREAREKSRESWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHK
SFVPNMIGGAAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLVNKMD
DPTVNWEEVRYNECKDKILPYLKKLGFKAKDLTFMPVSGITGMGLKEPIDKNLCPWYDGP
GFIPFIDDLPSLNRKTDGPFIMPIVDKYKDMGTVVMGKVESGMAKKGQNLLVMPNRTQVA
VDQLWSDEEEVTSVGPGENVKIKLKGIEEEDVSPGFVLCDASNPIKTGKIFDAQVVILEH
KSIICAGYSAVMHIHCAAEEVTVKALICLVDKKSGDKSKTRPRFVKQDQVAIMRIECSGM
ICLEQFKLFPQMGRFTLRDENKTIAIGKVLKVIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g5235.t6 CDD cd01883 EF1_alpha 33 251 7.62796E-138
18 g5235.t6 CDD cd04089 eRF3_II 259 340 4.89373E-50
19 g5235.t6 CDD cd03704 eRF3_C_III 346 452 4.77696E-59
14 g5235.t6 Gene3D G3DSA:3.40.50.300 - 14 254 3.0E-83
16 g5235.t6 Gene3D G3DSA:2.40.30.10 Translation factors 255 342 1.8E-26
15 g5235.t6 Gene3D G3DSA:2.40.30.10 Translation factors 344 452 1.1E-38
21 g5235.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
4 g5235.t6 PANTHER PTHR23115:SF125 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A 20 453 2.6E-243
5 g5235.t6 PANTHER PTHR23115 TRANSLATION FACTOR 20 453 2.6E-243
10 g5235.t6 PRINTS PR00315 GTP-binding elongation factor signature 33 46 4.8E-16
7 g5235.t6 PRINTS PR00315 GTP-binding elongation factor signature 92 100 4.8E-16
6 g5235.t6 PRINTS PR00315 GTP-binding elongation factor signature 112 122 4.8E-16
8 g5235.t6 PRINTS PR00315 GTP-binding elongation factor signature 128 139 4.8E-16
9 g5235.t6 PRINTS PR00315 GTP-binding elongation factor signature 172 181 4.8E-16
3 g5235.t6 Pfam PF00009 Elongation factor Tu GTP binding domain 29 227 1.9E-43
2 g5235.t6 Pfam PF03144 Elongation factor Tu domain 2 272 339 4.7E-9
1 g5235.t6 Pfam PF03143 Elongation factor Tu C-terminal domain 344 452 2.5E-28
20 g5235.t6 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 85 100 -
22 g5235.t6 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 29 254 53.01
12 g5235.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 27 272 1.04E-60
13 g5235.t6 SUPERFAMILY SSF50447 Translation proteins 254 344 9.98E-24
11 g5235.t6 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 350 453 8.43E-31

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5235/g5235.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t6.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

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