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.t7 TTS g5235.t7 7947867 7947867
chr_2 g5235 g5235.t7 isoform g5235.t7 7947936 7950336
chr_2 g5235 g5235.t7 exon g5235.t7.exon1 7947936 7947963
chr_2 g5235 g5235.t7 cds g5235.t7.CDS1 7947950 7947963
chr_2 g5235 g5235.t7 exon g5235.t7.exon2 7948046 7948214
chr_2 g5235 g5235.t7 cds g5235.t7.CDS2 7948046 7948214
chr_2 g5235 g5235.t7 exon g5235.t7.exon3 7948272 7948448
chr_2 g5235 g5235.t7 cds g5235.t7.CDS3 7948272 7948448
chr_2 g5235 g5235.t7 exon g5235.t7.exon4 7948517 7948603
chr_2 g5235 g5235.t7 cds g5235.t7.CDS4 7948517 7948603
chr_2 g5235 g5235.t7 exon g5235.t7.exon5 7948682 7948952
chr_2 g5235 g5235.t7 cds g5235.t7.CDS5 7948682 7948952
chr_2 g5235 g5235.t7 exon g5235.t7.exon6 7949020 7949222
chr_2 g5235 g5235.t7 cds g5235.t7.CDS6 7949020 7949222
chr_2 g5235 g5235.t7 exon g5235.t7.exon7 7949287 7949432
chr_2 g5235 g5235.t7 cds g5235.t7.CDS7 7949287 7949432
chr_2 g5235 g5235.t7 exon g5235.t7.exon8 7949501 7949647
chr_2 g5235 g5235.t7 cds g5235.t7.CDS8 7949501 7949647
chr_2 g5235 g5235.t7 exon g5235.t7.exon9 7949707 7949830
chr_2 g5235 g5235.t7 cds g5235.t7.CDS9 7949707 7949827
chr_2 g5235 g5235.t7 exon g5235.t7.exon10 7949888 7950336
chr_2 g5235 g5235.t7 TSS g5235.t7 7950481 7950481

Sequences

>g5235.t7 Gene=g5235 Length=1801
ATGGAAAACGATCAGGAAATTCATAAAATTGGTTCACAATTTTCAACGCTAAATGTTAAT
GCAGTTGAATTTGTTCCGAGCTTCGTTGTGTCTCATCAACCACAGAAAGATATTGAAAAT
AGCATCGAAGATCCTCCGCCTACAGCACCTTCAAAGCCAATTGAAACTCCTGAAAACAAT
GGAAATGGTAAGTAAATAAGTGTAAAATGCAAAATAATTTCAATCACGCAATACAGAAAA
GTTGCCACATCGAATGTCTCACAATGAAAAAGAGATCTGTGACCTATTTAAGAGCGCAAG
AAGTCGTATTTTTACAATCTTTGTTGAATAGTCCGATATAAATAACCGGATATATCTGCT
TTATAGTGGTCGAAAATGAACCTCTTGATACATGGGACGAAGAAGAAACAATTCTAACTC
CAGATGGAGACAATGAAAATGAAGAGGAGGAAATGGAAGTTGAAGATGGCAGCGATGCAC
TACCAAAACCATCAACTAAAAGGAAACCTCCAAAAGTTGAAGAAAATTGTAGCAAAAAGG
AGCATGTGAATGTTGTTTTTATCGGTCATGTTGATGCCGGAAAGTCTACTATTGGCGGTC
AAATTATGTCTTTGACTGGAATGGTTGATAAGCGTACATTGGAAAAATACGAACGTGAAG
CTCGTGAAAAATCAAGAGAAAGCTGGTATCTTTCGTGGGCCTTGGATACAAATCAGGAAG
AACGTGATAAAGGTAAAACTGTTGAAGTTGGCAGAGCCTATTTTGAGACTGAGAAAAAGC
ATTTCACCATACTCGATGCTCCTGGACATAAGAGCTTTGTACCAAACATGATTGGAGGAG
CAGCACAAGCCGATTTAGCAGTTCTGGTAATTTCCGCACGTAAAGGAGAATTTGAAACTG
GATTTGATCGAGGAGGTCAAACGAGAGAGCATGCAATGTTAGCAAAGACAGCTGGCGTCA
AGCACTTGGTAGTTTTAGTCAATAAAATGGACGATCCGACAGTTAACTGGGAGGAAGTTC
GCTACAACGAATGTAAAGATAAAATTTTACCATATCTCAAAAAACTCGGTTTTAAAGCAA
AGGACTTGACATTTATGCCAGTATCAGGAATCACGGGAATGGGACTTAAAGAACCAATTG
ATAAAAATTTATGCCCCTGGTATGATGGACCAGGTTTCATTCCATTCATCGACGACTTAC
CATCACTAAATCGCAAAACAGACGGCCCATTTATTATGCCAATTGTCGATAAATACAAAG
ATATGGGAACGGTGGTCATGGGAAAAGTTGAAAGTGGAATGGCCAAGAAGGGACAAAATT
TACTCGTAATGCCTAATAGAACACAAGTAGCAGTTGATCAATTGTGGTCTGATGAAGAGG
AAGTAACAAGTGTTGGTCCAGGTGAAAATGTAAAAATTAAACTCAAAGGCATCGAAGAAG
AAGATGTTTCACCCGGATTTGTCCTATGCGATGCTTCCAATCCAATCAAAACAGGAAAGA
TCTTCGACGCCCAAGTAGTTATATTAGAGCATAAATCAATTATCTGTGCGGGATATTCTG
CTGTAATGCATATTCATTGTGCAGCTGAAGAAGTCACTGTTAAAGCCCTTATTTGTTTAG
TAGATAAAAAGAGCGGAGACAAATCGAAAACTCGTCCAAGATTTGTTAAACAAGACCAAG
TCGCAATAATGCGAATTGAATGCTCTGGTATGATTTGCTTAGAACAATTTAAGCTCTTCC
CTCAGATGGGTCGATTCACGTTGCGTGATGAGACGGAAAAGTGTTAAAAGTTATTGAATA
A

>g5235.t7 Gene=g5235 Length=444
MEVEDGSDALPKPSTKRKPPKVEENCSKKEHVNVVFIGHVDAGKSTIGGQIMSLTGMVDK
RTLEKYEREAREKSRESWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHK
SFVPNMIGGAAQADLAVLVISARKGEFETGFDRGGQTREHAMLAKTAGVKHLVVLVNKMD
DPTVNWEEVRYNECKDKILPYLKKLGFKAKDLTFMPVSGITGMGLKEPIDKNLCPWYDGP
GFIPFIDDLPSLNRKTDGPFIMPIVDKYKDMGTVVMGKVESGMAKKGQNLLVMPNRTQVA
VDQLWSDEEEVTSVGPGENVKIKLKGIEEEDVSPGFVLCDASNPIKTGKIFDAQVVILEH
KSIICAGYSAVMHIHCAAEEVTVKALICLVDKKSGDKSKTRPRFVKQDQVAIMRIECSGM
ICLEQFKLFPQMGRFTLRDETEKC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g5235.t7 CDD cd01883 EF1_alpha 33 251 2.24531E-138
18 g5235.t7 CDD cd04089 eRF3_II 259 340 2.32558E-50
19 g5235.t7 CDD cd03704 eRF3_C_III 346 441 2.07647E-50
14 g5235.t7 Gene3D G3DSA:3.40.50.300 - 14 254 2.8E-83
16 g5235.t7 Gene3D G3DSA:2.40.30.10 Translation factors 255 342 1.7E-26
15 g5235.t7 Gene3D G3DSA:2.40.30.10 Translation factors 344 444 2.2E-32
21 g5235.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
4 g5235.t7 PANTHER PTHR23115:SF125 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A 20 442 3.0E-237
5 g5235.t7 PANTHER PTHR23115 TRANSLATION FACTOR 20 442 3.0E-237
10 g5235.t7 PRINTS PR00315 GTP-binding elongation factor signature 33 46 4.4E-16
7 g5235.t7 PRINTS PR00315 GTP-binding elongation factor signature 92 100 4.4E-16
6 g5235.t7 PRINTS PR00315 GTP-binding elongation factor signature 112 122 4.4E-16
8 g5235.t7 PRINTS PR00315 GTP-binding elongation factor signature 128 139 4.4E-16
9 g5235.t7 PRINTS PR00315 GTP-binding elongation factor signature 172 181 4.4E-16
3 g5235.t7 Pfam PF00009 Elongation factor Tu GTP binding domain 29 227 1.8E-43
2 g5235.t7 Pfam PF03144 Elongation factor Tu domain 2 272 339 4.6E-9
1 g5235.t7 Pfam PF03143 Elongation factor Tu C-terminal domain 344 440 3.4E-22
20 g5235.t7 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 85 100 -
22 g5235.t7 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 29 254 53.01
12 g5235.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 27 272 9.5E-61
13 g5235.t7 SUPERFAMILY SSF50447 Translation proteins 254 344 9.77E-24
11 g5235.t7 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 350 441 1.36E-24

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5235/g5235.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t7.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