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.t4 isoform g5235.t4 7947007 7950336
chr_2 g5235 g5235.t4 exon g5235.t4.exon1 7947007 7947979
chr_2 g5235 g5235.t4 TTS g5235.t4 7947026 7947026
chr_2 g5235 g5235.t4 cds g5235.t4.CDS1 7947936 7947979
chr_2 g5235 g5235.t4 exon g5235.t4.exon2 7948046 7948214
chr_2 g5235 g5235.t4 cds g5235.t4.CDS2 7948046 7948214
chr_2 g5235 g5235.t4 exon g5235.t4.exon3 7948272 7948448
chr_2 g5235 g5235.t4 cds g5235.t4.CDS3 7948272 7948448
chr_2 g5235 g5235.t4 exon g5235.t4.exon4 7948517 7948603
chr_2 g5235 g5235.t4 cds g5235.t4.CDS4 7948517 7948603
chr_2 g5235 g5235.t4 exon g5235.t4.exon5 7948682 7948952
chr_2 g5235 g5235.t4 cds g5235.t4.CDS5 7948682 7948952
chr_2 g5235 g5235.t4 exon g5235.t4.exon6 7949020 7949222
chr_2 g5235 g5235.t4 cds g5235.t4.CDS6 7949020 7949222
chr_2 g5235 g5235.t4 exon g5235.t4.exon7 7949287 7949432
chr_2 g5235 g5235.t4 cds g5235.t4.CDS7 7949287 7949432
chr_2 g5235 g5235.t4 exon g5235.t4.exon8 7949501 7949647
chr_2 g5235 g5235.t4 cds g5235.t4.CDS8 7949501 7949647
chr_2 g5235 g5235.t4 exon g5235.t4.exon9 7949707 7949830
chr_2 g5235 g5235.t4 cds g5235.t4.CDS9 7949707 7949830
chr_2 g5235 g5235.t4 exon g5235.t4.exon10 7949888 7949970
chr_2 g5235 g5235.t4 cds g5235.t4.CDS10 7949888 7949970
chr_2 g5235 g5235.t4 exon g5235.t4.exon11 7950146 7950336
chr_2 g5235 g5235.t4 cds g5235.t4.CDS11 7950146 7950158
chr_2 g5235 g5235.t4 TSS g5235.t4 7950481 7950481

Sequences

>g5235.t4 Gene=g5235 Length=2571
ATGGAAAACGATCAGGAAATTCATAAAATTGGTTCACAATTTTCAACGCTAAATGTTAAT
GCAGTTGAATTTGTTCCGAGCTTCGTTGTGTCTCATCAACCACAGAAAGATATTGAAAAT
AGCATCGAAGATCCTCCGCCTACAGCACCTTCAAAGCCAATTGAAACTCCTGAAAACAAT
GGAAATGGTAATGGTCGAAAATGAACCTCTTGATACATGGGACGAAGAAGAAACAATTCT
AACTCCAGATGGAGACAATGAAAATGAAGAGGAGGAAATGGAAGTTGAAGATGGCAGCGA
TGCACTACCAAAACCATCAACTAAAAGGAAACCTCCAAAAGTTGAAGAAAATTGTAGCAA
AAAGGAGCATGTGAATGTTGTTTTTATCGGTCATGTTGATGCCGGAAAGTCTACTATTGG
CGGTCAAATTATGTCTTTGACTGGAATGGTTGATAAGCGTACATTGGAAAAATACGAACG
TGAAGCTCGTGAAAAATCAAGAGAAAGCTGGTATCTTTCGTGGGCCTTGGATACAAATCA
GGAAGAACGTGATAAAGGTAAAACTGTTGAAGTTGGCAGAGCCTATTTTGAGACTGAGAA
AAAGCATTTCACCATACTCGATGCTCCTGGACATAAGAGCTTTGTACCAAACATGATTGG
AGGAGCAGCACAAGCCGATTTAGCAGTTCTGGTAATTTCCGCACGTAAAGGAGAATTTGA
AACTGGATTTGATCGAGGAGGTCAAACGAGAGAGCATGCAATGTTAGCAAAGACAGCTGG
CGTCAAGCACTTGGTAGTTTTAGTCAATAAAATGGACGATCCGACAGTTAACTGGGAGGA
AGTTCGCTACAACGAATGTAAAGATAAAATTTTACCATATCTCAAAAAACTCGGTTTTAA
AGCAAAGGACTTGACATTTATGCCAGTATCAGGAATCACGGGAATGGGACTTAAAGAACC
AATTGATAAAAATTTATGCCCCTGGTATGATGGACCAGGTTTCATTCCATTCATCGACGA
CTTACCATCACTAAATCGCAAAACAGACGGCCCATTTATTATGCCAATTGTCGATAAATA
CAAAGATATGGGAACGGTGGTCATGGGAAAAGTTGAAAGTGGAATGGCCAAGAAGGGACA
AAATTTACTCGTAATGCCTAATAGAACACAAGTAGCAGTTGATCAATTGTGGTCTGATGA
AGAGGAAGTAACAAGTGTTGGTCCAGGTGAAAATGTAAAAATTAAACTCAAAGGCATCGA
AGAAGAAGATGTTTCACCCGGATTTGTCCTATGCGATGCTTCCAATCCAATCAAAACAGG
AAAGATCTTCGACGCCCAAGTAGTTATATTAGAGCATAAATCAATTATCTGTGCGGGATA
TTCTGCTGTAATGCATATTCATTGTGCAGCTGAAGAAGTCACTGTTAAAGCCCTTATTTG
TTTAGTAGATAAAAAGAGCGGAGACAAATCGAAAACTCGTCCAAGATTTGTTAAACAAGA
CCAAGTCGCAATAATGCGAATTGAATGCTCTGGTATGATTTGCTTAGAACAATTTAAGCT
CTTCCCTCAGATGGGTCGATTCACGTTGCGTGATGAGAATAAAACAATTGCCATCGGAAA
AGTGTTAAAAGTTATTGAATAAACATTTGCGCTCTTTTACAAGTTACTATAATAAAACAT
TTTTATACCAATTTGCAACTTGATAACACGAAACAAGAAAAAAAATGAATTAAGTAAAAA
CTTTTAAGCTTACACATCCGATTATACAAAACAAACAAGCTGAGAGAAAAAAAATCTAAA
TGGGAAAGCGTGTACATATTTAATAAAATGCACATAACAATATGGGCTGAACATCATTAT
TACGAGTATCTTAACATTTGAACGCAATGTTAATTGATAAAAAGATGAAAACAAAAAAAC
ACTTAATGAATTGTTATATTGCTTTGCTTATTGAATCCTTAAAAATTTCATATATTGTTT
AAAGAATGCTATTCACACACACACACTCTTTTTATTAGTTTAAAAAAGTAAAGAAAAAAT
TCATTATCTCTTATGTCTAAAGAAGAAAGAGAAAGAATAGGAAATGATGGTAGGCAAGTG
AAGATTTTTGCGTGTATAATGCTTCAAATTAAGAAAATAATTTTTATATATCAACATATA
TATATTTAATTTTCAATTTCCTATAAGAAAGTCTAAGCAAGAATTAGAAAAGAGGATAAG
GAAGATGAATTTTCAAATTGTTCGTTAGCAATAATTATCATTTTTATGTTGCAAATATAA
GAAAGTACCTCTAATATATTTGCTTCACACAAACACTCTATATCCTTCCTCCTCTCGCCC
CTCTTATATATATCCATATTCATTATAATCATTAAGTTTTTCTTTTTTTTTTTTTGTTAG
CAATCCTATTAAAAAAATGATGAAAAAAATTTCTCTTGAAAAAATGAGGTCATGTCACTT
TTTTTAAAAAAAGAATTAAGAATTTAAGAAAACTGATAAATTTCTTGAAGAAGCATGACG
ATAATAATAATAAAGCAAAATGATTTAATATCAAAAAGATTAATTTTTTAT

>g5235.t4 Gene=g5235 Length=487
MEMVMVENEPLDTWDEEETILTPDGDNENEEEEMEVEDGSDALPKPSTKRKPPKVEENCS
KKEHVNVVFIGHVDAGKSTIGGQIMSLTGMVDKRTLEKYEREAREKSRESWYLSWALDTN
QEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGAAQADLAVLVISARKGEF
ETGFDRGGQTREHAMLAKTAGVKHLVVLVNKMDDPTVNWEEVRYNECKDKILPYLKKLGF
KAKDLTFMPVSGITGMGLKEPIDKNLCPWYDGPGFIPFIDDLPSLNRKTDGPFIMPIVDK
YKDMGTVVMGKVESGMAKKGQNLLVMPNRTQVAVDQLWSDEEEVTSVGPGENVKIKLKGI
EEEDVSPGFVLCDASNPIKTGKIFDAQVVILEHKSIICAGYSAVMHIHCAAEEVTVKALI
CLVDKKSGDKSKTRPRFVKQDQVAIMRIECSGMICLEQFKLFPQMGRFTLRDENKTIAIG
KVLKVIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g5235.t4 CDD cd01883 EF1_alpha 66 284 3.19098E-137
18 g5235.t4 CDD cd04089 eRF3_II 292 373 1.06643E-49
19 g5235.t4 CDD cd03704 eRF3_C_III 379 485 4.61852E-59
14 g5235.t4 Gene3D G3DSA:3.40.50.300 - 47 287 3.5E-83
15 g5235.t4 Gene3D G3DSA:2.40.30.10 Translation factors 288 375 2.0E-26
16 g5235.t4 Gene3D G3DSA:2.40.30.10 Translation factors 377 485 1.2E-38
23 g5235.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 58 -
22 g5235.t4 MobiDBLite mobidb-lite consensus disorder prediction 9 38 -
21 g5235.t4 MobiDBLite mobidb-lite consensus disorder prediction 39 58 -
4 g5235.t4 PANTHER PTHR23115:SF125 EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A 13 486 7.8E-244
5 g5235.t4 PANTHER PTHR23115 TRANSLATION FACTOR 13 486 7.8E-244
6 g5235.t4 PRINTS PR00315 GTP-binding elongation factor signature 66 79 6.5E-16
10 g5235.t4 PRINTS PR00315 GTP-binding elongation factor signature 125 133 6.5E-16
7 g5235.t4 PRINTS PR00315 GTP-binding elongation factor signature 145 155 6.5E-16
8 g5235.t4 PRINTS PR00315 GTP-binding elongation factor signature 161 172 6.5E-16
9 g5235.t4 PRINTS PR00315 GTP-binding elongation factor signature 205 214 6.5E-16
3 g5235.t4 Pfam PF00009 Elongation factor Tu GTP binding domain 62 260 2.3E-43
2 g5235.t4 Pfam PF03144 Elongation factor Tu domain 2 305 372 5.2E-9
1 g5235.t4 Pfam PF03143 Elongation factor Tu C-terminal domain 377 485 2.9E-28
20 g5235.t4 ProSitePatterns PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature. 118 133 -
24 g5235.t4 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 62 287 53.01
12 g5235.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 60 305 1.21E-60
13 g5235.t4 SUPERFAMILY SSF50447 Translation proteins 287 377 1.12E-23
11 g5235.t4 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 383 486 9.46E-31

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5235/g5235.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t4.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