General information for g5235.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Eukaryotic peptide chain release factor GTP-binding subunit ERF3A.
Parent gene
- The parent gene g5235 is located on chr_2: 7949744..7951196 (- strand)
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.t1 | TTS | g5235.t1 | 7947867 | 7947867 |
| chr_2 | g5235 | g5235.t1 | isoform | g5235.t1 | 7947936 | 7950336 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon1 | 7947936 | 7947979 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS1 | 7947936 | 7947979 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon2 | 7948046 | 7948214 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS2 | 7948046 | 7948214 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon3 | 7948272 | 7948448 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS3 | 7948272 | 7948448 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon4 | 7948517 | 7948603 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS4 | 7948517 | 7948603 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon5 | 7948682 | 7948952 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS5 | 7948682 | 7948952 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon6 | 7949020 | 7949222 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS6 | 7949020 | 7949222 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon7 | 7949287 | 7949432 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS7 | 7949287 | 7949432 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon8 | 7949501 | 7949647 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS8 | 7949501 | 7949647 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon9 | 7949707 | 7949830 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS9 | 7949707 | 7949830 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon10 | 7949888 | 7949970 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS10 | 7949888 | 7949970 |
| chr_2 | g5235 | g5235.t1 | exon | g5235.t1.exon11 | 7950150 | 7950336 |
| chr_2 | g5235 | g5235.t1 | cds | g5235.t1.CDS11 | 7950150 | 7950336 |
| chr_2 | g5235 | g5235.t1 | TSS | g5235.t1 | 7950481 | 7950481 |
Sequences
>g5235.t1 Gene=g5235 Length=1638
ATGGAAAACGATCAGGAAATTCATAAAATTGGTTCACAATTTTCAACGCTAAATGTTAAT
GCAGTTGAATTTGTTCCGAGCTTCGTTGTGTCTCATCAACCACAGAAAGATATTGAAAAT
AGCATCGAAGATCCTCCGCCTACAGCACCTTCAAAGCCAATTGAAACTCCTGAAAACAAT
GGAAATGTGGTCGAAAATGAACCTCTTGATACATGGGACGAAGAAGAAACAATTCTAACT
CCAGATGGAGACAATGAAAATGAAGAGGAGGAAATGGAAGTTGAAGATGGCAGCGATGCA
CTACCAAAACCATCAACTAAAAGGAAACCTCCAAAAGTTGAAGAAAATTGTAGCAAAAAG
GAGCATGTGAATGTTGTTTTTATCGGTCATGTTGATGCCGGAAAGTCTACTATTGGCGGT
CAAATTATGTCTTTGACTGGAATGGTTGATAAGCGTACATTGGAAAAATACGAACGTGAA
GCTCGTGAAAAATCAAGAGAAAGCTGGTATCTTTCGTGGGCCTTGGATACAAATCAGGAA
GAACGTGATAAAGGTAAAACTGTTGAAGTTGGCAGAGCCTATTTTGAGACTGAGAAAAAG
CATTTCACCATACTCGATGCTCCTGGACATAAGAGCTTTGTACCAAACATGATTGGAGGA
GCAGCACAAGCCGATTTAGCAGTTCTGGTAATTTCCGCACGTAAAGGAGAATTTGAAACT
GGATTTGATCGAGGAGGTCAAACGAGAGAGCATGCAATGTTAGCAAAGACAGCTGGCGTC
AAGCACTTGGTAGTTTTAGTCAATAAAATGGACGATCCGACAGTTAACTGGGAGGAAGTT
CGCTACAACGAATGTAAAGATAAAATTTTACCATATCTCAAAAAACTCGGTTTTAAAGCA
AAGGACTTGACATTTATGCCAGTATCAGGAATCACGGGAATGGGACTTAAAGAACCAATT
GATAAAAATTTATGCCCCTGGTATGATGGACCAGGTTTCATTCCATTCATCGACGACTTA
CCATCACTAAATCGCAAAACAGACGGCCCATTTATTATGCCAATTGTCGATAAATACAAA
GATATGGGAACGGTGGTCATGGGAAAAGTTGAAAGTGGAATGGCCAAGAAGGGACAAAAT
TTACTCGTAATGCCTAATAGAACACAAGTAGCAGTTGATCAATTGTGGTCTGATGAAGAG
GAAGTAACAAGTGTTGGTCCAGGTGAAAATGTAAAAATTAAACTCAAAGGCATCGAAGAA
GAAGATGTTTCACCCGGATTTGTCCTATGCGATGCTTCCAATCCAATCAAAACAGGAAAG
ATCTTCGACGCCCAAGTAGTTATATTAGAGCATAAATCAATTATCTGTGCGGGATATTCT
GCTGTAATGCATATTCATTGTGCAGCTGAAGAAGTCACTGTTAAAGCCCTTATTTGTTTA
GTAGATAAAAAGAGCGGAGACAAATCGAAAACTCGTCCAAGATTTGTTAAACAAGACCAA
GTCGCAATAATGCGAATTGAATGCTCTGGTATGATTTGCTTAGAACAATTTAAGCTCTTC
CCTCAGATGGGTCGATTCACGTTGCGTGATGAGAATAAAACAATTGCCATCGGAAAAGTG
TTAAAAGTTATTGAATAA
>g5235.t1 Gene=g5235 Length=545
MENDQEIHKIGSQFSTLNVNAVEFVPSFVVSHQPQKDIENSIEDPPPTAPSKPIETPENN
GNVVENEPLDTWDEEETILTPDGDNENEEEEMEVEDGSDALPKPSTKRKPPKVEENCSKK
EHVNVVFIGHVDAGKSTIGGQIMSLTGMVDKRTLEKYEREAREKSRESWYLSWALDTNQE
ERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGAAQADLAVLVISARKGEFET
GFDRGGQTREHAMLAKTAGVKHLVVLVNKMDDPTVNWEEVRYNECKDKILPYLKKLGFKA
KDLTFMPVSGITGMGLKEPIDKNLCPWYDGPGFIPFIDDLPSLNRKTDGPFIMPIVDKYK
DMGTVVMGKVESGMAKKGQNLLVMPNRTQVAVDQLWSDEEEVTSVGPGENVKIKLKGIEE
EDVSPGFVLCDASNPIKTGKIFDAQVVILEHKSIICAGYSAVMHIHCAAEEVTVKALICL
VDKKSGDKSKTRPRFVKQDQVAIMRIECSGMICLEQFKLFPQMGRFTLRDENKTIAIGKV
LKVIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g5235.t1 | CDD | cd01883 | EF1_alpha | 124 | 342 | 3.91685E-137 |
| 19 | g5235.t1 | CDD | cd04089 | eRF3_II | 350 | 431 | 8.56913E-50 |
| 20 | g5235.t1 | CDD | cd03704 | eRF3_C_III | 437 | 543 | 5.35816E-59 |
| 15 | g5235.t1 | Gene3D | G3DSA:3.40.50.300 | - | 105 | 345 | 4.6E-83 |
| 17 | g5235.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 346 | 433 | 2.4E-26 |
| 16 | g5235.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 435 | 543 | 1.4E-38 |
| 23 | g5235.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 32 | 116 | - |
| 22 | g5235.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 68 | 96 | - |
| 24 | g5235.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 97 | 116 | - |
| 5 | g5235.t1 | PANTHER | PTHR23115:SF125 | EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A | 55 | 544 | 1.4E-243 |
| 6 | g5235.t1 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 55 | 544 | 1.4E-243 |
| 9 | g5235.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 124 | 137 | 1.1E-15 |
| 8 | g5235.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 183 | 191 | 1.1E-15 |
| 11 | g5235.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 203 | 213 | 1.1E-15 |
| 10 | g5235.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 219 | 230 | 1.1E-15 |
| 7 | g5235.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 263 | 272 | 1.1E-15 |
| 4 | g5235.t1 | Pfam | PF07145 | Ataxin-2 C-terminal region | 13 | 28 | 2.8E-5 |
| 3 | g5235.t1 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 120 | 318 | 3.0E-43 |
| 2 | g5235.t1 | Pfam | PF03144 | Elongation factor Tu domain 2 | 363 | 430 | 6.2E-9 |
| 1 | g5235.t1 | Pfam | PF03143 | Elongation factor Tu C-terminal domain | 435 | 543 | 3.5E-28 |
| 21 | g5235.t1 | ProSitePatterns | PS00301 | Translational (tr)-type guanine nucleotide-binding (G) domain signature. | 176 | 191 | - |
| 25 | g5235.t1 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 120 | 345 | 53.01 |
| 13 | g5235.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 118 | 363 | 1.63E-60 |
| 14 | g5235.t1 | SUPERFAMILY | SSF50447 | Translation proteins | 345 | 435 | 1.35E-23 |
| 12 | g5235.t1 | SUPERFAMILY | SSF50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 441 | 544 | 1.15E-30 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5235/g5235.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t1.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 transcript has been annotated with K03267 (peptide chain release factor subunit 3)
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.
