General information for g5235.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t10 | isoform | g5235.t10 | 7949501 | 7950409 |
| chr_2 | g5235 | g5235.t10 | exon | g5235.t10.exon1 | 7949501 | 7949647 |
| chr_2 | g5235 | g5235.t10 | cds | g5235.t10.CDS1 | 7949502 | 7949647 |
| chr_2 | g5235 | g5235.t10 | exon | g5235.t10.exon2 | 7949707 | 7949830 |
| chr_2 | g5235 | g5235.t10 | cds | g5235.t10.CDS2 | 7949707 | 7949830 |
| chr_2 | g5235 | g5235.t10 | exon | g5235.t10.exon3 | 7949888 | 7949970 |
| chr_2 | g5235 | g5235.t10 | cds | g5235.t10.CDS3 | 7949888 | 7949970 |
| chr_2 | g5235 | g5235.t10 | exon | g5235.t10.exon4 | 7950150 | 7950409 |
| chr_2 | g5235 | g5235.t10 | cds | g5235.t10.CDS4 | 7950150 | 7950336 |
| chr_2 | g5235 | g5235.t10 | TSS | g5235.t10 | 7950481 | 7950481 |
| chr_2 | g5235 | g5235.t10 | TTS | g5235.t10 | NA | NA |
Sequences
>g5235.t10 Gene=g5235 Length=614
AGTGAAAGTCTTTCCTTTAGTTTTTCCAATCGCTCAATAGATAAAGCAAGTGTATCGTCT
ATCGTTAGTGAAAATGGAAAACGATCAGGAAATTCATAAAATTGGTTCACAATTTTCAAC
GCTAAATGTTAATGCAGTTGAATTTGTTCCGAGCTTCGTTGTGTCTCATCAACCACAGAA
AGATATTGAAAATAGCATCGAAGATCCTCCGCCTACAGCACCTTCAAAGCCAATTGAAAC
TCCTGAAAACAATGGAAATGTGGTCGAAAATGAACCTCTTGATACATGGGACGAAGAAGA
AACAATTCTAACTCCAGATGGAGACAATGAAAATGAAGAGGAGGAAATGGAAGTTGAAGA
TGGCAGCGATGCACTACCAAAACCATCAACTAAAAGGAAACCTCCAAAAGTTGAAGAAAA
TTGTAGCAAAAAGGAGCATGTGAATGTTGTTTTTATCGGTCATGTTGATGCCGGAAAGTC
TACTATTGGCGGTCAAATTATGTCTTTGACTGGAATGGTTGATAAGCGTACATTGGAAAA
ATACGAACGTGAAGCTCGTGAAAAATCAAGAGAAAGCTGGTATCTTTCGTGGGCCTTGGA
TACAAATCAGGAAG
>g5235.t10 Gene=g5235 Length=180
MENDQEIHKIGSQFSTLNVNAVEFVPSFVVSHQPQKDIENSIEDPPPTAPSKPIETPENN
GNVVENEPLDTWDEEETILTPDGDNENEEEEMEVEDGSDALPKPSTKRKPPKVEENCSKK
EHVNVVFIGHVDAGKSTIGGQIMSLTGMVDKRTLEKYEREAREKSRESWYLSWALDTNQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5235.t10 | Gene3D | G3DSA:3.40.50.300 | - | 111 | 180 | 4.9E-19 |
| 8 | g5235.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 32 | 119 | - |
| 7 | g5235.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 68 | 96 | - |
| 6 | g5235.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 97 | 119 | - |
| 3 | g5235.t10 | PANTHER | PTHR23115:SF125 | EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A | 51 | 180 | 1.2E-38 |
| 4 | g5235.t10 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 51 | 180 | 1.2E-38 |
| 2 | g5235.t10 | Pfam | PF07145 | Ataxin-2 C-terminal region | 13 | 28 | 7.0E-6 |
| 1 | g5235.t10 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 120 | 159 | 2.5E-8 |
| 5 | g5235.t10 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 114 | 179 | 6.56E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5235/g5235.t10; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t10.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.
