General information for g5235.t9
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.t9 | isoform | g5235.t9 | 7949501 | 7950336 |
| chr_2 | g5235 | g5235.t9 | exon | g5235.t9.exon1 | 7949501 | 7949663 |
| chr_2 | g5235 | g5235.t9 | cds | g5235.t9.CDS1 | 7949502 | 7949663 |
| chr_2 | g5235 | g5235.t9 | exon | g5235.t9.exon2 | 7949729 | 7949830 |
| chr_2 | g5235 | g5235.t9 | cds | g5235.t9.CDS2 | 7949729 | 7949830 |
| chr_2 | g5235 | g5235.t9 | exon | g5235.t9.exon3 | 7949888 | 7949970 |
| chr_2 | g5235 | g5235.t9 | cds | g5235.t9.CDS3 | 7949888 | 7949970 |
| chr_2 | g5235 | g5235.t9 | exon | g5235.t9.exon4 | 7950150 | 7950336 |
| chr_2 | g5235 | g5235.t9 | cds | g5235.t9.CDS4 | 7950150 | 7950336 |
| chr_2 | g5235 | g5235.t9 | TSS | g5235.t9 | 7950481 | 7950481 |
| chr_2 | g5235 | g5235.t9 | TTS | g5235.t9 | NA | NA |
Sequences
>g5235.t9 Gene=g5235 Length=535
ATGGAAAACGATCAGGAAATTCATAAAATTGGTTCACAATTTTCAACGCTAAATGTTAAT
GCAGTTGAATTTGTTCCGAGCTTCGTTGTGTCTCATCAACCACAGAAAGATATTGAAAAT
AGCATCGAAGATCCTCCGCCTACAGCACCTTCAAAGCCAATTGAAACTCCTGAAAACAAT
GGAAATGTGGTCGAAAATGAACCTCTTGATACATGGGACGAAGAAGAAACAATTCTAACT
CCAGATGGAGACAATGAAAATGAAGAGGAGGAAATGGAAGTTGAAGATGGCAGCGATGCA
CTACCAAAACCATCAACTAAAAGGAAACCTCCAAAAGTTGAAGAAAATTGTAGCAAAAAG
GAGCATGTGAATAAATTTGCATTTTTAGATGCCGGAAAGTCTACTATTGGCGGTCAAATT
ATGTCTTTGACTGGAATGGTTGATAAGCGTACATTGGAAAAATACGAACGTGAAGCTCGT
GAAAAATCAAGAGAAAGCTGGTATCTTTCGTGGGCCTTGGATACAAATCAGGAAG
>g5235.t9 Gene=g5235 Length=178
MENDQEIHKIGSQFSTLNVNAVEFVPSFVVSHQPQKDIENSIEDPPPTAPSKPIETPENN
GNVVENEPLDTWDEEETILTPDGDNENEEEEMEVEDGSDALPKPSTKRKPPKVEENCSKK
EHVNKFAFLDAGKSTIGGQIMSLTGMVDKRTLEKYEREAREKSRESWYLSWALDTNQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5235.t9 | Gene3D | G3DSA:3.40.50.300 | - | 112 | 178 | 4.5E-11 |
| 7 | g5235.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 32 | 120 | - |
| 6 | g5235.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 68 | 96 | - |
| 5 | g5235.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 97 | 120 | - |
| 2 | g5235.t9 | PANTHER | PTHR23115:SF125 | EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR GTP-BINDING SUBUNIT ERF3A | 51 | 178 | 2.3E-30 |
| 3 | g5235.t9 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 51 | 178 | 2.3E-30 |
| 1 | g5235.t9 | Pfam | PF07145 | Ataxin-2 C-terminal region | 13 | 28 | 6.9E-6 |
| 4 | g5235.t9 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 128 | 177 | 1.95E-5 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5235/g5235.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5235.t9.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
