General information for g293.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Translational regulator orb2.
Parent gene
- The parent gene g293 is located on chr_3: 2550085..2553267 (- 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_3 | g293 | g293.t1 | TTS | g293.t1 | 2549523 | 2549523 |
| chr_3 | g293 | g293.t1 | isoform | g293.t1 | 2550085 | 2553267 |
| chr_3 | g293 | g293.t1 | exon | g293.t1.exon1 | 2550085 | 2550201 |
| chr_3 | g293 | g293.t1 | cds | g293.t1.CDS1 | 2550085 | 2550201 |
| chr_3 | g293 | g293.t1 | exon | g293.t1.exon2 | 2550435 | 2550641 |
| chr_3 | g293 | g293.t1 | cds | g293.t1.CDS2 | 2550435 | 2550641 |
| chr_3 | g293 | g293.t1 | exon | g293.t1.exon3 | 2550729 | 2550814 |
| chr_3 | g293 | g293.t1 | cds | g293.t1.CDS3 | 2550729 | 2550814 |
| chr_3 | g293 | g293.t1 | exon | g293.t1.exon4 | 2550881 | 2551091 |
| chr_3 | g293 | g293.t1 | cds | g293.t1.CDS4 | 2550881 | 2551091 |
| chr_3 | g293 | g293.t1 | exon | g293.t1.exon5 | 2553073 | 2553185 |
| chr_3 | g293 | g293.t1 | cds | g293.t1.CDS5 | 2553073 | 2553185 |
| chr_3 | g293 | g293.t1 | exon | g293.t1.exon6 | 2553237 | 2553267 |
| chr_3 | g293 | g293.t1 | cds | g293.t1.CDS6 | 2553237 | 2553267 |
| chr_3 | g293 | g293.t1 | TSS | g293.t1 | NA | NA |
Sequences
>g293.t1 Gene=g293 Length=765
ATGTTTCTAGTGACATTAAAGGAGCAATTTGATGAAATAACTGCTTCTTTCCGTCGCTAT
GGACCGTTAGTAGTCGATTGGCCTCATAAAGCTGAATCAAAATCATATTTTCCACCGAAA
GGATATGCATTCTTACTGTTTCAGGATGAAAGTTCTGTCCAAACTTTGATTGAAAATTGC
ATTGTGGAAGAAGACAAATTATATATTTGTGTCTCATCGCCAACCATCAAGAATAAACCC
GTTCAGATTCGTCCATGGCGCCTTTCAGATGCTGATTTTGTACTAAATGGTTCAATGCCA
TTAGATCCACGTAAAACTGTTTTTGTGGGTGGTGTTCCACGACCATTGAAAGCATTGGAA
CTAGCAATGATTATGGATCGTCTATATGGTGGAGTTTGTTATGCTGGAATTGACACTGAT
CCCGAATTGAAATATCCAAAGGGCGCTGGTCGTGTAGCATTTTCAAATCAACAAAGCTAT
ATTGCAGCAATTTCCGCTCGTTTCGTTCAATTGCAACACAATGACATTGACAAACGCGTT
GAAGTGAAACCGTACGTTCTCGACGATCAAATGTGCGATGAATGTCAAGGGCAAAGATGC
AGCGGCAAATTTGCTCCATTCTTCTGCGCCAATGTTACTTGCTTGCAGTACTACTGTGAG
CATTGCTGGGCATCTATTCATTCACGTCCTGGACGCGAATATCACAAGCCGTTGGTGAAG
GAAGGCGCTGATCGTCCTCGTGCTGTTCCATTTCGTTGGTGTTAA
>g293.t1 Gene=g293 Length=254
MFLVTLKEQFDEITASFRRYGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQTLIENC
IVEEDKLYICVSSPTIKNKPVQIRPWRLSDADFVLNGSMPLDPRKTVFVGGVPRPLKALE
LAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAISARFVQLQHNDIDKRV
EVKPYVLDDQMCDECQGQRCSGKFAPFFCANVTCLQYYCEHCWASIHSRPGREYHKPLVK
EGADRPRAVPFRWC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g293.t1 | CDD | cd12726 | RRM2_CPEB2_like | 105 | 185 | 0.0000000 |
| 10 | g293.t1 | CDD | cd19757 | Bbox1 | 191 | 229 | 0.0000763 |
| 6 | g293.t1 | Gene3D | G3DSA:3.30.70.330 | - | 5 | 85 | 0.0000000 |
| 7 | g293.t1 | Gene3D | G3DSA:3.30.70.330 | - | 89 | 182 | 0.0000000 |
| 8 | g293.t1 | Gene3D | G3DSA:3.30.40.130 | - | 183 | 248 | 0.0000000 |
| 3 | g293.t1 | PANTHER | PTHR12566 | CYTOPLASMIC POLYADENYLATION ELEMENT BINDING PROTEIN CPEB | 11 | 253 | 0.0000000 |
| 4 | g293.t1 | PANTHER | PTHR12566:SF2 | CYTOPLASMIC POLYADENYLATION ELEMENT-BINDING PROTEIN 4 | 11 | 253 | 0.0000000 |
| 2 | g293.t1 | Pfam | PF16367 | RNA recognition motif | 11 | 85 | 0.0000000 |
| 1 | g293.t1 | Pfam | PF16366 | Cytoplasmic polyadenylation element-binding protein ZZ domain | 178 | 240 | 0.0000000 |
| 9 | g293.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 105 | 183 | 9.1490000 |
| 5 | g293.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 11 | 166 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0045182 | translation regulator activity | MF |
| GO:0006417 | regulation of translation | BP |
| GO:0003730 | mRNA 3’-UTR binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K02602 (cytoplasmic polyadenylation element-binding protein)
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. There were no conditions that were differentially expressed