General information for g9497.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transformer-2 protein homolog beta.
Parent gene
- The parent gene g9497 is located on chr_1: 3795435..3796041 (+ 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_1 | g9497 | g9497.t1 | TSS | g9497.t1 | 3795365 | 3795365 |
| chr_1 | g9497 | g9497.t1 | isoform | g9497.t1 | 3795435 | 3796041 |
| chr_1 | g9497 | g9497.t1 | exon | g9497.t1.exon1 | 3795435 | 3795741 |
| chr_1 | g9497 | g9497.t1 | cds | g9497.t1.CDS1 | 3795435 | 3795741 |
| chr_1 | g9497 | g9497.t1 | exon | g9497.t1.exon2 | 3795797 | 3796041 |
| chr_1 | g9497 | g9497.t1 | cds | g9497.t1.CDS2 | 3795797 | 3796041 |
| chr_1 | g9497 | g9497.t1 | TTS | g9497.t1 | 3796287 | 3796287 |
Sequences
>g9497.t1 Gene=g9497 Length=552
ATGCCTAATTTAAAGTCCGAAGTAGCTGAATCAGAAGATTACAGCTCAAGAAAACATGAA
TCATCAAGATCAAGCTCGAATCAACTGCATTACGAAAGAAATTCAAGAAAATATGAAAAT
CGTAGCACTTCATCAACTTCACGTTCAAGGTCGAGATCCAGTAGCAGTGATCGAGATCGA
GATTATAAACGTCGTCGTCGTTATTATGGAACTCGTGAGCATCCCTACGAATCTTCTGTT
CTTGGTGTATTTGGACTAAGGAGTTTTATCAATTGTTCTGACTTGTATAAGCTGTTTTCG
TATTATGGGAAAATTGAAGATATTCATATTATTTATGATAAAAAAACACAATATTCGCGC
GGATTTGCTTTCGTTTACTTCCGAAAAAGAGAGGATGCATCTTATGCTCGTCGAAAATGC
AATGGGATGCAATTTTTTGGCCGAAGAATTCGCGTTGATTATTCAATTACTCGAAGAGCT
CATACACCAACACCTGGCATTTATATGGGATTTCGTTCAAGAAGCCGCAATTCTTCCTCT
AATCGTCGTTAA
>g9497.t1 Gene=g9497 Length=183
MPNLKSEVAESEDYSSRKHESSRSSSNQLHYERNSRKYENRSTSSTSRSRSRSSSSDRDR
DYKRRRRYYGTREHPYESSVLGVFGLRSFINCSDLYKLFSYYGKIEDIHIIYDKKTQYSR
GFAFVYFRKREDASYARRKCNGMQFFGRRIRVDYSITRRAHTPTPGIYMGFRSRSRNSSS
NRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9497.t1 | Gene3D | G3DSA:3.30.70.330 | - | 5 | 163 | 2.8E-29 |
| 7 | g9497.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 68 | - |
| 8 | g9497.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 10 | 39 | - |
| 6 | g9497.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 68 | - |
| 2 | g9497.t1 | PANTHER | PTHR48034:SF1 | TRANSFORMER-2 PROTEIN HOMOLOG BETA | 14 | 171 | 3.5E-39 |
| 3 | g9497.t1 | PANTHER | PTHR48034 | TRANSFORMER-2 SEX-DETERMINING PROTEIN-RELATED | 14 | 171 | 3.5E-39 |
| 1 | g9497.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 83 | 151 | 2.7E-17 |
| 10 | g9497.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 79 | 157 | 16.023 |
| 5 | g9497.t1 | SMART | SM00360 | rrm1_1 | 80 | 153 | 1.2E-20 |
| 4 | g9497.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 75 | 181 | 4.7E-28 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12897 (transformer-2 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