General information for g12398.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as REST corepressor.
Parent gene
- The parent gene g12398 is located on chr_1: 23337727..23339315 (+ 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 | g12398 | g12398.t3 | TSS | g12398.t3 | 23336730 | 23336730 |
| chr_1 | g12398 | g12398.t3 | isoform | g12398.t3 | 23337727 | 23338808 |
| chr_1 | g12398 | g12398.t3 | exon | g12398.t3.exon1 | 23337727 | 23337865 |
| chr_1 | g12398 | g12398.t3 | cds | g12398.t3.CDS1 | 23337727 | 23337865 |
| chr_1 | g12398 | g12398.t3 | exon | g12398.t3.exon2 | 23337951 | 23338001 |
| chr_1 | g12398 | g12398.t3 | cds | g12398.t3.CDS2 | 23337951 | 23338001 |
| chr_1 | g12398 | g12398.t3 | exon | g12398.t3.exon3 | 23338396 | 23338584 |
| chr_1 | g12398 | g12398.t3 | cds | g12398.t3.CDS3 | 23338396 | 23338584 |
| chr_1 | g12398 | g12398.t3 | exon | g12398.t3.exon4 | 23338654 | 23338808 |
| chr_1 | g12398 | g12398.t3 | cds | g12398.t3.CDS4 | 23338654 | 23338808 |
| chr_1 | g12398 | g12398.t3 | TTS | g12398.t3 | NA | NA |
Sequences
>g12398.t3 Gene=g12398 Length=534
ATGACAATGAGCTCCGAAGGCAAAGAAGCCATTAAATCGAATGGAACGAAATCTGAGAGA
ACAACATCACCGTTATCTACATCTTCAGCAAAACATCAGACGAGTGATTTGACTCCTGAT
ACATCTGACGATGACTTTCAATCGAGAAAAAATATGAATAAACCGAATAAGCCGAAGAGT
GAATTTGAAGAAAAAATTAGAGTTGGAAAGGATTATCAAGTTGTTGTACCAGAAATGAAT
CCACATCTAAAGCTTGAAAATTACAACGATAAGGCACTGCTGGTTTGGTCGCCTGTTAAA
GATATTAGTGAAGAGCGATTAGATGAGTATATTGTGCTAGCTCAACAAAAATATGGATAT
AATGCAGAACAAGCTTTAGGAATGCTTTTTTGGCATAAGCATGATCTTCAAAAAGCTGTA
ATGGACTTGCAAAATTTCACTCCATTTCCCGATGAATGGACAAAAGAAGATAAAATTTTA
TTTGAACAGGCCTATCAATTTCATGGAAAATGCTTTCATCGTATACGACAAATG
>g12398.t3 Gene=g12398 Length=178
MTMSSEGKEAIKSNGTKSERTTSPLSTSSAKHQTSDLTPDTSDDDFQSRKNMNKPNKPKS
EFEEKIRVGKDYQVVVPEMNPHLKLENYNDKALLVWSPVKDISEERLDEYIVLAQQKYGY
NAEQALGMLFWHKHDLQKAVMDLQNFTPFPDEWTKEDKILFEQAYQFHGKCFHRIRQM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12398.t3 | Gene3D | G3DSA:1.10.1740.200 | - | 62 | 120 | 4.3E-5 |
| 10 | g12398.t3 | Gene3D | G3DSA:1.10.10.60 | - | 151 | 178 | 5.2E-8 |
| 6 | g12398.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 64 | - |
| 7 | g12398.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 36 | - |
| 8 | g12398.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 37 | 64 | - |
| 2 | g12398.t3 | PANTHER | PTHR16089:SF28 | GEO13032P1-RELATED | 12 | 178 | 1.3E-52 |
| 3 | g12398.t3 | PANTHER | PTHR16089 | REST COREPRESSOR COREST PROTEIN-RELATED | 12 | 178 | 1.3E-52 |
| 1 | g12398.t3 | Pfam | PF01448 | ELM2 domain | 66 | 115 | 1.1E-9 |
| 11 | g12398.t3 | ProSiteProfiles | PS51156 | ELM2 domain profile. | 64 | 147 | 23.842 |
| 12 | g12398.t3 | ProSiteProfiles | PS51293 | SANT domain profile. | 148 | 178 | 9.132 |
| 5 | g12398.t3 | SMART | SM01189 | ELM2_2 | 66 | 118 | 8.2E-13 |
| 4 | g12398.t3 | SUPERFAMILY | SSF46689 | Homeodomain-like | 136 | 177 | 8.69E-6 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
