General information for g12398.t1
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.t1 | TSS | g12398.t1 | 23336730 | 23336730 |
| chr_1 | g12398 | g12398.t1 | isoform | g12398.t1 | 23337727 | 23339315 |
| chr_1 | g12398 | g12398.t1 | exon | g12398.t1.exon1 | 23337727 | 23337865 |
| chr_1 | g12398 | g12398.t1 | cds | g12398.t1.CDS1 | 23337727 | 23337865 |
| chr_1 | g12398 | g12398.t1 | exon | g12398.t1.exon2 | 23337951 | 23338001 |
| chr_1 | g12398 | g12398.t1 | cds | g12398.t1.CDS2 | 23337951 | 23338001 |
| chr_1 | g12398 | g12398.t1 | exon | g12398.t1.exon3 | 23338396 | 23338584 |
| chr_1 | g12398 | g12398.t1 | cds | g12398.t1.CDS3 | 23338396 | 23338584 |
| chr_1 | g12398 | g12398.t1 | exon | g12398.t1.exon4 | 23338654 | 23338808 |
| chr_1 | g12398 | g12398.t1 | cds | g12398.t1.CDS4 | 23338654 | 23338808 |
| chr_1 | g12398 | g12398.t1 | exon | g12398.t1.exon5 | 23338865 | 23339017 |
| chr_1 | g12398 | g12398.t1 | cds | g12398.t1.CDS5 | 23338865 | 23339017 |
| chr_1 | g12398 | g12398.t1 | exon | g12398.t1.exon6 | 23339082 | 23339315 |
| chr_1 | g12398 | g12398.t1 | cds | g12398.t1.CDS6 | 23339082 | 23339315 |
| chr_1 | g12398 | g12398.t1 | TTS | g12398.t1 | NA | NA |
Sequences
>g12398.t1 Gene=g12398 Length=921
ATGACAATGAGCTCCGAAGGCAAAGAAGCCATTAAATCGAATGGAACGAAATCTGAGAGA
ACAACATCACCGTTATCTACATCTTCAGCAAAACATCAGACGAGTGATTTGACTCCTGAT
ACATCTGACGATGACTTTCAATCGAGAAAAAATATGAATAAACCGAATAAGCCGAAGAGT
GAATTTGAAGAAAAAATTAGAGTTGGAAAGGATTATCAAGTTGTTGTACCAGAAATGAAT
CCACATCTAAAGCTTGAAAATTACAACGATAAGGCACTGCTGGTTTGGTCGCCTGTTAAA
GATATTAGTGAAGAGCGATTAGATGAGTATATTGTGCTAGCTCAACAAAAATATGGATAT
AATGCAGAACAAGCTTTAGGAATGCTTTTTTGGCATAAGCATGATCTTCAAAAAGCTGTA
ATGGACTTGCAAAATTTCACTCCATTTCCCGATGAATGGACAAAAGAAGATAAAATTTTA
TTTGAACAGGCCTATCAATTTCATGGAAAATGCTTTCATCGTATACGACAAATGTTGCCT
GATAAATCAATTGCCAGTTTAGTAAAGTTCTATTATTCATGGAAAAAAGCTAGAACTCGA
TCGAGTACAGAACGTCAAGAGAAAAGAAAACATGAAGAAAATGGAAGTGAAAATGGTAGT
CCAAATGATTCTGACATTGAGGAAAAAAATGACTCTGAAATAGGCGATATTGAAGAGATA
ATTGGAATACCTACAAAGGACAGTTCAGATCAAAAATCGAACAAAACAAGTATAATGACG
ACCAGTAATAAATCATTAAAACGCAAACATGAAGATGAGAGCTATAACATAAATGATGAT
GTTGCAGCTGAAAAGAAGCTAGCTACCGAGAAATTATTGAATGATAAGCCAGAACTCACA
ATTACATTAGCTAAAGACTAA
>g12398.t1 Gene=g12398 Length=306
MTMSSEGKEAIKSNGTKSERTTSPLSTSSAKHQTSDLTPDTSDDDFQSRKNMNKPNKPKS
EFEEKIRVGKDYQVVVPEMNPHLKLENYNDKALLVWSPVKDISEERLDEYIVLAQQKYGY
NAEQALGMLFWHKHDLQKAVMDLQNFTPFPDEWTKEDKILFEQAYQFHGKCFHRIRQMLP
DKSIASLVKFYYSWKKARTRSSTERQEKRKHEENGSENGSPNDSDIEEKNDSEIGDIEEI
IGIPTKDSSDQKSNKTSIMTTSNKSLKRKHEDESYNINDDVAAEKKLATEKLLNDKPELT
ITLAKD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g12398.t1 | Gene3D | G3DSA:1.10.10.60 | - | 151 | 198 | 4.5E-21 |
| 10 | g12398.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 64 | - |
| 11 | g12398.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 36 | - |
| 12 | g12398.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 37 | 64 | - |
| 9 | g12398.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 273 | - |
| 13 | g12398.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 228 | - |
| 8 | g12398.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 246 | 263 | - |
| 3 | g12398.t1 | PANTHER | PTHR16089:SF28 | GEO13032P1-RELATED | 12 | 287 | 7.1E-71 |
| 4 | g12398.t1 | PANTHER | PTHR16089 | REST COREPRESSOR COREST PROTEIN-RELATED | 12 | 287 | 7.1E-71 |
| 1 | g12398.t1 | Pfam | PF01448 | ELM2 domain | 66 | 115 | 2.7E-9 |
| 2 | g12398.t1 | Pfam | PF00249 | Myb-like DNA-binding domain | 152 | 195 | 1.1E-5 |
| 15 | g12398.t1 | ProSiteProfiles | PS51156 | ELM2 domain profile. | 64 | 147 | 23.842 |
| 16 | g12398.t1 | ProSiteProfiles | PS51293 | SANT domain profile. | 148 | 199 | 13.215 |
| 6 | g12398.t1 | SMART | SM01189 | ELM2_2 | 66 | 118 | 8.2E-13 |
| 7 | g12398.t1 | SMART | SM00717 | sant | 149 | 197 | 6.1E-8 |
| 5 | g12398.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 136 | 196 | 8.2E-13 |
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 transcript has been annotated with K11829 (REST corepressor 1)
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.
