General information for g12470.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone deacetylase complex subunit SAP18.
Parent gene
- The parent gene g12470 is located on chr_1: 23919831..23922323 (- 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 | g12470 | g12470.t9 | TTS | g12470.t9 | 23919128 | 23919128 |
| chr_1 | g12470 | g12470.t9 | isoform | g12470.t9 | 23919141 | 23919697 |
| chr_1 | g12470 | g12470.t9 | exon | g12470.t9.exon1 | 23919141 | 23919697 |
| chr_1 | g12470 | g12470.t9 | cds | g12470.t9.CDS1 | 23919238 | 23919642 |
| chr_1 | g12470 | g12470.t9 | TSS | g12470.t9 | 23919923 | 23919923 |
Sequences
>g12470.t9 Gene=g12470 Length=557
GACATGTCCTCTTTTATTGCGTGTATTTTGTTCTTCATCAGGCAGGCACCATTCAATGAG
TGAATATTCGCATGGAAATACACCAGCTAATGAATTACAAATTTATACATGGCTTGATGC
AACATTAAAGGAATTGACAAGTTTGATACGAGATGTGAATCCTGAAACAAGAAAGAAGGG
AACATACTTTGATTTCGCTTTGGTTTTCCCTGATAATCGGCCAAATGCATATCGAATGCG
TGAAATCGGTGTAACATGCAGTGGTCAAAAAGGAGCTGATGACAACAAAACACTCGCTCA
AGCTAAATTTCAAATTGGTGATTATTTGGACATCAATATAACAAGCCGAGGAAAAGACCA
AATGAGAAACGATAGACGTGATAGAGATCGTGATCGAGACCGCGATCGAGATAACAGAGA
CATTAGAGACAGAGATCATCGAGATAGACGACCATATTAAATTAAATACTTCACTAAATT
TGCATTAAAATTTATTTCTTCTTTCTAAGAGTGACAAAATGTTCAAATTCATAATTTTTC
GATTGCATCAATAAACT
>g12470.t9 Gene=g12470 Length=134
MSEYSHGNTPANELQIYTWLDATLKELTSLIRDVNPETRKKGTYFDFALVFPDNRPNAYR
MREIGVTCSGQKGADDNKTLAQAKFQIGDYLDINITSRGKDQMRNDRRDRDRDRDRDRDN
RDIRDRDHRDRRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12470.t9 | Gene3D | G3DSA:3.10.20.550 | - | 1 | 101 | 2.1E-39 |
| 4 | g12470.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 134 | - |
| 5 | g12470.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 134 | - |
| 2 | g12470.t9 | PANTHER | PTHR13082:SF1 | HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18 | 1 | 99 | 6.4E-38 |
| 3 | g12470.t9 | PANTHER | PTHR13082 | SAP18 | 1 | 99 | 6.4E-38 |
| 1 | g12470.t9 | Pfam | PF06487 | Sin3 associated polypeptide p18 (SAP18) | 1 | 95 | 4.0E-27 |
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.
