General information for g12470.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g12470.t1 | 23919128 | 23919128 |
| chr_1 | g12470 | g12470.t1 | isoform | g12470.t1 | 23919238 | 23919831 |
| chr_1 | g12470 | g12470.t1 | exon | g12470.t1.exon1 | 23919238 | 23919696 |
| chr_1 | g12470 | g12470.t1 | cds | g12470.t1.CDS1 | 23919238 | 23919696 |
| chr_1 | g12470 | g12470.t1 | exon | g12470.t1.exon2 | 23919760 | 23919831 |
| chr_1 | g12470 | g12470.t1 | cds | g12470.t1.CDS2 | 23919760 | 23919831 |
| chr_1 | g12470 | g12470.t1 | TSS | g12470.t1 | 23919923 | 23919923 |
Sequences
>g12470.t1 Gene=g12470 Length=531
ATGGCTAACGTTGAGTCAATGATTGTCGATGAAAAACCAAAAGATGTACGTCCTGCAATT
GATCGAGAAAAGACATGTCCTCTTTTATTGCGTGTATTTTGTTCTTCATCAGGCAGGCAC
CATTCAATGAGTGAATATTCGCATGGAAATACACCAGCTAATGAATTACAAATTTATACA
TGGCTTGATGCAACATTAAAGGAATTGACAAGTTTGATACGAGATGTGAATCCTGAAACA
AGAAAGAAGGGAACATACTTTGATTTCGCTTTGGTTTTCCCTGATAATCGGCCAAATGCA
TATCGAATGCGTGAAATCGGTGTAACATGCAGTGGTCAAAAAGGAGCTGATGACAACAAA
ACACTCGCTCAAGCTAAATTTCAAATTGGTGATTATTTGGACATCAATATAACAAGCCGA
GGAAAAGACCAAATGAGAAACGATAGACGTGATAGAGATCGTGATCGAGACCGCGATCGA
GATAACAGAGACATTAGAGACAGAGATCATCGAGATAGACGACCATATTAA
>g12470.t1 Gene=g12470 Length=176
MANVESMIVDEKPKDVRPAIDREKTCPLLLRVFCSSSGRHHSMSEYSHGNTPANELQIYT
WLDATLKELTSLIRDVNPETRKKGTYFDFALVFPDNRPNAYRMREIGVTCSGQKGADDNK
TLAQAKFQIGDYLDINITSRGKDQMRNDRRDRDRDRDRDRDNRDIRDRDHRDRRPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12470.t1 | Gene3D | G3DSA:3.10.20.550 | - | 3 | 142 | 4.5E-56 |
| 5 | g12470.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 140 | 176 | - |
| 4 | g12470.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 176 | - |
| 2 | g12470.t1 | PANTHER | PTHR13082:SF1 | HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18 | 4 | 140 | 6.6E-54 |
| 3 | g12470.t1 | PANTHER | PTHR13082 | SAP18 | 4 | 140 | 6.6E-54 |
| 7 | g12470.t1 | PIRSF | PIRSF037637 | SAP18 | 1 | 154 | 6.9E-68 |
| 1 | g12470.t1 | Pfam | PF06487 | Sin3 associated polypeptide p18 (SAP18) | 20 | 137 | 1.8E-39 |
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 K14324 (histone deacetylase complex subunit SAP18)
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.
