General information for g3724.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Paired amphipathic helix protein Sin3a.
Parent gene
- The parent gene g3724 is located on chr_3: 27659526..27666799 (+ 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_3 | g3724 | g3724.t2 | isoform | g3724.t2 | 27655388 | 27660267 |
| chr_3 | g3724 | g3724.t2 | exon | g3724.t2.exon1 | 27655388 | 27655805 |
| chr_3 | g3724 | g3724.t2 | exon | g3724.t2.exon2 | 27659403 | 27659978 |
| chr_3 | g3724 | g3724.t2 | cds | g3724.t2.CDS1 | 27659526 | 27659978 |
| chr_3 | g3724 | g3724.t2 | exon | g3724.t2.exon3 | 27660057 | 27660267 |
| chr_3 | g3724 | g3724.t2 | cds | g3724.t2.CDS2 | 27660057 | 27660266 |
| chr_3 | g3724 | g3724.t2 | TSS | g3724.t2 | NA | NA |
| chr_3 | g3724 | g3724.t2 | TTS | g3724.t2 | NA | NA |
Sequences
>g3724.t2 Gene=g3724 Length=1205
TCTTGTACAAACAAACTGGTTAAAATCTTATAATTATTATACTATCAAGTACTATCAATT
TTTTATTAGAAAAATGAAAAATGTCTTTCTACTTCTTTCTTTGCTGCTGTTCTTTTATGA
CTTGACTTGTGTACCCCACATTTTAAAAAAATAAAAATCCAGTAGAATAAGGGAAAAATA
TTTTAATAGTGTATAACATCCATTTTAAATTTAAACAAGGGGTCTTCAGCTTAGTTGCAT
ACCATGATTTTGAAAGAAAAGCATAAACTCTGTAAAGTTTGAAAATTAAATAAAAAATCA
AGATATACGCGTCCTATTTCTTTTTTAGGCGCTAGTTCAAATAATAAAAGGACTATTAAG
TGCGATTTCAAGTCAAGAAAAGTGAAGATAATATTTTTTGATAAACATAACGTGCAAGCT
CATTTCACAAATGTGAATAACTTTTAGCGTGTTTGTGTATCTAAAGTTATTAAATTTACT
TAAAGTCTAAGCATTATCATCATCATCATTGATATAGAAAGAAAGATAAAATTATACGGT
AATGAAGAAAAGAGTGGATGAAATTCAAACTTTTCACAGTACAGCACGTGTAACTGGAGG
TACGGCTCGAATATTAACGCCACCGCAGCATAATAACAGTCCAAATGCCACGCAAAGTCA
GTTTCAAATTTTAAACGTTCTACGCGATTCAGCTCCAGCAGCACAAAGCGTCCAATATAC
ATATACTCCAGCAATAACTACTACAAACATTCAAAGAAATAATGTAGCACAGCAGCAACA
GCAACAATCACAGAATCAACCAACAGTGCAGGTTGTCACTGCTTCAGCTATAGCAAATAC
TGTTCGTCCAAAACCTCCAGTTACATCTGGAAGTATAACGCCAACGCCAGTTACTGTTAC
AAGTCCAACTGGCAATTCGATTCCAGCTCAAAATGCTAGTAGCCAAAATTTTCCACGATT
AAAAGTAGAAGACGCTCTTAGTTATCTCGATCAGGTCAAATACAAATTTGGGAATCAACC
ACAAGTGTACAATGATTTTCTTGATATAATGAAAGAATTCAAATCTCAAAGCATCGATAC
ACCAGGTGTCATTCAACGTGTATCAAATCTCTTCAAAGGGCATCCTGAATTGATTGTTGG
ATTTAATACTTTTCTACCGCCTGGATATAAAATTGAAGTTCAGGCCAATGATCAAGGTTT
CGCAT
>g3724.t2 Gene=g3724 Length=221
MKKRVDEIQTFHSTARVTGGTARILTPPQHNNSPNATQSQFQILNVLRDSAPAAQSVQYT
YTPAITTTNIQRNNVAQQQQQQSQNQPTVQVVTASAIANTVRPKPPVTSGSITPTPVTVT
SPTGNSIPAQNASSQNFPRLKVEDALSYLDQVKYKFGNQPQVYNDFLDIMKEFKSQSIDT
PGVIQRVSNLFKGHPELIVGFNTFLPPGYKIEVQANDQGFA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3724.t2 | Gene3D | G3DSA:1.20.1160.11 | PAH2 domain | 144 | 206 | 0.000 |
| 2 | g3724.t2 | PANTHER | PTHR12346 | SIN3B-RELATED | 63 | 219 | 0.000 |
| 3 | g3724.t2 | PANTHER | PTHR12346:SF2 | PAIRED AMPHIPATHIC HELIX PROTEIN SIN3A | 63 | 219 | 0.000 |
| 1 | g3724.t2 | Pfam | PF02671 | Paired amphipathic helix repeat | 161 | 205 | 0.000 |
| 6 | g3724.t2 | ProSiteProfiles | PS51477 | PAH domain profile. | 138 | 208 | 19.493 |
| 4 | g3724.t2 | SUPERFAMILY | SSF47762 | PAH2 domain | 138 | 207 | 0.000 |
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:0003714 | transcription corepressor activity | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0016580 | Sin3 complex | CC |
KEGG
Orthology
- This transcript has been annotated with K11644 (paired amphipathic helix protein Sin3a)
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.
