General information for g13221.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone deacetylase 1.
Parent gene
- The parent gene g13221 is located on chr_1: 28601781..28603261 (+ 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 | g13221 | g13221.t1 | isoform | g13221.t1 | 28601781 | 28603261 |
| chr_1 | g13221 | g13221.t1 | exon | g13221.t1.exon1 | 28601781 | 28601829 |
| chr_1 | g13221 | g13221.t1 | cds | g13221.t1.CDS1 | 28601781 | 28601829 |
| chr_1 | g13221 | g13221.t1 | exon | g13221.t1.exon2 | 28601907 | 28602044 |
| chr_1 | g13221 | g13221.t1 | cds | g13221.t1.CDS2 | 28601907 | 28602044 |
| chr_1 | g13221 | g13221.t1 | exon | g13221.t1.exon3 | 28602121 | 28602843 |
| chr_1 | g13221 | g13221.t1 | cds | g13221.t1.CDS3 | 28602121 | 28602843 |
| chr_1 | g13221 | g13221.t1 | exon | g13221.t1.exon4 | 28602906 | 28603261 |
| chr_1 | g13221 | g13221.t1 | cds | g13221.t1.CDS4 | 28602906 | 28603261 |
| chr_1 | g13221 | g13221.t1 | TSS | g13221.t1 | NA | NA |
| chr_1 | g13221 | g13221.t1 | TTS | g13221.t1 | NA | NA |
Sequences
>g13221.t1 Gene=g13221 Length=1266
ATGGCTTTCGGTGATCCGTATAAACGAAAGATCTGCTATTATTACGATCAGGATATCGGA
GATTGTCATTTTGGTAATAAACATCCAATGAAACCTCATCGCTTAATCATTACTCATGAA
TTGATAGTAAAATATGGATTATTTCAAAAAATGGACGTTTTCAAACCTTATTTAGCAACT
GCAGAAGATATGCAAGAATTTCATAGTGAAGACTACGTTAGCTTTTTGCAATCACTTAAT
GCTACTAGAATATCAAATGATATGAAAAATTTAATGAGCAGATTTCAAATAGGAACAAAG
GAAAATGACTGTCCTGTTTTTGATGGAGTCTTTAAGTTTGCACAAATAAGTGCTGGTGGA
TCGCTTGCTGCAGCCGCTCATATAAACGACAATACTGCTGATATTGCAATCAATTGGGCT
GGCGGTTTACATCACGCAAAAAAATCACAAGCAAGTGGATTTTGCTACATTAATGATATT
GTTCTTTGCATATTAGAATTGTTAAAGTATCATCCAAGAGTTCTGTATGTTGATATTGAT
GTTCATCATGCTGATGGGGTTGAAGAAGCATTTTATACTTCTAATCGAGTTATGACTGTC
AGTTTTCATCGTTATGGTGAAAATTTTTTCCCTGGAACTGGCAATTTTACTGAATGTGGT
GAAGCTGAAGGCAGAGGATATTCAGTAAATGTTCCACTTAAATCTGGCATTATTGATGAA
GATTATGAAGCTGTTTTTGCTTCAGTTATGTCTAAAGTCTTACAAGTTTTTAGTCCAAGT
GTTGTTGTTATGCAATGTGGAAGCGATTCAATTGCTGGTGATCAACTTGGCGATTTCAAT
TTAACACTCAATGCTCATGGACGTTGTATAAAATTTATGAGGAAAAAAAATATTCCTTTA
ATTTTACTTGGCGGTGGGGGATACACAATTGAAAATGTCAGTAGATGTTGGTGTTTCGAT
ACTTCAATTGCATTAAACGAAACAATTCCTAATGATTTGCCAGAAAATAATTATTCAAAA
TATTTTGCACCATTAAATAAATTACATATTGAACCAGATCCTACACTTCCAAATCGAAAT
GGACAGCAGTATTTGAGTAAACTTATCGTGCAGATTGTTCAAAATTTAAAAAATATTGAA
CCAGTTCCAAGTGTTCAATTTCAAAATATGATGGAACCAATTGTCATTGAAGATTCTCCT
AAAAGAACTAAAAGTACAATGTCTTATAATAACGAAGTAATAGAAATATCAGATGATGAA
GATTAA
>g13221.t1 Gene=g13221 Length=421
MAFGDPYKRKICYYYDQDIGDCHFGNKHPMKPHRLIITHELIVKYGLFQKMDVFKPYLAT
AEDMQEFHSEDYVSFLQSLNATRISNDMKNLMSRFQIGTKENDCPVFDGVFKFAQISAGG
SLAAAAHINDNTADIAINWAGGLHHAKKSQASGFCYINDIVLCILELLKYHPRVLYVDID
VHHADGVEEAFYTSNRVMTVSFHRYGENFFPGTGNFTECGEAEGRGYSVNVPLKSGIIDE
DYEAVFASVMSKVLQVFSPSVVVMQCGSDSIAGDQLGDFNLTLNAHGRCIKFMRKKNIPL
ILLGGGGYTIENVSRCWCFDTSIALNETIPNDLPENNYSKYFAPLNKLHIEPDPTLPNRN
GQQYLSKLIVQIVQNLKNIEPVPSVQFQNMMEPIVIEDSPKRTKSTMSYNNEVIEISDDE
D
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g13221.t1 | Gene3D | G3DSA:3.40.800.20 | - | 7 | 386 | 0 |
| 2 | g13221.t1 | PANTHER | PTHR10625 | HISTONE DEACETYLASE | 8 | 406 | 0 |
| 3 | g13221.t1 | PANTHER | PTHR10625:SF132 | HISTONE DEACETYLASE RPD3 | 8 | 406 | 0 |
| 16 | g13221.t1 | PIRSF | PIRSF037913 | HDAC_I_euk | 2 | 421 | 0 |
| 8 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 30 | 47 | 0 |
| 12 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 63 | 81 | 0 |
| 13 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 98 | 115 | 0 |
| 7 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 119 | 139 | 0 |
| 5 | g13221.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 141 | 164 | 0 |
| 9 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 160 | 176 | 0 |
| 6 | g13221.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 173 | 188 | 0 |
| 11 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 220 | 233 | 0 |
| 10 | g13221.t1 | PRINTS | PR01271 | Histone deacetylase signature | 237 | 255 | 0 |
| 4 | g13221.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 259 | 269 | 0 |
| 1 | g13221.t1 | Pfam | PF00850 | Histone deacetylase domain | 28 | 318 | 0 |
| 14 | g13221.t1 | SUPERFAMILY | SSF52768 | Arginase/deacetylase | 9 | 379 | 0 |
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:0004407 | histone deacetylase activity | MF |
| GO:0016575 | histone deacetylation | BP |
KEGG
Orthology
- This transcript has been annotated with K04768 (acetoin utilization protein AcuC)
Pathway
This gene does not belong to any 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. There were no conditions that were differentially expressed