General information for g11299.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone deacetylase 3.
Parent gene
- The parent gene g11299 is located on chr_1: 15487660..15497552 (+ 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 | g11299 | g11299.t1 | TSS | g11299.t1 | 15485996 | 15485996 |
| chr_1 | g11299 | g11299.t1 | isoform | g11299.t1 | 15486111 | 15487660 |
| chr_1 | g11299 | g11299.t1 | exon | g11299.t1.exon1 | 15486111 | 15486169 |
| chr_1 | g11299 | g11299.t1 | cds | g11299.t1.CDS1 | 15486111 | 15486169 |
| chr_1 | g11299 | g11299.t1 | exon | g11299.t1.exon2 | 15486229 | 15486327 |
| chr_1 | g11299 | g11299.t1 | cds | g11299.t1.CDS2 | 15486229 | 15486327 |
| chr_1 | g11299 | g11299.t1 | exon | g11299.t1.exon3 | 15486391 | 15487112 |
| chr_1 | g11299 | g11299.t1 | cds | g11299.t1.CDS3 | 15486391 | 15487112 |
| chr_1 | g11299 | g11299.t1 | exon | g11299.t1.exon4 | 15487184 | 15487332 |
| chr_1 | g11299 | g11299.t1 | cds | g11299.t1.CDS4 | 15487184 | 15487332 |
| chr_1 | g11299 | g11299.t1 | exon | g11299.t1.exon5 | 15487394 | 15487660 |
| chr_1 | g11299 | g11299.t1 | cds | g11299.t1.CDS5 | 15487394 | 15487660 |
| chr_1 | g11299 | g11299.t1 | TTS | g11299.t1 | 15487722 | 15487722 |
Sequences
>g11299.t1 Gene=g11299 Length=1296
ATGAGTTCAAGAAAGGTTTCATATGCCTTTTGTGGTGAAGTGGGTAATTTTCATTATGGA
CCTGGACACCCAATGAAGCCTCATCGTTTATCAGTCATTCATCATTTAGTAATGAATTAT
GGTCTTCATAAAAAAATGTCAATTTTTAGACCATACAAAGCAACTGCACAAGACATGACT
CGATTTCATGATTCAGATTACATAGACTTTCTTCAAAAGACCCTCCCCGGGAATGTATCA
TTACAAGATCATAAACAATTCAATTTAGGTGATGACTGTCCTATTTTTGATGGATTATTT
GATTTTTGCTCTATGTATACTGGTGCAAGTCTTGAAGGAGCACAAAAATTAAATCACAAT
CAAAGTGATATATGTATAAACTGGAGTGGTGGTCTTCATCATGCAAAAAAATTTGAACCT
TCTGGCTTTTGCTATGTAAATGACATTGTTATTTCAATCTTGGAGCTGCTTAAATATCAT
CCTCGAGTTTTATACATTGACATTGATGTACATCATGGTGATGGTGTACAAGAAGCTTTC
TATCTCACTGATCGTGTTATGACAGTCAGTTTTCACAAATACGGTGATAAATTTTTTCCT
GGAACAGGCTCAATGTACGAAATCGGGGCTGAAAGTGGTCGCTACTATTCCGTCAATGTA
CCTTTTAAAGAAGGAATTGATGATCAAAGTTATTTTCAAGTTTTTAAACCAGTAATATCT
CAAGTAATGGAATTTTATAGACCCACAGTCATTGTCTTACAATGTGGAGCTGATTCACTT
GCTGGTGACCGTCTCGGTTGTTTCAGTTTGTCGACACGTGGTCATGGAGACTGTGTTAAG
TTTGTTAAAGAATTAAATGTTCCGACTTTGATTTTAGGAGGTGGTGGATATACTTTAAGA
AATGTCGCAAGATGCTGGACATATGAAACTTCATTATGTGTCGATGAACAGATTTCAAAT
GAACTTCCAATGAATCTTTATATAGAATTTTTCAAACCCGAATTTGTATTGCACGTGGAT
GAGTCACAGGGTCGTCGCATTGAGAATGCTAATTCGAAACAGTATTTGGAAGCTATTACG
AAACACACTTATGATATATTAAAAATGTGTCAAAATTCACCTTCAGTTCAATTTATGTCA
ATCCCAGAAGACGCTTTACCCGATGAAAAAGATCGAATAACTGAAGAACCCGATGCTGAT
GTAAGAATGAGTCAACGTGACATTGATAGCATGGTTGAAAAAAATAATGAATTTTATGAT
GATGAAAATGACAATGATAAAAATGAAGGTGATTGA
>g11299.t1 Gene=g11299 Length=431
MSSRKVSYAFCGEVGNFHYGPGHPMKPHRLSVIHHLVMNYGLHKKMSIFRPYKATAQDMT
RFHDSDYIDFLQKTLPGNVSLQDHKQFNLGDDCPIFDGLFDFCSMYTGASLEGAQKLNHN
QSDICINWSGGLHHAKKFEPSGFCYVNDIVISILELLKYHPRVLYIDIDVHHGDGVQEAF
YLTDRVMTVSFHKYGDKFFPGTGSMYEIGAESGRYYSVNVPFKEGIDDQSYFQVFKPVIS
QVMEFYRPTVIVLQCGADSLAGDRLGCFSLSTRGHGDCVKFVKELNVPTLILGGGGYTLR
NVARCWTYETSLCVDEQISNELPMNLYIEFFKPEFVLHVDESQGRRIENANSKQYLEAIT
KHTYDILKMCQNSPSVQFMSIPEDALPDEKDRITEEPDADVRMSQRDIDSMVEKNNEFYD
DENDNDKNEGD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g11299.t1 | Gene3D | G3DSA:3.40.800.20 | - | 2 | 377 | 4.3E-158 |
| 15 | g11299.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 431 | - |
| 14 | g11299.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 384 | 421 | - |
| 2 | g11299.t1 | PANTHER | PTHR10625 | HISTONE DEACETYLASE | 4 | 429 | 1.1E-220 |
| 3 | g11299.t1 | PANTHER | PTHR10625:SF201 | HISTONE DEACETYLASE 3 | 4 | 429 | 1.1E-220 |
| 17 | g11299.t1 | PIRSF | PIRSF037913 | HDAC_I_euk | 1 | 431 | 1.5E-199 |
| 12 | g11299.t1 | PRINTS | PR01271 | Histone deacetylase signature | 25 | 42 | 6.9E-53 |
| 11 | g11299.t1 | PRINTS | PR01271 | Histone deacetylase signature | 87 | 104 | 6.9E-53 |
| 10 | g11299.t1 | PRINTS | PR01271 | Histone deacetylase signature | 108 | 128 | 6.9E-53 |
| 6 | g11299.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 130 | 153 | 6.2E-23 |
| 9 | g11299.t1 | PRINTS | PR01271 | Histone deacetylase signature | 149 | 165 | 6.9E-53 |
| 5 | g11299.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 162 | 177 | 6.2E-23 |
| 7 | g11299.t1 | PRINTS | PR01271 | Histone deacetylase signature | 209 | 222 | 6.9E-53 |
| 8 | g11299.t1 | PRINTS | PR01271 | Histone deacetylase signature | 226 | 244 | 6.9E-53 |
| 4 | g11299.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 248 | 258 | 6.2E-23 |
| 1 | g11299.t1 | Pfam | PF00850 | Histone deacetylase domain | 23 | 311 | 2.1E-87 |
| 13 | g11299.t1 | SUPERFAMILY | SSF52768 | Arginase/deacetylase | 16 | 370 | 1.92E-118 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
## Warning: Removed 1 row(s) containing missing values (geom_path).
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 K11404 (histone deacetylase 3)
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.
