Gene loci information

Transcript annotation

  • This transcript has been annotated as Histone deacetylase 3.

Parent gene

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.t2 TSS g11299.t2 15485996 15485996
chr_1 g11299 g11299.t2 isoform g11299.t2 15486111 15486889
chr_1 g11299 g11299.t2 exon g11299.t2.exon1 15486111 15486169
chr_1 g11299 g11299.t2 cds g11299.t2.CDS1 15486111 15486169
chr_1 g11299 g11299.t2 exon g11299.t2.exon2 15486229 15486327
chr_1 g11299 g11299.t2 cds g11299.t2.CDS2 15486229 15486327
chr_1 g11299 g11299.t2 exon g11299.t2.exon3 15486391 15486889
chr_1 g11299 g11299.t2 cds g11299.t2.CDS3 15486391 15486889
chr_1 g11299 g11299.t2 TTS g11299.t2 15487722 15487722

Sequences

>g11299.t2 Gene=g11299 Length=657
ATGAGTTCAAGAAAGGTTTCATATGCCTTTTGTGGTGAAGTGGGTAATTTTCATTATGGA
CCTGGACACCCAATGAAGCCTCATCGTTTATCAGTCATTCATCATTTAGTAATGAATTAT
GGTCTTCATAAAAAAATGTCAATTTTTAGACCATACAAAGCAACTGCACAAGACATGACT
CGATTTCATGATTCAGATTACATAGACTTTCTTCAAAAGACCCTCCCCGGGAATGTATCA
TTACAAGATCATAAACAATTCAATTTAGGTGATGACTGTCCTATTTTTGATGGATTATTT
GATTTTTGCTCTATGTATACTGGTGCAAGTCTTGAAGGAGCACAAAAATTAAATCACAAT
CAAAGTGATATATGTATAAACTGGAGTGGTGGTCTTCATCATGCAAAAAAATTTGAACCT
TCTGGCTTTTGCTATGTAAATGACATTGTTATTTCAATCTTGGAGCTGCTTAAATATCAT
CCTCGAGTTTTATACATTGACATTGATGTACATCATGGTGATGGTGTACAAGAAGCTTTC
TATCTCACTGATCGTGTTATGACAGTCAGTTTTCACAAATACGGTGATAAATTTTTTCCT
GGAACAGGCTCAATGTACGAAATCGGGGCTGAAAGTGGTCGCTACTATTCCGTCAAT

>g11299.t2 Gene=g11299 Length=219
MSSRKVSYAFCGEVGNFHYGPGHPMKPHRLSVIHHLVMNYGLHKKMSIFRPYKATAQDMT
RFHDSDYIDFLQKTLPGNVSLQDHKQFNLGDDCPIFDGLFDFCSMYTGASLEGAQKLNHN
QSDICINWSGGLHHAKKFEPSGFCYVNDIVISILELLKYHPRVLYIDIDVHHGDGVQEAF
YLTDRVMTVSFHKYGDKFFPGTGSMYEIGAESGRYYSVN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11299.t2 Gene3D G3DSA:3.40.800.20 - 2 219 0
2 g11299.t2 PANTHER PTHR10625 HISTONE DEACETYLASE 4 219 0
3 g11299.t2 PANTHER PTHR10625:SF201 HISTONE DEACETYLASE 3 4 219 0
10 g11299.t2 PRINTS PR01271 Histone deacetylase signature 25 42 0
9 g11299.t2 PRINTS PR01271 Histone deacetylase signature 87 104 0
8 g11299.t2 PRINTS PR01271 Histone deacetylase signature 108 128 0
5 g11299.t2 PRINTS PR01270 Histone deacetylase superfamily signature 130 153 0
7 g11299.t2 PRINTS PR01271 Histone deacetylase signature 149 165 0
4 g11299.t2 PRINTS PR01270 Histone deacetylase superfamily signature 162 177 0
6 g11299.t2 PRINTS PR01271 Histone deacetylase signature 209 219 0
1 g11299.t2 Pfam PF00850 Histone deacetylase domain 23 219 0
11 g11299.t2 SUPERFAMILY SSF52768 Arginase/deacetylase 16 219 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 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.

Raw TPM values