General information for g4819.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Histone deacetylase 6.
Parent gene
- The parent gene g4819 is located on chr_2: 5089516..5089945 (- 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_2 | g4819 | g4819.t2 | TTS | g4819.t2 | 5084997 | 5084997 |
| chr_2 | g4819 | g4819.t2 | isoform | g4819.t2 | 5085452 | 5085833 |
| chr_2 | g4819 | g4819.t2 | exon | g4819.t2.exon1 | 5085452 | 5085833 |
| chr_2 | g4819 | g4819.t2 | cds | g4819.t2.CDS1 | 5085452 | 5085796 |
| chr_2 | g4819 | g4819.t2 | TSS | g4819.t2 | NA | NA |
Sequences
>g4819.t2 Gene=g4819 Length=382
TGTATGTAGAAAAAATTACAAAAAAATAAATTTTTAAATGGAATTCTCTTCCTCAGCAAT
TGACCATAAGAGTGAATGTAATGAATGTCAAACAGCTATTGAAAACTGGGCTTGTTTAAT
TTGTTACAAAACATTTTGCTCACGATACATTAATGAACACAGTTATCTGCATTTTGTATC
AACTGAACATCCATTGACCCTCAGTTTTAGTGATCTTTCTGTATGGTGTTACAAATGCGA
AGCATACATCGATAATCCGCAATTGTATAAATTTAAAAATTTAGTTCATCGCAGCAAATT
CGGAGAAGATTTAGTTTGGAGCTATGGTGACTCAACTATGTTAATTGACATGCGACAAAA
TGATGATGACGACAGTGAATGA
>g4819.t2 Gene=g4819 Length=114
MEFSSSAIDHKSECNECQTAIENWACLICYKTFCSRYINEHSYLHFVSTEHPLTLSFSDL
SVWCYKCEAYIDNPQLYKFKNLVHRSKFGEDLVWSYGDSTMLIDMRQNDDDDSE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4819.t2 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 1 | 108 | 0.000 |
| 2 | g4819.t2 | PANTHER | PTHR47665 | HISTONE DEACETYLASE-LIKE PROTEIN | 14 | 90 | 0.000 |
| 1 | g4819.t2 | Pfam | PF02148 | Zn-finger in ubiquitin-hydrolases and other protein | 14 | 75 | 0.000 |
| 6 | g4819.t2 | ProSiteProfiles | PS50271 | Zinc finger UBP-type profile. | 12 | 73 | 17.343 |
| 4 | g4819.t2 | SMART | SM00290 | Zf_UBP_1 | 13 | 62 | 0.000 |
| 3 | g4819.t2 | SUPERFAMILY | SSF57850 | RING/U-box | 8 | 86 | 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:0008270 | zinc ion binding | MF |
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.
