General information for g3585.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Histone deacetylase HDAC1.
Parent gene
- The parent gene g3585 is located on chr_3: 26556736..26557658 (- 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 | g3585 | g3585.t1 | TTS | g3585.t1 | 26555600 | 26555600 |
| chr_3 | g3585 | g3585.t1 | isoform | g3585.t1 | 26555781 | 26557658 |
| chr_3 | g3585 | g3585.t1 | exon | g3585.t1.exon1 | 26555781 | 26556657 |
| chr_3 | g3585 | g3585.t1 | cds | g3585.t1.CDS1 | 26555781 | 26556657 |
| chr_3 | g3585 | g3585.t1 | exon | g3585.t1.exon2 | 26556723 | 26556818 |
| chr_3 | g3585 | g3585.t1 | cds | g3585.t1.CDS2 | 26556723 | 26556818 |
| chr_3 | g3585 | g3585.t1 | exon | g3585.t1.exon3 | 26556885 | 26557374 |
| chr_3 | g3585 | g3585.t1 | cds | g3585.t1.CDS3 | 26556885 | 26557374 |
| chr_3 | g3585 | g3585.t1 | exon | g3585.t1.exon4 | 26557610 | 26557658 |
| chr_3 | g3585 | g3585.t1 | cds | g3585.t1.CDS4 | 26557610 | 26557658 |
| chr_3 | g3585 | g3585.t1 | TSS | g3585.t1 | 26557724 | 26557724 |
Sequences
>g3585.t1 Gene=g3585 Length=1512
ATGGCTACACAAGCTCATTCAAAGAAGCGTGTTTGTTATTACTATGATAGTGATATCGGA
AACTACTATTATGGCCAGGGACATCCAATGAAGCCGCATCGTATTCGTATGACGCATAAT
CTACTTCTAAATTACGGACTTTATCGTAAAATGGAAATTTATCGACCACATAAAGCAACT
CAAGATGAAATGACAAAATTCCATTCTGATGAATATATAAGATTTTTACGATCAATTCGA
CCAGATAACATGAATGAGTATTCGAAGCAAATGCAAAGATTCAATGTGGGTGAAGATTGT
CCTGTTTTTGATGGTCTCTATGAGTTTTGTCAATTATCTGCTGGTGGTTCAGTAGCGTCA
GCTGTAAAACTGAATAAACAAGCATCGGAAATTTGTATCAATTGGGGTGGAGGACTTCAT
CATGCAAAAAAATCAGAAGCTTCTGGTTTTTGCTATGTTAATGATATTGTTCTTGGTATT
TTAGAACTTCTAAAATATCATCAACGTGTTCTCTACATTGATATTGATGTACATCATGGT
GATGGAGTTGAAGAAGCTTTTTTTACTACTGATCGTGTAATGACTGCAAGTTTCCACAAA
TATGGAGAATATTTCCCGGGAACTGGCGATTTAAGGGATATTGGAGCAGGACGCGGCAAA
TATTATGCAGTAAATGTTCCTCTTCGTGATGGAATGGATGATGAATCATATGAATCGATT
TTTGTTCCAATCATGACGAAAGTAATGGAAACTTTTCAACCATCAGCAGTCGTTTTACAG
TGTGGTGCAGACTCATTAACTGGTGATCGCTTGGGATGCTTCAATCTTACTGTAAAAGGT
CATGGAAAATGCGTAGAATTTGTCAAGAAATATAATCTTCCCTTCATGGTTTTGGGTGGA
GGAGGCTACACAATTCGAAATGTCTCAAGATGCTGGACATATGAAACATCTGTTGCTCTT
GGCGTTGAAATTGCAAATGAACTGCCCTATAATGATTACTTTGAATATTTTGGTCCAGAC
TTCAAATTACACATTTCACCTTCTAATATGACAAATCTCAATACAACAGACTATTTGGAA
AAAGTCAAATCTAGACTATTCGAAAATCTGAGAATGTTACCACATGCGCCTGGCGTTCAA
GTGCAGGCAATCCCTGAAGATGGAATAAAAATGGATATTGATGATCAAGATGGTGCACCT
GATACCGAAGAGGCAGAAAAAGACGAACGCGTACCCCAATCGATTAAAGATAAGAGAATT
ATGGGTGATAATGAATATTCAGATTCAGAAGATGAAGGACCCACAGGTGATGGCAGAAGA
AATCGTGAGTCTCATAAAAACCCACGCAAAAAGCAAAAAACAACAGAAGCTAAAGTAGAT
AGTGAGGCAGTCAAGGAAGAAAAGACTGAAGAGAAAGAAAAATCCACTGAAGTTGCAACA
GAAAAGAAGGAAGAAAATGGGACAGCAACTAAGAAGGAAGAATCAAATGAGCCAGTCACT
TGCGAAACTTAA
>g3585.t1 Gene=g3585 Length=503
MATQAHSKKRVCYYYDSDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAT
QDEMTKFHSDEYIRFLRSIRPDNMNEYSKQMQRFNVGEDCPVFDGLYEFCQLSAGGSVAS
AVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELLKYHQRVLYIDIDVHHG
DGVEEAFFTTDRVMTASFHKYGEYFPGTGDLRDIGAGRGKYYAVNVPLRDGMDDESYESI
FVPIMTKVMETFQPSAVVLQCGADSLTGDRLGCFNLTVKGHGKCVEFVKKYNLPFMVLGG
GGYTIRNVSRCWTYETSVALGVEIANELPYNDYFEYFGPDFKLHISPSNMTNLNTTDYLE
KVKSRLFENLRMLPHAPGVQVQAIPEDGIKMDIDDQDGAPDTEEAEKDERVPQSIKDKRI
MGDNEYSDSEDEGPTGDGRRNRESHKNPRKKQKTTEAKVDSEAVKEEKTEEKEKSTEVAT
EKKEENGTATKKEESNEPVTCET
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g3585.t1 | Coils | Coil | Coil | 465 | 485 | - |
| 15 | g3585.t1 | Gene3D | G3DSA:3.40.800.20 | - | 1 | 376 | 1.8E-171 |
| 18 | g3585.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 397 | 503 | - |
| 19 | g3585.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 403 | 503 | - |
| 2 | g3585.t1 | PANTHER | PTHR10625:SF203 | HISTONE DEACETYLASE 2 | 3 | 468 | 6.3E-268 |
| 3 | g3585.t1 | PANTHER | PTHR10625 | HISTONE DEACETYLASE | 3 | 468 | 6.3E-268 |
| 17 | g3585.t1 | PIRSF | PIRSF037913 | HDAC_I_euk | 1 | 500 | 1.2E-223 |
| 11 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 30 | 47 | 9.4E-70 |
| 13 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 63 | 81 | 9.4E-70 |
| 9 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 94 | 111 | 9.4E-70 |
| 10 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 115 | 135 | 9.4E-70 |
| 6 | g3585.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 137 | 160 | 3.4E-24 |
| 8 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 156 | 172 | 9.4E-70 |
| 4 | g3585.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 169 | 184 | 3.4E-24 |
| 12 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 215 | 228 | 9.4E-70 |
| 7 | g3585.t1 | PRINTS | PR01271 | Histone deacetylase signature | 232 | 250 | 9.4E-70 |
| 5 | g3585.t1 | PRINTS | PR01270 | Histone deacetylase superfamily signature | 254 | 264 | 3.4E-24 |
| 1 | g3585.t1 | Pfam | PF00850 | Histone deacetylase domain | 28 | 317 | 5.6E-87 |
| 14 | g3585.t1 | SUPERFAMILY | SSF52768 | Arginase/deacetylase | 9 | 373 | 5.28E-129 |
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 K06067 (histone deacetylase 1/2)
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.
