Gene loci information

Transcript annotation

  • This transcript has been annotated as Histone deacetylase 6.

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_2 g4819 g4819.t1 TTS g4819.t1 5084997 5084997
chr_2 g4819 g4819.t1 isoform g4819.t1 5085452 5089516
chr_2 g4819 g4819.t1 exon g4819.t1.exon1 5085452 5085777
chr_2 g4819 g4819.t1 cds g4819.t1.CDS1 5085452 5085777
chr_2 g4819 g4819.t1 exon g4819.t1.exon2 5085833 5085920
chr_2 g4819 g4819.t1 cds g4819.t1.CDS2 5085833 5085920
chr_2 g4819 g4819.t1 exon g4819.t1.exon3 5085977 5087222
chr_2 g4819 g4819.t1 cds g4819.t1.CDS3 5085977 5087222
chr_2 g4819 g4819.t1 exon g4819.t1.exon4 5087284 5087616
chr_2 g4819 g4819.t1 cds g4819.t1.CDS4 5087284 5087616
chr_2 g4819 g4819.t1 exon g4819.t1.exon5 5087679 5087875
chr_2 g4819 g4819.t1 cds g4819.t1.CDS5 5087679 5087875
chr_2 g4819 g4819.t1 exon g4819.t1.exon6 5088072 5088131
chr_2 g4819 g4819.t1 cds g4819.t1.CDS6 5088072 5088131
chr_2 g4819 g4819.t1 exon g4819.t1.exon7 5088225 5088467
chr_2 g4819 g4819.t1 cds g4819.t1.CDS7 5088225 5088467
chr_2 g4819 g4819.t1 exon g4819.t1.exon8 5088534 5089070
chr_2 g4819 g4819.t1 cds g4819.t1.CDS8 5088534 5089070
chr_2 g4819 g4819.t1 exon g4819.t1.exon9 5089140 5089322
chr_2 g4819 g4819.t1 cds g4819.t1.CDS9 5089140 5089322
chr_2 g4819 g4819.t1 exon g4819.t1.exon10 5089514 5089516
chr_2 g4819 g4819.t1 cds g4819.t1.CDS10 5089514 5089516
chr_2 g4819 g4819.t1 TSS g4819.t1 5089949 5089949

Sequences

>g4819.t1 Gene=g4819 Length=3216
ATGCAAAAAACTGTGATTACACGCAAAGATGCTCAAGAAGCAAAAATCAAAACACGAGCA
ATGGCAAAGGCTAAAGAAAATAAAATTTCATTAATCGAAGCGAAACGAAATAGCCGCCAA
AAAATGCTTCTAGCAAAATCGAGTGAACCTTCACCCACGACATCGGTCAAGGATATTTAT
GGAAATGCATTGAGTGCTATCAACATGGTACGAGGTGAAACTGGCATAATTTATCATGAT
TCAATGACTAAACATTATTGCACATGGGATCCGAATTATCCAGAAAATCCTCAAAGATTT
ACGTCTGTGATTAATCGATGTAAAGAATTAAATCTGTTTGATCGATGCAAAACACTTCAA
ACGCGATTAGCGACTAAAAACGAAATTTTGACCATTCATACTGAGAAACATTATGAACTT
TTAGAATCAACCAATGACTGTACTGACGAGGACCAATTAGAAGAATTAAGTTCACACTAT
GACGCGATTTACATTAATTCATCGACTTTTAACCTTTCATTGCTCGCATGTGGTTCAACA
ATTGAACTCGTTGACAATATTCTTGATGGTCGGATTCAAAATGGAATGGCAATTATTCGT
CCACCTGGTCATCATGCTATGAAAGCTGAATATAATGGTTACTGTTTTTTTAATAATGTT
GCAGTGGCAGCTAAACATGCACTCGATAATAAAGATATAAAGAAGATTTTAATAGTTGAT
TGGGACGTTCATCATGGACAGGGAACGCAACGCGCATTTTATGACGACCCTCGAGTTGTA
TATTTTTCAATTCATCGTTTCGAACATGGTAAATTTTGGCCAAATTTGCGAGAAAGCGAT
TATGACTATATTGGTAATGGAGAAGGAGCTGGAAAAAATATCAATGTTCCATTGAACAAA
ACTGGTATGACGAATGGAGATTATTTGGCAATATTTCAACAACTTTTGATGCCTATAGCG
ATTGAGTTTCAACCAGAATTAATTTTCATATCAGCTGGATATGATTGTGCTGTTGGATGC
CCAGAGGGTGAAATGGAAGTTACACCAGCTTGTTATTCTCATTTGCTATCACCACTTCTT
ACACTGGCAAATGGACGCGTTGCGGTTGTACTTGAGGGTGGCTACTGTTTAGAATCTCTA
GCTGAAGGCGCTGCATTAACTCTTAAAACGTTATTAGGTGATCCATGTCCAAATATGGAA
CCAATTGAAACACCATGTGAAAGCATTCAAGAAACGATACTTAATTGCATTTATTTACAT
CGCCATTATTGGAAAAATTTGTGCCTGCAACAAGTCTATAATATTGAAGAGCTCAATAAT
GTTAATCCACAATCAAATTTACATAAAATTTCTCATGATACTTTCATTGGTGGTGATCCA
ATACCTGAAAGGTTTTTAACTCGAAATTGCTATCCCGTACAGAATGAAGCTTTTAAAATT
CGAGTTGCTGATAGATTACTCAAACTCAAATTATCAACAAATTTAACATATCCAACAAAT
AGAGTTTGTTATGTTTACGATGAAATTATGTTACAACATAAAAACAATTTTGAAAATGGT
CATCCAGAGCAGCCGGATAGAATTCGCAAAATCAAATCACGATTCAGTGAATACAATATT
GTTAATCGAATGAAACATTTGCCATCAAGAGAAATTACAGAAGAAGAATTGCTTCTGGTT
CACTCACTATCACATATTAAATATATGGCAGAAATTGAAAAACTCGATGATTTAGCAGCA
GTTGGTGAAAGATTTAACTCTGTGTATTTCCATAAAAAGACATTTGAATGTGCAAAATAT
GCAGCTGGTAGTGTGCTACAAGTAGTTGATGAAGTACTTAATAATCTTTCACTAAGTGGT
TTGTGTGTTGTTCGTCCACCTGGTCATCATTCTGAATCTGATGAACCTCATGGCTTCTGT
ATTTTTAACAATGTTGCATTAGCTGCTCAATATGCAATTAAAAATCATGGATTAAAGAGA
GTTCTTATTGTTGATTGGGATGTACATCATGGTCAAGGAACTCAGCATATTTTTGAGACT
GATCCAAAAGTTTTGTATATGTCAATTCATCGTTATGATCATGGAAGTTTCTTTCCTCGT
AGTAAAGATGCTAATTACACAGAAGTTGGATATGAAAATGGTAAAGGTTTTAATGTGAAT
ATTCCGTGGAATAAAAAGGGAATGGGTGACATAGAATATTCACTTGCTTTTCAAAATATT
ATCATGCCAATAGCTTACGAATTTGATCCAGAATTGGTTCTTGTATCTGCTGGTTTTGAT
GCTGCAATAGGTGATCAACTTGGAGGTTGTAGAGTAAGCCCAGAAGCTTATGGCCATTTT
ACCAGTTGGCTACATACTTTAGCTAATGGAAAAATAATTTTAGTACTCGAAGGTGGATAT
AATGTCAACTCAATATCACATTCTATGACTATTTGTGCAAAATCATTACTCGCTGATCCT
TTGCCATCAATTAACATTTCATCACGATGGAATGGTATAAATACAACTGCATTAGAAAGT
TTACAAAATGTCATTAAGACACACGAAGTTTATTGGAAATGTTTGAAATTTAACAAAAAA
TTGCCGGACTATGATGTGAATGAAAATAAAATGGATAATGTGACTATGAAATTTGAGTCA
ATTAAATTAAACATACCAAATGATAGTGATGATAAAGGCAATAGTTCTCAACAATCGTCA
AATATTTCAGCTTGTAGCTCTGATTCTTGTGATGCAGGACCATCAAATGTTAATACAGAG
AAAAAACAAACTCTTACAGATTTTCTTAATGAAAATATGGAGGCACTGAACAATGAAGAA
ATGTATGCCATTGTACCTCTTAAGAATTGTCCACATTTATCACTTTTACATCCAGAAAGT
GCTCCTAATTCAATTGACCATAAGAGTGAATGTAATGAATGTCAAACAGCTATTGAAAAC
TGGGCTTGTTTAATTTGTTACAAAACATTTTGCTCACGATACATTAATGAACACAGTTAT
CTGCATTTTGTATCAACTGAACATCCATTGACCCTCAGTTTTAGTGATCTTTCTGTATGG
TGTTACAAATGCGAAGCATACATCGATAATCCGCAATTGTATAAATTTAAAAATTTAGTT
CATCGCAGCAAATTCGGAGAAGATTTAGTTTGGAGCTATGGTGACTCAACTATGTTAATT
GACATGCGACAAAATGATGATGACGACAGTGAATGA

>g4819.t1 Gene=g4819 Length=1071
MQKTVITRKDAQEAKIKTRAMAKAKENKISLIEAKRNSRQKMLLAKSSEPSPTTSVKDIY
GNALSAINMVRGETGIIYHDSMTKHYCTWDPNYPENPQRFTSVINRCKELNLFDRCKTLQ
TRLATKNEILTIHTEKHYELLESTNDCTDEDQLEELSSHYDAIYINSSTFNLSLLACGST
IELVDNILDGRIQNGMAIIRPPGHHAMKAEYNGYCFFNNVAVAAKHALDNKDIKKILIVD
WDVHHGQGTQRAFYDDPRVVYFSIHRFEHGKFWPNLRESDYDYIGNGEGAGKNINVPLNK
TGMTNGDYLAIFQQLLMPIAIEFQPELIFISAGYDCAVGCPEGEMEVTPACYSHLLSPLL
TLANGRVAVVLEGGYCLESLAEGAALTLKTLLGDPCPNMEPIETPCESIQETILNCIYLH
RHYWKNLCLQQVYNIEELNNVNPQSNLHKISHDTFIGGDPIPERFLTRNCYPVQNEAFKI
RVADRLLKLKLSTNLTYPTNRVCYVYDEIMLQHKNNFENGHPEQPDRIRKIKSRFSEYNI
VNRMKHLPSREITEEELLLVHSLSHIKYMAEIEKLDDLAAVGERFNSVYFHKKTFECAKY
AAGSVLQVVDEVLNNLSLSGLCVVRPPGHHSESDEPHGFCIFNNVALAAQYAIKNHGLKR
VLIVDWDVHHGQGTQHIFETDPKVLYMSIHRYDHGSFFPRSKDANYTEVGYENGKGFNVN
IPWNKKGMGDIEYSLAFQNIIMPIAYEFDPELVLVSAGFDAAIGDQLGGCRVSPEAYGHF
TSWLHTLANGKIILVLEGGYNVNSISHSMTICAKSLLADPLPSINISSRWNGINTTALES
LQNVIKTHEVYWKCLKFNKKLPDYDVNENKMDNVTMKFESIKLNIPNDSDDKGNSSQQSS
NISACSSDSCDAGPSNVNTEKKQTLTDFLNENMEALNNEEMYAIVPLKNCPHLSLLHPES
APNSIDHKSECNECQTAIENWACLICYKTFCSRYINEHSYLHFVSTEHPLTLSFSDLSVW
CYKCEAYIDNPQLYKFKNLVHRSKFGEDLVWSYGDSTMLIDMRQNDDDDSE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g4819.t1 CDD cd10002 HDAC10_HDAC6-dom1 87 424 0.000
12 g4819.t1 Gene3D G3DSA:3.40.800.20 - 71 430 0.000
13 g4819.t1 Gene3D G3DSA:3.40.800.20 - 494 878 0.000
14 g4819.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 944 1052 0.000
4 g4819.t1 PANTHER PTHR45634 HISTONE DEACETYLASE 84 901 0.000
5 g4819.t1 PANTHER PTHR45634:SF25 HISTONE DEACETYLASE 6, ISOFORM G 84 901 0.000
7 g4819.t1 PRINTS PR01270 Histone deacetylase superfamily signature 626 649 0.000
8 g4819.t1 PRINTS PR01270 Histone deacetylase superfamily signature 660 675 0.000
6 g4819.t1 PRINTS PR01270 Histone deacetylase superfamily signature 750 760 0.000
2 g4819.t1 Pfam PF00850 Histone deacetylase domain 94 390 0.000
3 g4819.t1 Pfam PF00850 Histone deacetylase domain 521 814 0.000
1 g4819.t1 Pfam PF02148 Zn-finger in ubiquitin-hydrolases and other protein 971 1032 0.000
17 g4819.t1 ProSiteProfiles PS50271 Zinc finger UBP-type profile. 969 1030 17.343
16 g4819.t1 SMART SM00290 Zf_UBP_1 970 1019 0.000
11 g4819.t1 SUPERFAMILY SSF52768 Arginase/deacetylase 72 426 0.000
10 g4819.t1 SUPERFAMILY SSF52768 Arginase/deacetylase 499 856 0.000
9 g4819.t1 SUPERFAMILY SSF57850 RING/U-box 948 1042 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

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.

Raw TPM values