RLG00000015028

histone deacetylase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr3
OG0000538
Physical Location & Seq
Forward (+)
60798442 .. 60800924
2483 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000015028

Sequence Viewer

Length: 822 bp
ATGAGCCAGACACAATGCGCTCACCACCAGGCTGTTGTTTCCTGTGATCTCACTGGAGTTCCCAGCCCTGACACTCCCTGCAAAAGAATTGGTTTAATTTGTTTGTCCTGCAAGGACATCTTCCGCAGTAGTAGTGTGTATGGACATTTTATTCAGCATTATCAGGAGACAAAGCATTGTCTTTGTGTCAACTGCAGTGGCGACGCCATGTCCAAGCTAGAGTGCATTGATGCAATGATTGTTGATGTTATTGATCTCTTATCGAAGCCATTTCCTAGCATCAGTGTTCATCCACAGTTGGATGCTGAGTCGTTTGTAGGCCAGGATGAGCTTGCATTGGCTGAGGAGGGACTCAAGAAGATCTTTGATTGCGGATTAAAGGCTCTAGCTGATCTCAAAGTGCAAGAAGAATGCAATCTTCCGGAGGAAACCTCTGCGTTCATCAAAGCTCAAGATGAGTTGAAGGTGGCCTCAGACTTGTCGGCCTCAATCACTCAGAAGAAGTTTGTGGTGCGGCAACAAACTTCAAAGTATGATGAGGTGAAGAACAAAATTGTCTCCTCGGACGAGAAAGTTGCCAACTTCAAGGCCACGATCAACGAGTTGGAAGCACAAATAAAAAGGTTGGAAGCTTGTTTAGCCACAAAAGAGAGCAACAAGGCAAAGATTGATGAGGCTATTGATTCCATCAAGAAACAAGTCACCTCCGCGAGAGATGGATTGGTCTCGGACTTGGCACGAGTGTCTTCCATGGAAGGATCGACCCAAGCAACTAACGACAGCACAACATATCAGATAGATAAACCTCCCTTCTCTGATTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
zf-UBP

Protein Analysis

274

Amino Acids

29.93

Weight (kDa)

5.17

Isoelectric Point (pI)

41.87

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-UBP PF02148 33 - 66 2.7e-06 Zn-finger in ubiquitin-hydrolases and other protein
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000538)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g04050 FvH4_2g04050 FvH4_2g04050 FvH4_2g04050 FvH4_2g04050
rosa_chinensis RchiOBHm_Chr6g0253231 RchiOBHm_Chr6g0253251 RchiOBHm_Chr6g0253261 RchiOBHm_Chr6g0253271 RchiOBHm_Chr6g0253291 RchiOBHm_Chr6g0253321 RchiOBHm_Chr6g0253331 RchiOBHm_Chr6g0253341 RchiOBHm_Chr6g0253371 RchiOBHm_Chr6g0253401
rosa_laevigata RLG00000015022 RLG00000015023 RLG00000015024 RLG00000015027 RLG00000015028 RLG00000015030 RLG00000015031 RLG00000015034 RLG00000015035 RLG00000015038 RLG00000015041
rosa_multiflora Rmu_sc0001257.1_g000004 Rmu_sc0001257.1_g000008 Rmu_sc0001257.1_g000014 Rmu_sc0001257.1_g000016 Rmu_sc0001257.1_g000019 Rmu_sc0001257.1_g000026 Rmu_sc0002560.1_g000013 Rmu_sc0002560.1_g000020 Rmu_sc0002560.1_g000021 Rmu_sc0003855.1_g000005 Rmu_sc0003855.1_g000011 Rmu_sc0003898.1_g000003 Rmu_sc0003898.1_g000005 Rmu_sc0003898.1_g000016 Rmu_sc0003898.1_g000017 Rmu_sc0005439.1_g000007 Rmu_sc0005439.1_g000014 Rmu_sc0005439.1_g000021
rosa_roxburghii Rroxscaffold_7G00211930 Rroxscaffold_7G00211940 Rroxscaffold_7G00211960 Rroxscaffold_7G00211980 Rroxscaffold_7G00211990 Rroxscaffold_7G00212000 Rroxscaffold_7G00212050 Rroxscaffold_7G00212060 Rroxscaffold_7G00212070 Rroxscaffold_7G00212080 Rroxscaffold_7G00212160
rosa_rugosa Rorug05G0542900 Rorug05G0542900 Rorug05G0543000 Rorug05G0543100 Rorug05G0543100 Rorug05G0543200 Rorug05G0543300 Rorug05G0543400 Rorug05G0543400 Rorug05G0543500 Rorug05G0543600 Rorug05G0543700
rosa_samantha Rh6CG050000 Rh6DG045200 Rh6DG045500 Rh6DG045600 Rh6DG045700 Rh6DG045800 Rh6DG046200 Rh6DG046300 Rh6DG046400 Rh6DG046500 Rh6DG046700 Rh6DG046800
rosa_wichuraiana Rw0G000070 Rw6G005230 Rw6G005240 Rw6G005280 Rw6G005290

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 710
AccIII TCCGGA 1 cut(s) 421
AciI CCGC 4 cut(s) 124, 372, 514, 708
AclWI GGATC 1 cut(s) 766
AcyI GRCGYC 1 cut(s) 204
AgsI TTSAA 3 cut(s) 463, 528, 586
AhdI GACNNNNNGTC 1 cut(s) 208
AjnI CCWGG 2 cut(s) 27, 321
AluBI AGCT 5 cut(s) 217, 331, 389, 449, 632
AluI AGCT 5 cut(s) 217, 331, 389, 449, 632
Alw26I GTCTC 3 cut(s) 161, 562, 730
AlwI GGATC 1 cut(s) 766
Aor13HI TCCGGA 1 cut(s) 421
AoxI GGCC 4 cut(s) 319, 468, 483, 588
AspLEI GCGC 1 cut(s) 20
AsuHPI GGTGA 3 cut(s) 14, 553, 694
BauI CACGAG 1 cut(s) 738
BbsI GAAGAC 1 cut(s) 738
BbvCI CCTCAGC 1 cut(s) 342
BccI CCATC 2 cut(s) 695, 710
BcgI CGANNNNNNTGC 2 cut(s) 557, 591
BciT130I CCWGG 2 cut(s) 29, 323
BcoDI GTCTC 3 cut(s) 161, 562, 730
BfaI CTAG 3 cut(s) 218, 276, 386
BfmI CTRYAG 1 cut(s) 193
BglII AGATCT 1 cut(s) 360
BisI GCNGC 1 cut(s) 515
BlsI GCNGC 1 cut(s) 516
Bme1390I CCNGG 2 cut(s) 29, 323
BmeRI GACNNNNNGTC 1 cut(s) 208
BmrFI CCNGG 2 cut(s) 29, 323
BmsI GCATC 3 cut(s) 220, 288, 292
BpiI GAAGAC 1 cut(s) 738
BplI GAGNNNNNCTC 2 cut(s) 416, 448
BpmI CTGGAG 1 cut(s) 75
Bpu10I CCTNAGC 1 cut(s) 342
BpuEI CTTGAG 2 cut(s) 338, 435
BsaHI GRCGYC 1 cut(s) 204
BsaI GGTCTC 1 cut(s) 730
BsaJI CCNNGG 2 cut(s) 561, 750
BsaWI WCCGGW 1 cut(s) 421
Bse1I ACTGG 1 cut(s) 58
Bse3DI GCAATG 1 cut(s) 240
BseAI TCCGGA 1 cut(s) 421
BseBI CCWGG 2 cut(s) 29, 323
BseDI CCNNGG 2 cut(s) 561, 750
BseGI GGATG 3 cut(s) 289, 307, 331
BseMI GCAATG 1 cut(s) 240
BseMII CTCAG 4 cut(s) 297, 333, 486, 509
BseNI ACTGG 1 cut(s) 58
BseRI GAGGAG 2 cut(s) 359, 550
BseYI CCCAGC 1 cut(s) 62
Bsh1236I CGCG 1 cut(s) 710
BshFI GGCC 4 cut(s) 321, 470, 485, 590
BsiSI CCGG 1 cut(s) 422
BslFI GGGAC 1 cut(s) 363
BsmAI GTCTC 3 cut(s) 161, 562, 730
BsmFI GGGAC 1 cut(s) 363
BsmI GAATGC 1 cut(s) 416
BsnI GGCC 4 cut(s) 321, 470, 485, 590
Bso31I GGTCTC 1 cut(s) 730
Bsp13I TCCGGA 1 cut(s) 421
Bsp143I GATC 6 cut(s) 46, 253, 360, 391, 594, 758
Bsp19I CCATGG 1 cut(s) 750
BspACI CCGC 4 cut(s) 124, 372, 514, 708
BspANI GGCC 4 cut(s) 321, 470, 485, 590
BspCNI CTCAG 4 cut(s) 298, 334, 485, 508
BspEI TCCGGA 1 cut(s) 421
BspFNI CGCG 1 cut(s) 710
BspMAI CTGCAG 1 cut(s) 197
BspPI GGATC 1 cut(s) 766
BspTNI GGTCTC 1 cut(s) 730
BsrDI GCAATG 1 cut(s) 240
BsrI ACTGG 1 cut(s) 58
BssECI CCNNGG 2 cut(s) 561, 750
BssMI GATC 6 cut(s) 46, 253, 360, 391, 594, 758
BssNI GRCGYC 1 cut(s) 204
BssSI CACGAG 1 cut(s) 738
BssT1I CCWWGG 1 cut(s) 750
Bst2BI CACGAG 1 cut(s) 738
Bst2UI CCWGG 2 cut(s) 29, 323
Bst4CI ACNGT 1 cut(s) 297
BstACI GRCGYC 1 cut(s) 204
BstC8I GCNNGC 1 cut(s) 333
BstDEI CTNAG 4 cut(s) 306, 342, 472, 495
BstDSI CCRYGG 1 cut(s) 750
BstF5I GGATG 3 cut(s) 289, 307, 331
BstFNI CGCG 1 cut(s) 710
BstHHI GCGC 1 cut(s) 20
BstKTI GATC 6 cut(s) 49, 256, 363, 394, 597, 761
BstMAI GTCTC 3 cut(s) 161, 562, 730
BstMBI GATC 6 cut(s) 46, 253, 360, 391, 594, 758
BstMWI GCNNNNNNNGC 1 cut(s) 638
BstNI CCWGG 2 cut(s) 29, 323
BstSCI CCNGG 2 cut(s) 27, 321
BstSFI CTRYAG 1 cut(s) 193
BstUI CGCG 1 cut(s) 710
BstV2I GAAGAC 1 cut(s) 738
BstX2I RGATCY 1 cut(s) 360
BstYI RGATCY 1 cut(s) 360
BsuRI GGCC 4 cut(s) 321, 470, 485, 590
BtgI CCRYGG 1 cut(s) 750
BtsCI GGATG 3 cut(s) 289, 307, 331
BtsI GCAGTG 1 cut(s) 202
BtsIMutI CAGTG 3 cut(s) 51, 202, 289
Cac8I GCNNGC 1 cut(s) 333
CfoI GCGC 1 cut(s) 20
CseI GACGC 1 cut(s) 212
CspCI CAANNNNNGTGG 2 cut(s) 178, 213
CviAII CATG 2 cut(s) 208, 751
DdeI CTNAG 4 cut(s) 306, 342, 472, 495
DpnI GATC 6 cut(s) 48, 255, 362, 393, 596, 760
DpnII GATC 6 cut(s) 46, 253, 360, 391, 594, 758
DriI GACNNNNNGTC 1 cut(s) 208
Eam1105I GACNNNNNGTC 1 cut(s) 208
Eco130I CCWWGG 1 cut(s) 750
Eco31I GGTCTC 1 cut(s) 730
EcoRII CCWGG 2 cut(s) 27, 321
EcoT14I CCWWGG 1 cut(s) 750
ErhI CCWWGG 1 cut(s) 750
FaeI CATG 2 cut(s) 211, 754
FaiI YATR 5 cut(s) 141, 209, 534, 752, 790
FalI AAGNNNNNCTT 4 cut(s) 104, 136, 347, 379
FaqI GGGAC 1 cut(s) 363
FatI CATG 2 cut(s) 207, 750
Fnu4HI GCNGC 1 cut(s) 515
FokI GGATG 3 cut(s) 276, 314, 338
Fsp4HI GCNGC 1 cut(s) 515
FspBI CTAG 3 cut(s) 218, 276, 386
GlaI GCGC 1 cut(s) 19
GluI GCNGC 1 cut(s) 515
GsaI CCCAGC 1 cut(s) 66
GsuI CTGGAG 1 cut(s) 75
HaeIII GGCC 4 cut(s) 321, 470, 485, 590
HapII CCGG 1 cut(s) 422
HgaI GACGC 1 cut(s) 212
HhaI GCGC 1 cut(s) 20
Hin1I GRCGYC 1 cut(s) 204
Hin1II CATG 2 cut(s) 211, 754
Hin6I GCGC 1 cut(s) 18
HinP1I GCGC 1 cut(s) 18
HincII GTYRAC 1 cut(s) 190
HindII GTYRAC 1 cut(s) 190
HindIII AAGCTT 1 cut(s) 630
HinfI GANTC 3 cut(s) 308, 351, 683
HpaII CCGG 1 cut(s) 422
HphI GGTGA 3 cut(s) 14, 553, 694
Hpy166II GTNNAC 1 cut(s) 190
Hpy188I TCNGA 6 cut(s) 475, 498, 565, 730, 795, 817
Hpy188III TCNNGA 5 cut(s) 164, 355, 422, 452, 691
Hpy8I GTNNAC 1 cut(s) 190
Hpy99I CGWCG 1 cut(s) 206
HpyAV CCTTC 3 cut(s) 457, 749, 820
HpyCH4III ACNGT 1 cut(s) 297
HpyCH4V TGCA 8 cut(s) 81, 111, 195, 225, 233, 335, 403, 414
HpyF10VI GCNNNNNNNGC 1 cut(s) 638
HpyF3I CTNAG 4 cut(s) 306, 342, 472, 495
Hsp92I GRCGYC 1 cut(s) 204
Hsp92II CATG 2 cut(s) 211, 754
HspAI GCGC 1 cut(s) 18
Kpn2I TCCGGA 1 cut(s) 421
Kzo9I GATC 6 cut(s) 46, 253, 360, 391, 594, 758
LweI GCATC 3 cut(s) 220, 288, 292
MaeI CTAG 3 cut(s) 218, 276, 386
MaeIII GTNAC 1 cut(s) 700
MalI GATC 6 cut(s) 48, 255, 362, 393, 596, 760
MboI GATC 6 cut(s) 46, 253, 360, 391, 594, 758
MboII GAAGA 7 cut(s) 112, 370, 410, 419, 511, 556, 738
MflI RGATCY 1 cut(s) 360
MluCI AATT 3 cut(s) 87, 96, 552
MlyI GAGTC 2 cut(s) 317, 345
MmeI TCCRAC 3 cut(s) 279, 585, 606
MroI TCCGGA 1 cut(s) 421
MseI TTAA 2 cut(s) 95, 377
MspI CCGG 1 cut(s) 422
MspR9I CCNGG 2 cut(s) 29, 323
Mva1269I GAATGC 1 cut(s) 416
MvaI CCWGG 2 cut(s) 29, 323
MvnI CGCG 1 cut(s) 710
MwoI GCNNNNNNNGC 1 cut(s) 638
NcoI CCATGG 1 cut(s) 750
NdeII GATC 6 cut(s) 46, 253, 360, 391, 594, 758
NlaIII CATG 2 cut(s) 211, 754
NmuCI GTSAC 1 cut(s) 700
PctI GAATGC 1 cut(s) 416
PfeI GAWTC 1 cut(s) 683
PkrI GCNGC 1 cut(s) 516
PleI GAGTC 2 cut(s) 316, 345
PpsI GAGTC 2 cut(s) 316, 345
Psp6I CCWGG 2 cut(s) 27, 321
PspFI CCCAGC 1 cut(s) 62
PspGI CCWGG 2 cut(s) 27, 321
PstI CTGCAG 1 cut(s) 197
PsuI RGATCY 1 cut(s) 360
SaqAI TTAA 2 cut(s) 95, 377
SatI GCNGC 1 cut(s) 515
Sau3AI GATC 6 cut(s) 46, 253, 360, 391, 594, 758
SchI GAGTC 2 cut(s) 317, 345
ScrFI CCNGG 2 cut(s) 29, 323
SfaNI GCATC 3 cut(s) 220, 288, 292
SfcI CTRYAG 1 cut(s) 193
SmlI CTYRAG 2 cut(s) 353, 450
SmoI CTYRAG 2 cut(s) 353, 450
Sse9I AATT 3 cut(s) 87, 96, 552
SsiI CCGC 4 cut(s) 124, 372, 514, 708
SspMI CTAG 3 cut(s) 218, 276, 386
StyD4I CCNGG 2 cut(s) 27, 321
StyI CCWWGG 1 cut(s) 750
TaaI ACNGT 1 cut(s) 297
TaqI TCGA 2 cut(s) 263, 761
TasI AATT 3 cut(s) 87, 96, 552
TauI GCSGC 1 cut(s) 517
TfiI GAWTC 1 cut(s) 683
Tru1I TTAA 2 cut(s) 95, 377
Tru9I TTAA 2 cut(s) 95, 377
TscAI CASTG 3 cut(s) 58, 202, 289
TseFI GTSAC 1 cut(s) 700
Tsp45I GTSAC 1 cut(s) 700
TspDTI ATGAA 2 cut(s) 278, 430
TspRI CASTG 3 cut(s) 58, 202, 289
XspI CTAG 3 cut(s) 218, 276, 386
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.