Rw6G005240

histone deacetylase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000538
Physical Location & Seq
Reverse (-)
8443062 .. 8457846
14785 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G005240.1

Sequence Viewer

Length: 1164 bp
ATGGAGATGAAGAGGAATCTGGAGGGTTTGGATAGGGAGGAACATGAACACAGTCGACCTTGCCGAGTCTACAACTCTACAAGAAATTGGGGAAAAGGTTCCCTCACACCTCCAGAACAGGAGAGCAAGGTCAACAGCAACTTCGCCATGACCCAGACACAGTGCGCTCACTCCTTGGCTTTCATTTCCTGTGACCCCAGTGTCGTTCCCAACCCTGACACTCCCTGCAAAAGATGTCAGCATCCAGGACCAAAAGGGAATTGGTTTTGTTTGTCCTGTAAGGACATCTTCTGTTGTACTAGTGTGAAGGGACATTTTATGCAGCATTATCAGGAGACCAAGCATGGTCTTTGTGTCAACTGCAGCACAAAATCAATTTACTGTTGCTCCTGTAGTAAAACTCTAGATGCGCAAGTGATCCAACAATTATGGATCAAGGGTCGATCCACTTCATCCAAGCTAGAGAGCATTGATGTAATGATTGTTGATGTTATTGATCTCTTGTCTAAACCGTTTCCTAGCATCAATGTTCATCCACAGTTGGGTGCTCAGTCATTTGTAGGCCAGGATGAATTTGCATTGGCTAAGGAGGGACTGCAAAAGATCTTTGATAACGGGTTAATAGCTGTAGCTGATCCCAAAGTGCAAGAAAAGTTTCTCCTTTACTCAGCCACATTGCTATCAGCCGAGTCATGCCCCTCAGAATTGAAGGTTAACCTCTCATCATTCAGATGCAATCTTCCGGAGGAAACCTCTGCTTTCATCAAAGCTCAAGATGAGTTGAAGGTGGCTTCAGACTTATCAGCCTCAATCACTCAGAAGAAGTTTGTAGTGCGGCAACAAACTTCAAAGTATGATGAGGTGAAGAAAGAAATTGTGGCCTCGGACGAGAAAGTTTCTAACTTCAAGGCCATGATCAAAGAATTGAAAGCACAAATCAAAAGGTTGGAAGCTTGTTTAGCCACGGAAAAGAGCAACAGAGCAAAGAATGATGAGGCTATTGATTCCATCGAGAAACAAGTCACCACCGCGAGAGATGGGTTGGTCTCGGACTTGGCACAAGTGTCTTCCATGGAAGGATCGACCCAAGCAGCTAACGAGTTAGTAGCTCGAAAACAGTCGGACTGGGATAACTTAAAGCTTAGTTTTACCAAGTTTGCATGA
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

387

Amino Acids

43.1

Weight (kDa)

7.44

Isoelectric Point (pI)

33.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-UBP PF02148 76 - 136 3.2e-13 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)
AasI GACNNNNNNGTC 1 cut(s) 200
Acc16I TGCGCA 1 cut(s) 411
AccI GTMKAC 2 cut(s) 55, 69
AccII CGCG 1 cut(s) 1031
AccIII TCCGGA 1 cut(s) 742
AciI CCGC 2 cut(s) 835, 1029
AclWI GGATC 5 cut(s) 412, 438, 440, 629, 1087
AcsI RAATTY 1 cut(s) 572
AcuI CTGAAG 1 cut(s) 777
AfaI GTAC 1 cut(s) 298
AfiI CCNNNNNNNGG 1 cut(s) 542
AgsI TTSAA 5 cut(s) 709, 784, 849, 907, 928
AhlI ACTAGT 1 cut(s) 299
AjnI CCWGG 2 cut(s) 244, 564
AluBI AGCT 8 cut(s) 460, 626, 632, 770, 953, 1094, 1109, 1141
AluI AGCT 8 cut(s) 460, 626, 632, 770, 953, 1094, 1109, 1141
Alw21I GWGCWC 1 cut(s) 550
Alw26I GTCTC 2 cut(s) 329, 1051
AlwI GGATC 5 cut(s) 412, 438, 440, 629, 1087
Aor13HI TCCGGA 1 cut(s) 742
AoxI GGCC 3 cut(s) 562, 879, 909
ApeKI GCWGC 3 cut(s) 322, 363, 1091
ApoI RAATTY 1 cut(s) 572
Asp700I GAANNNNTTC 2 cut(s) 97, 654
AspLEI GCGC 2 cut(s) 167, 412
AspS9I GGNCC 1 cut(s) 248
AsuHPI GGTGA 2 cut(s) 874, 1015
AvaII GGWCC 1 cut(s) 248
BbsI GAAGAC 1 cut(s) 1059
Bbv12I GWGCWC 1 cut(s) 550
BbvI GCAGC 3 cut(s) 334, 375, 1103
BccI CCATC 2 cut(s) 1016, 1031
BciT130I CCWGG 2 cut(s) 246, 566
BclI TGATCA 1 cut(s) 915
BcoDI GTCTC 2 cut(s) 329, 1051
BcuI ACTAGT 1 cut(s) 299
BfaI CTAG 4 cut(s) 300, 404, 461, 519
BfmI CTRYAG 3 cut(s) 361, 391, 627
BglII AGATCT 1 cut(s) 603
BisI GCNGC 4 cut(s) 323, 364, 836, 1092
BlsI GCNGC 4 cut(s) 324, 365, 837, 1093
Bme1390I CCNGG 2 cut(s) 246, 566
Bme18I GGWCC 1 cut(s) 248
BmgT120I GGNCC 1 cut(s) 248
BmiI GGNNCC 1 cut(s) 100
BmrFI CCNGG 2 cut(s) 246, 566
BmrI ACTGGG 2 cut(s) 192, 1135
BmsI GCATC 4 cut(s) 250, 397, 531, 722
BmuI ACTGGG 2 cut(s) 192, 1135
BpiI GAAGAC 1 cut(s) 1059
BplI GAGNNNNNCTC 2 cut(s) 737, 769
BpmI CTGGAG 2 cut(s) 41, 96
Bpu10I CCTNAGC 1 cut(s) 585
BpuEI CTTGAG 1 cut(s) 756
BsaI GGTCTC 2 cut(s) 329, 1051
BsaJI CCNNGG 4 cut(s) 174, 882, 963, 1071
BsaWI WCCGGW 1 cut(s) 742
BsaXI ACNNNNNCTCC 2 cut(s) 371, 401
Bsc4I CCNNNNNNNGG 1 cut(s) 542
Bse1I ACTGG 2 cut(s) 198, 1130
Bse3DI GCAATG 1 cut(s) 674
BseAI TCCGGA 1 cut(s) 742
BseBI CCWGG 2 cut(s) 246, 566
BseDI CCNNGG 4 cut(s) 174, 882, 963, 1071
BseGI GGATG 4 cut(s) 241, 452, 532, 574
BseLI CCNNNNNNNGG 1 cut(s) 542
BseMI GCAATG 1 cut(s) 674
BseMII CTCAG 4 cut(s) 563, 681, 714, 830
BseNI ACTGG 2 cut(s) 198, 1130
BseXI GCAGC 3 cut(s) 334, 375, 1103
Bsh1236I CGCG 1 cut(s) 1031
BshFI GGCC 3 cut(s) 564, 881, 911
BsiHKAI GWGCWC 1 cut(s) 550
BsiSI CCGG 1 cut(s) 743
BslFI GGGAC 2 cut(s) 324, 606
BslI CCNNNNNNNGG 1 cut(s) 542
BsmAI GTCTC 2 cut(s) 329, 1051
BsmFI GGGAC 2 cut(s) 324, 606
BsnI GGCC 3 cut(s) 564, 881, 911
Bso31I GGTCTC 2 cut(s) 329, 1051
Bsp1286I GDGCHC 1 cut(s) 550
Bsp13I TCCGGA 1 cut(s) 742
Bsp143I GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
Bsp19I CCATGG 1 cut(s) 1071
BspACI CCGC 2 cut(s) 835, 1029
BspANI GGCC 3 cut(s) 564, 881, 911
BspCNI CTCAG 4 cut(s) 562, 680, 713, 829
BspEI TCCGGA 1 cut(s) 742
BspFNI CGCG 1 cut(s) 1031
BspLI GGNNCC 1 cut(s) 100
BspMAI CTGCAG 1 cut(s) 365
BspPI GGATC 5 cut(s) 412, 438, 440, 629, 1087
BspTNI GGTCTC 2 cut(s) 329, 1051
BsrDI GCAATG 1 cut(s) 674
BsrI ACTGG 2 cut(s) 198, 1130
BssECI CCNNGG 4 cut(s) 174, 882, 963, 1071
BssMI GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
BssT1I CCWWGG 2 cut(s) 174, 1071
Bst2UI CCWGG 2 cut(s) 246, 566
Bst4CI ACNGT 6 cut(s) 53, 162, 383, 513, 540, 1119
Bst6I CTCTTC 1 cut(s) 5
BstDEI CTNAG 6 cut(s) 549, 585, 667, 700, 816, 1142
BstDSI CCRYGG 2 cut(s) 963, 1071
BstF5I GGATG 4 cut(s) 241, 452, 532, 574
BstFNI CGCG 1 cut(s) 1031
BstHHI GCGC 2 cut(s) 167, 412
BstKTI GATC 8 cut(s) 420, 435, 446, 499, 606, 637, 918, 1082
BstMAI GTCTC 2 cut(s) 329, 1051
BstMBI GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
BstMWI GCNNNNNNNGC 1 cut(s) 959
BstNI CCWGG 2 cut(s) 246, 566
BstSCI CCNGG 2 cut(s) 244, 564
BstSFI CTRYAG 3 cut(s) 361, 391, 627
BstUI CGCG 1 cut(s) 1031
BstV1I GCAGC 3 cut(s) 334, 375, 1103
BstV2I GAAGAC 1 cut(s) 1059
BstX2I RGATCY 1 cut(s) 603
BstYI RGATCY 1 cut(s) 603
BsuRI GGCC 3 cut(s) 564, 881, 911
BtgI CCRYGG 2 cut(s) 963, 1071
BtsCI GGATG 4 cut(s) 241, 452, 532, 574
BtsIMutI CAGTG 2 cut(s) 167, 205
CfoI GCGC 2 cut(s) 167, 412
Cfr13I GGNCC 1 cut(s) 248
Csp6I GTAC 1 cut(s) 297
CviAII CATG 7 cut(s) 44, 148, 344, 693, 913, 1072, 1161
CviQI GTAC 1 cut(s) 297
DdeI CTNAG 6 cut(s) 549, 585, 667, 700, 816, 1142
DpnI GATC 8 cut(s) 419, 434, 445, 498, 605, 636, 917, 1081
DpnII GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
DrdI GACNNNNNNGTC 1 cut(s) 200
DseDI GACNNNNNNGTC 1 cut(s) 200
Eam1104I CTCTTC 1 cut(s) 5
EarI CTCTTC 1 cut(s) 5
Eco130I CCWWGG 2 cut(s) 174, 1071
Eco31I GGTCTC 2 cut(s) 329, 1051
Eco47I GGWCC 1 cut(s) 248
Eco57I CTGAAG 1 cut(s) 777
EcoRII CCWGG 2 cut(s) 244, 564
EcoT14I CCWWGG 2 cut(s) 174, 1071
ErhI CCWWGG 2 cut(s) 174, 1071
FaeI CATG 7 cut(s) 47, 151, 347, 696, 916, 1075, 1164
FalI AAGNNNNNCTT 2 cut(s) 272, 304
FaqI GGGAC 2 cut(s) 324, 606
FatI CATG 7 cut(s) 43, 147, 343, 692, 912, 1071, 1160
FbaI TGATCA 1 cut(s) 915
FblI GTMKAC 2 cut(s) 55, 69
Fnu4HI GCNGC 4 cut(s) 323, 364, 836, 1092
FokI GGATG 4 cut(s) 228, 439, 519, 581
Fsp4HI GCNGC 4 cut(s) 323, 364, 836, 1092
FspBI CTAG 4 cut(s) 300, 404, 461, 519
FspI TGCGCA 1 cut(s) 411
GlaI GCGC 2 cut(s) 166, 411
GluI GCNGC 4 cut(s) 323, 364, 836, 1092
GsuI CTGGAG 2 cut(s) 41, 96
HaeIII GGCC 3 cut(s) 564, 881, 911
HapII CCGG 1 cut(s) 743
HhaI GCGC 2 cut(s) 167, 412
Hin1II CATG 7 cut(s) 47, 151, 347, 696, 916, 1075, 1164
Hin6I GCGC 2 cut(s) 165, 410
HinP1I GCGC 2 cut(s) 165, 410
HincII GTYRAC 4 cut(s) 56, 133, 358, 715
HindII GTYRAC 4 cut(s) 56, 133, 358, 715
HindIII AAGCTT 2 cut(s) 951, 1139
HinfI GANTC 4 cut(s) 16, 66, 689, 1004
HpaI GTTAAC 1 cut(s) 715
HpaII CCGG 1 cut(s) 743
HphI GGTGA 2 cut(s) 874, 1015
Hpy166II GTNNAC 5 cut(s) 56, 70, 133, 358, 715
Hpy188I TCNGA 7 cut(s) 703, 731, 796, 819, 886, 1051, 1123
Hpy188III TCNNGA 7 cut(s) 20, 113, 332, 404, 743, 773, 1012
Hpy8I GTNNAC 5 cut(s) 56, 70, 133, 358, 715
HpyAV CCTTC 4 cut(s) 301, 703, 778, 1070
HpyCH4III ACNGT 6 cut(s) 53, 162, 383, 513, 540, 1119
HpyCH4V TGCA 8 cut(s) 228, 322, 363, 578, 598, 646, 735, 1160
HpyF10VI GCNNNNNNNGC 1 cut(s) 959
HpyF3I CTNAG 6 cut(s) 549, 585, 667, 700, 816, 1142
Hsp92II CATG 7 cut(s) 47, 151, 347, 696, 916, 1075, 1164
HspAI GCGC 2 cut(s) 165, 410
Kpn2I TCCGGA 1 cut(s) 742
Ksp22I TGATCA 1 cut(s) 915
KspAI GTTAAC 1 cut(s) 715
Kzo9I GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
LmnI GCTCC 1 cut(s) 392
Lsp1109I GCAGC 3 cut(s) 334, 375, 1103
LweI GCATC 4 cut(s) 250, 397, 531, 722
MaeI CTAG 4 cut(s) 300, 404, 461, 519
MaeIII GTNAC 2 cut(s) 191, 1021
MalI GATC 8 cut(s) 419, 434, 445, 498, 605, 636, 917, 1081
MboI GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
MboII GAAGA 6 cut(s) 22, 280, 731, 832, 877, 1059
MflI RGATCY 1 cut(s) 603
MhlI GDGCHC 1 cut(s) 550
MluCI AATT 8 cut(s) 85, 259, 375, 425, 572, 704, 873, 923
MlyI GAGTC 2 cut(s) 75, 698
MmeI TCCRAC 3 cut(s) 445, 927, 1101
MroI TCCGGA 1 cut(s) 742
MroXI GAANNNNTTC 2 cut(s) 97, 654
MseI TTAA 3 cut(s) 620, 714, 1136
MslI CAYNNNNRTG 1 cut(s) 730
MspI CCGG 1 cut(s) 743
MspR9I CCNGG 2 cut(s) 246, 566
MvaI CCWGG 2 cut(s) 246, 566
MvnI CGCG 1 cut(s) 1031
MwoI GCNNNNNNNGC 1 cut(s) 959
NcoI CCATGG 1 cut(s) 1071
NdeII GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
NlaIII CATG 7 cut(s) 47, 151, 347, 696, 916, 1075, 1164
NlaIV GGNNCC 1 cut(s) 100
NmeAIII GCCGAG 2 cut(s) 89, 712
NmuCI GTSAC 2 cut(s) 191, 1021
NsbI TGCGCA 1 cut(s) 411
PcsI WCGNNNNNNNCGW 1 cut(s) 61
PdmI GAANNNNTTC 2 cut(s) 97, 654
PfeI GAWTC 2 cut(s) 16, 1004
PfoI TCCNGGA 1 cut(s) 244
PkrI GCNGC 4 cut(s) 324, 365, 837, 1093
PleI GAGTC 2 cut(s) 74, 697
PpsI GAGTC 2 cut(s) 74, 697
Psp6I CCWGG 2 cut(s) 244, 564
PspGI CCWGG 2 cut(s) 244, 564
PspN4I GGNNCC 1 cut(s) 100
PspPI GGNCC 1 cut(s) 248
PstI CTGCAG 1 cut(s) 365
PsuI RGATCY 1 cut(s) 603
RsaI GTAC 1 cut(s) 298
RsaNI GTAC 1 cut(s) 297
RseI CAYNNNNRTG 1 cut(s) 730
SalI GTCGAC 1 cut(s) 54
SaqAI TTAA 3 cut(s) 620, 714, 1136
SatI GCNGC 4 cut(s) 323, 364, 836, 1092
Sau3AI GATC 8 cut(s) 417, 432, 443, 496, 603, 634, 915, 1079
Sau96I GGNCC 1 cut(s) 248
SchI GAGTC 2 cut(s) 75, 698
ScrFI CCNGG 2 cut(s) 246, 566
SduI GDGCHC 1 cut(s) 550
SfaNI GCATC 4 cut(s) 250, 397, 531, 722
SfcI CTRYAG 3 cut(s) 361, 391, 627
SinI GGWCC 1 cut(s) 248
SmiMI CAYNNNNRTG 1 cut(s) 730
SmlI CTYRAG 1 cut(s) 771
SmoI CTYRAG 1 cut(s) 771
SpeI ACTAGT 1 cut(s) 299
Sse9I AATT 8 cut(s) 85, 259, 375, 425, 572, 704, 873, 923
SsiI CCGC 2 cut(s) 835, 1029
SspMI CTAG 4 cut(s) 300, 404, 461, 519
StyD4I CCNGG 2 cut(s) 244, 564
StyI CCWWGG 2 cut(s) 174, 1071
TaaI ACNGT 6 cut(s) 53, 162, 383, 513, 540, 1119
TaqI TCGA 5 cut(s) 55, 442, 1011, 1082, 1111
TasI AATT 8 cut(s) 85, 259, 375, 425, 572, 704, 873, 923
TatI WGTACW 1 cut(s) 296
TauI GCSGC 1 cut(s) 838
TfiI GAWTC 2 cut(s) 16, 1004
Tru1I TTAA 3 cut(s) 620, 714, 1136
Tru9I TTAA 3 cut(s) 620, 714, 1136
TscAI CASTG 2 cut(s) 167, 205
TseFI GTSAC 2 cut(s) 191, 1021
TseI GCWGC 3 cut(s) 322, 363, 1091
Tsp45I GTSAC 2 cut(s) 191, 1021
TspDTI ATGAA 7 cut(s) 23, 60, 172, 441, 521, 585, 751
TspGWI ACGGA 1 cut(s) 980
TspRI CASTG 2 cut(s) 167, 205
VpaK11BI GGWCC 1 cut(s) 248
XapI RAATTY 1 cut(s) 572
XbaI TCTAGA 1 cut(s) 403
XcmI CCANNNNNNNNNTGG 1 cut(s) 258
XmiI GTMKAC 2 cut(s) 55, 69
XmnI GAANNNNTTC 2 cut(s) 97, 654
XspI CTAG 4 cut(s) 300, 404, 461, 519
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.