Rroxscaffold_1G00067240

Histone deacetylase HDT1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0002833
Physical Location & Seq
Forward (+)
88618002 .. 88623730
5729 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00067240.1

Sequence Viewer

Length: 1659 bp
ATGTCACCGTTTTGCCCTAACTGTGACCGAGAACCTGAGTTTTGGGGTGCTGAAGTGAAATCCGGCGAGAAGTTGAAAGTGAAGCCAGATGCGGGCGTGGTTTTGCATCTCACTCAGGCATGTGTGGGCTTAAATCAAAGATGTCATGGCGTCGTTTATGTGAGCATCGGGGAAGAGAGAAGAGTCTTGGGAAGTCTCTTGCCACCAAGAGTACCTCAATTTTCCTGCGATCTGGTCTTTGACCAAGAATTTCTGCTTTCACACAACTTGGAGATGGGAAGCGTCTTCTTTGCCGGTTATTCTTGCTTTAGTAAAAATAAGCTTGAGGAAACAAAGCAAACTACAAGTAAGACCAAATCTTCTGATGAGAATCCAATCTGTGAGGAAAAGAGAGAGCCTCTTAGGCAAGCAAGGCCGGCAATAGGGAAGACCAGATCTTCTGTTAAGAATCCAATCATTGAGGAAAATAGAGTACCTATTGACAAAGCTGACTTTGTTGTGCGCCCACTGGTGGTGAGAAGTCCAGAGAACATAAGTAAGGAGCTCGAATTCTATAGAACTATTTTTGAGGCTGAACCGATTGCTGGCCCCCAGATTGGGTCTGAAAGATCGCATGAGTTCAAGATTGGAAATAATTCATTATATGTTGTTGCTGCTTCGACTATTGAGGAACTTGAGCCTCTTGGGCCTGCCCTTTGTGTGGAGACGGGAGATGTAGCAACTTTTATTGAGAAAGCGGAAAATGCTGGGTGGAAGTGCTCTGTCCTTGAAAGGTATCGGCCCAATATCACGCCAGATGATAAGTTGAGTGGCACTAGAATGAGAACTAAATTCGGTCAGATCTGTTACATCTGTCAGACACCCCAAACAAGAAACAATGAAGAAGAGCAGCAAACAAAAATCAAGTCCATATGCCCTACAATGCTATTTTATGAAGATGAGTTTGCTGAGGCAGTTGCAAATTATGAGGCTGTTTTCGGAAGGTCTCAAGGCTCGTTCTTTCAGTTGTTCCGGAGACGATCTACCTCTTTTTCAGACTGCCTCTATGCTGCAGCCAAGGATAGGGGTATTGGCAGTTCTACATGTCTCTGCATAGAGCCGGAGGATATTGTCATTTTCATGGAGTCGTTCTTTACTTTGAAGTCGTCCTTAGGTTTCTTCTATCTCAATTGTGAAGTGGTTCTACATGACTGGGGAAAGACAGTTGTGAGATTGATATCTCCTAAGCGTCACACTCTTTATGTTTACAGCAGCAAGCCATCATTGACTGTGCTCTCATGTAACGTAAAGCATGGTGCTATACAGCCACTGATTCAGTTCCTTGGCTCAGTCAGTCAAGTAAAATGGGTCAAAATCCATGTAGATGAAATTCCTCGTTGCTTGTCCTTCCCTTACCCGGATTTGCTGATTATTGGTGATGAGATGATACTTACTCTTGAGAGGATGGAAAAAAAACTGTCTTCAAGGAATTCGGATACCAAGTTATTGCAGGTTCATGGGCAACCAGTATCAGAAGACATGAAAAGATTGTTGAAGAGGCATGAAGCAAAATATGTAGGTTTGCCTTTGACAATTGAGAATGTTGAACAAGTTTATTCGAGTCTTTCTGCTCCAAAATCAGACAAGTGGGTCTATCTTCCTCACTTAGAATGGGCATGA
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
No domains found.

Protein Analysis

552

Amino Acids

62.5

Weight (kDa)

6.46

Isoelectric Point (pI)

50.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NPL PF17800 14 - 100 1.9e-11 Nucleoplasmin-like domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 1628
Acc36I ACCTGC 1 cut(s) 1480
AccIII TCCGGA 1 cut(s) 1011
AciI CCGC 2 cut(s) 92, 737
AcsI RAATTY 5 cut(s) 248, 548, 830, 1368, 1468
AcuI CTGAAG 1 cut(s) 72
AcyI GRCGYC 1 cut(s) 150
AfaI GTAC 2 cut(s) 213, 474
AfiI CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1062, 1396
AflIII ACRYGT 1 cut(s) 1082
AgsI TTSAA 7 cut(s) 76, 622, 770, 1141, 1464, 1534, 1586
AluBI AGCT 3 cut(s) 322, 488, 544
AluI AGCT 3 cut(s) 322, 488, 544
Alw21I GWGCWC 3 cut(s) 546, 761, 1275
Alw26I GTCTC 5 cut(s) 200, 698, 990, 1009, 1091
AlwNI CAGNNNCTG 1 cut(s) 1309
Aor13HI TCCGGA 1 cut(s) 1011
AoxI GGCC 4 cut(s) 413, 586, 686, 779
ApeKI GCWGC 5 cut(s) 653, 889, 1049, 1052, 1251
ApoI RAATTY 5 cut(s) 248, 548, 830, 1368, 1468
ArsI GACNNNNNNTTYG 2 cut(s) 890, 922
Asp700I GAANNNNTTC 2 cut(s) 634, 1179
AspLEI GCGC 1 cut(s) 504
AspS9I GGNCC 3 cut(s) 587, 686, 780
AsuC2I CCSGG 1 cut(s) 1397
AsuHPI GGTGA 2 cut(s) 526, 1427
AxyI CCTNAGG 1 cut(s) 1150
BanII GRGCYC 1 cut(s) 546
BarI GAAGNNNNNNTAC 2 cut(s) 1167, 1199
BbsI GAAGAC 4 cut(s) 277, 434, 1452, 1521
Bbv12I GWGCWC 3 cut(s) 546, 761, 1275
BbvCI CCTCAGC 1 cut(s) 948
BbvI GCAGC 5 cut(s) 640, 901, 1036, 1064, 1263
BccI CCATC 3 cut(s) 268, 1267, 1438
BciVI GTATCC 1 cut(s) 1468
BcnI CCSGG 1 cut(s) 1397
BcoDI GTCTC 5 cut(s) 200, 698, 990, 1009, 1091
BfaI CTAG 1 cut(s) 816
BfmI CTRYAG 2 cut(s) 553, 1050
BfuAI ACCTGC 1 cut(s) 1480
BfuI GTATCC 1 cut(s) 1468
BglI GCCNNNNNGGC 2 cut(s) 403, 685
BglII AGATCT 2 cut(s) 434, 840
BisI GCNGC 5 cut(s) 654, 890, 1050, 1053, 1252
BlsI GCNGC 5 cut(s) 655, 891, 1051, 1054, 1253
Bme1390I CCNGG 1 cut(s) 1397
BmgT120I GGNCC 3 cut(s) 587, 686, 780
BmiI GGNNCC 1 cut(s) 589
BmrFI CCNGG 1 cut(s) 1397
BmrI ACTGGG 1 cut(s) 1201
BmsI GCATC 3 cut(s) 79, 115, 174
BmuI ACTGGG 1 cut(s) 1201
BpiI GAAGAC 4 cut(s) 277, 434, 1452, 1521
BplI GAGNNNNNCTC 2 cut(s) 382, 414
Bpu10I CCTNAGC 2 cut(s) 948, 1224
BpuEI CTTGAG 4 cut(s) 344, 695, 972, 1457
BpuMI CCSGG 1 cut(s) 1397
BsaBI GATNNNNATC 2 cut(s) 369, 1216
BsaHI GRCGYC 1 cut(s) 150
BsaI GGTCTC 1 cut(s) 990
BsaJI CCNNGG 2 cut(s) 1056, 1321
BsaWI WCCGGW 1 cut(s) 1011
Bsc4I CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1062, 1396
Bse118I RCCGGY 2 cut(s) 293, 415
Bse1I ACTGG 3 cut(s) 513, 1196, 1505
Bse21I CCTNAGG 1 cut(s) 1150
Bse8I GATNNNNATC 2 cut(s) 369, 1216
BseAI TCCGGA 1 cut(s) 1011
BseDI CCNNGG 2 cut(s) 1056, 1321
BseGI GGATG 1 cut(s) 1449
BseJI GATNNNNATC 2 cut(s) 369, 1216
BseLI CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1062, 1396
BseMII CTCAG 4 cut(s) 27, 128, 939, 1341
BseNI ACTGG 3 cut(s) 513, 1196, 1505
BseXI GCAGC 5 cut(s) 640, 901, 1036, 1064, 1263
BseYI CCCAGC 1 cut(s) 746
BshFI GGCC 4 cut(s) 415, 588, 688, 781
BsiHKAI GWGCWC 3 cut(s) 546, 761, 1275
BsiSI CCGG 6 cut(s) 63, 294, 416, 1012, 1100, 1397
BslI CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1062, 1396
BsmAI GTCTC 5 cut(s) 200, 698, 990, 1009, 1091
BsmBI CGTCTC 2 cut(s) 698, 1009
BsnI GGCC 4 cut(s) 415, 588, 688, 781
Bso31I GGTCTC 1 cut(s) 990
Bsp1286I GDGCHC 3 cut(s) 546, 761, 1275
Bsp13I TCCGGA 1 cut(s) 1011
Bsp143I GATC 5 cut(s) 229, 434, 608, 840, 1019
BspACI CCGC 2 cut(s) 92, 737
BspANI GGCC 4 cut(s) 415, 588, 688, 781
BspCNI CTCAG 4 cut(s) 28, 127, 940, 1340
BspEI TCCGGA 1 cut(s) 1011
BspLI GGNNCC 1 cut(s) 589
BspMAI CTGCAG 1 cut(s) 1054
BspMI ACCTGC 1 cut(s) 1480
BspQI GCTCTTC 1 cut(s) 879
BspTNI GGTCTC 1 cut(s) 990
BsrFI RCCGGY 2 cut(s) 293, 415
BsrI ACTGG 3 cut(s) 513, 1196, 1505
BssAI RCCGGY 2 cut(s) 293, 415
BssECI CCNNGG 2 cut(s) 1056, 1321
BssMI GATC 5 cut(s) 229, 434, 608, 840, 1019
BssNI GRCGYC 1 cut(s) 150
BssT1I CCWWGG 2 cut(s) 1056, 1321
Bst4CI ACNGT 5 cut(s) 9, 23, 1204, 1270, 1458
Bst6I CTCTTC 4 cut(s) 168, 175, 879, 1529
BstACI GRCGYC 1 cut(s) 150
BstC8I GCNNGC 6 cut(s) 94, 408, 417, 586, 690, 1256
BstDEI CTNAG 8 cut(s) 36, 114, 401, 948, 1150, 1224, 1327, 1645
BstF5I GGATG 1 cut(s) 1449
BstHHI GCGC 1 cut(s) 504
BstKTI GATC 5 cut(s) 232, 437, 611, 843, 1022
BstMAI GTCTC 5 cut(s) 200, 698, 990, 1009, 1091
BstMBI GATC 5 cut(s) 229, 434, 608, 840, 1019
BstMWI GCNNNNNNNGC 5 cut(s) 403, 412, 416, 685, 743
BstNSI RCATGY 2 cut(s) 123, 1086
BstSCI CCNGG 1 cut(s) 1395
BstSFI CTRYAG 2 cut(s) 553, 1050
BstV1I GCAGC 5 cut(s) 640, 901, 1036, 1064, 1263
BstV2I GAAGAC 4 cut(s) 277, 434, 1452, 1521
BstX2I RGATCY 2 cut(s) 434, 840
BstYI RGATCY 2 cut(s) 434, 840
Bsu36I CCTNAGG 1 cut(s) 1150
BsuI GTATCC 1 cut(s) 1468
BsuRI GGCC 4 cut(s) 415, 588, 688, 781
BtsCI GGATG 1 cut(s) 1449
BtsIMutI CAGTG 2 cut(s) 506, 1307
BveI ACCTGC 1 cut(s) 1480
Cac8I GCNNGC 6 cut(s) 94, 408, 417, 586, 690, 1256
CaiI CAGNNNCTG 1 cut(s) 1309
CfoI GCGC 1 cut(s) 504
Cfr10I RCCGGY 2 cut(s) 293, 415
Cfr13I GGNCC 3 cut(s) 587, 686, 780
CseI GACGC 3 cut(s) 139, 271, 1217
Csp6I GTAC 2 cut(s) 212, 473
CviQI GTAC 2 cut(s) 212, 473
DdeI CTNAG 8 cut(s) 36, 114, 401, 948, 1150, 1224, 1327, 1645
DpnI GATC 5 cut(s) 231, 436, 610, 842, 1021
DpnII GATC 5 cut(s) 229, 434, 608, 840, 1019
DrdI GACNNNNNNGTC 1 cut(s) 1628
DseDI GACNNNNNNGTC 1 cut(s) 1628
Eam1104I CTCTTC 4 cut(s) 168, 175, 879, 1529
EarI CTCTTC 4 cut(s) 168, 175, 879, 1529
Ecl136II GAGCTC 1 cut(s) 544
Eco130I CCWWGG 2 cut(s) 1056, 1321
Eco24I GRGCYC 1 cut(s) 546
Eco31I GGTCTC 1 cut(s) 990
Eco32I GATATC 1 cut(s) 1218
Eco53kI GAGCTC 1 cut(s) 544
Eco57I CTGAAG 1 cut(s) 72
Eco81I CCTNAGG 1 cut(s) 1150
EcoICRI GAGCTC 1 cut(s) 544
EcoRI GAATTC 2 cut(s) 548, 1468
EcoRV GATATC 1 cut(s) 1218
EcoT14I CCWWGG 2 cut(s) 1056, 1321
EcoT38I GRGCYC 1 cut(s) 546
ErhI CCWWGG 2 cut(s) 1056, 1321
Esp3I CGTCTC 2 cut(s) 698, 1009
FalI AAGNNNNNCTT 2 cut(s) 1133, 1165
FauI CCCGC 1 cut(s) 85
FauNDI CATATG 1 cut(s) 911
Fnu4HI GCNGC 5 cut(s) 654, 890, 1050, 1053, 1252
FokI GGATG 1 cut(s) 1456
FriOI GRGCYC 1 cut(s) 546
Fsp4HI GCNGC 5 cut(s) 654, 890, 1050, 1053, 1252
FspBI CTAG 1 cut(s) 816
GlaI GCGC 1 cut(s) 503
GluI GCNGC 5 cut(s) 654, 890, 1050, 1053, 1252
GsaI CCCAGC 1 cut(s) 750
HaeIII GGCC 4 cut(s) 415, 588, 688, 781
HapII CCGG 6 cut(s) 63, 294, 416, 1012, 1100, 1397
HgaI GACGC 3 cut(s) 139, 271, 1217
HhaI GCGC 1 cut(s) 504
Hin1I GRCGYC 1 cut(s) 150
Hin6I GCGC 1 cut(s) 502
HinP1I GCGC 1 cut(s) 502
HindIII AAGCTT 1 cut(s) 320
HinfI GANTC 6 cut(s) 183, 370, 448, 1124, 1312, 1600
HpaII CCGG 6 cut(s) 63, 294, 416, 1012, 1100, 1397
HphI GGTGA 2 cut(s) 526, 1427
Hpy166II GTNNAC 1 cut(s) 1246
Hpy188I TCNGA 9 cut(s) 364, 604, 840, 858, 980, 1036, 1474, 1513, 1621
Hpy188III TCNNGA 4 cut(s) 524, 622, 1012, 1436
Hpy8I GTNNAC 1 cut(s) 1246
Hpy99I CGWCG 1 cut(s) 155
HpyAV CCTTC 2 cut(s) 975, 1396
HpyCH4III ACNGT 5 cut(s) 9, 23, 1204, 1270, 1458
HpyCH4IV ACGT 1 cut(s) 1284
HpyCH4V TGCA 5 cut(s) 106, 959, 1052, 1092, 1489
HpyF10VI GCNNNNNNNGC 5 cut(s) 403, 412, 416, 685, 743
HpyF3I CTNAG 8 cut(s) 36, 114, 401, 948, 1150, 1224, 1327, 1645
HpySE526I ACGT 1 cut(s) 1284
Hsp92I GRCGYC 1 cut(s) 150
HspAI GCGC 1 cut(s) 502
Kpn2I TCCGGA 1 cut(s) 1011
KroI GCCGGC 1 cut(s) 415
KroNI GCCGGC 1 cut(s) 417
Kzo9I GATC 5 cut(s) 229, 434, 608, 840, 1019
LguI GCTCTTC 1 cut(s) 879
LmnI GCTCC 2 cut(s) 541, 1615
Lsp1109I GCAGC 5 cut(s) 640, 901, 1036, 1064, 1263
LweI GCATC 3 cut(s) 79, 115, 174
MaeI CTAG 1 cut(s) 816
MaeII ACGT 1 cut(s) 1284
MaeIII GTNAC 5 cut(s) 3, 23, 845, 1229, 1280
MalI GATC 5 cut(s) 231, 436, 610, 842, 1021
MboI GATC 5 cut(s) 229, 434, 608, 840, 1019
MfeI CAATTG 2 cut(s) 1168, 1572
MflI RGATCY 2 cut(s) 434, 840
MhlI GDGCHC 3 cut(s) 546, 761, 1275
MlyI GAGTC 3 cut(s) 192, 1133, 1609
MroI TCCGGA 1 cut(s) 1011
MroNI GCCGGC 1 cut(s) 415
MroXI GAANNNNTTC 2 cut(s) 634, 1179
MseI TTAA 2 cut(s) 131, 444
MslI CAYNNNNRTG 3 cut(s) 818, 1118, 1362
MspI CCGG 6 cut(s) 63, 294, 416, 1012, 1100, 1397
MspR9I CCNGG 1 cut(s) 1397
MunI CAATTG 2 cut(s) 1168, 1572
MwoI GCNNNNNNNGC 5 cut(s) 403, 412, 416, 685, 743
NaeI GCCGGC 1 cut(s) 417
NciI CCSGG 1 cut(s) 1397
NdeI CATATG 1 cut(s) 911
NdeII GATC 5 cut(s) 229, 434, 608, 840, 1019
NgoMIV GCCGGC 1 cut(s) 415
NlaIV GGNNCC 1 cut(s) 589
NmuCI GTSAC 3 cut(s) 3, 23, 1229
NspI RCATGY 2 cut(s) 123, 1086
PciI ACATGT 1 cut(s) 1082
PciSI GCTCTTC 1 cut(s) 879
PdiI GCCGGC 1 cut(s) 417
PdmI GAANNNNTTC 2 cut(s) 634, 1179
PfeI GAWTC 3 cut(s) 370, 448, 1312
PkrI GCNGC 5 cut(s) 655, 891, 1051, 1054, 1253
PleI GAGTC 3 cut(s) 191, 1132, 1608
PpsI GAGTC 3 cut(s) 191, 1132, 1608
PscI ACATGT 1 cut(s) 1082
Psp124BI GAGCTC 1 cut(s) 546
PspFI CCCAGC 1 cut(s) 746
PspN4I GGNNCC 1 cut(s) 589
PspPI GGNCC 3 cut(s) 587, 686, 780
PsrI GAACNNNNNNTAC 2 cut(s) 1060, 1092
PstI CTGCAG 1 cut(s) 1054
PstNI CAGNNNCTG 1 cut(s) 1309
PsuI RGATCY 2 cut(s) 434, 840
RsaI GTAC 2 cut(s) 213, 474
RsaNI GTAC 2 cut(s) 212, 473
RseI CAYNNNNRTG 3 cut(s) 818, 1118, 1362
SacI GAGCTC 1 cut(s) 546
SapI GCTCTTC 1 cut(s) 879
SaqAI TTAA 2 cut(s) 131, 444
SatI GCNGC 5 cut(s) 654, 890, 1050, 1053, 1252
Sau3AI GATC 5 cut(s) 229, 434, 608, 840, 1019
Sau96I GGNCC 3 cut(s) 587, 686, 780
SchI GAGTC 3 cut(s) 192, 1133, 1609
ScrFI CCNGG 1 cut(s) 1397
SduI GDGCHC 3 cut(s) 546, 761, 1275
SfaNI GCATC 3 cut(s) 79, 115, 174
SfcI CTRYAG 2 cut(s) 553, 1050
SmiMI CAYNNNNRTG 3 cut(s) 818, 1118, 1362
SmlI CTYRAG 4 cut(s) 323, 674, 987, 1436
SmoI CTYRAG 4 cut(s) 323, 674, 987, 1436
SsiI CCGC 2 cut(s) 92, 737
SspMI CTAG 1 cut(s) 816
SstI GAGCTC 1 cut(s) 546
StyD4I CCNGG 1 cut(s) 1395
StyI CCWWGG 2 cut(s) 1056, 1321
TaaI ACNGT 5 cut(s) 9, 23, 1204, 1270, 1458
TaiI ACGT 1 cut(s) 1287
TaqI TCGA 3 cut(s) 546, 659, 1598
TaqII GACCGA 2 cut(s) 42, 824
TfiI GAWTC 3 cut(s) 370, 448, 1312
Tru1I TTAA 2 cut(s) 131, 444
Tru9I TTAA 2 cut(s) 131, 444
TscAI CASTG 2 cut(s) 513, 1314
TseFI GTSAC 3 cut(s) 3, 23, 1229
TseI GCWGC 5 cut(s) 653, 889, 1049, 1052, 1251
Tsp45I GTSAC 3 cut(s) 3, 23, 1229
TspDTI ATGAA 8 cut(s) 627, 894, 948, 1108, 1380, 1484, 1535, 1557
TspRI CASTG 2 cut(s) 513, 1314
XapI RAATTY 5 cut(s) 248, 548, 830, 1368, 1468
XceI RCATGY 2 cut(s) 123, 1086
XmnI GAANNNNTTC 2 cut(s) 634, 1179
XspI CTAG 1 cut(s) 816
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.