Rroxscaffold_1G00067840

Histone deacetylase HDT1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0002833
Physical Location & Seq
Forward (+)
89131601 .. 89137325
5725 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00067840.1

Sequence Viewer

Length: 1662 bp
ATGTCACCGTTTTGCCCTAACTGTGACCGAGAACCTGAGTTTTGGGGTGCTGAAGTGAAATCCGGCGAGAAGTTGAAAGTGAAGCCAGATGCGGGCGTGGTTTTGCATCTCACTCAGGCATGTGTGGGCTTAAATCAAAGATGTCATGGCGTCGTTTATGTGAGCATCGGGGAAGAGAGAAGAGTCTTGGGAAGTCTCTTGCCACCAAGAGTACCTCAATTTTCCTGCGATCTGGTCTTTGACCAAGAATTTCTGCTTTCACACAACTTGGAGATGGGAAGCGTCTTCTTTGCCGGTTATTCTTGCTTTAGTAAAAATAAGCTTGAGGAAACAAAGCAAACTACAAGTAAGACCAAATCTTCTGATGAGAATCCAATCTGTGAGGAAAAGAGAGAGCCTCTTAGGCAAGCAAGGCCGGCAATAGGGAAGACCAGATCTTCTGTTAAGAATCCAATCATTGAGGAAAATAGAGTACCTATTGACAAAGCTGACTTTGTTGTGCGCCCACTGGTGGTGAGAAGTCCAGAGAACATAAGTAAGGAGCTCGAATTCTATAGAACTATTTTTGAGGCTGAACCGATTGCTGGCCCCCAGATTGGGTCTGAAAGATCGCATGAGTTCAAGATTGGAAATAATTCATTATATGTTGTTGCTGCTTCGACTATTGAGGAACTTGAGCCTCTTGGGCCTGCCCTTTGTGTGGAGACGGGAGATGTAGCAACTTTTATTGAGAAAGCGGAAAATGCTGGGTGGAAGTGCTCTGTCCTTGAAAGGTATCGGCCCAATATCACGCCAGATGATAAGTTGAGTGGCACTAGAATGAGAACTAAATTCGGTCAGATCTGTTACATCTGTCAGACACCCCAAACAAGAAACAATGTAGAAGAAGAGCAGCAAACAAAAATCAAGTCCATATGCCCTACAATGCTATTTTATGAAGATGAGTTTGCTGAGGCAGTTGCAAATTATGAGGCTGTTTTCGGAAGGTCTCAAGGCTCGTTCTTTCAGTTGTTCCGGAGACGATCTACCTCTTTTTCAGACTGCCTCTATGCTGCAGCCAAGGATAGGGGTATTGGCAGTTCTACATGTCTCTGCATAGAGCCGGAGGATATTGTCATTTTCATGGAGTCGTTCTTTACTTTGAAGTCGTCCTTAGGTTTCTTCTATCTCAATTGTGAAGTGGTTCTACATGACTGGGGAAAGACAGTTGTGAGATTGATATCTCCTAAGCGTCACACTCTTTATGTTTACAGCAGCAAGCCATCATTGACTGTGCTCTCATGTAACGTAAAGCATGGTGCTATACAGCCACTGATTCAGTTCCTTGGCTCAGTCAGTCAAGTAAAATGGGTCAAAATCCATGTAGATGAAATTCCTCGTTGCTTGTCCTTCCCTTACCCGGATTTGCTGATTATTGGTGATGAGATGATACTTACTCTTGAGAGGATGGAAAAAAAACTGTCTTCAAGGAATTCGGATACCAAGTTATTGCAGGTTCATGGGCAACCAGTATCAGAAGACATGAAAAGATTGTTGAAGAGGCATGAAGCAAAATATGTAGGTTTGCCTTTGACAATTGAGAATGTTGAACAAGTTTATTCGAGTCTTTCTGCTCCAAAATCAGACAAGTGGGTCTATCTTCCTCACTTAGAATGGGCATGA
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

553

Amino Acids

62.6

Weight (kDa)

6.46

Isoelectric Point (pI)

49.94

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) 1631
Acc36I ACCTGC 1 cut(s) 1483
AccIII TCCGGA 1 cut(s) 1014
AciI CCGC 2 cut(s) 92, 737
AcsI RAATTY 5 cut(s) 248, 548, 830, 1371, 1471
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, 1065, 1399
AflIII ACRYGT 1 cut(s) 1085
AgsI TTSAA 7 cut(s) 76, 622, 770, 1144, 1467, 1537, 1589
AluBI AGCT 3 cut(s) 322, 488, 544
AluI AGCT 3 cut(s) 322, 488, 544
Alw21I GWGCWC 3 cut(s) 546, 761, 1278
Alw26I GTCTC 5 cut(s) 200, 698, 993, 1012, 1094
AlwNI CAGNNNCTG 1 cut(s) 1312
Aor13HI TCCGGA 1 cut(s) 1014
AoxI GGCC 4 cut(s) 413, 586, 686, 779
ApeKI GCWGC 5 cut(s) 653, 892, 1052, 1055, 1254
ApoI RAATTY 5 cut(s) 248, 548, 830, 1371, 1471
ArsI GACNNNNNNTTYG 2 cut(s) 893, 925
Asp700I GAANNNNTTC 2 cut(s) 634, 1182
AspLEI GCGC 1 cut(s) 504
AspS9I GGNCC 3 cut(s) 587, 686, 780
AsuC2I CCSGG 1 cut(s) 1400
AsuHPI GGTGA 2 cut(s) 526, 1430
AxyI CCTNAGG 1 cut(s) 1153
BanII GRGCYC 1 cut(s) 546
BarI GAAGNNNNNNTAC 2 cut(s) 1170, 1202
BbsI GAAGAC 4 cut(s) 277, 434, 1455, 1524
Bbv12I GWGCWC 3 cut(s) 546, 761, 1278
BbvCI CCTCAGC 1 cut(s) 951
BbvI GCAGC 5 cut(s) 640, 904, 1039, 1067, 1266
BccI CCATC 3 cut(s) 268, 1270, 1441
BciVI GTATCC 1 cut(s) 1471
BcnI CCSGG 1 cut(s) 1400
BcoDI GTCTC 5 cut(s) 200, 698, 993, 1012, 1094
BfaI CTAG 1 cut(s) 816
BfmI CTRYAG 2 cut(s) 553, 1053
BfuAI ACCTGC 1 cut(s) 1483
BfuI GTATCC 1 cut(s) 1471
BglI GCCNNNNNGGC 2 cut(s) 403, 685
BglII AGATCT 2 cut(s) 434, 840
BisI GCNGC 5 cut(s) 654, 893, 1053, 1056, 1255
BlsI GCNGC 5 cut(s) 655, 894, 1054, 1057, 1256
Bme1390I CCNGG 1 cut(s) 1400
BmgT120I GGNCC 3 cut(s) 587, 686, 780
BmiI GGNNCC 1 cut(s) 589
BmrFI CCNGG 1 cut(s) 1400
BmrI ACTGGG 1 cut(s) 1204
BmsI GCATC 3 cut(s) 79, 115, 174
BmuI ACTGGG 1 cut(s) 1204
BpiI GAAGAC 4 cut(s) 277, 434, 1455, 1524
BplI GAGNNNNNCTC 2 cut(s) 382, 414
Bpu10I CCTNAGC 2 cut(s) 951, 1227
BpuEI CTTGAG 4 cut(s) 344, 695, 975, 1460
BpuMI CCSGG 1 cut(s) 1400
BsaBI GATNNNNATC 2 cut(s) 369, 1219
BsaHI GRCGYC 1 cut(s) 150
BsaI GGTCTC 1 cut(s) 993
BsaJI CCNNGG 2 cut(s) 1059, 1324
BsaWI WCCGGW 1 cut(s) 1014
Bsc4I CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1065, 1399
Bse118I RCCGGY 2 cut(s) 293, 415
Bse1I ACTGG 3 cut(s) 513, 1199, 1508
Bse21I CCTNAGG 1 cut(s) 1153
Bse8I GATNNNNATC 2 cut(s) 369, 1219
BseAI TCCGGA 1 cut(s) 1014
BseDI CCNNGG 2 cut(s) 1059, 1324
BseGI GGATG 1 cut(s) 1452
BseJI GATNNNNATC 2 cut(s) 369, 1219
BseLI CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1065, 1399
BseMII CTCAG 4 cut(s) 27, 128, 942, 1344
BseNI ACTGG 3 cut(s) 513, 1199, 1508
BseXI GCAGC 5 cut(s) 640, 904, 1039, 1067, 1266
BseYI CCCAGC 1 cut(s) 746
BshFI GGCC 4 cut(s) 415, 588, 688, 781
BsiHKAI GWGCWC 3 cut(s) 546, 761, 1278
BsiSI CCGG 6 cut(s) 63, 294, 416, 1015, 1103, 1400
BslI CCNNNNNNNGG 9 cut(s) 92, 422, 511, 584, 596, 597, 700, 1065, 1399
BsmAI GTCTC 5 cut(s) 200, 698, 993, 1012, 1094
BsmBI CGTCTC 2 cut(s) 698, 1012
BsnI GGCC 4 cut(s) 415, 588, 688, 781
Bso31I GGTCTC 1 cut(s) 993
Bsp1286I GDGCHC 3 cut(s) 546, 761, 1278
Bsp13I TCCGGA 1 cut(s) 1014
Bsp143I GATC 5 cut(s) 229, 434, 608, 840, 1022
BspACI CCGC 2 cut(s) 92, 737
BspANI GGCC 4 cut(s) 415, 588, 688, 781
BspCNI CTCAG 4 cut(s) 28, 127, 943, 1343
BspEI TCCGGA 1 cut(s) 1014
BspLI GGNNCC 1 cut(s) 589
BspMAI CTGCAG 1 cut(s) 1057
BspMI ACCTGC 1 cut(s) 1483
BspQI GCTCTTC 1 cut(s) 882
BspTNI GGTCTC 1 cut(s) 993
BsrFI RCCGGY 2 cut(s) 293, 415
BsrI ACTGG 3 cut(s) 513, 1199, 1508
BssAI RCCGGY 2 cut(s) 293, 415
BssECI CCNNGG 2 cut(s) 1059, 1324
BssMI GATC 5 cut(s) 229, 434, 608, 840, 1022
BssNI GRCGYC 1 cut(s) 150
BssT1I CCWWGG 2 cut(s) 1059, 1324
Bst4CI ACNGT 5 cut(s) 9, 23, 1207, 1273, 1461
Bst6I CTCTTC 4 cut(s) 168, 175, 882, 1532
BstACI GRCGYC 1 cut(s) 150
BstC8I GCNNGC 6 cut(s) 94, 408, 417, 586, 690, 1259
BstDEI CTNAG 8 cut(s) 36, 114, 401, 951, 1153, 1227, 1330, 1648
BstF5I GGATG 1 cut(s) 1452
BstHHI GCGC 1 cut(s) 504
BstKTI GATC 5 cut(s) 232, 437, 611, 843, 1025
BstMAI GTCTC 5 cut(s) 200, 698, 993, 1012, 1094
BstMBI GATC 5 cut(s) 229, 434, 608, 840, 1022
BstMWI GCNNNNNNNGC 5 cut(s) 403, 412, 416, 685, 743
BstNSI RCATGY 2 cut(s) 123, 1089
BstSCI CCNGG 1 cut(s) 1398
BstSFI CTRYAG 2 cut(s) 553, 1053
BstV1I GCAGC 5 cut(s) 640, 904, 1039, 1067, 1266
BstV2I GAAGAC 4 cut(s) 277, 434, 1455, 1524
BstX2I RGATCY 2 cut(s) 434, 840
BstYI RGATCY 2 cut(s) 434, 840
Bsu36I CCTNAGG 1 cut(s) 1153
BsuI GTATCC 1 cut(s) 1471
BsuRI GGCC 4 cut(s) 415, 588, 688, 781
BtsCI GGATG 1 cut(s) 1452
BtsIMutI CAGTG 2 cut(s) 506, 1310
BveI ACCTGC 1 cut(s) 1483
Cac8I GCNNGC 6 cut(s) 94, 408, 417, 586, 690, 1259
CaiI CAGNNNCTG 1 cut(s) 1312
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, 1220
Csp6I GTAC 2 cut(s) 212, 473
CviQI GTAC 2 cut(s) 212, 473
DdeI CTNAG 8 cut(s) 36, 114, 401, 951, 1153, 1227, 1330, 1648
DpnI GATC 5 cut(s) 231, 436, 610, 842, 1024
DpnII GATC 5 cut(s) 229, 434, 608, 840, 1022
DrdI GACNNNNNNGTC 1 cut(s) 1631
DseDI GACNNNNNNGTC 1 cut(s) 1631
Eam1104I CTCTTC 4 cut(s) 168, 175, 882, 1532
EarI CTCTTC 4 cut(s) 168, 175, 882, 1532
Ecl136II GAGCTC 1 cut(s) 544
Eco130I CCWWGG 2 cut(s) 1059, 1324
Eco24I GRGCYC 1 cut(s) 546
Eco31I GGTCTC 1 cut(s) 993
Eco32I GATATC 1 cut(s) 1221
Eco53kI GAGCTC 1 cut(s) 544
Eco57I CTGAAG 1 cut(s) 72
Eco81I CCTNAGG 1 cut(s) 1153
EcoICRI GAGCTC 1 cut(s) 544
EcoRI GAATTC 2 cut(s) 548, 1471
EcoRV GATATC 1 cut(s) 1221
EcoT14I CCWWGG 2 cut(s) 1059, 1324
EcoT38I GRGCYC 1 cut(s) 546
ErhI CCWWGG 2 cut(s) 1059, 1324
Esp3I CGTCTC 2 cut(s) 698, 1012
FalI AAGNNNNNCTT 2 cut(s) 1136, 1168
FauI CCCGC 1 cut(s) 85
FauNDI CATATG 1 cut(s) 914
Fnu4HI GCNGC 5 cut(s) 654, 893, 1053, 1056, 1255
FokI GGATG 1 cut(s) 1459
FriOI GRGCYC 1 cut(s) 546
Fsp4HI GCNGC 5 cut(s) 654, 893, 1053, 1056, 1255
FspBI CTAG 1 cut(s) 816
GlaI GCGC 1 cut(s) 503
GluI GCNGC 5 cut(s) 654, 893, 1053, 1056, 1255
GsaI CCCAGC 1 cut(s) 750
HaeIII GGCC 4 cut(s) 415, 588, 688, 781
HapII CCGG 6 cut(s) 63, 294, 416, 1015, 1103, 1400
HgaI GACGC 3 cut(s) 139, 271, 1220
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, 1127, 1315, 1603
HpaII CCGG 6 cut(s) 63, 294, 416, 1015, 1103, 1400
HphI GGTGA 2 cut(s) 526, 1430
Hpy166II GTNNAC 1 cut(s) 1249
Hpy188I TCNGA 9 cut(s) 364, 604, 840, 858, 983, 1039, 1477, 1516, 1624
Hpy188III TCNNGA 4 cut(s) 524, 622, 1015, 1439
Hpy8I GTNNAC 1 cut(s) 1249
Hpy99I CGWCG 1 cut(s) 155
HpyAV CCTTC 2 cut(s) 978, 1399
HpyCH4III ACNGT 5 cut(s) 9, 23, 1207, 1273, 1461
HpyCH4IV ACGT 1 cut(s) 1287
HpyCH4V TGCA 5 cut(s) 106, 962, 1055, 1095, 1492
HpyF10VI GCNNNNNNNGC 5 cut(s) 403, 412, 416, 685, 743
HpyF3I CTNAG 8 cut(s) 36, 114, 401, 951, 1153, 1227, 1330, 1648
HpySE526I ACGT 1 cut(s) 1287
Hsp92I GRCGYC 1 cut(s) 150
HspAI GCGC 1 cut(s) 502
Kpn2I TCCGGA 1 cut(s) 1014
KroI GCCGGC 1 cut(s) 415
KroNI GCCGGC 1 cut(s) 417
Kzo9I GATC 5 cut(s) 229, 434, 608, 840, 1022
LguI GCTCTTC 1 cut(s) 882
LmnI GCTCC 2 cut(s) 541, 1618
Lsp1109I GCAGC 5 cut(s) 640, 904, 1039, 1067, 1266
LweI GCATC 3 cut(s) 79, 115, 174
MaeI CTAG 1 cut(s) 816
MaeII ACGT 1 cut(s) 1287
MaeIII GTNAC 5 cut(s) 3, 23, 845, 1232, 1283
MalI GATC 5 cut(s) 231, 436, 610, 842, 1024
MboI GATC 5 cut(s) 229, 434, 608, 840, 1022
MfeI CAATTG 2 cut(s) 1171, 1575
MflI RGATCY 2 cut(s) 434, 840
MhlI GDGCHC 3 cut(s) 546, 761, 1278
MlyI GAGTC 3 cut(s) 192, 1136, 1612
MroI TCCGGA 1 cut(s) 1014
MroNI GCCGGC 1 cut(s) 415
MroXI GAANNNNTTC 2 cut(s) 634, 1182
MseI TTAA 2 cut(s) 131, 444
MslI CAYNNNNRTG 3 cut(s) 818, 1121, 1365
MspI CCGG 6 cut(s) 63, 294, 416, 1015, 1103, 1400
MspR9I CCNGG 1 cut(s) 1400
MunI CAATTG 2 cut(s) 1171, 1575
MwoI GCNNNNNNNGC 5 cut(s) 403, 412, 416, 685, 743
NaeI GCCGGC 1 cut(s) 417
NciI CCSGG 1 cut(s) 1400
NdeI CATATG 1 cut(s) 914
NdeII GATC 5 cut(s) 229, 434, 608, 840, 1022
NgoMIV GCCGGC 1 cut(s) 415
NlaIV GGNNCC 1 cut(s) 589
NmuCI GTSAC 3 cut(s) 3, 23, 1232
NspI RCATGY 2 cut(s) 123, 1089
PciI ACATGT 1 cut(s) 1085
PciSI GCTCTTC 1 cut(s) 882
PdiI GCCGGC 1 cut(s) 417
PdmI GAANNNNTTC 2 cut(s) 634, 1182
PfeI GAWTC 3 cut(s) 370, 448, 1315
PkrI GCNGC 5 cut(s) 655, 894, 1054, 1057, 1256
PleI GAGTC 3 cut(s) 191, 1135, 1611
PpsI GAGTC 3 cut(s) 191, 1135, 1611
PscI ACATGT 1 cut(s) 1085
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) 1063, 1095
PstI CTGCAG 1 cut(s) 1057
PstNI CAGNNNCTG 1 cut(s) 1312
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, 1121, 1365
SacI GAGCTC 1 cut(s) 546
SapI GCTCTTC 1 cut(s) 882
SaqAI TTAA 2 cut(s) 131, 444
SatI GCNGC 5 cut(s) 654, 893, 1053, 1056, 1255
Sau3AI GATC 5 cut(s) 229, 434, 608, 840, 1022
Sau96I GGNCC 3 cut(s) 587, 686, 780
SchI GAGTC 3 cut(s) 192, 1136, 1612
ScrFI CCNGG 1 cut(s) 1400
SduI GDGCHC 3 cut(s) 546, 761, 1278
SfaNI GCATC 3 cut(s) 79, 115, 174
SfcI CTRYAG 2 cut(s) 553, 1053
SmiMI CAYNNNNRTG 3 cut(s) 818, 1121, 1365
SmlI CTYRAG 4 cut(s) 323, 674, 990, 1439
SmoI CTYRAG 4 cut(s) 323, 674, 990, 1439
SsiI CCGC 2 cut(s) 92, 737
SspMI CTAG 1 cut(s) 816
SstI GAGCTC 1 cut(s) 546
StyD4I CCNGG 1 cut(s) 1398
StyI CCWWGG 2 cut(s) 1059, 1324
TaaI ACNGT 5 cut(s) 9, 23, 1207, 1273, 1461
TaiI ACGT 1 cut(s) 1290
TaqI TCGA 3 cut(s) 546, 659, 1601
TaqII GACCGA 2 cut(s) 42, 824
TfiI GAWTC 3 cut(s) 370, 448, 1315
Tru1I TTAA 2 cut(s) 131, 444
Tru9I TTAA 2 cut(s) 131, 444
TscAI CASTG 2 cut(s) 513, 1317
TseFI GTSAC 3 cut(s) 3, 23, 1232
TseI GCWGC 5 cut(s) 653, 892, 1052, 1055, 1254
Tsp45I GTSAC 3 cut(s) 3, 23, 1232
TspDTI ATGAA 7 cut(s) 627, 951, 1111, 1383, 1487, 1538, 1560
TspRI CASTG 2 cut(s) 513, 1317
XapI RAATTY 5 cut(s) 248, 548, 830, 1371, 1471
XceI RCATGY 2 cut(s) 123, 1089
XmnI GAANNNNTTC 2 cut(s) 634, 1182
XspI CTAG 1 cut(s) 816
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.