Rroxscaffold_4G00296330

mediator of RNA polymerase II transcription subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0003446
Physical Location & Seq
Reverse (-)
16394992 .. 16402201
7210 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00296330.1

Sequence Viewer

Length: 1263 bp
ATGGTGGAGGGTGGTGTGGAAGAGACGCCTAATGATGAAGGAATTGGGGCTGTGAAAGAAATGAACTCCAACATGCCTCAGCACCAAATTGTGCAATCCCCAGCTAGGCTAGGCCTGGCAAATCCCACTTCACCATCTCTTCAAAACCCTAATCCTCCAAAACCCCCTTCACAGCAATCCAATGCCTCTTCGACTCTTATCTCTCTTCTCCCACCCCTCCCTAGAGCACAGTCCCTTCTTGTCCAAATGGCCTCTCTAGCCTCCAAGCTCTTTGAAGTCTCGCCTAATCGGTCCCTCTGGCTCAATGCATTCCGTGGCTCGCTCCCAACCTTTCTGCCTTCCCAAAACCAGTCAGTGCCCATAGCCCCACTTGACTCCAATCCTTCCTCCACCAAAGACATTCTGTCCCAGTTCACAGTGCTTCAAACCCAACTCTTTCAGGCTGTTGCCGAGCTGCAGGAAATTCTTGATCTTCAGGACTCTAAGCTGAAAATTGCACAGGAAATCCGGTCCAAGGATGCTGCACTTCTTGCCTTTTCCAAGAAACTCAAGGATGCTGAGCAGATTCTTGATAACCTCGTTGATGACTACTCTGACTATCGCCGCCCCAAACGGCCAAAACTGGAGGATGATGATGCAGAGGATGAGGAATCTTCATGCACTACTACTGTTACATCTAAGTTGAAGTTATCAGATATTTTGTCATATGCCCACCGGATAAGCTACACAACCTTTGCACCGCCAGATTTTGGTGCCGGGCAAGCTCCTCTTCGTGGGGCACTACCACCTGCACCACAGGATGAGCAAATGCGTGCTTCTCAGCTATACCATTTTGCAAACCTTGATGTGGGATTACCTAAGACAGTTGAGAGCGAGGAGAAAACAATTGAAACAATTATTGAGCCCCCACCTCCACAACCAACAGAATACAATCAGGGTATTGAGAGCATGGTTCCATTTCAGGGTATGCTTCCTCCAAATTTCACAATTCCGTCAGGTTGGAAACCAGGAATGCCTGTGGAATTGCCAACTGATTTACCTGTTCCCCCACCTGGATGGAAGCCTGGGGACCCAGTGCCTCTGCCTCCATTGGACAATCTCCCCATACCTTTACCCCCACAAACACGGACTAATGCTCCTCAAGGAATACATAAACCACCAGAGACAATACAGGTTCAGCATGTTCAGCTCGATATTCTGGATCAAGATGATGATAGTAGTGATTATAGTAGCGACGAGGGAAGCTCTGAAGATGATGATTGA

Protein Analysis

420

Amino Acids

45.9

Weight (kDa)

4.47

Isoelectric Point (pI)

71.96

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Med4 PF10018 134 - 296 4.4e-12 Vitamin-D-receptor interacting Mediator subunit 4
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 796
Acc36I ACCTGC 1 cut(s) 796
AccB1I GGYRCC 1 cut(s) 752
AccB7I CCANNNNNTGG 1 cut(s) 749
AciI CCGC 2 cut(s) 604, 740
AclWI GGATC 1 cut(s) 1209
AcoI YGGCCR 1 cut(s) 614
AcsI RAATTY 2 cut(s) 462, 979
AcuI CTGAAG 1 cut(s) 458
AcyI GRCGYC 1 cut(s) 26
AfiI CCNNNNNNNGG 7 cut(s) 105, 514, 749, 773, 847, 962, 1052
AgsI TTSAA 5 cut(s) 143, 275, 425, 685, 890
AhdI GACNNNNNGTC 1 cut(s) 403
AjnI CCWGG 4 cut(s) 114, 1006, 1051, 1063
AjuI GAANNNNNNNTTGG 2 cut(s) 151, 183
AluBI AGCT 9 cut(s) 104, 268, 454, 487, 723, 764, 823, 1189, 1245
AluI AGCT 9 cut(s) 104, 268, 454, 487, 723, 764, 823, 1189, 1245
Alw21I GWGCWC 1 cut(s) 229
Alw26I GTCTC 3 cut(s) 17, 283, 1157
AlwI GGATC 1 cut(s) 1209
AoxI GGCC 3 cut(s) 112, 249, 614
ApeKI GCWGC 2 cut(s) 454, 521
ApoI RAATTY 2 cut(s) 462, 979
AspS9I GGNCC 3 cut(s) 291, 510, 1069
AsuC2I CCSGG 1 cut(s) 757
AsuHPI GGTGA 1 cut(s) 123
AvaII GGWCC 3 cut(s) 291, 510, 1069
BaeGI GKGCMC 2 cut(s) 360, 781
BanI GGYRCC 1 cut(s) 752
BanII GRGCYC 1 cut(s) 906
Bbv12I GWGCWC 1 cut(s) 229
BbvCI CCTCAGC 1 cut(s) 78
BbvI GCAGC 2 cut(s) 441, 508
BccI CCATC 2 cut(s) 142, 1050
BceAI ACGGC 1 cut(s) 629
BciT130I CCWGG 4 cut(s) 116, 1008, 1053, 1065
BcnI CCSGG 1 cut(s) 757
BcoDI GTCTC 3 cut(s) 17, 283, 1157
BfaI CTAG 4 cut(s) 105, 110, 222, 257
BfmI CTRYAG 1 cut(s) 455
BfuAI ACCTGC 1 cut(s) 796
BisI GCNGC 3 cut(s) 455, 522, 604
BlpI GCTNAGC 1 cut(s) 558
BlsI GCNGC 3 cut(s) 456, 523, 605
Bme1390I CCNGG 5 cut(s) 116, 757, 1008, 1053, 1065
Bme18I GGWCC 3 cut(s) 291, 510, 1069
BmeRI GACNNNNNGTC 1 cut(s) 403
BmgT120I GGNCC 3 cut(s) 291, 510, 1069
BmiI GGNNCC 5 cut(s) 293, 754, 954, 1070, 1071
BmrFI CCNGG 5 cut(s) 116, 757, 1008, 1053, 1065
BmrI ACTGGG 2 cut(s) 403, 1067
BmsI GCATC 3 cut(s) 508, 544, 625
BmuI ACTGGG 2 cut(s) 403, 1067
BplI GAGNNNNNCTC 2 cut(s) 1229, 1261
BpmI CTGGAG 1 cut(s) 644
Bpu10I CCTNAGC 1 cut(s) 78
Bpu1102I GCTNAGC 1 cut(s) 558
BpuEI CTTGAG 2 cut(s) 533, 1125
BpuMI CCSGG 1 cut(s) 757
BsaHI GRCGYC 1 cut(s) 26
BsaJI CCNNGG 3 cut(s) 313, 513, 1064
BsaWI WCCGGW 2 cut(s) 507, 714
BsaXI ACNNNNNCTCC 2 cut(s) 1120, 1150
Bsc4I CCNNNNNNNGG 7 cut(s) 105, 514, 749, 773, 847, 962, 1052
Bse1I ACTGG 4 cut(s) 349, 409, 627, 1073
BseBI CCWGG 4 cut(s) 116, 1008, 1053, 1065
BseDI CCNNGG 3 cut(s) 313, 513, 1064
BseGI GGATG 6 cut(s) 523, 559, 634, 649, 805, 1061
BseLI CCNNNNNNNGG 7 cut(s) 105, 514, 749, 773, 847, 962, 1052
BseMII CTCAG 3 cut(s) 92, 549, 833
BseNI ACTGG 4 cut(s) 349, 409, 627, 1073
BseRI GAGGAG 3 cut(s) 756, 890, 1128
BseSI GKGCMC 2 cut(s) 360, 781
BseXI GCAGC 2 cut(s) 441, 508
BseYI CCCAGC 1 cut(s) 100
BsgI GTGCAG 2 cut(s) 507, 774
BshFI GGCC 3 cut(s) 114, 251, 616
BshNI GGYRCC 1 cut(s) 752
BsiHKAI GWGCWC 1 cut(s) 229
BsiSI CCGG 3 cut(s) 508, 715, 756
BslFI GGGAC 4 cut(s) 217, 277, 391, 1082
BslI CCNNNNNNNGG 7 cut(s) 105, 514, 749, 773, 847, 962, 1052
BsmAI GTCTC 3 cut(s) 17, 283, 1157
BsmBI CGTCTC 1 cut(s) 17
BsmFI GGGAC 4 cut(s) 217, 277, 391, 1082
BsmI GAATGC 2 cut(s) 308, 1017
BsnI GGCC 3 cut(s) 114, 251, 616
Bsp1286I GDGCHC 4 cut(s) 229, 360, 781, 906
Bsp143I GATC 2 cut(s) 469, 1201
Bsp1720I GCTNAGC 1 cut(s) 558
BspACI CCGC 2 cut(s) 604, 740
BspANI GGCC 3 cut(s) 114, 251, 616
BspCNI CTCAG 3 cut(s) 91, 550, 832
BspLI GGNNCC 5 cut(s) 293, 754, 954, 1070, 1071
BspMAI CTGCAG 1 cut(s) 459
BspMI ACCTGC 1 cut(s) 796
BspPI GGATC 1 cut(s) 1209
BspT107I GGYRCC 1 cut(s) 752
BsrI ACTGG 4 cut(s) 349, 409, 627, 1073
BssECI CCNNGG 3 cut(s) 313, 513, 1064
BssMI GATC 2 cut(s) 469, 1201
BssNI GRCGYC 1 cut(s) 26
BssT1I CCWWGG 1 cut(s) 513
Bst2UI CCWGG 4 cut(s) 116, 1008, 1053, 1065
Bst4CI ACNGT 4 cut(s) 231, 418, 670, 865
Bst6I CTCTTC 5 cut(s) 15, 144, 193, 210, 774
BstACI GRCGYC 1 cut(s) 26
BstAPI GCANNNNNTGC 1 cut(s) 530
BstC8I GCNNGC 3 cut(s) 320, 762, 813
BstDEI CTNAG 6 cut(s) 78, 483, 558, 678, 819, 858
BstDSI CCRYGG 1 cut(s) 313
BstF5I GGATG 6 cut(s) 523, 559, 634, 649, 805, 1061
BstKTI GATC 2 cut(s) 472, 1204
BstMAI GTCTC 3 cut(s) 17, 283, 1157
BstMBI GATC 2 cut(s) 469, 1201
BstMWI GCNNNNNNNGC 4 cut(s) 257, 530, 761, 1186
BstNI CCWGG 4 cut(s) 116, 1008, 1053, 1065
BstNSI RCATGY 2 cut(s) 76, 1184
BstSCI CCNGG 5 cut(s) 114, 755, 1006, 1051, 1063
BstSFI CTRYAG 1 cut(s) 455
BstSLI GKGCMC 2 cut(s) 360, 781
BstV1I GCAGC 2 cut(s) 441, 508
BstXI CCANNNNNNTGG 1 cut(s) 1056
BsuRI GGCC 3 cut(s) 114, 251, 616
BtgI CCRYGG 1 cut(s) 313
BtsCI GGATG 6 cut(s) 523, 559, 634, 649, 805, 1061
BtsIMutI CAGTG 3 cut(s) 360, 423, 1080
BveI ACCTGC 1 cut(s) 796
Cac8I GCNNGC 3 cut(s) 320, 762, 813
Cfr13I GGNCC 3 cut(s) 291, 510, 1069
CseI GACGC 1 cut(s) 34
CviAII CATG 4 cut(s) 73, 657, 949, 1181
DdeI CTNAG 6 cut(s) 78, 483, 558, 678, 819, 858
DpnI GATC 2 cut(s) 471, 1203
DpnII GATC 2 cut(s) 469, 1201
DriI GACNNNNNGTC 1 cut(s) 403
EaeI YGGCCR 1 cut(s) 614
Eam1104I CTCTTC 5 cut(s) 15, 144, 193, 210, 774
Eam1105I GACNNNNNGTC 1 cut(s) 403
EarI CTCTTC 5 cut(s) 15, 144, 193, 210, 774
Eco130I CCWWGG 1 cut(s) 513
Eco147I AGGCCT 1 cut(s) 114
Eco24I GRGCYC 1 cut(s) 906
Eco47I GGWCC 3 cut(s) 291, 510, 1069
Eco57I CTGAAG 1 cut(s) 458
EcoO109I RGGNCCY 1 cut(s) 1069
EcoRII CCWGG 4 cut(s) 114, 1006, 1051, 1063
EcoT14I CCWWGG 1 cut(s) 513
EcoT22I ATGCAT 1 cut(s) 310
EcoT38I GRGCYC 1 cut(s) 906
ErhI CCWWGG 1 cut(s) 513
Esp3I CGTCTC 1 cut(s) 17
FaeI CATG 4 cut(s) 76, 660, 952, 1184
FalI AAGNNNNNCTT 2 cut(s) 753, 785
FaqI GGGAC 4 cut(s) 217, 277, 391, 1082
FatI CATG 4 cut(s) 72, 656, 948, 1180
FauNDI CATATG 1 cut(s) 706
Fnu4HI GCNGC 3 cut(s) 455, 522, 604
FokI GGATG 6 cut(s) 530, 566, 641, 656, 812, 1068
FriOI GRGCYC 1 cut(s) 906
Fsp4HI GCNGC 3 cut(s) 455, 522, 604
FspBI CTAG 4 cut(s) 105, 110, 222, 257
GluI GCNGC 3 cut(s) 455, 522, 604
GsaI CCCAGC 1 cut(s) 104
GsuI CTGGAG 1 cut(s) 644
HaeIII GGCC 3 cut(s) 114, 251, 616
HapII CCGG 3 cut(s) 508, 715, 756
HgaI GACGC 1 cut(s) 34
Hin1I GRCGYC 1 cut(s) 26
Hin1II CATG 4 cut(s) 76, 660, 952, 1184
HinfI GANTC 5 cut(s) 193, 374, 479, 565, 650
HpaII CCGG 3 cut(s) 508, 715, 756
HphI GGTGA 1 cut(s) 123
Hpy166II GTNNAC 1 cut(s) 414
Hpy188I TCNGA 3 cut(s) 595, 694, 1249
Hpy188III TCNNGA 5 cut(s) 467, 476, 569, 1199, 1205
Hpy8I GTNNAC 1 cut(s) 414
Hpy99I CGWCG 1 cut(s) 1238
HpyAV CCTTC 5 cut(s) 32, 177, 245, 348, 393
HpyCH4III ACNGT 4 cut(s) 231, 418, 670, 865
HpyF10VI GCNNNNNNNGC 4 cut(s) 257, 530, 761, 1186
HpyF3I CTNAG 6 cut(s) 78, 483, 558, 678, 819, 858
Hsp92I GRCGYC 1 cut(s) 26
Hsp92II CATG 4 cut(s) 76, 660, 952, 1184
KflI GGGWCCC 1 cut(s) 1069
Kzo9I GATC 2 cut(s) 469, 1201
LmnI GCTCC 3 cut(s) 327, 769, 1141
Lsp1109I GCAGC 2 cut(s) 441, 508
LweI GCATC 3 cut(s) 508, 544, 625
MaeI CTAG 4 cut(s) 105, 110, 222, 257
MaeIII GTNAC 1 cut(s) 670
MalI GATC 2 cut(s) 471, 1203
MboI GATC 2 cut(s) 469, 1201
MboII GAAGA 8 cut(s) 32, 131, 180, 197, 464, 645, 761, 1262
MfeI CAATTG 1 cut(s) 885
MhlI GDGCHC 4 cut(s) 229, 360, 781, 906
MluCI AATT 9 cut(s) 42, 87, 462, 492, 885, 894, 979, 987, 1022
MlyI GAGTC 3 cut(s) 187, 368, 473
MmeI TCCRAC 2 cut(s) 93, 980
Mph1103I ATGCAT 1 cut(s) 310
MslI CAYNNNNRTG 1 cut(s) 1054
MspI CCGG 3 cut(s) 508, 715, 756
MspR9I CCNGG 5 cut(s) 116, 757, 1008, 1053, 1065
MunI CAATTG 1 cut(s) 885
Mva1269I GAATGC 2 cut(s) 308, 1017
MvaI CCWGG 4 cut(s) 116, 1008, 1053, 1065
MwoI GCNNNNNNNGC 4 cut(s) 257, 530, 761, 1186
NciI CCSGG 1 cut(s) 757
NdeI CATATG 1 cut(s) 706
NdeII GATC 2 cut(s) 469, 1201
NlaIII CATG 4 cut(s) 76, 660, 952, 1184
NlaIV GGNNCC 5 cut(s) 293, 754, 954, 1070, 1071
NmeAIII GCCGAG 1 cut(s) 475
NsiI ATGCAT 1 cut(s) 310
NspI RCATGY 2 cut(s) 76, 1184
PaqCI CACCTGC 1 cut(s) 796
PceI AGGCCT 1 cut(s) 114
PctI GAATGC 2 cut(s) 308, 1017
PfeI GAWTC 2 cut(s) 565, 650
PflMI CCANNNNNTGG 1 cut(s) 749
PkrI GCNGC 3 cut(s) 456, 523, 605
PleI GAGTC 3 cut(s) 187, 368, 473
PpsI GAGTC 3 cut(s) 187, 368, 473
PpuMI RGGWCCY 1 cut(s) 1069
Psp5II RGGWCCY 1 cut(s) 1069
Psp6I CCWGG 4 cut(s) 114, 1006, 1051, 1063
PspFI CCCAGC 1 cut(s) 100
PspGI CCWGG 4 cut(s) 114, 1006, 1051, 1063
PspN4I GGNNCC 5 cut(s) 293, 754, 954, 1070, 1071
PspPI GGNCC 3 cut(s) 291, 510, 1069
PspPPI RGGWCCY 1 cut(s) 1069
PstI CTGCAG 1 cut(s) 459
RseI CAYNNNNRTG 1 cut(s) 1054
SatI GCNGC 3 cut(s) 455, 522, 604
Sau3AI GATC 2 cut(s) 469, 1201
Sau96I GGNCC 3 cut(s) 291, 510, 1069
SchI GAGTC 3 cut(s) 187, 368, 473
ScrFI CCNGG 5 cut(s) 116, 757, 1008, 1053, 1065
SduI GDGCHC 4 cut(s) 229, 360, 781, 906
SfaNI GCATC 3 cut(s) 508, 544, 625
SfcI CTRYAG 1 cut(s) 455
SinI GGWCC 3 cut(s) 291, 510, 1069
SmiMI CAYNNNNRTG 1 cut(s) 1054
SmlI CTYRAG 2 cut(s) 548, 1140
SmoI CTYRAG 2 cut(s) 548, 1140
Sse9I AATT 9 cut(s) 42, 87, 462, 492, 885, 894, 979, 987, 1022
SseBI AGGCCT 1 cut(s) 114
SsiI CCGC 2 cut(s) 604, 740
SspMI CTAG 4 cut(s) 105, 110, 222, 257
StuI AGGCCT 1 cut(s) 114
StyD4I CCNGG 5 cut(s) 114, 755, 1006, 1051, 1063
StyI CCWWGG 1 cut(s) 513
TaaI ACNGT 4 cut(s) 231, 418, 670, 865
TaqI TCGA 2 cut(s) 191, 1191
TaqII GACCGA 1 cut(s) 279
TasI AATT 9 cut(s) 42, 87, 462, 492, 885, 894, 979, 987, 1022
TauI GCSGC 1 cut(s) 606
TfiI GAWTC 2 cut(s) 565, 650
TscAI CASTG 3 cut(s) 360, 423, 1080
TseI GCWGC 2 cut(s) 454, 521
TspDTI ATGAA 3 cut(s) 51, 77, 645
TspGWI ACGGA 3 cut(s) 302, 981, 1141
TspRI CASTG 3 cut(s) 360, 423, 1080
Van91I CCANNNNNTGG 1 cut(s) 749
VpaK11BI GGWCC 3 cut(s) 291, 510, 1069
XapI RAATTY 2 cut(s) 462, 979
XceI RCATGY 2 cut(s) 76, 1184
XspI CTAG 4 cut(s) 105, 110, 222, 257
Zsp2I ATGCAT 1 cut(s) 310
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.