Rw3G006790

RNA polymerase II-associated protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0005138
Physical Location & Seq
Reverse (-)
6320835 .. 6324259
3425 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G006790.1

Sequence Viewer

Length: 1215 bp
ATGGCCAGGGCTCCAAGCAAGCACGGTCGCGACCAACCTCTGGATTTCCGGGGGTTTTTGAGTGACTTGCAGGACCGGAAGCTTTCACGCAAGGACAAGGATAAAAAAATGAGGCCACAACAACCCAACAAGGATATTCAGTGTTCTCTTCCATATGTTATTGATTGGCATTTCCTAATGCTGTTGCTGTTTCAGAAATCAGGAGATTTTGGAACTAGTTTCGGTTCTGAAGATAGTCTTCCAGATGCTGCCGCTTCGGAAAAGGACTTGGGTAATGAGTATTTTAAGCAGAAGAAGTTTAAGGAAGCTATTGACTGCTATTCAAGAAGCATTGCCTTATCTCCAACTGCTGTAGCTTTTGCAAATAGGGCAATGTCATATATCAAAATCAAAAGATTCCAGGAAGCGGAGAATGACTGTAGGGAGGCCTTGAATTTGGATGATCGCTATATAAAAGCATACTCACGACGTGCAACAGCTAGAAAAGAACTGGGAAAACTTAAAGAATCTATTGAGGATGCAGAGTTTGCTCTGAGGTTGGAGCCACACAACCAAGAAATCAAGAAACAGTATGCTGAGGCCAAATCTTTGTATGAGAAAAGAATTCTTCAGAAAATTTCTGAACAAGAAAAGCAGAACGTGGGAAAGTTGGATACCAAAGTGAATGGACACATCATCCAGCCTGTATCTAGTAGTACTCAAAGGAAAGAAATGACTGCAGTTGAGGATCACACTAAGAAGATTAACAAAAGTGGGAAGCAAGCATGGAAGGTATCGGTACAAGAGCTTGCTTCTAGAGCCGCTTCACGAGCCAAGGTTCTAGCTGCACAAAACATCACACGACCAACTACAGCATATCATTTTGAGGCTTCTTGGAGAGGACTCTCTGGAGATCGTGCTCTTCAGGCTAAATTGTTGAAGGCTATATATCCCAGAGAACTGCCGTATATATTCAAAAATGCTTTGACTGTTCACATACTAGTTGATATCATCAAGTGTGTGACAACCTTTTTTATTGATGAAATGGCTTTAACAGTCAGTTTTTTGGAGAACTTAACTAAGGTTCCTAGATTTGACACACTCATCATGTTTCTTTCTTCCAAGGACAAGGATGATCTTGCTAAGACATGGGATGAAGTGTTCTACTATGAGGTGATCCCCATTGAGTTTGCTGAAAAGCTTGATAACCTGCGTACAAAGTACTGCCTTAAGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0032991 GO:0044424 GO:0044444 GO:0044464 GO:0097255
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RPAP3_C TPR_1 TPR_8

Protein Analysis

404

Amino Acids

46.55

Weight (kDa)

9.29

Isoelectric Point (pI)

39.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TPR_BSK1_C PF25575 86 - 152 4.2e-07 Serine/threonine-protein kinase BSK1-like, TPR repeats
TPR_1 PF00515 88 - 116 5.6e-08 Tetratricopeptide repeat
RPAP3_C PF13877 282 - 370 1.3e-24 Potential Monad-binding region of RPAP3
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 1197
AccB7I CCANNNNNTGG 1 cut(s) 40
AccII CGCG 1 cut(s) 30
AciI CCGC 3 cut(s) 252, 407, 801
AclWI GGATC 2 cut(s) 735, 1150
AcoI YGGCCR 1 cut(s) 3
AcsI RAATTY 3 cut(s) 433, 603, 615
AcuI CTGAAG 3 cut(s) 249, 593, 887
AdeI CACNNNGTG 1 cut(s) 470
AfaI GTAC 4 cut(s) 697, 780, 1195, 1202
AfiI CCNNNNNNNGG 2 cut(s) 40, 406
AflII CTTAAG 1 cut(s) 1208
AgsI TTSAA 4 cut(s) 324, 433, 919, 955
AhlI ACTAGT 2 cut(s) 215, 979
AjiI CACGTC 1 cut(s) 470
AjnI CCWGG 2 cut(s) 5, 399
AloI GAACNNNNNNTCC 2 cut(s) 1124, 1156
AluBI AGCT 7 cut(s) 82, 308, 356, 479, 787, 824, 1180
AluI AGCT 7 cut(s) 82, 308, 356, 479, 787, 824, 1180
Alw21I GWGCWC 1 cut(s) 901
AlwI GGATC 2 cut(s) 735, 1150
AlwNI CAGNNNCTG 1 cut(s) 248
AoxI GGCC 4 cut(s) 3, 113, 426, 579
ApeKI GCWGC 2 cut(s) 248, 824
ApoI RAATTY 3 cut(s) 433, 603, 615
AspS9I GGNCC 1 cut(s) 73
AsuC2I CCSGG 1 cut(s) 50
AsuHPI GGTGA 1 cut(s) 1165
AvaII GGWCC 1 cut(s) 73
BaeI ACNNNNGTAYC 2 cut(s) 645, 678
BalI TGGCCA 1 cut(s) 5
BanII GRGCYC 1 cut(s) 13
BauI CACGAG 1 cut(s) 807
BbsI GAAGAC 1 cut(s) 230
Bbv12I GWGCWC 1 cut(s) 901
BbvCI CCTCAGC 1 cut(s) 576
BbvI GCAGC 2 cut(s) 235, 811
BceAI ACGGC 1 cut(s) 928
BciT130I CCWGG 2 cut(s) 7, 401
BciVI GTATCC 1 cut(s) 646
BcnI CCSGG 1 cut(s) 50
BcuI ACTAGT 2 cut(s) 215, 979
BfaI CTAG 7 cut(s) 216, 480, 690, 795, 821, 980, 1068
BfmI CTRYAG 4 cut(s) 351, 418, 717, 849
BfrI CTTAAG 1 cut(s) 1208
BfuAI ACCTGC 1 cut(s) 1197
BfuI GTATCC 1 cut(s) 646
BisI GCNGC 4 cut(s) 249, 252, 801, 825
BlsI GCNGC 4 cut(s) 250, 253, 802, 826
BmcAI AGTACT 2 cut(s) 697, 1202
Bme1390I CCNGG 3 cut(s) 7, 50, 401
Bme18I GGWCC 1 cut(s) 73
BmgBI CACGTC 1 cut(s) 470
BmgT120I GGNCC 1 cut(s) 73
BmiI GGNNCC 3 cut(s) 12, 543, 1065
BmrFI CCNGG 3 cut(s) 7, 50, 401
BmrI ACTGGG 1 cut(s) 500
BmsI GCATC 2 cut(s) 235, 508
BmuI ACTGGG 1 cut(s) 500
BpiI GAAGAC 1 cut(s) 230
BpmI CTGGAG 1 cut(s) 909
Bpu10I CCTNAGC 1 cut(s) 576
BpuMI CCSGG 1 cut(s) 50
BsaJI CCNNGG 4 cut(s) 6, 49, 813, 1101
BsaWI WCCGGW 1 cut(s) 75
Bsc4I CCNNNNNNNGG 2 cut(s) 40, 406
Bse1I ACTGG 1 cut(s) 495
Bse3DI GCAATG 2 cut(s) 330, 378
BseBI CCWGG 2 cut(s) 7, 401
BseDI CCNNGG 4 cut(s) 6, 49, 813, 1101
BseGI GGATG 5 cut(s) 445, 523, 675, 1117, 1138
BseLI CCNNNNNNNGG 2 cut(s) 40, 406
BseMI GCAATG 2 cut(s) 330, 378
BseMII CTCAG 2 cut(s) 524, 567
BseNI ACTGG 1 cut(s) 495
BseXI GCAGC 2 cut(s) 235, 811
BsgI GTGCAG 1 cut(s) 810
Bsh1236I CGCG 1 cut(s) 30
Bsh1285I CGRYCG 1 cut(s) 28
BshFI GGCC 4 cut(s) 5, 115, 428, 581
BsiEI CGRYCG 1 cut(s) 28
BsiHKAI GWGCWC 1 cut(s) 901
BsiSI CCGG 2 cut(s) 49, 76
BslI CCNNNNNNNGG 2 cut(s) 40, 406
BsnI GGCC 4 cut(s) 5, 115, 428, 581
Bsp1286I GDGCHC 2 cut(s) 13, 901
Bsp143I GATC 5 cut(s) 442, 727, 892, 1114, 1155
Bsp68I TCGCGA 1 cut(s) 30
BspACI CCGC 3 cut(s) 252, 407, 801
BspANI GGCC 4 cut(s) 5, 115, 428, 581
BspCNI CTCAG 2 cut(s) 525, 568
BspFNI CGCG 1 cut(s) 30
BspLI GGNNCC 3 cut(s) 12, 543, 1065
BspMAI CTGCAG 1 cut(s) 721
BspMI ACCTGC 1 cut(s) 1197
BspPI GGATC 2 cut(s) 735, 1150
BspQI GCTCTTC 1 cut(s) 906
BspTI CTTAAG 1 cut(s) 1208
BsrDI GCAATG 2 cut(s) 330, 378
BsrI ACTGG 1 cut(s) 495
BssECI CCNNGG 4 cut(s) 6, 49, 813, 1101
BssMI GATC 5 cut(s) 442, 727, 892, 1114, 1155
BssSI CACGAG 1 cut(s) 807
BssT1I CCWWGG 2 cut(s) 813, 1101
Bst2BI CACGAG 1 cut(s) 807
Bst2UI CCWGG 2 cut(s) 7, 401
Bst4CI ACNGT 5 cut(s) 26, 419, 570, 970, 1036
Bst6I CTCTTC 2 cut(s) 153, 906
BstAFI CTTAAG 1 cut(s) 1208
BstAPI GCANNNNNTGC 1 cut(s) 527
BstC8I GCNNGC 3 cut(s) 20, 762, 789
BstDEI CTNAG 5 cut(s) 533, 576, 735, 1059, 1122
BstF5I GGATG 5 cut(s) 445, 523, 675, 1117, 1138
BstFNI CGCG 1 cut(s) 30
BstKTI GATC 5 cut(s) 445, 730, 895, 1117, 1158
BstMBI GATC 5 cut(s) 442, 727, 892, 1114, 1155
BstMCI CGRYCG 1 cut(s) 28
BstMWI GCNNNNNNNGC 5 cut(s) 368, 527, 797, 809, 905
BstNI CCWGG 2 cut(s) 7, 401
BstSCI CCNGG 3 cut(s) 5, 48, 399
BstSFI CTRYAG 4 cut(s) 351, 418, 717, 849
BstUI CGCG 1 cut(s) 30
BstV1I GCAGC 2 cut(s) 235, 811
BstV2I GAAGAC 1 cut(s) 230
BsuI GTATCC 1 cut(s) 646
BsuRI GGCC 4 cut(s) 5, 115, 428, 581
BtrI CACGTC 1 cut(s) 470
BtsCI GGATG 5 cut(s) 445, 523, 675, 1117, 1138
BtsIMutI CAGTG 1 cut(s) 146
BtuMI TCGCGA 1 cut(s) 30
BveI ACCTGC 1 cut(s) 1197
Cac8I GCNNGC 3 cut(s) 20, 762, 789
CaiI CAGNNNCTG 1 cut(s) 248
Cfr13I GGNCC 1 cut(s) 73
Csp6I GTAC 4 cut(s) 696, 779, 1194, 1201
CviAII CATG 3 cut(s) 765, 1087, 1128
CviQI GTAC 4 cut(s) 696, 779, 1194, 1201
DdeI CTNAG 5 cut(s) 533, 576, 735, 1059, 1122
DpnI GATC 5 cut(s) 444, 729, 894, 1116, 1157
DpnII GATC 5 cut(s) 442, 727, 892, 1114, 1155
DraIII CACNNNGTG 1 cut(s) 470
EaeI YGGCCR 1 cut(s) 3
Eam1104I CTCTTC 2 cut(s) 153, 906
EarI CTCTTC 2 cut(s) 153, 906
Eco130I CCWWGG 2 cut(s) 813, 1101
Eco147I AGGCCT 1 cut(s) 428
Eco24I GRGCYC 1 cut(s) 13
Eco32I GATATC 1 cut(s) 988
Eco47I GGWCC 1 cut(s) 73
Eco57I CTGAAG 3 cut(s) 249, 593, 887
EcoRI GAATTC 1 cut(s) 603
EcoRII CCWGG 2 cut(s) 5, 399
EcoRV GATATC 1 cut(s) 988
EcoT14I CCWWGG 2 cut(s) 813, 1101
EcoT38I GRGCYC 1 cut(s) 13
ErhI CCWWGG 2 cut(s) 813, 1101
FaeI CATG 3 cut(s) 768, 1090, 1131
FalI AAGNNNNNCTT 2 cut(s) 222, 254
FatI CATG 3 cut(s) 764, 1086, 1127
FauNDI CATATG 1 cut(s) 154
Fnu4HI GCNGC 4 cut(s) 249, 252, 801, 825
FokI GGATG 5 cut(s) 452, 530, 662, 1124, 1145
FriOI GRGCYC 1 cut(s) 13
Fsp4HI GCNGC 4 cut(s) 249, 252, 801, 825
FspBI CTAG 7 cut(s) 216, 480, 690, 795, 821, 980, 1068
GluI GCNGC 4 cut(s) 249, 252, 801, 825
GsuI CTGGAG 1 cut(s) 909
HaeIII GGCC 4 cut(s) 5, 115, 428, 581
HapII CCGG 2 cut(s) 49, 76
Hin1II CATG 3 cut(s) 768, 1090, 1131
HindIII AAGCTT 2 cut(s) 80, 1178
HinfI GANTC 3 cut(s) 396, 506, 882
HpaII CCGG 2 cut(s) 49, 76
HphI GGTGA 1 cut(s) 1165
Hpy166II GTNNAC 1 cut(s) 973
Hpy188I TCNGA 6 cut(s) 195, 229, 259, 534, 612, 622
Hpy8I GTNNAC 1 cut(s) 973
Hpy99I CGWCG 1 cut(s) 471
HpyAV CCTTC 2 cut(s) 763, 913
HpyCH4III ACNGT 5 cut(s) 26, 419, 570, 970, 1036
HpyCH4IV ACGT 2 cut(s) 469, 639
HpyCH4V TGCA 6 cut(s) 70, 362, 473, 521, 719, 827
HpyF10VI GCNNNNNNNGC 5 cut(s) 368, 527, 797, 809, 905
HpyF3I CTNAG 5 cut(s) 533, 576, 735, 1059, 1122
HpySE526I ACGT 2 cut(s) 469, 639
Hsp92II CATG 3 cut(s) 768, 1090, 1131
Kzo9I GATC 5 cut(s) 442, 727, 892, 1114, 1155
LguI GCTCTTC 1 cut(s) 906
LmnI GCTCC 2 cut(s) 16, 541
Lsp1109I GCAGC 2 cut(s) 235, 811
LweI GCATC 2 cut(s) 235, 508
MaeI CTAG 7 cut(s) 216, 480, 690, 795, 821, 980, 1068
MaeII ACGT 2 cut(s) 469, 639
MaeIII GTNAC 2 cut(s) 62, 1000
MalI GATC 5 cut(s) 444, 729, 894, 1116, 1157
MboI GATC 5 cut(s) 442, 727, 892, 1114, 1155
MboII GAAGA 8 cut(s) 140, 230, 242, 304, 599, 751, 893, 1089
MhlI GDGCHC 2 cut(s) 13, 901
MlsI TGGCCA 1 cut(s) 5
MluCI AATT 4 cut(s) 433, 603, 615, 911
MluNI TGGCCA 1 cut(s) 5
MlyI GAGTC 1 cut(s) 876
MmeI TCCRAC 3 cut(s) 368, 519, 630
Mox20I TGGCCA 1 cut(s) 5
MscI TGGCCA 1 cut(s) 5
MseI TTAA 7 cut(s) 285, 300, 501, 744, 1031, 1055, 1209
Msp20I TGGCCA 1 cut(s) 5
MspCI CTTAAG 1 cut(s) 1208
MspI CCGG 2 cut(s) 49, 76
MspR9I CCNGG 3 cut(s) 7, 50, 401
MvaI CCWGG 2 cut(s) 7, 401
MvnI CGCG 1 cut(s) 30
MwoI GCNNNNNNNGC 5 cut(s) 368, 527, 797, 809, 905
NciI CCSGG 1 cut(s) 50
NdeI CATATG 1 cut(s) 154
NdeII GATC 5 cut(s) 442, 727, 892, 1114, 1155
NlaIII CATG 3 cut(s) 768, 1090, 1131
NlaIV GGNNCC 3 cut(s) 12, 543, 1065
NmuCI GTSAC 2 cut(s) 62, 1000
NruI TCGCGA 1 cut(s) 30
PceI AGGCCT 1 cut(s) 428
PciSI GCTCTTC 1 cut(s) 906
PfeI GAWTC 2 cut(s) 396, 506
PflMI CCANNNNNTGG 1 cut(s) 40
PfoI TCCNGGA 1 cut(s) 399
PkrI GCNGC 4 cut(s) 250, 253, 802, 826
PleI GAGTC 1 cut(s) 876
PpsI GAGTC 1 cut(s) 876
Psp6I CCWGG 2 cut(s) 5, 399
PspGI CCWGG 2 cut(s) 5, 399
PspN4I GGNNCC 3 cut(s) 12, 543, 1065
PspPI GGNCC 1 cut(s) 73
PstI CTGCAG 1 cut(s) 721
PstNI CAGNNNCTG 1 cut(s) 248
RruI TCGCGA 1 cut(s) 30
RsaI GTAC 4 cut(s) 697, 780, 1195, 1202
RsaNI GTAC 4 cut(s) 696, 779, 1194, 1201
SapI GCTCTTC 1 cut(s) 906
SaqAI TTAA 7 cut(s) 285, 300, 501, 744, 1031, 1055, 1209
SatI GCNGC 4 cut(s) 249, 252, 801, 825
Sau3AI GATC 5 cut(s) 442, 727, 892, 1114, 1155
Sau96I GGNCC 1 cut(s) 73
ScaI AGTACT 2 cut(s) 697, 1202
SchI GAGTC 1 cut(s) 876
ScrFI CCNGG 3 cut(s) 7, 50, 401
SduI GDGCHC 2 cut(s) 13, 901
SfaNI GCATC 2 cut(s) 235, 508
SfcI CTRYAG 4 cut(s) 351, 418, 717, 849
SinI GGWCC 1 cut(s) 73
SmlI CTYRAG 1 cut(s) 1208
SmoI CTYRAG 1 cut(s) 1208
SpeI ACTAGT 2 cut(s) 215, 979
Sse9I AATT 4 cut(s) 433, 603, 615, 911
SseBI AGGCCT 1 cut(s) 428
SsiI CCGC 3 cut(s) 252, 407, 801
SspMI CTAG 7 cut(s) 216, 480, 690, 795, 821, 980, 1068
StuI AGGCCT 1 cut(s) 428
StyD4I CCNGG 3 cut(s) 5, 48, 399
StyI CCWWGG 2 cut(s) 813, 1101
TaaI ACNGT 5 cut(s) 26, 419, 570, 970, 1036
TaiI ACGT 2 cut(s) 472, 642
TasI AATT 4 cut(s) 433, 603, 615, 911
TatI WGTACW 2 cut(s) 695, 1200
TauI GCSGC 2 cut(s) 254, 803
TfiI GAWTC 2 cut(s) 396, 506
Tru1I TTAA 7 cut(s) 285, 300, 501, 744, 1031, 1055, 1209
Tru9I TTAA 7 cut(s) 285, 300, 501, 744, 1031, 1055, 1209
TscAI CASTG 1 cut(s) 146
TseFI GTSAC 2 cut(s) 62, 1000
TseI GCWGC 2 cut(s) 248, 824
Tsp45I GTSAC 2 cut(s) 62, 1000
TspDTI ATGAA 2 cut(s) 1035, 1149
TspRI CASTG 1 cut(s) 146
Van91I CCANNNNNTGG 1 cut(s) 40
Vha464I CTTAAG 1 cut(s) 1208
VpaK11BI GGWCC 1 cut(s) 73
XapI RAATTY 3 cut(s) 433, 603, 615
XbaI TCTAGA 1 cut(s) 794
XspI CTAG 7 cut(s) 216, 480, 690, 795, 821, 980, 1068
ZrmI AGTACT 2 cut(s) 697, 1202
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.