RchiOBHm_Chr3g0457141

RNA polymerase II-associated protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0005138
Physical Location & Seq
Reverse (-)
6363614 .. 6367625
4012 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ42390

Sequence Viewer

Length: 1209 bp
ATGGCTAGGGCTCCAAGCAAGCACGGTCGCGACCAAGCCCTGGATTTCCAGGGGTTTTTGAGTGACTTGCAGGACTGGGAGCTTTCACTCAAGGACAAGGATAAAAAAATGAGGCCACAAGAACCCAACAAGGAAATTCCGAAATCAGGAGATTTTGGAACTAGTTCCTACTCGAGGAATTATGATCCAATCAACACTATATCCAGTAGTTTCGGTTCTGAAGATAGTCTTCCAGATGCTGCTTCGGAAAAGGACTTGGGTAATGAGTATTTTAAGCAGAAGAAGTTTAAGGAAGCTATTGACTGCTATTCAAGAAGCATTGCCTTATCTCCAACTGCTGTAGCTTTTGCAAATAGGGCAATGTCATATATCAAAATCAAAAGATTCCAGGAAGCCGAGAATGACTGTACGGAGGCCTTGAATTTGGATGATCGCTATATAAAAGCATACTCACGACGTGCGACAACTAGAAAAGAACTGGGAAAACTTAAAGAATCTATTGAGGATGCAGAGTTTGCTCTGAGGTTGGAGCCACATAACCAAGAAATCAAGAAACAATATGCTGAGGTCAAATCTTTGTATGAAAAAAGAATTCTTCAGAAAATTTCTGAACAAGAAAAGCAGAAAGTGGGAAAGTTGGATACCAAAGTGAATGGACACAGCATCCAGACTGTTTCTAGTAGTACTCAAAGGACAGAAATGACTGCAGTTGTGGATCACACTAAGAAAATTAACACAAGTGGAAAGCAAGCGTCGAAGGTATCGGTACAGGAGCTTGCTTCTCGAGCTGCTTTGCGAGCCAAGGTTCTAGCTGCAGAAAACATCACACCACCAACTTCAGCATATCAATTTGAGGCTTCTTGGAGAGGACTCTCTGGAGATCGTGCTCTTCAGGCTAAATTTTTGAAGGCTATATCTCCCAGTGCACTGCCGCAGATATTCAAAAATGCTTTGACTGTTCACATACTAGTTGATATCATCAAGTGTGTGACAACCTTTTTTATGGACGAAATGGATTTGGCGGTCAACATTTTGGAGAACTTAACTAAGGTTCCTAGATTTGACACACTCGTCATGTTTCTTTCATCCAACGACAAGGCTGATCTTGCTAAGATATGGGATGAAGTGTTCTACAATGAAGCAACCCCCATTGAGTTTGCTGAAAAGCTTGATAACCTGCGTACAAAGTACTGCCTTAAGCGATTATGA
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

402

Amino Acids

45.56

Weight (kDa)

8.83

Isoelectric Point (pI)

43.32

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TPR_BSK1_C PF25575 75 - 149 7.8e-08 Serine/threonine-protein kinase BSK1-like, TPR repeats
TPR_1 PF00515 84 - 112 5.6e-08 Tetratricopeptide repeat
RPAP3_C PF13877 277 - 366 1.5e-27 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)
AasI GACNNNNNNGTC 1 cut(s) 1070
Acc36I ACCTGC 1 cut(s) 1185
AccB7I CCANNNNNTGG 1 cut(s) 40
AccII CGCG 1 cut(s) 30
AciI CCGC 2 cut(s) 932, 1022
AclWI GGATC 2 cut(s) 179, 723
AcsI RAATTY 5 cut(s) 135, 421, 591, 603, 899
AcuI CTGAAG 4 cut(s) 240, 581, 822, 875
AdeI CACNNNGTG 1 cut(s) 458
AfaI GTAC 5 cut(s) 409, 685, 768, 1183, 1190
AfiI CCNNNNNNNGG 3 cut(s) 40, 146, 174
AflII CTTAAG 1 cut(s) 1196
AgsI TTSAA 4 cut(s) 312, 421, 907, 943
AhlI ACTAGT 2 cut(s) 161, 967
AjiI CACGTC 1 cut(s) 458
AjnI CCWGG 3 cut(s) 39, 48, 387
AloI GAACNNNNNNTCC 2 cut(s) 1112, 1144
AluBI AGCT 7 cut(s) 82, 296, 344, 775, 788, 812, 1168
AluI AGCT 7 cut(s) 82, 296, 344, 775, 788, 812, 1168
Alw21I GWGCWC 2 cut(s) 889, 928
Alw44I GTGCAC 1 cut(s) 924
AlwI GGATC 2 cut(s) 179, 723
AlwNI CAGNNNCTG 1 cut(s) 239
Ama87I CYCGRG 2 cut(s) 172, 783
AoxI GGCC 2 cut(s) 113, 414
ApaLI GTGCAC 1 cut(s) 924
ApeKI GCWGC 3 cut(s) 239, 788, 812
ApoI RAATTY 5 cut(s) 135, 421, 591, 603, 899
Asp700I GAANNNNTTC 1 cut(s) 163
AvaI CYCGRG 2 cut(s) 172, 783
BaeGI GKGCMC 1 cut(s) 928
BaeI ACNNNNGTAYC 2 cut(s) 633, 666
BanII GRGCYC 1 cut(s) 13
BbsI GAAGAC 1 cut(s) 221
Bbv12I GWGCWC 2 cut(s) 889, 928
BbvCI CCTCAGC 1 cut(s) 564
BbvI GCAGC 3 cut(s) 226, 775, 799
BciT130I CCWGG 3 cut(s) 41, 50, 389
BciVI GTATCC 1 cut(s) 634
BcuI ACTAGT 2 cut(s) 161, 967
BfaI CTAG 7 cut(s) 6, 162, 468, 678, 809, 968, 1056
BfmI CTRYAG 3 cut(s) 339, 705, 813
BfrI CTTAAG 1 cut(s) 1196
BfuAI ACCTGC 1 cut(s) 1185
BfuI GTATCC 1 cut(s) 634
BisI GCNGC 4 cut(s) 240, 789, 813, 932
BlsI GCNGC 4 cut(s) 241, 790, 814, 933
BmcAI AGTACT 2 cut(s) 685, 1190
Bme1390I CCNGG 3 cut(s) 41, 50, 389
BmeT110I CYCGRG 2 cut(s) 172, 783
BmgBI CACGTC 1 cut(s) 458
BmiI GGNNCC 3 cut(s) 12, 531, 1053
BmrFI CCNGG 3 cut(s) 41, 50, 389
BmrI ACTGGG 3 cut(s) 85, 488, 915
BmsI GCATC 3 cut(s) 226, 496, 672
BmuI ACTGGG 3 cut(s) 85, 488, 915
BpiI GAAGAC 1 cut(s) 221
BpmI CTGGAG 1 cut(s) 897
Bpu10I CCTNAGC 1 cut(s) 564
BpuEI CTTGAG 1 cut(s) 74
BsaJI CCNNGG 3 cut(s) 39, 49, 801
Bsc4I CCNNNNNNNGG 3 cut(s) 40, 146, 174
Bse1I ACTGG 4 cut(s) 80, 204, 483, 921
Bse3DI GCAATG 2 cut(s) 318, 366
BseBI CCWGG 3 cut(s) 41, 50, 389
BseDI CCNNGG 3 cut(s) 39, 49, 801
BseGI GGATG 5 cut(s) 433, 511, 663, 1085, 1126
BseLI CCNNNNNNNGG 3 cut(s) 40, 146, 174
BseMI GCAATG 2 cut(s) 318, 366
BseMII CTCAG 2 cut(s) 512, 555
BseNI ACTGG 4 cut(s) 80, 204, 483, 921
BseSI GKGCMC 1 cut(s) 928
BseXI GCAGC 3 cut(s) 226, 775, 799
Bsh1236I CGCG 1 cut(s) 30
Bsh1285I CGRYCG 1 cut(s) 28
BshFI GGCC 2 cut(s) 115, 416
BsiEI CGRYCG 1 cut(s) 28
BsiHKAI GWGCWC 2 cut(s) 889, 928
BsiHKCI CYCGRG 2 cut(s) 172, 783
BslI CCNNNNNNNGG 3 cut(s) 40, 146, 174
BsnI GGCC 2 cut(s) 115, 416
BsoBI CYCGRG 2 cut(s) 172, 783
Bsp1286I GDGCHC 3 cut(s) 13, 889, 928
Bsp143I GATC 5 cut(s) 184, 430, 715, 880, 1102
Bsp68I TCGCGA 1 cut(s) 30
BspACI CCGC 2 cut(s) 932, 1022
BspANI GGCC 2 cut(s) 115, 416
BspCNI CTCAG 2 cut(s) 513, 556
BspFNI CGCG 1 cut(s) 30
BspLI GGNNCC 3 cut(s) 12, 531, 1053
BspMAI CTGCAG 2 cut(s) 709, 817
BspMI ACCTGC 1 cut(s) 1185
BspPI GGATC 2 cut(s) 179, 723
BspQI GCTCTTC 1 cut(s) 894
BspTI CTTAAG 1 cut(s) 1196
BsrDI GCAATG 2 cut(s) 318, 366
BsrI ACTGG 4 cut(s) 80, 204, 483, 921
BssECI CCNNGG 3 cut(s) 39, 49, 801
BssMI GATC 5 cut(s) 184, 430, 715, 880, 1102
BssT1I CCWWGG 1 cut(s) 801
Bst2UI CCWGG 3 cut(s) 41, 50, 389
Bst4CI ACNGT 4 cut(s) 26, 407, 673, 958
Bst6I CTCTTC 1 cut(s) 894
BstAFI CTTAAG 1 cut(s) 1196
BstAPI GCANNNNNTGC 1 cut(s) 515
BstC8I GCNNGC 4 cut(s) 20, 750, 777, 798
BstDEI CTNAG 5 cut(s) 521, 564, 723, 1047, 1110
BstENI CCTNNNNNAGG 1 cut(s) 172
BstF5I GGATG 5 cut(s) 433, 511, 663, 1085, 1126
BstFNI CGCG 1 cut(s) 30
BstKTI GATC 5 cut(s) 187, 433, 718, 883, 1105
BstMBI GATC 5 cut(s) 184, 430, 715, 880, 1102
BstMCI CGRYCG 1 cut(s) 28
BstMWI GCNNNNNNNGC 6 cut(s) 356, 515, 785, 797, 893, 1106
BstNI CCWGG 3 cut(s) 41, 50, 389
BstSCI CCNGG 3 cut(s) 39, 48, 387
BstSFI CTRYAG 3 cut(s) 339, 705, 813
BstSLI GKGCMC 1 cut(s) 928
BstUI CGCG 1 cut(s) 30
BstV1I GCAGC 3 cut(s) 226, 775, 799
BstV2I GAAGAC 1 cut(s) 221
BsuI GTATCC 1 cut(s) 634
BsuRI GGCC 2 cut(s) 115, 416
BtrI CACGTC 1 cut(s) 458
BtsCI GGATG 5 cut(s) 433, 511, 663, 1085, 1126
BtsI GCAGTG 1 cut(s) 926
BtsIMutI CAGTG 2 cut(s) 926, 928
BtuMI TCGCGA 1 cut(s) 30
BveI ACCTGC 1 cut(s) 1185
Cac8I GCNNGC 4 cut(s) 20, 750, 777, 798
CaiI CAGNNNCTG 1 cut(s) 239
CseI GACGC 1 cut(s) 741
Csp6I GTAC 5 cut(s) 408, 684, 767, 1182, 1189
CviAII CATG 1 cut(s) 1075
CviQI GTAC 5 cut(s) 408, 684, 767, 1182, 1189
DdeI CTNAG 5 cut(s) 521, 564, 723, 1047, 1110
DpnI GATC 5 cut(s) 186, 432, 717, 882, 1104
DpnII GATC 5 cut(s) 184, 430, 715, 880, 1102
DraIII CACNNNGTG 1 cut(s) 458
DrdI GACNNNNNNGTC 1 cut(s) 1070
DseDI GACNNNNNNGTC 1 cut(s) 1070
Eam1104I CTCTTC 1 cut(s) 894
EarI CTCTTC 1 cut(s) 894
Eco130I CCWWGG 1 cut(s) 801
Eco147I AGGCCT 1 cut(s) 416
Eco24I GRGCYC 1 cut(s) 13
Eco32I GATATC 1 cut(s) 976
Eco57I CTGAAG 4 cut(s) 240, 581, 822, 875
Eco88I CYCGRG 2 cut(s) 172, 783
EcoNI CCTNNNNNAGG 1 cut(s) 172
EcoRI GAATTC 1 cut(s) 591
EcoRII CCWGG 3 cut(s) 39, 48, 387
EcoRV GATATC 1 cut(s) 976
EcoT14I CCWWGG 1 cut(s) 801
EcoT38I GRGCYC 1 cut(s) 13
ErhI CCWWGG 1 cut(s) 801
FaeI CATG 1 cut(s) 1078
FalI AAGNNNNNCTT 2 cut(s) 213, 245
FatI CATG 1 cut(s) 1074
Fnu4HI GCNGC 4 cut(s) 240, 789, 813, 932
FokI GGATG 5 cut(s) 440, 518, 650, 1072, 1133
FriOI GRGCYC 1 cut(s) 13
Fsp4HI GCNGC 4 cut(s) 240, 789, 813, 932
FspBI CTAG 7 cut(s) 6, 162, 468, 678, 809, 968, 1056
GluI GCNGC 4 cut(s) 240, 789, 813, 932
GsuI CTGGAG 1 cut(s) 897
HaeIII GGCC 2 cut(s) 115, 416
HgaI GACGC 1 cut(s) 741
Hin1II CATG 1 cut(s) 1078
HincII GTYRAC 1 cut(s) 1027
HindII GTYRAC 1 cut(s) 1027
HindIII AAGCTT 1 cut(s) 1166
HinfI GANTC 3 cut(s) 384, 494, 870
Hpy166II GTNNAC 3 cut(s) 926, 961, 1027
Hpy188I TCNGA 6 cut(s) 141, 220, 247, 522, 600, 610
Hpy188III TCNNGA 9 cut(s) 29, 147, 233, 312, 453, 550, 667, 783, 876
Hpy8I GTNNAC 3 cut(s) 926, 961, 1027
Hpy99I CGWCG 2 cut(s) 459, 757
HpyAV CCTTC 2 cut(s) 751, 901
HpyCH4III ACNGT 4 cut(s) 26, 407, 673, 958
HpyCH4IV ACGT 1 cut(s) 457
HpyCH4V TGCA 6 cut(s) 70, 350, 509, 707, 815, 926
HpyF10VI GCNNNNNNNGC 6 cut(s) 356, 515, 785, 797, 893, 1106
HpyF3I CTNAG 5 cut(s) 521, 564, 723, 1047, 1110
HpySE526I ACGT 1 cut(s) 457
Hsp92II CATG 1 cut(s) 1078
Kzo9I GATC 5 cut(s) 184, 430, 715, 880, 1102
LguI GCTCTTC 1 cut(s) 894
LmnI GCTCC 4 cut(s) 16, 79, 529, 772
Lsp1109I GCAGC 3 cut(s) 226, 775, 799
LweI GCATC 3 cut(s) 226, 496, 672
MaeI CTAG 7 cut(s) 6, 162, 468, 678, 809, 968, 1056
MaeII ACGT 1 cut(s) 457
MaeIII GTNAC 2 cut(s) 62, 988
MalI GATC 5 cut(s) 186, 432, 717, 882, 1104
MboI GATC 5 cut(s) 184, 430, 715, 880, 1102
MboII GAAGA 5 cut(s) 221, 233, 292, 587, 881
MhlI GDGCHC 3 cut(s) 13, 889, 928
MluCI AATT 8 cut(s) 135, 178, 421, 591, 603, 729, 848, 899
MlyI GAGTC 1 cut(s) 864
MmeI TCCRAC 4 cut(s) 356, 507, 618, 1113
MnlI CCTC 8 cut(s) 105, 168, 406, 496, 516, 559, 847, 860
MroXI GAANNNNTTC 1 cut(s) 163
MseI TTAA 6 cut(s) 273, 288, 489, 732, 1043, 1197
MspCI CTTAAG 1 cut(s) 1196
MspR9I CCNGG 3 cut(s) 41, 50, 389
MvaI CCWGG 3 cut(s) 41, 50, 389
MvnI CGCG 1 cut(s) 30
MwoI GCNNNNNNNGC 6 cut(s) 356, 515, 785, 797, 893, 1106
NdeII GATC 5 cut(s) 184, 430, 715, 880, 1102
NlaIII CATG 1 cut(s) 1078
NlaIV GGNNCC 3 cut(s) 12, 531, 1053
NmeAIII GCCGAG 1 cut(s) 421
NmuCI GTSAC 2 cut(s) 62, 988
NruI TCGCGA 1 cut(s) 30
PaeR7I CTCGAG 2 cut(s) 172, 783
PceI AGGCCT 1 cut(s) 416
PciSI GCTCTTC 1 cut(s) 894
PdmI GAANNNNTTC 1 cut(s) 163
PfeI GAWTC 2 cut(s) 384, 494
PflMI CCANNNNNTGG 1 cut(s) 40
PfoI TCCNGGA 1 cut(s) 387
PkrI GCNGC 4 cut(s) 241, 790, 814, 933
PleI GAGTC 1 cut(s) 864
PpsI GAGTC 1 cut(s) 864
Psp6I CCWGG 3 cut(s) 39, 48, 387
PspGI CCWGG 3 cut(s) 39, 48, 387
PspN4I GGNNCC 3 cut(s) 12, 531, 1053
PspXI VCTCGAGB 1 cut(s) 172
PsrI GAACNNNNNNTAC 2 cut(s) 199, 231
PstI CTGCAG 2 cut(s) 709, 817
PstNI CAGNNNCTG 1 cut(s) 239
RruI TCGCGA 1 cut(s) 30
RsaI GTAC 5 cut(s) 409, 685, 768, 1183, 1190
RsaNI GTAC 5 cut(s) 408, 684, 767, 1182, 1189
SapI GCTCTTC 1 cut(s) 894
SaqAI TTAA 6 cut(s) 273, 288, 489, 732, 1043, 1197
SatI GCNGC 4 cut(s) 240, 789, 813, 932
Sau3AI GATC 5 cut(s) 184, 430, 715, 880, 1102
ScaI AGTACT 2 cut(s) 685, 1190
SchI GAGTC 1 cut(s) 864
ScrFI CCNGG 3 cut(s) 41, 50, 389
SduI GDGCHC 3 cut(s) 13, 889, 928
SfaNI GCATC 3 cut(s) 226, 496, 672
SfcI CTRYAG 3 cut(s) 339, 705, 813
Sfr274I CTCGAG 2 cut(s) 172, 783
SlaI CTCGAG 2 cut(s) 172, 783
SmlI CTYRAG 4 cut(s) 89, 172, 783, 1196
SmoI CTYRAG 4 cut(s) 89, 172, 783, 1196
SpeI ACTAGT 2 cut(s) 161, 967
Sse9I AATT 8 cut(s) 135, 178, 421, 591, 603, 729, 848, 899
SseBI AGGCCT 1 cut(s) 416
SsiI CCGC 2 cut(s) 932, 1022
SspMI CTAG 7 cut(s) 6, 162, 468, 678, 809, 968, 1056
StuI AGGCCT 1 cut(s) 416
StyD4I CCNGG 3 cut(s) 39, 48, 387
StyI CCWWGG 1 cut(s) 801
TaaI ACNGT 4 cut(s) 26, 407, 673, 958
TaiI ACGT 1 cut(s) 460
TaqI TCGA 3 cut(s) 173, 755, 784
TasI AATT 8 cut(s) 135, 178, 421, 591, 603, 729, 848, 899
TatI WGTACW 2 cut(s) 683, 1188
TauI GCSGC 1 cut(s) 934
TfiI GAWTC 2 cut(s) 384, 494
Tru1I TTAA 6 cut(s) 273, 288, 489, 732, 1043, 1197
Tru9I TTAA 6 cut(s) 273, 288, 489, 732, 1043, 1197
TscAI CASTG 2 cut(s) 928, 933
TseFI GTSAC 2 cut(s) 62, 988
TseI GCWGC 3 cut(s) 239, 788, 812
Tsp45I GTSAC 2 cut(s) 62, 988
TspDTI ATGAA 4 cut(s) 597, 1074, 1137, 1152
TspGWI ACGGA 1 cut(s) 425
TspRI CASTG 2 cut(s) 928, 933
Van91I CCANNNNNTGG 1 cut(s) 40
Vha464I CTTAAG 1 cut(s) 1196
VneI GTGCAC 1 cut(s) 924
XagI CCTNNNNNAGG 1 cut(s) 172
XapI RAATTY 5 cut(s) 135, 421, 591, 603, 899
XhoI CTCGAG 2 cut(s) 172, 783
XmnI GAANNNNTTC 1 cut(s) 163
XspI CTAG 7 cut(s) 6, 162, 468, 678, 809, 968, 1056
ZrmI AGTACT 2 cut(s) 685, 1190
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.