Rh3DG082700

RNA polymerase II-associated protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3D
OG0005138
Physical Location & Seq
Reverse (-)
6350753 .. 6354173
3421 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3DG082700.1

Sequence Viewer

Length: 1158 bp
ATGGCTAGGGCTCCAAGCAAGCACGGTCGCGACCAACCTCTGGATTTCCGGGGGTTTTTGAGTGACTTGCAGGACCGGAAGCTTTCACGCAAGGACAAGGATAAAAAAATGAGGCCACAACAACCCAACAAGGATATTCCGAAATCAGGAGATTTTGGAACTAGTTTCGGTTCTGAAGATAGTCTTCCAGATGCTGCTTCGGAAAAGGACTTGGGTAATGAGTATTTTAAGCAGAAGAAGTTTAAGGAAGCTATTGACTGCTATTCAAGAAGCATTGCCTTATCTCCAACTGCTGTAGCTTTTGCAAATAGGGCAATGTCATATATCAAAATCAAAAGATTCCAGGAAGCGGAGAATGACTGTACGGAGGCCTTGAATTTGGATGATCGCTATATAAAAGCATACTCACGACGTGCAACAGCTAGAAAAGAACTGGGAAAACTTAAAGAATCTATTGAGGATGCAGAGTTTGCTCTGAGGTTGGAGCCACACAACCAAGAAATCAAGAAACAGTATGCTGAGGCCAAATCTTTGTATGAGAAAAGAATTCTTCAGAAAATTTCTGAACAAGAAAAGCAGAACGTGGGAAAGTTGGATACCAAAGTGAATGGACACATCATCCAGCCTGTATCTAGTAGTACTCAAAGGAAAGAAATGACTGCAGTTGAGGATCACACTAAGAAGATTAACAAAAGTGGGAAGCAAGCATGGAAGGTATCGGTACAAGAGCTTGCTTCTAGAGCTGCTTCACGAGCCAAGGTTCTAGCTGCACAAAACATCACACGACCAACTACAGCATATGAATTTGAGGCTTCTTGGAGAGGACTCTCTGGAGATCGTGCTCTTCAGGCTAAATTGTTGAAGGCTATATATCCCAGAGAACTGCCGTATATATTCAAAAATGCTTTGACTGTTCACATACTAGTTGATATCATCAAGTGTGTGACAACCTTTTTTATTGATGAAATGGCTTTAACAGTCAGTTTTTTGGAGAACTTAACTAAGGTTCCTAGATTTGACACACTCATCATGTTTCTTTCTTCCAAGGACAAGGATGATCTTGCTAAGACATGGGATGAAGTGTTCTACTATGAGGTGATCCCCATTGAGTTTGCTGAAAAGCTTGATAACCTGCGTACAAAGTACTGCCTTAAGTGA
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

385

Amino Acids

44.16

Weight (kDa)

9.28

Isoelectric Point (pI)

41.52

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TPR_BSK1_C PF25575 62 - 134 1.1e-07 Serine/threonine-protein kinase BSK1-like, TPR repeats
TPR_1 PF00515 69 - 97 5.3e-08 Tetratricopeptide repeat
RPAP3_C PF13877 263 - 351 3.5e-25 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) 1140
AccB7I CCANNNNNTGG 1 cut(s) 40
AccII CGCG 1 cut(s) 30
AciI CCGC 1 cut(s) 350
AclWI GGATC 2 cut(s) 678, 1093
AcsI RAATTY 4 cut(s) 376, 546, 558, 803
AcuI CTGAAG 3 cut(s) 195, 536, 830
AdeI CACNNNGTG 1 cut(s) 413
AfaI GTAC 5 cut(s) 364, 640, 723, 1138, 1145
AfiI CCNNNNNNNGG 3 cut(s) 40, 146, 349
AflII CTTAAG 1 cut(s) 1151
AgsI TTSAA 4 cut(s) 267, 376, 862, 898
AhlI ACTAGT 2 cut(s) 161, 922
AjiI CACGTC 1 cut(s) 413
AjnI CCWGG 1 cut(s) 342
AloI GAACNNNNNNTCC 2 cut(s) 1067, 1099
AluBI AGCT 8 cut(s) 82, 251, 299, 422, 730, 743, 767, 1123
AluI AGCT 8 cut(s) 82, 251, 299, 422, 730, 743, 767, 1123
Alw21I GWGCWC 1 cut(s) 844
AlwI GGATC 2 cut(s) 678, 1093
AlwNI CAGNNNCTG 1 cut(s) 194
AoxI GGCC 3 cut(s) 113, 369, 522
ApeKI GCWGC 3 cut(s) 194, 743, 767
ApoI RAATTY 4 cut(s) 376, 546, 558, 803
AspS9I GGNCC 1 cut(s) 73
AsuC2I CCSGG 1 cut(s) 50
AsuHPI GGTGA 1 cut(s) 1108
AvaII GGWCC 1 cut(s) 73
BaeI ACNNNNGTAYC 2 cut(s) 588, 621
BanII GRGCYC 1 cut(s) 13
BauI CACGAG 1 cut(s) 750
BbsI GAAGAC 1 cut(s) 176
Bbv12I GWGCWC 1 cut(s) 844
BbvCI CCTCAGC 1 cut(s) 519
BbvI GCAGC 3 cut(s) 181, 730, 754
BceAI ACGGC 1 cut(s) 871
BciT130I CCWGG 1 cut(s) 344
BciVI GTATCC 1 cut(s) 589
BcnI CCSGG 1 cut(s) 50
BcuI ACTAGT 2 cut(s) 161, 922
BfaI CTAG 8 cut(s) 6, 162, 423, 633, 738, 764, 923, 1011
BfmI CTRYAG 3 cut(s) 294, 660, 792
BfrI CTTAAG 1 cut(s) 1151
BfuAI ACCTGC 1 cut(s) 1140
BfuI GTATCC 1 cut(s) 589
BisI GCNGC 3 cut(s) 195, 744, 768
BlsI GCNGC 3 cut(s) 196, 745, 769
BmcAI AGTACT 2 cut(s) 640, 1145
Bme1390I CCNGG 2 cut(s) 50, 344
Bme18I GGWCC 1 cut(s) 73
BmgBI CACGTC 1 cut(s) 413
BmgT120I GGNCC 1 cut(s) 73
BmiI GGNNCC 3 cut(s) 12, 486, 1008
BmrFI CCNGG 2 cut(s) 50, 344
BmrI ACTGGG 1 cut(s) 443
BmsI GCATC 2 cut(s) 181, 451
BmuI ACTGGG 1 cut(s) 443
BpiI GAAGAC 1 cut(s) 176
BpmI CTGGAG 1 cut(s) 852
Bpu10I CCTNAGC 1 cut(s) 519
BpuMI CCSGG 1 cut(s) 50
BsaJI CCNNGG 3 cut(s) 49, 756, 1044
BsaWI WCCGGW 1 cut(s) 75
Bsc4I CCNNNNNNNGG 3 cut(s) 40, 146, 349
Bse1I ACTGG 1 cut(s) 438
Bse3DI GCAATG 2 cut(s) 273, 321
BseBI CCWGG 1 cut(s) 344
BseDI CCNNGG 3 cut(s) 49, 756, 1044
BseGI GGATG 5 cut(s) 388, 466, 618, 1060, 1081
BseLI CCNNNNNNNGG 3 cut(s) 40, 146, 349
BseMI GCAATG 2 cut(s) 273, 321
BseMII CTCAG 2 cut(s) 467, 510
BseNI ACTGG 1 cut(s) 438
BseXI GCAGC 3 cut(s) 181, 730, 754
BsgI GTGCAG 1 cut(s) 753
Bsh1236I CGCG 1 cut(s) 30
Bsh1285I CGRYCG 1 cut(s) 28
BshFI GGCC 3 cut(s) 115, 371, 524
BsiEI CGRYCG 1 cut(s) 28
BsiHKAI GWGCWC 1 cut(s) 844
BsiSI CCGG 2 cut(s) 49, 76
BslI CCNNNNNNNGG 3 cut(s) 40, 146, 349
BsnI GGCC 3 cut(s) 115, 371, 524
Bsp1286I GDGCHC 2 cut(s) 13, 844
Bsp143I GATC 5 cut(s) 385, 670, 835, 1057, 1098
Bsp68I TCGCGA 1 cut(s) 30
BspACI CCGC 1 cut(s) 350
BspANI GGCC 3 cut(s) 115, 371, 524
BspCNI CTCAG 2 cut(s) 468, 511
BspFNI CGCG 1 cut(s) 30
BspLI GGNNCC 3 cut(s) 12, 486, 1008
BspMAI CTGCAG 1 cut(s) 664
BspMI ACCTGC 1 cut(s) 1140
BspPI GGATC 2 cut(s) 678, 1093
BspQI GCTCTTC 1 cut(s) 849
BspTI CTTAAG 1 cut(s) 1151
BsrDI GCAATG 2 cut(s) 273, 321
BsrI ACTGG 1 cut(s) 438
BssECI CCNNGG 3 cut(s) 49, 756, 1044
BssMI GATC 5 cut(s) 385, 670, 835, 1057, 1098
BssSI CACGAG 1 cut(s) 750
BssT1I CCWWGG 2 cut(s) 756, 1044
Bst2BI CACGAG 1 cut(s) 750
Bst2UI CCWGG 1 cut(s) 344
Bst4CI ACNGT 5 cut(s) 26, 362, 513, 913, 979
Bst6I CTCTTC 1 cut(s) 849
BstAFI CTTAAG 1 cut(s) 1151
BstAPI GCANNNNNTGC 1 cut(s) 470
BstC8I GCNNGC 3 cut(s) 20, 705, 732
BstDEI CTNAG 5 cut(s) 476, 519, 678, 1002, 1065
BstF5I GGATG 5 cut(s) 388, 466, 618, 1060, 1081
BstFNI CGCG 1 cut(s) 30
BstKTI GATC 5 cut(s) 388, 673, 838, 1060, 1101
BstMBI GATC 5 cut(s) 385, 670, 835, 1057, 1098
BstMCI CGRYCG 1 cut(s) 28
BstMWI GCNNNNNNNGC 5 cut(s) 311, 470, 740, 752, 848
BstNI CCWGG 1 cut(s) 344
BstSCI CCNGG 2 cut(s) 48, 342
BstSFI CTRYAG 3 cut(s) 294, 660, 792
BstUI CGCG 1 cut(s) 30
BstV1I GCAGC 3 cut(s) 181, 730, 754
BstV2I GAAGAC 1 cut(s) 176
BsuI GTATCC 1 cut(s) 589
BsuRI GGCC 3 cut(s) 115, 371, 524
BtrI CACGTC 1 cut(s) 413
BtsCI GGATG 5 cut(s) 388, 466, 618, 1060, 1081
BtuMI TCGCGA 1 cut(s) 30
BveI ACCTGC 1 cut(s) 1140
Cac8I GCNNGC 3 cut(s) 20, 705, 732
CaiI CAGNNNCTG 1 cut(s) 194
Cfr13I GGNCC 1 cut(s) 73
Csp6I GTAC 5 cut(s) 363, 639, 722, 1137, 1144
CviAII CATG 3 cut(s) 708, 1030, 1071
CviQI GTAC 5 cut(s) 363, 639, 722, 1137, 1144
DdeI CTNAG 5 cut(s) 476, 519, 678, 1002, 1065
DpnI GATC 5 cut(s) 387, 672, 837, 1059, 1100
DpnII GATC 5 cut(s) 385, 670, 835, 1057, 1098
DraIII CACNNNGTG 1 cut(s) 413
Eam1104I CTCTTC 1 cut(s) 849
EarI CTCTTC 1 cut(s) 849
Eco130I CCWWGG 2 cut(s) 756, 1044
Eco147I AGGCCT 1 cut(s) 371
Eco24I GRGCYC 1 cut(s) 13
Eco32I GATATC 1 cut(s) 931
Eco47I GGWCC 1 cut(s) 73
Eco57I CTGAAG 3 cut(s) 195, 536, 830
EcoRI GAATTC 1 cut(s) 546
EcoRII CCWGG 1 cut(s) 342
EcoRV GATATC 1 cut(s) 931
EcoT14I CCWWGG 2 cut(s) 756, 1044
EcoT38I GRGCYC 1 cut(s) 13
ErhI CCWWGG 2 cut(s) 756, 1044
FaeI CATG 3 cut(s) 711, 1033, 1074
FalI AAGNNNNNCTT 2 cut(s) 168, 200
FatI CATG 3 cut(s) 707, 1029, 1070
FauNDI CATATG 1 cut(s) 799
Fnu4HI GCNGC 3 cut(s) 195, 744, 768
FokI GGATG 5 cut(s) 395, 473, 605, 1067, 1088
FriOI GRGCYC 1 cut(s) 13
Fsp4HI GCNGC 3 cut(s) 195, 744, 768
FspBI CTAG 8 cut(s) 6, 162, 423, 633, 738, 764, 923, 1011
GluI GCNGC 3 cut(s) 195, 744, 768
GsuI CTGGAG 1 cut(s) 852
HaeIII GGCC 3 cut(s) 115, 371, 524
HapII CCGG 2 cut(s) 49, 76
Hin1II CATG 3 cut(s) 711, 1033, 1074
HindIII AAGCTT 2 cut(s) 80, 1121
HinfI GANTC 3 cut(s) 339, 449, 825
HpaII CCGG 2 cut(s) 49, 76
HphI GGTGA 1 cut(s) 1108
Hpy166II GTNNAC 1 cut(s) 916
Hpy188I TCNGA 6 cut(s) 141, 175, 202, 477, 555, 565
Hpy8I GTNNAC 1 cut(s) 916
Hpy99I CGWCG 1 cut(s) 414
HpyAV CCTTC 2 cut(s) 706, 856
HpyCH4III ACNGT 5 cut(s) 26, 362, 513, 913, 979
HpyCH4IV ACGT 2 cut(s) 412, 582
HpyCH4V TGCA 6 cut(s) 70, 305, 416, 464, 662, 770
HpyF10VI GCNNNNNNNGC 5 cut(s) 311, 470, 740, 752, 848
HpyF3I CTNAG 5 cut(s) 476, 519, 678, 1002, 1065
HpySE526I ACGT 2 cut(s) 412, 582
Hsp92II CATG 3 cut(s) 711, 1033, 1074
Kzo9I GATC 5 cut(s) 385, 670, 835, 1057, 1098
LguI GCTCTTC 1 cut(s) 849
LmnI GCTCC 2 cut(s) 16, 484
Lsp1109I GCAGC 3 cut(s) 181, 730, 754
LweI GCATC 2 cut(s) 181, 451
MaeI CTAG 8 cut(s) 6, 162, 423, 633, 738, 764, 923, 1011
MaeII ACGT 2 cut(s) 412, 582
MaeIII GTNAC 2 cut(s) 62, 943
MalI GATC 5 cut(s) 387, 672, 837, 1059, 1100
MboI GATC 5 cut(s) 385, 670, 835, 1057, 1098
MboII GAAGA 7 cut(s) 176, 188, 247, 542, 694, 836, 1032
MhlI GDGCHC 2 cut(s) 13, 844
MluCI AATT 5 cut(s) 376, 546, 558, 803, 854
MlyI GAGTC 1 cut(s) 819
MmeI TCCRAC 3 cut(s) 311, 462, 573
MseI TTAA 7 cut(s) 228, 243, 444, 687, 974, 998, 1152
MspCI CTTAAG 1 cut(s) 1151
MspI CCGG 2 cut(s) 49, 76
MspR9I CCNGG 2 cut(s) 50, 344
MvaI CCWGG 1 cut(s) 344
MvnI CGCG 1 cut(s) 30
MwoI GCNNNNNNNGC 5 cut(s) 311, 470, 740, 752, 848
NciI CCSGG 1 cut(s) 50
NdeI CATATG 1 cut(s) 799
NdeII GATC 5 cut(s) 385, 670, 835, 1057, 1098
NlaIII CATG 3 cut(s) 711, 1033, 1074
NlaIV GGNNCC 3 cut(s) 12, 486, 1008
NmuCI GTSAC 2 cut(s) 62, 943
NruI TCGCGA 1 cut(s) 30
PceI AGGCCT 1 cut(s) 371
PciSI GCTCTTC 1 cut(s) 849
PfeI GAWTC 2 cut(s) 339, 449
PflMI CCANNNNNTGG 1 cut(s) 40
PfoI TCCNGGA 1 cut(s) 342
PkrI GCNGC 3 cut(s) 196, 745, 769
PleI GAGTC 1 cut(s) 819
PpsI GAGTC 1 cut(s) 819
Psp6I CCWGG 1 cut(s) 342
PspGI CCWGG 1 cut(s) 342
PspN4I GGNNCC 3 cut(s) 12, 486, 1008
PspPI GGNCC 1 cut(s) 73
PstI CTGCAG 1 cut(s) 664
PstNI CAGNNNCTG 1 cut(s) 194
RruI TCGCGA 1 cut(s) 30
RsaI GTAC 5 cut(s) 364, 640, 723, 1138, 1145
RsaNI GTAC 5 cut(s) 363, 639, 722, 1137, 1144
SapI GCTCTTC 1 cut(s) 849
SaqAI TTAA 7 cut(s) 228, 243, 444, 687, 974, 998, 1152
SatI GCNGC 3 cut(s) 195, 744, 768
Sau3AI GATC 5 cut(s) 385, 670, 835, 1057, 1098
Sau96I GGNCC 1 cut(s) 73
ScaI AGTACT 2 cut(s) 640, 1145
SchI GAGTC 1 cut(s) 819
ScrFI CCNGG 2 cut(s) 50, 344
SduI GDGCHC 2 cut(s) 13, 844
SfaNI GCATC 2 cut(s) 181, 451
SfcI CTRYAG 3 cut(s) 294, 660, 792
SinI GGWCC 1 cut(s) 73
SmlI CTYRAG 1 cut(s) 1151
SmoI CTYRAG 1 cut(s) 1151
SpeI ACTAGT 2 cut(s) 161, 922
Sse9I AATT 5 cut(s) 376, 546, 558, 803, 854
SseBI AGGCCT 1 cut(s) 371
SsiI CCGC 1 cut(s) 350
SspMI CTAG 8 cut(s) 6, 162, 423, 633, 738, 764, 923, 1011
StuI AGGCCT 1 cut(s) 371
StyD4I CCNGG 2 cut(s) 48, 342
StyI CCWWGG 2 cut(s) 756, 1044
TaaI ACNGT 5 cut(s) 26, 362, 513, 913, 979
TaiI ACGT 2 cut(s) 415, 585
TasI AATT 5 cut(s) 376, 546, 558, 803, 854
TatI WGTACW 2 cut(s) 638, 1143
TfiI GAWTC 2 cut(s) 339, 449
Tru1I TTAA 7 cut(s) 228, 243, 444, 687, 974, 998, 1152
Tru9I TTAA 7 cut(s) 228, 243, 444, 687, 974, 998, 1152
TseFI GTSAC 2 cut(s) 62, 943
TseI GCWGC 3 cut(s) 194, 743, 767
Tsp45I GTSAC 2 cut(s) 62, 943
TspDTI ATGAA 3 cut(s) 816, 978, 1092
TspGWI ACGGA 1 cut(s) 380
Van91I CCANNNNNTGG 1 cut(s) 40
Vha464I CTTAAG 1 cut(s) 1151
VpaK11BI GGWCC 1 cut(s) 73
XapI RAATTY 4 cut(s) 376, 546, 558, 803
XbaI TCTAGA 1 cut(s) 737
XspI CTAG 8 cut(s) 6, 162, 423, 633, 738, 764, 923, 1011
ZrmI AGTACT 2 cut(s) 640, 1145
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.