Rroxscaffold_2G00119100

RNA polymerase Rpb1, domain 5

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0004622
Physical Location & Seq
Forward (+)
50907147 .. 50909120
1974 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00119100.1

Sequence Viewer

Length: 1974 bp
ATGGATAAGATATTCCGACACAATGGCATCTTGATACCGCCAGGAACAAATTCTAAGGAATCAAAAAAGCGGAACAATTGGATTTATGTCCAATGGATCACACCCACCAAGAAAAAGTATTTTGTTTTGGTTCGACCCGTAATCATATATGAAATTGCGGACGGTATAAATTTAGCAACACTTTTCCCCCAGGATCCATTGCGGGAAAGGGATAATCTAGAACTTCGAGTTGTAAATTATATACTTTATGGAAATGGCAAACCAATTTGGGGAATTTCCGGCACAAGTATTCAATTAGTTCGGACCTGTTTAATCTTGAACTGGGACAAAAACAAAAAAAGTTCTTCTATCGAAGAGGCCCACGCTTCCTTTGTTGAAGTAAGTGCGAATGGTCTGATTCAAGATTTCCTCAGAATCAACTTAGTGAAATCCCATACTTCGTATATCCGAAAAAGGAATGATCCATTAGGTTCAGGATTGATCTCTGATAATAGGTCGGATCGTACCAATATCAATCCATTTTATTCTATTTATTCCAAGGAAAGAATTCAACAATCGCTTAGACAAAATCAAGGAACTTTTCGTACGTTGTTGAATAGAAATAAGGAATCCCAATCTTTGATAATTTTGTCATCATATAATTGTTTTCAAATGAGTCCATTCAACGATGTAAAATATTACGATGGGATAAAAGAATCAATTAAAAGAGATAGGGATTCCCTAATTCAAATTACAAATTTGTTAGGCCCCTTAGGAACAGCCTCTCAAATTGATCTTTTTTATTCGTTTTACCATTTACTAACTCATAATCATATTTCGGTAACTAAATATTTCTATTTGCAACTCGACAATTTAAAACAGACTTTTCAAGTATTTAAGTATTATTTAATGGATGAAAACGGGAGAATTTCGAATTCCGATCCGTGCAGTAGCATCCTTTTGAATCCACTTAACTTGAATTGGCATTTTCTCGACCATAATTATTGTGAGGAAACATCCACAATAATTAGTCTCGGGCAGTTTATTTGTGAAAATCTATGTATAGCCAAAAAAGGATCGCCCCTAAAATCGGGTCAAGTTATAGTCGTTCAACTTGACTCTTTAGTAATAAGATCGGCGAAGCCTTATTTAGCTACTCCAGGAGCAACTGTTCATGGACATTATGGAGAAATCCTTTCCGAAGGAGATACATTAGTTACATTTATATATGAAAAATCTCGATCTGGTGATATAACGCAAGGTCTTCCAAAAGTAGAACAGGTTTTAGAGGTACGTTCGATTGATTCAATATCGATGAACCTAGAAAAGAGAGTTGAGGGTTGGAATGAGTGTATAACAAGAATTCTTGGAATTCCTTGGGGATTCTTGATTGGCGCTGAGCTAACTATAGCGCAAAGTCGTATCTCTTTGGTTAATAAGATCCAAAAAGTTTATAGATCCCAGGGGGTACAGATCCATAATAGGCATATCGAAATCATTGTACGTCAAATAACATCAAAAGTGTTGGTTTCAGAAGATGGAATGTCTAATGTTTTTTCACCCGGAGAACTGATTGGATTGCTGCGAGCTGAACGAACGGGGCGCGCTTTAGAAGAAGCGATTTGTTACCGAGCCATATTATTAGGAATAACGAAAGCATCTCTAAATACTCAAAGTTTCATATCCGAAGCAAGTTTTCAAGAAACTGCTCGAGTTTTAGCAAAAGCTGCCCTCCGGGGTCGTATCGATTGGTTGAAAGGTCTGAAAGAGAACGTTGTTCTAGGAGGGATGATACCCGTTGGTACCGGATTCAAAGGATTCGTGCCCCGTTCAAGGCAACATAACAACATTTCTTTGGAAACCAAAAATAAGAGTTTATTCGAGGGGGAAATGAGAGATATTTTGGTCCACCACAGAGAATTATTTGATTTTTGCATTTCAAAAAATTTACATGATACATCAGAACAATCTTTTTTCGGATTTAATGATTCCTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00190 ko00195 ko00230 ko00240 ko01100 ko03020 map00190 map00195 map00230 map00240 map01100 map03020
Pfam Domains
Protein Families
RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5 Ribosomal_S2

Protein Analysis

657

Amino Acids

74.73

Weight (kDa)

9.1

Isoelectric Point (pI)

44.45

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb1_5 PF04998 461 - 548 6.7e-08 RNA polymerase Rpb1, domain 5
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 1781
AccB1I GGYRCC 1 cut(s) 1781
AccII CGCG 1 cut(s) 1584
AciI CCGC 4 cut(s) 38, 70, 158, 202
AclI AACGTT 1 cut(s) 1752
AfaI GTAC 6 cut(s) 505, 586, 1272, 1449, 1482, 1783
AfiI CCNNNNNNNGG 3 cut(s) 269, 1069, 1812
AjnI CCWGG 4 cut(s) 40, 189, 1138, 1440
AloI GAACNNNNNNTCC 2 cut(s) 1134, 1166
AluBI AGCT 4 cut(s) 1133, 1381, 1568, 1706
AluI AGCT 4 cut(s) 1133, 1381, 1568, 1706
Alw26I GTCTC 1 cut(s) 1016
Ama87I CYCGRG 2 cut(s) 1013, 1689
AoxI GGCC 2 cut(s) 357, 745
ApeKI GCWGC 2 cut(s) 1561, 1706
Asp700I GAANNNNTTC 2 cut(s) 49, 546
Asp718I GGTACC 1 cut(s) 1781
AspLEI GCGC 4 cut(s) 1376, 1393, 1584, 1586
AspS9I GGNCC 4 cut(s) 303, 358, 746, 1885
AsuC2I CCSGG 2 cut(s) 1542, 1715
AsuHPI GGTGA 2 cut(s) 1238, 1530
AsuII TTCGAA 1 cut(s) 911
AvaI CYCGRG 2 cut(s) 1013, 1689
AvaII GGWCC 2 cut(s) 303, 1885
AxyI CCTNAGG 1 cut(s) 751
BaeGI GKGCMC 1 cut(s) 1806
BaeI ACNNNNGTAYC 2 cut(s) 1179, 1212
BamHI GGATCC 1 cut(s) 193
BanI GGYRCC 1 cut(s) 1781
BbsI GAAGAC 1 cut(s) 1235
BbvI GCAGC 2 cut(s) 1548, 1693
BccI CCATC 2 cut(s) 677, 1511
BciT130I CCWGG 4 cut(s) 42, 191, 1140, 1442
BcnI CCSGG 2 cut(s) 1542, 1715
BcoDI GTCTC 1 cut(s) 1016
BfaI CTAG 3 cut(s) 218, 1301, 1760
BfmI CTRYAG 1 cut(s) 1386
BfoI RGCGCY 1 cut(s) 1377
BisI GCNGC 2 cut(s) 1562, 1707
BlpI GCTNAGC 1 cut(s) 1377
BlsI GCNGC 2 cut(s) 1563, 1708
Bme1390I CCNGG 6 cut(s) 42, 191, 1140, 1442, 1542, 1715
Bme18I GGWCC 2 cut(s) 303, 1885
BmeT110I CYCGRG 2 cut(s) 1013, 1689
BmgT120I GGNCC 4 cut(s) 303, 358, 746, 1885
BmiI GGNNCC 3 cut(s) 195, 748, 1783
BmrFI CCNGG 6 cut(s) 42, 191, 1140, 1442, 1542, 1715
BmrI ACTGGG 1 cut(s) 331
BmsI GCATC 3 cut(s) 36, 942, 1646
BmuI ACTGGG 1 cut(s) 331
BpiI GAAGAC 1 cut(s) 1235
BpmI CTGGAG 1 cut(s) 1122
Bpu1102I GCTNAGC 1 cut(s) 1377
Bpu14I TTCGAA 1 cut(s) 911
BpuMI CCSGG 2 cut(s) 1542, 1715
Bsa29I ATCGAT 2 cut(s) 1292, 1725
BsaJI CCNNGG 6 cut(s) 189, 537, 1355, 1440, 1441, 1714
BsaWI WCCGGW 1 cut(s) 1784
BsaXI ACNNNNNCTCC 2 cut(s) 1134, 1164
Bsc4I CCNNNNNNNGG 3 cut(s) 269, 1069, 1812
Bse1I ACTGG 1 cut(s) 326
Bse21I CCTNAGG 1 cut(s) 751
Bse3DI GCAATG 1 cut(s) 197
BseBI CCWGG 4 cut(s) 42, 191, 1140, 1442
BseCI ATCGAT 2 cut(s) 1292, 1725
BseDI CCNNGG 6 cut(s) 189, 537, 1355, 1440, 1441, 1714
BseGI GGATG 4 cut(s) 898, 933, 995, 1773
BseLI CCNNNNNNNGG 3 cut(s) 269, 1069, 1812
BseMI GCAATG 1 cut(s) 197
BseMII CTCAG 2 cut(s) 424, 1368
BseNI ACTGG 1 cut(s) 326
BsePI GCGCGC 1 cut(s) 1582
BseSI GKGCMC 1 cut(s) 1806
BseXI GCAGC 2 cut(s) 1548, 1693
BsgI GTGCAG 1 cut(s) 946
Bsh1236I CGCG 1 cut(s) 1584
BshFI GGCC 2 cut(s) 359, 747
BshNI GGYRCC 1 cut(s) 1781
BshVI ATCGAT 2 cut(s) 1292, 1725
BsiHKCI CYCGRG 2 cut(s) 1013, 1689
BsiSI CCGG 4 cut(s) 279, 1542, 1714, 1785
BsiWI CGTACG 1 cut(s) 584
BslFI GGGAC 1 cut(s) 338
BslI CCNNNNNNNGG 3 cut(s) 269, 1069, 1812
BsmAI GTCTC 1 cut(s) 1016
BsmFI GGGAC 1 cut(s) 338
BsnI GGCC 2 cut(s) 359, 747
BsoBI CYCGRG 2 cut(s) 1013, 1689
Bsp119I TTCGAA 1 cut(s) 911
Bsp1286I GDGCHC 1 cut(s) 1806
Bsp1720I GCTNAGC 1 cut(s) 1377
BspACI CCGC 4 cut(s) 38, 70, 158, 202
BspANI GGCC 2 cut(s) 359, 747
BspCNI CTCAG 2 cut(s) 423, 1369
BspDI ATCGAT 2 cut(s) 1292, 1725
BspFNI CGCG 1 cut(s) 1584
BspLI GGNNCC 3 cut(s) 195, 748, 1783
BspT104I TTCGAA 1 cut(s) 911
BspT107I GGYRCC 1 cut(s) 1781
BsrDI GCAATG 1 cut(s) 197
BsrI ACTGG 1 cut(s) 326
BssECI CCNNGG 6 cut(s) 189, 537, 1355, 1440, 1441, 1714
BssHII GCGCGC 1 cut(s) 1582
BssT1I CCWWGG 2 cut(s) 537, 1355
Bst2UI CCWGG 4 cut(s) 42, 191, 1140, 1442
Bst4CI ACNGT 2 cut(s) 164, 1150
Bst6I CTCTTC 1 cut(s) 348
BstAPI GCANNNNNTGC 1 cut(s) 1706
BstBI TTCGAA 1 cut(s) 911
BstC8I GCNNGC 2 cut(s) 1566, 1584
BstDEI CTNAG 6 cut(s) 54, 410, 421, 560, 751, 1377
BstF5I GGATG 4 cut(s) 898, 933, 995, 1773
BstFNI CGCG 1 cut(s) 1584
BstH2I RGCGCY 1 cut(s) 1377
BstHHI GCGC 4 cut(s) 1376, 1393, 1584, 1586
BstMAI GTCTC 1 cut(s) 1016
BstMWI GCNNNNNNNGC 1 cut(s) 1706
BstNI CCWGG 4 cut(s) 42, 191, 1140, 1442
BstSCI CCNGG 6 cut(s) 40, 189, 1138, 1440, 1540, 1713
BstSFI CTRYAG 1 cut(s) 1386
BstSLI GKGCMC 1 cut(s) 1806
BstUI CGCG 1 cut(s) 1584
BstV1I GCAGC 2 cut(s) 1548, 1693
BstV2I GAAGAC 1 cut(s) 1235
BstX2I RGATCY 4 cut(s) 193, 1419, 1436, 1452
BstYI RGATCY 4 cut(s) 193, 1419, 1436, 1452
Bsu15I ATCGAT 2 cut(s) 1292, 1725
Bsu36I CCTNAGG 1 cut(s) 751
BsuRI GGCC 2 cut(s) 359, 747
BsuTUI ATCGAT 2 cut(s) 1292, 1725
BtsCI GGATG 4 cut(s) 898, 933, 995, 1773
Cac8I GCNNGC 2 cut(s) 1566, 1584
CfoI GCGC 4 cut(s) 1376, 1393, 1584, 1586
Cfr13I GGNCC 4 cut(s) 303, 358, 746, 1885
ClaI ATCGAT 2 cut(s) 1292, 1725
Csp6I GTAC 6 cut(s) 504, 585, 1271, 1448, 1481, 1782
CspCI CAANNNNNGTGG 2 cut(s) 936, 971
CviAII CATG 2 cut(s) 1154, 1931
CviQI GTAC 6 cut(s) 504, 585, 1271, 1448, 1481, 1782
DdeI CTNAG 6 cut(s) 54, 410, 421, 560, 751, 1377
DraI TTTAAA 1 cut(s) 855
Eam1104I CTCTTC 1 cut(s) 348
EarI CTCTTC 1 cut(s) 348
Eco130I CCWWGG 2 cut(s) 537, 1355
Eco47I GGWCC 2 cut(s) 303, 1885
Eco81I CCTNAGG 1 cut(s) 751
Eco88I CYCGRG 2 cut(s) 1013, 1689
EcoO109I RGGNCCY 1 cut(s) 746
EcoRI GAATTC 4 cut(s) 546, 913, 1341, 1350
EcoRII CCWGG 4 cut(s) 40, 189, 1138, 1440
EcoT14I CCWWGG 2 cut(s) 537, 1355
ErhI CCWWGG 2 cut(s) 537, 1355
FaeI CATG 2 cut(s) 1157, 1934
FaqI GGGAC 1 cut(s) 338
FatI CATG 2 cut(s) 1153, 1930
FauI CCCGC 1 cut(s) 195
Fnu4HI GCNGC 2 cut(s) 1562, 1707
FokI GGATG 4 cut(s) 905, 920, 982, 1780
Fsp4HI GCNGC 2 cut(s) 1562, 1707
FspBI CTAG 3 cut(s) 218, 1301, 1760
GlaI GCGC 4 cut(s) 1375, 1392, 1583, 1585
GluI GCNGC 2 cut(s) 1562, 1707
GsuI CTGGAG 1 cut(s) 1122
HaeII RGCGCY 1 cut(s) 1377
HaeIII GGCC 2 cut(s) 359, 747
HapII CCGG 4 cut(s) 279, 1542, 1714, 1785
HhaI GCGC 4 cut(s) 1376, 1393, 1584, 1586
Hin1II CATG 2 cut(s) 1157, 1934
Hin6I GCGC 4 cut(s) 1374, 1391, 1582, 1584
HinP1I GCGC 4 cut(s) 1374, 1391, 1582, 1584
HpaII CCGG 4 cut(s) 279, 1542, 1714, 1785
HphI GGTGA 2 cut(s) 1238, 1530
Hpy166II GTNNAC 1 cut(s) 1888
Hpy188III TCNNGA 9 cut(s) 31, 218, 316, 401, 474, 971, 1218, 1366, 1679
Hpy8I GTNNAC 1 cut(s) 1888
HpyAV CCTTC 1 cut(s) 1175
HpyCH4III ACNGT 2 cut(s) 164, 1150
HpyCH4IV ACGT 4 cut(s) 587, 1273, 1483, 1752
HpyCH4V TGCA 3 cut(s) 841, 927, 1914
HpyF10VI GCNNNNNNNGC 1 cut(s) 1706
HpyF3I CTNAG 6 cut(s) 54, 410, 421, 560, 751, 1377
HpySE526I ACGT 4 cut(s) 587, 1273, 1483, 1752
Hsp92II CATG 2 cut(s) 1157, 1934
HspAI GCGC 4 cut(s) 1374, 1391, 1582, 1584
KpnI GGTACC 1 cut(s) 1785
LmnI GCTCC 1 cut(s) 1142
Lsp1109I GCAGC 2 cut(s) 1548, 1693
LweI GCATC 3 cut(s) 36, 942, 1646
MaeI CTAG 3 cut(s) 218, 1301, 1760
MaeII ACGT 4 cut(s) 587, 1273, 1483, 1752
MaeIII GTNAC 3 cut(s) 820, 1195, 1604
MboII GAAGA 5 cut(s) 336, 365, 1235, 1526, 1604
MfeI CAATTG 1 cut(s) 76
MflI RGATCY 4 cut(s) 193, 1419, 1436, 1452
MhlI GDGCHC 1 cut(s) 1806
MlyI GAGTC 2 cut(s) 664, 1091
MmeI TCCRAC 3 cut(s) 40, 477, 1301
MnlI CCTC 9 cut(s) 349, 419, 772, 982, 1261, 1309, 1721, 1757, 1855
MroXI GAANNNNTTC 2 cut(s) 49, 546
MseI TTAA 8 cut(s) 311, 702, 854, 876, 887, 951, 1413, 1962
MspI CCGG 4 cut(s) 279, 1542, 1714, 1785
MspR9I CCNGG 6 cut(s) 42, 191, 1140, 1442, 1542, 1715
MunI CAATTG 1 cut(s) 76
MvaI CCWGG 4 cut(s) 42, 191, 1140, 1442
MvnI CGCG 1 cut(s) 1584
MwoI GCNNNNNNNGC 1 cut(s) 1706
NciI CCSGG 2 cut(s) 1542, 1715
NlaIII CATG 2 cut(s) 1157, 1934
NlaIV GGNNCC 3 cut(s) 195, 748, 1783
NspV TTCGAA 1 cut(s) 911
PaeR7I CTCGAG 1 cut(s) 1689
PasI CCCWGGG 1 cut(s) 1441
PauI GCGCGC 1 cut(s) 1582
PdmI GAANNNNTTC 2 cut(s) 49, 546
Pfl23II CGTACG 1 cut(s) 584
PfoI TCCNGGA 1 cut(s) 1138
PkrI GCNGC 2 cut(s) 1563, 1708
PleI GAGTC 2 cut(s) 663, 1091
PpsI GAGTC 2 cut(s) 663, 1091
Psp1406I AACGTT 1 cut(s) 1752
Psp6I CCWGG 4 cut(s) 40, 189, 1138, 1440
PspGI CCWGG 4 cut(s) 40, 189, 1138, 1440
PspLI CGTACG 1 cut(s) 584
PspN4I GGNNCC 3 cut(s) 195, 748, 1783
PspPI GGNCC 4 cut(s) 303, 358, 746, 1885
PspXI VCTCGAGB 1 cut(s) 1689
PsrI GAACNNNNNNTAC 2 cut(s) 568, 600
PsuI RGATCY 4 cut(s) 193, 1419, 1436, 1452
PteI GCGCGC 1 cut(s) 1582
RsaI GTAC 6 cut(s) 505, 586, 1272, 1449, 1482, 1783
RsaNI GTAC 6 cut(s) 504, 585, 1271, 1448, 1481, 1782
SaqAI TTAA 8 cut(s) 311, 702, 854, 876, 887, 951, 1413, 1962
SatI GCNGC 2 cut(s) 1562, 1707
Sau96I GGNCC 4 cut(s) 303, 358, 746, 1885
SchI GAGTC 2 cut(s) 664, 1091
ScrFI CCNGG 6 cut(s) 42, 191, 1140, 1442, 1542, 1715
SduI GDGCHC 1 cut(s) 1806
SfaNI GCATC 3 cut(s) 36, 942, 1646
SfcI CTRYAG 1 cut(s) 1386
Sfr274I CTCGAG 1 cut(s) 1689
SfuI TTCGAA 1 cut(s) 911
SinI GGWCC 2 cut(s) 303, 1885
SlaI CTCGAG 1 cut(s) 1689
SmlI CTYRAG 1 cut(s) 1689
SmoI CTYRAG 1 cut(s) 1689
SsiI CCGC 4 cut(s) 38, 70, 158, 202
SspI AATATT 2 cut(s) 677, 830
SspMI CTAG 3 cut(s) 218, 1301, 1760
StyD4I CCNGG 6 cut(s) 40, 189, 1138, 1440, 1540, 1713
StyI CCWWGG 2 cut(s) 537, 1355
TaaI ACNGT 2 cut(s) 164, 1150
TaiI ACGT 4 cut(s) 590, 1276, 1486, 1755
Tru1I TTAA 8 cut(s) 311, 702, 854, 876, 887, 951, 1413, 1962
Tru9I TTAA 8 cut(s) 311, 702, 854, 876, 887, 951, 1413, 1962
TseI GCWGC 2 cut(s) 1561, 1706
TspDTI ATGAA 6 cut(s) 165, 909, 1142, 1224, 1310, 1648
TspGWI ACGGA 1 cut(s) 912
VpaK11BI GGWCC 2 cut(s) 303, 1885
XbaI TCTAGA 1 cut(s) 217
XhoI CTCGAG 1 cut(s) 1689
XmnI GAANNNNTTC 2 cut(s) 49, 546
XspI CTAG 3 cut(s) 218, 1301, 1760
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.