RchiOBHm_Chr5g0042251

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0018192
Physical Location & Seq
Reverse (-)
37010140 .. 37012585
2446 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ32066

Sequence Viewer

Length: 756 bp
ATGGCGGTATGCTTCCGTCAGGTTTGGGGCAGTGCTATGAATGATAGGGAGTATTATATGCTACCTAGGCATGCTTGGCTTCAAAATATGACTTACTCAGCTAAGATCAAAAGCGAAAAGTTTAAAACTGGAGAAGAACAATGTCTTGACAAGCAGATTGTGACTACGGAGAGTAGAGATGTCTTTATTGGTAAGCTCCCAGTGATGGTGAAGTCTGACTTGTGTTGGCTGAAAGACGAGAGAGCTGACTGTGAATTTGACCATGGAGGTTATTTTATAATCAAGGGTGCAGAGAAGACCTTTATTGCGCAAGAGCAGACCTGTCTGAAGAGACTTCTAATTACAAGTAATCAGGGGCTCACAGTAGCATATAGGTCTGATGTCAAGCAGCATAGACTAATAATAAGATTATCTGGGATTTCTCAACTTGAAAACATTGAAGGATTAGAGAAAGTTTTGTCAGTGTACTTTATGTCAGCAGAAATCCCTGTCTGGATTTGGTTTTTTGCCCTTGGGGTTTCTTCGGACAATGAAGTTATAGATCTGATTGATTATGGCAAAGAAGATGCAAGCATTTCAAACATTCTAGTTGCCTCAATTCTTGATGCTGACCAACGAAAAGATATCTTCCGAAGAGGGAAGAATGCTCTCAGATATGTTGAAGAGATGATAAAGAATACCACGTTTCCTCCTTGGGAAAGCATTGAAGAATGCATCAGCATGTATCTGTTCCCCAATCTGAGAGGCATGAAGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000228 GO:0000418 GO:0000419 GO:0000428 GO:0000785 GO:0000790 GO:0000792 GO:0002682 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005694 GO:0005720 GO:0005730 GO:0005736 GO:0006139 GO:0006259 GO:0006304 GO:0006305 GO:0006306 GO:0006396 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009605 GO:0009607 GO:0009620 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016020 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0030422 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032259 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034654 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043207 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043331 GO:0043412 GO:0043414 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044454 GO:0044464 GO:0044728 GO:0046483 GO:0048519 GO:0048583 GO:0050776 GO:0050789 GO:0050832 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0097747 GO:0098542 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1901698 GO:1901699 GO:1902494 GO:1990234
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169
Pfam Domains
Protein Families
RNA_pol_Rpb2_1 RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_4 RNA_pol_Rpb2_5 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

251

Amino Acids

29.06

Weight (kDa)

5.77

Isoelectric Point (pI)

47.63

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb2_1 PF04563 14 - 217 2.3e-18 RNA polymerase beta subunit
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)
AanI TTATAA 1 cut(s) 278
Acc16I TGCGCA 1 cut(s) 309
AciI CCGC 1 cut(s) 5
AcsI RAATTY 1 cut(s) 254
AcuI CTGAAG 1 cut(s) 347
AfaI GTAC 1 cut(s) 467
AfiI CCNNNNNNNGG 1 cut(s) 205
AgsI TTSAA 6 cut(s) 83, 431, 440, 579, 662, 707
AluBI AGCT 3 cut(s) 101, 196, 245
AluI AGCT 3 cut(s) 101, 196, 245
Alw26I GTCTC 1 cut(s) 325
ApeKI GCWGC 1 cut(s) 388
ApoI RAATTY 1 cut(s) 254
ArsI GACNNNNNNTTYG 2 cut(s) 239, 271
AspA2I CCTAGG 1 cut(s) 65
AspLEI GCGC 1 cut(s) 310
AsuHPI GGTGA 1 cut(s) 220
AvrII CCTAGG 1 cut(s) 65
BanII GRGCYC 1 cut(s) 360
BbsI GAAGAC 1 cut(s) 302
BbvI GCAGC 1 cut(s) 400
BccI CCATC 1 cut(s) 199
BcoDI GTCTC 1 cut(s) 325
BfaI CTAG 2 cut(s) 66, 587
BglII AGATCT 1 cut(s) 541
BisI GCNGC 1 cut(s) 389
BlnI CCTAGG 1 cut(s) 65
BlsI GCNGC 1 cut(s) 390
BmrI ACTGGG 1 cut(s) 194
BmsI GCATC 3 cut(s) 556, 595, 723
BmuI ACTGGG 1 cut(s) 194
BpiI GAAGAC 1 cut(s) 302
BpmI CTGGAG 1 cut(s) 150
BsaJI CCNNGG 4 cut(s) 65, 262, 511, 692
BsaXI ACNNNNNCTCC 2 cut(s) 673, 703
Bsc4I CCNNNNNNNGG 1 cut(s) 205
Bse1I ACTGG 2 cut(s) 133, 200
BseDI CCNNGG 4 cut(s) 65, 262, 511, 692
BseLI CCNNNNNNNGG 1 cut(s) 205
BseMII CTCAG 3 cut(s) 111, 664, 731
BseNI ACTGG 2 cut(s) 133, 200
BseXI GCAGC 1 cut(s) 400
BsgI GTGCAG 1 cut(s) 309
BslI CCNNNNNNNGG 1 cut(s) 205
BsmAI GTCTC 1 cut(s) 325
BsmI GAATGC 2 cut(s) 649, 716
Bsp1286I GDGCHC 1 cut(s) 360
Bsp143I GATC 2 cut(s) 105, 541
Bsp19I CCATGG 1 cut(s) 262
BspACI CCGC 1 cut(s) 5
BspCNI CTCAG 3 cut(s) 110, 663, 732
BsrI ACTGG 2 cut(s) 133, 200
BssECI CCNNGG 4 cut(s) 65, 262, 511, 692
BssMI GATC 2 cut(s) 105, 541
BssT1I CCWWGG 4 cut(s) 65, 262, 511, 692
Bst4CI ACNGT 2 cut(s) 251, 364
Bst6I CTCTTC 3 cut(s) 323, 628, 657
BstC8I GCNNGC 2 cut(s) 72, 571
BstDEI CTNAG 4 cut(s) 97, 102, 650, 740
BstDSI CCRYGG 1 cut(s) 262
BstHHI GCGC 1 cut(s) 310
BstKTI GATC 2 cut(s) 108, 544
BstMAI GTCTC 1 cut(s) 325
BstMBI GATC 2 cut(s) 105, 541
BstMWI GCNNNNNNNGC 2 cut(s) 67, 76
BstNSI RCATGY 2 cut(s) 74, 724
BstV1I GCAGC 1 cut(s) 400
BstV2I GAAGAC 1 cut(s) 302
BstX2I RGATCY 1 cut(s) 541
BstYI RGATCY 1 cut(s) 541
BtgI CCRYGG 1 cut(s) 262
BtsI GCAGTG 1 cut(s) 37
BtsIMutI CAGTG 3 cut(s) 37, 207, 468
Cac8I GCNNGC 2 cut(s) 72, 571
CfoI GCGC 1 cut(s) 310
Csp6I GTAC 1 cut(s) 466
CviAII CATG 4 cut(s) 71, 263, 721, 748
CviJI RGCY 6 cut(s) 79, 101, 196, 229, 245, 358
CviKI_1 RGCY 6 cut(s) 79, 101, 196, 229, 245, 358
CviQI GTAC 1 cut(s) 466
DdeI CTNAG 4 cut(s) 97, 102, 650, 740
DpnI GATC 2 cut(s) 107, 543
DpnII GATC 2 cut(s) 105, 541
DraI TTTAAA 1 cut(s) 124
Eam1104I CTCTTC 3 cut(s) 323, 628, 657
EarI CTCTTC 3 cut(s) 323, 628, 657
Eco130I CCWWGG 4 cut(s) 65, 262, 511, 692
Eco24I GRGCYC 1 cut(s) 360
Eco32I GATATC 1 cut(s) 625
Eco57I CTGAAG 1 cut(s) 347
EcoRV GATATC 1 cut(s) 625
EcoT14I CCWWGG 4 cut(s) 65, 262, 511, 692
EcoT22I ATGCAT 1 cut(s) 716
EcoT38I GRGCYC 1 cut(s) 360
ErhI CCWWGG 4 cut(s) 65, 262, 511, 692
FaeI CATG 4 cut(s) 74, 266, 724, 751
FalI AAGNNNNNCTT 2 cut(s) 203, 235
FatI CATG 4 cut(s) 70, 262, 720, 747
Fnu4HI GCNGC 1 cut(s) 389
FriOI GRGCYC 1 cut(s) 360
Fsp4HI GCNGC 1 cut(s) 389
FspBI CTAG 2 cut(s) 66, 587
FspI TGCGCA 1 cut(s) 309
GlaI GCGC 1 cut(s) 309
GluI GCNGC 1 cut(s) 389
GsuI CTGGAG 1 cut(s) 150
HhaI GCGC 1 cut(s) 310
Hin1II CATG 4 cut(s) 74, 266, 724, 751
Hin6I GCGC 1 cut(s) 308
HinP1I GCGC 1 cut(s) 308
HphI GGTGA 1 cut(s) 220
Hpy166II GTNNAC 1 cut(s) 466
Hpy188I TCNGA 8 cut(s) 217, 327, 379, 526, 546, 632, 653, 741
Hpy188III TCNNGA 3 cut(s) 146, 493, 602
Hpy8I GTNNAC 1 cut(s) 466
HpyAV CCTTC 1 cut(s) 434
HpyCH4III ACNGT 2 cut(s) 251, 364
HpyCH4IV ACGT 1 cut(s) 683
HpyCH4V TGCA 3 cut(s) 290, 569, 714
HpyF10VI GCNNNNNNNGC 2 cut(s) 67, 76
HpyF3I CTNAG 4 cut(s) 97, 102, 650, 740
HpySE526I ACGT 1 cut(s) 683
Hsp92II CATG 4 cut(s) 74, 266, 724, 751
HspAI GCGC 1 cut(s) 308
Kzo9I GATC 2 cut(s) 105, 541
LmnI GCTCC 1 cut(s) 201
LpnPI CCDG 8 cut(s) 5, 114, 213, 334, 338, 399, 478, 501
Lsp1109I GCAGC 1 cut(s) 400
LweI GCATC 3 cut(s) 556, 595, 723
MaeI CTAG 2 cut(s) 66, 587
MaeII ACGT 1 cut(s) 683
MaeIII GTNAC 1 cut(s) 160
MalI GATC 2 cut(s) 107, 543
MboI GATC 2 cut(s) 105, 541
MflI RGATCY 1 cut(s) 541
MhlI GDGCHC 1 cut(s) 360
MluCI AATT 3 cut(s) 254, 339, 597
MnlI CCTC 5 cut(s) 260, 604, 629, 699, 737
Mph1103I ATGCAT 1 cut(s) 716
MseI TTAA 1 cut(s) 123
MslI CAYNNNNRTG 1 cut(s) 719
Mva1269I GAATGC 2 cut(s) 649, 716
MwoI GCNNNNNNNGC 2 cut(s) 67, 76
NcoI CCATGG 1 cut(s) 262
NdeII GATC 2 cut(s) 105, 541
NlaIII CATG 4 cut(s) 74, 266, 724, 751
NmuCI GTSAC 1 cut(s) 160
NsbI TGCGCA 1 cut(s) 309
NsiI ATGCAT 1 cut(s) 716
NspI RCATGY 2 cut(s) 74, 724
PaeI GCATGC 1 cut(s) 74
PctI GAATGC 2 cut(s) 649, 716
PkrI GCNGC 1 cut(s) 390
PsiI TTATAA 1 cut(s) 278
PsuI RGATCY 1 cut(s) 541
RsaI GTAC 1 cut(s) 467
RsaNI GTAC 1 cut(s) 466
RseI CAYNNNNRTG 1 cut(s) 719
SaqAI TTAA 1 cut(s) 123
SatI GCNGC 1 cut(s) 389
Sau3AI GATC 2 cut(s) 105, 541
SduI GDGCHC 1 cut(s) 360
SfaNI GCATC 3 cut(s) 556, 595, 723
SmiMI CAYNNNNRTG 1 cut(s) 719
SphI GCATGC 1 cut(s) 74
Sse9I AATT 3 cut(s) 254, 339, 597
SsiI CCGC 1 cut(s) 5
SspMI CTAG 2 cut(s) 66, 587
StyI CCWWGG 4 cut(s) 65, 262, 511, 692
TaaI ACNGT 2 cut(s) 251, 364
TaiI ACGT 1 cut(s) 686
TasI AATT 3 cut(s) 254, 339, 597
TatI WGTACW 1 cut(s) 465
Tru1I TTAA 1 cut(s) 123
Tru9I TTAA 1 cut(s) 123
TscAI CASTG 3 cut(s) 37, 207, 468
TseFI GTSAC 1 cut(s) 160
TseI GCWGC 1 cut(s) 388
Tsp45I GTSAC 1 cut(s) 160
TspDTI ATGAA 2 cut(s) 53, 546
TspGWI ACGGA 2 cut(s) 5, 182
TspRI CASTG 3 cut(s) 37, 207, 468
XapI RAATTY 1 cut(s) 254
XceI RCATGY 2 cut(s) 74, 724
XmaJI CCTAGG 1 cut(s) 65
XspI CTAG 2 cut(s) 66, 587
Zsp2I ATGCAT 1 cut(s) 716
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.