Rh4DG026400

DNA-directed RNA polymerase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0018596
Physical Location & Seq
Reverse (-)
4782412 .. 4783085
674 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4DG026400.1

Sequence Viewer

Length: 531 bp
ATGTTTCTCAAAGTAGAATTGCCCTGGAATGTAGTAATCCCGCCTGCAAACCTGGTTGCAAAAGGATTGATGCTTAAAAAATCAATCAGTCTCCGATTGCTCAAAGGCTTTGCTGCAAATAAGGCAACCAAAGATCATGGGTACTTTCTTGCGATCACAACCGTGGAAAGCATAGGAGAGGGAAAAGTCAGGCGCTCCGGGGATGTGTTGTATCCAGTTGTGTTTAGTTGCATCACTTTTAAGCTTTTCAGGGGGGAGATCATAGAGGGGGTTGTTCACCATGTGCTGAGAAATGGAGTTTTGATGAGCTGCGGCCCCGTTGAAAACATATTTCTATATAAGGACTTAATGCCTGATTACCGATATGTCCCCGGAGAGAATCCCATTTTCTTGAACGAAAAGACGGGCTCTAAGATTGTGAAAGATGTATTGGTTCGTTGTATTGTTCTTGGGACTAAGTGGCTTGAAGAAGAAAGGGAGTTTCGGGGACTGGTTAGCTTGGAGGGTGATTATCTAGGACCAGTTTCATAA

Protein Analysis

176

Amino Acids

19.73

Weight (kDa)

8.94

Isoelectric Point (pI)

35.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SHS2_Rpb7-N PF03876 10 - 67 8.2e-06 SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0018596)

Species Orthologous Gene IDs
rosa_chinensis RchiOBHm_Chr4g0390261
rosa_multiflora Rmu_sc0004432.1_g000008 Rmu_sc0014620.1_g000004
rosa_roxburghii Rroxscaffold_5G00336380
rosa_rugosa Rorug03G0328700 Rorug03G0328800
rosa_samantha Rh4AG031200 Rh4BG025200 Rh4CG034200 Rh4DG026400

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 2 cut(s) 41, 312
AdeI CACNNNGTG 1 cut(s) 283
AfaI GTAC 1 cut(s) 143
AgsI TTSAA 3 cut(s) 323, 394, 467
AjnI CCWGG 2 cut(s) 23, 51
AjuI GAANNNNNNNTTGG 2 cut(s) 413, 445
AleI CACNNNNGTG 1 cut(s) 161
AluBI AGCT 3 cut(s) 244, 309, 498
AluI AGCT 3 cut(s) 244, 309, 498
Alw26I GTCTC 1 cut(s) 95
AoxI GGCC 1 cut(s) 313
ApeKI GCWGC 2 cut(s) 113, 309
AspLEI GCGC 1 cut(s) 195
AspS9I GGNCC 2 cut(s) 314, 518
AsuC2I CCSGG 2 cut(s) 199, 372
AsuHPI GGTGA 2 cut(s) 269, 518
AvaII GGWCC 1 cut(s) 518
BanII GRGCYC 1 cut(s) 410
BbvI GCAGC 2 cut(s) 100, 296
BciT130I CCWGG 2 cut(s) 25, 53
BciVI GTATCC 1 cut(s) 222
BcnI CCSGG 2 cut(s) 199, 372
BcoDI GTCTC 1 cut(s) 95
BfaI CTAG 1 cut(s) 515
BfoI RGCGCY 1 cut(s) 196
BfuI GTATCC 1 cut(s) 222
BisI GCNGC 3 cut(s) 114, 310, 313
BlsI GCNGC 3 cut(s) 115, 311, 314
Bme1390I CCNGG 4 cut(s) 25, 53, 199, 372
Bme18I GGWCC 1 cut(s) 518
BmgT120I GGNCC 2 cut(s) 314, 518
BmiI GGNNCC 1 cut(s) 316
BmrFI CCNGG 4 cut(s) 25, 53, 199, 372
BmsI GCATC 2 cut(s) 60, 240
BpuMI CCSGG 2 cut(s) 199, 372
BsaJI CCNNGG 4 cut(s) 23, 162, 198, 370
Bse1I ACTGG 3 cut(s) 215, 495, 521
BseBI CCWGG 2 cut(s) 25, 53
BseDI CCNNGG 4 cut(s) 23, 162, 198, 370
BseGI GGATG 1 cut(s) 208
BseMII CTCAG 1 cut(s) 278
BseNI ACTGG 3 cut(s) 215, 495, 521
BseXI GCAGC 2 cut(s) 100, 296
BshFI GGCC 1 cut(s) 315
BsiSI CCGG 2 cut(s) 198, 372
BslFI GGGAC 3 cut(s) 353, 466, 501
BsmAI GTCTC 1 cut(s) 95
BsmFI GGGAC 3 cut(s) 353, 466, 501
BsnI GGCC 1 cut(s) 315
Bsp1286I GDGCHC 1 cut(s) 410
Bsp143I GATC 3 cut(s) 133, 153, 258
BspACI CCGC 2 cut(s) 41, 312
BspANI GGCC 1 cut(s) 315
BspCNI CTCAG 1 cut(s) 279
BspLI GGNNCC 1 cut(s) 316
BsrI ACTGG 3 cut(s) 215, 495, 521
BssECI CCNNGG 4 cut(s) 23, 162, 198, 370
BssMI GATC 3 cut(s) 133, 153, 258
Bst2UI CCWGG 2 cut(s) 25, 53
Bst4CI ACNGT 1 cut(s) 163
BstC8I GCNNGC 1 cut(s) 45
BstDEI CTNAG 3 cut(s) 287, 411, 456
BstDSI CCRYGG 1 cut(s) 162
BstF5I GGATG 1 cut(s) 208
BstH2I RGCGCY 1 cut(s) 196
BstHHI GCGC 1 cut(s) 195
BstKTI GATC 3 cut(s) 136, 156, 261
BstMAI GTCTC 1 cut(s) 95
BstMBI GATC 3 cut(s) 133, 153, 258
BstMWI GCNNNNNNNGC 1 cut(s) 122
BstNI CCWGG 2 cut(s) 25, 53
BstSCI CCNGG 4 cut(s) 23, 51, 197, 370
BstV1I GCAGC 2 cut(s) 100, 296
BsuI GTATCC 1 cut(s) 222
BsuRI GGCC 1 cut(s) 315
BtgI CCRYGG 1 cut(s) 162
BtsCI GGATG 1 cut(s) 208
Cac8I GCNNGC 1 cut(s) 45
CfoI GCGC 1 cut(s) 195
Cfr13I GGNCC 2 cut(s) 314, 518
CsiI ACCWGGT 1 cut(s) 51
Csp6I GTAC 1 cut(s) 142
CviAII CATG 2 cut(s) 137, 281
CviJI RGCY 7 cut(s) 108, 244, 309, 315, 408, 463, 498
CviKI_1 RGCY 7 cut(s) 108, 244, 309, 315, 408, 463, 498
CviQI GTAC 1 cut(s) 142
DdeI CTNAG 3 cut(s) 287, 411, 456
DpnI GATC 3 cut(s) 135, 155, 260
DpnII GATC 3 cut(s) 133, 153, 258
DraIII CACNNNGTG 1 cut(s) 283
Eco24I GRGCYC 1 cut(s) 410
Eco47I GGWCC 1 cut(s) 518
EcoRII CCWGG 2 cut(s) 23, 51
EcoT38I GRGCYC 1 cut(s) 410
FaeI CATG 2 cut(s) 140, 284
FaiI YATR 9 cut(s) 138, 173, 263, 282, 329, 337, 339, 366, 529
FaqI GGGAC 3 cut(s) 353, 466, 501
FatI CATG 2 cut(s) 136, 280
FauI CCCGC 1 cut(s) 48
Fnu4HI GCNGC 3 cut(s) 114, 310, 313
FokI GGATG 1 cut(s) 215
FriOI GRGCYC 1 cut(s) 410
Fsp4HI GCNGC 3 cut(s) 114, 310, 313
FspBI CTAG 1 cut(s) 515
GlaI GCGC 1 cut(s) 194
GluI GCNGC 3 cut(s) 114, 310, 313
HaeII RGCGCY 1 cut(s) 196
HaeIII GGCC 1 cut(s) 315
HapII CCGG 2 cut(s) 198, 372
HhaI GCGC 1 cut(s) 195
Hin1II CATG 2 cut(s) 140, 284
Hin6I GCGC 1 cut(s) 193
HinP1I GCGC 1 cut(s) 193
HindIII AAGCTT 1 cut(s) 242
HinfI GANTC 1 cut(s) 379
HpaII CCGG 2 cut(s) 198, 372
HphI GGTGA 2 cut(s) 269, 518
Hpy166II GTNNAC 1 cut(s) 277
Hpy188I TCNGA 1 cut(s) 95
Hpy188III TCNNGA 1 cut(s) 391
Hpy8I GTNNAC 1 cut(s) 277
HpyCH4III ACNGT 1 cut(s) 163
HpyCH4V TGCA 4 cut(s) 47, 59, 116, 231
HpyF10VI GCNNNNNNNGC 1 cut(s) 122
HpyF3I CTNAG 3 cut(s) 287, 411, 456
Hsp92II CATG 2 cut(s) 140, 284
HspAI GCGC 1 cut(s) 193
Kzo9I GATC 3 cut(s) 133, 153, 258
LmnI GCTCC 1 cut(s) 200
Lsp1109I GCAGC 2 cut(s) 100, 296
LweI GCATC 2 cut(s) 60, 240
MabI ACCWGGT 1 cut(s) 51
MaeI CTAG 1 cut(s) 515
MalI GATC 3 cut(s) 135, 155, 260
MboI GATC 3 cut(s) 133, 153, 258
MboII GAAGA 2 cut(s) 479, 482
MhlI GDGCHC 1 cut(s) 410
MluCI AATT 1 cut(s) 17
MnlI CCTC 3 cut(s) 172, 259, 496
MseI TTAA 3 cut(s) 75, 240, 347
MslI CAYNNNNRTG 1 cut(s) 161
MspI CCGG 2 cut(s) 198, 372
MspR9I CCNGG 4 cut(s) 25, 53, 199, 372
MvaI CCWGG 2 cut(s) 25, 53
MwoI GCNNNNNNNGC 1 cut(s) 122
NciI CCSGG 2 cut(s) 199, 372
NdeII GATC 3 cut(s) 133, 153, 258
NlaIII CATG 2 cut(s) 140, 284
NlaIV GGNNCC 1 cut(s) 316
OliI CACNNNNGTG 1 cut(s) 161
PfeI GAWTC 1 cut(s) 379
PkrI GCNGC 3 cut(s) 115, 311, 314
Psp6I CCWGG 2 cut(s) 23, 51
PspGI CCWGG 2 cut(s) 23, 51
PspN4I GGNNCC 1 cut(s) 316
PspPI GGNCC 2 cut(s) 314, 518
RsaI GTAC 1 cut(s) 143
RsaNI GTAC 1 cut(s) 142
RseI CAYNNNNRTG 1 cut(s) 161
SaqAI TTAA 3 cut(s) 75, 240, 347
SatI GCNGC 3 cut(s) 114, 310, 313
Sau3AI GATC 3 cut(s) 133, 153, 258
Sau96I GGNCC 2 cut(s) 314, 518
ScrFI CCNGG 4 cut(s) 25, 53, 199, 372
SduI GDGCHC 1 cut(s) 410
SetI ASST 4 cut(s) 54, 246, 311, 500
SexAI ACCWGGT 1 cut(s) 51
SfaNI GCATC 2 cut(s) 60, 240
SinI GGWCC 1 cut(s) 518
SmiMI CAYNNNNRTG 1 cut(s) 161
Sse9I AATT 1 cut(s) 17
SsiI CCGC 2 cut(s) 41, 312
SspMI CTAG 1 cut(s) 515
StyD4I CCNGG 4 cut(s) 23, 51, 197, 370
TaaI ACNGT 1 cut(s) 163
TasI AATT 1 cut(s) 17
TauI GCSGC 1 cut(s) 315
TfiI GAWTC 1 cut(s) 379
Tru1I TTAA 3 cut(s) 75, 240, 347
Tru9I TTAA 3 cut(s) 75, 240, 347
TseI GCWGC 2 cut(s) 113, 309
TspDTI ATGAA 1 cut(s) 516
VpaK11BI GGWCC 1 cut(s) 518
XspI CTAG 1 cut(s) 515
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.