Prupe.1G018500_v2.0.a1

RNA-directed DNA methylation 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
prunus_persica
Pp01
OG0012911
Physical Location & Seq
Forward (+)
1294454 .. 1297977
3524 bp
Loading structure...
UTR
Exon/CDS
Intron
Prupe.1G018500.1

Sequence Viewer

Length: 786 bp
ATGGAGAGGGAGAGAGATAGCGGAGGAGGAGAAGAAGGGTTGAAGAGATTGGCGAGAGCGATTGAGAGGTTCGGGGAGGTGTATCAGAGAGTGGAGGCCGAGAAGTTGAGGCAGATGGTGGAGTTGGAGAAGCAGAGGATGCAATTCGCCAATGATTTGGAGGTGCAGAGGATGAATATGTTCATGGACACGCAGCAGAGCAACCACGGCGAGCGATCGGGCTCTAATGGTTACAGTCCATATACCATGAAGAGGGCATTTCCATGGGATGAGCAGGTTGATGTTATATCATCAGATGACTCTTCTTCCTCAGACATGGAGATGGAAACCAATATTGAGTCTGATAGCAAGCAGTTAACCAATAATACCACATCTGATCAACCTGCCAAAGAAAGAACATCCGAAGGTGCTTTGACGCGAAGGGCAGAGATGTATCAGGAGTACATGAAGCAGATCCCGATCCCAGCGCACCGTGGCTCTGTTATCCCATTCACCTCATGGATGGGGTTAGGTAAATCCATTAAGCAGTTATATGGACAACCTTTGCATTACCTCACCAATATTCTCCTAAAACAGTGGGACCAATTGAGGATGGGCAGTGAGGAAGAGTACAGGCCCTTGGATACCATAATTCATCCGTGTAAAGCCGAAGCCACCATCTGGCTCATGGAAGAAGTCCACCGGCACACCTCATCTCATTATCATATAGCCAATCTCTGGCTATCAGATCCGATGCACCATGCCTTTGTGGATTCCATCTTTCCGCAGTTAAGAAGCAAATCATGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RdDM_RDM1

Protein Analysis

262

Amino Acids

30.36

Weight (kDa)

5.61

Isoelectric Point (pI)

60.99

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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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Orthologous Genes (Group: OG0012911)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G22680
fragaria_vesca FvH4_4g00760 FvH4_4g00760 FvH4_5g32450
malus_domestica MD16G1197500.v1.1
prunus_persica Prupe.1G018500_v2.0.a1
pyrus_communis pycom16g16640
rosa_chinensis RchiOBHm_Chr4g0407591
rosa_laevigata RLG00000008706 RLG00000010156
rosa_multiflora Rmu_sc0001942.1_g000058
rosa_roxburghii Rroxscaffold_5G00352200
rosa_rugosa Rorug04G0080600 Rorug04G0080700 Rorug04G0080800
rosa_samantha Rh4AG145400 Rh4CG152100
rosa_wichuraiana Rw4G011810

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 2 cut(s) 265, 391
AccB7I CCANNNNNTGG 2 cut(s) 660, 717
AccII CGCG 1 cut(s) 418
AciI CCGC 2 cut(s) 21, 764
AclWI GGATC 3 cut(s) 448, 454, 722
AfaI GTAC 2 cut(s) 443, 611
AfiI CCNNNNNNNGG 3 cut(s) 252, 660, 717
AgsI TTSAA 1 cut(s) 43
AlwI GGATC 3 cut(s) 448, 454, 722
AoxI GGCC 2 cut(s) 96, 614
ApeKI GCWGC 1 cut(s) 193
Asp700I GAANNNNTTC 1 cut(s) 179
AspLEI GCGC 1 cut(s) 469
AspS9I GGNCC 2 cut(s) 580, 615
AsuHPI GGTGA 2 cut(s) 484, 547
AvaII GGWCC 1 cut(s) 580
BanII GRGCYC 1 cut(s) 224
BbvI GCAGC 1 cut(s) 205
BccI CCATC 6 cut(s) 109, 316, 496, 586, 665, 764
BceAI ACGGC 1 cut(s) 223
BciVI GTATCC 1 cut(s) 616
BclI TGATCA 1 cut(s) 376
BfuAI ACCTGC 2 cut(s) 265, 391
BfuI GTATCC 1 cut(s) 616
BisI GCNGC 1 cut(s) 194
BlsI GCNGC 1 cut(s) 195
Bme18I GGWCC 1 cut(s) 580
BmgT120I GGNCC 2 cut(s) 580, 615
BmiI GGNNCC 1 cut(s) 581
BmsI GCATC 2 cut(s) 129, 723
BsaBI GATNNNNATC 1 cut(s) 458
BsaJI CCNNGG 4 cut(s) 205, 263, 472, 618
Bsc4I CCNNNNNNNGG 3 cut(s) 252, 660, 717
Bse118I RCCGGY 1 cut(s) 681
Bse8I GATNNNNATC 1 cut(s) 458
BseDI CCNNGG 4 cut(s) 205, 263, 472, 618
BseGI GGATG 7 cut(s) 144, 177, 274, 398, 507, 597, 634
BseJI GATNNNNATC 1 cut(s) 458
BseLI CCNNNNNNNGG 3 cut(s) 252, 660, 717
BseMII CTCAG 1 cut(s) 324
BseRI GAGGAG 2 cut(s) 39, 42
BseXI GCAGC 1 cut(s) 205
BseYI CCCAGC 1 cut(s) 463
BsgI GTGCAG 1 cut(s) 185
Bsh1236I CGCG 1 cut(s) 418
Bsh1285I CGRYCG 1 cut(s) 218
BshFI GGCC 2 cut(s) 98, 616
BsiEI CGRYCG 1 cut(s) 218
BsiSI CCGG 1 cut(s) 682
BslFI GGGAC 1 cut(s) 593
BslI CCNNNNNNNGG 3 cut(s) 252, 660, 717
BsmFI GGGAC 1 cut(s) 593
BsnI GGCC 2 cut(s) 98, 616
Bsp1286I GDGCHC 1 cut(s) 224
Bsp143I GATC 5 cut(s) 215, 376, 453, 459, 727
Bsp19I CCATGG 1 cut(s) 263
BspACI CCGC 2 cut(s) 21, 764
BspANI GGCC 2 cut(s) 98, 616
BspCNI CTCAG 1 cut(s) 323
BspFNI CGCG 1 cut(s) 418
BspHI TCATGA 1 cut(s) 782
BspLI GGNNCC 1 cut(s) 581
BspMI ACCTGC 2 cut(s) 265, 391
BspPI GGATC 3 cut(s) 448, 454, 722
BsrFI RCCGGY 1 cut(s) 681
BssAI RCCGGY 1 cut(s) 681
BssECI CCNNGG 4 cut(s) 205, 263, 472, 618
BssMI GATC 5 cut(s) 215, 376, 453, 459, 727
BssT1I CCWWGG 2 cut(s) 263, 618
Bst4CI ACNGT 3 cut(s) 236, 473, 576
Bst6I CTCTTC 4 cut(s) 38, 245, 307, 600
BstAPI GCANNNNNTGC 1 cut(s) 139
BstC8I GCNNGC 2 cut(s) 212, 350
BstDEI CTNAG 1 cut(s) 310
BstDSI CCRYGG 3 cut(s) 205, 263, 472
BstF5I GGATG 7 cut(s) 144, 177, 274, 398, 507, 597, 634
BstFNI CGCG 1 cut(s) 418
BstHHI GCGC 1 cut(s) 469
BstKTI GATC 5 cut(s) 218, 379, 456, 462, 730
BstMBI GATC 5 cut(s) 215, 376, 453, 459, 727
BstMCI CGRYCG 1 cut(s) 218
BstMWI GCNNNNNNNGC 2 cut(s) 139, 207
BstUI CGCG 1 cut(s) 418
BstV1I GCAGC 1 cut(s) 205
BstX2I RGATCY 2 cut(s) 453, 727
BstXI CCANNNNNNTGG 1 cut(s) 157
BstYI RGATCY 2 cut(s) 453, 727
BsuI GTATCC 1 cut(s) 616
BsuRI GGCC 2 cut(s) 98, 616
BtgI CCRYGG 3 cut(s) 205, 263, 472
BtsCI GGATG 7 cut(s) 144, 177, 274, 398, 507, 597, 634
BtsI GCAGTG 1 cut(s) 604
BtsIMutI CAGTG 2 cut(s) 581, 604
BveI ACCTGC 2 cut(s) 265, 391
Cac8I GCNNGC 2 cut(s) 212, 350
CciI TCATGA 1 cut(s) 782
CfoI GCGC 1 cut(s) 469
Cfr10I RCCGGY 1 cut(s) 681
Cfr13I GGNCC 2 cut(s) 580, 615
CseI GACGC 1 cut(s) 424
Csp6I GTAC 2 cut(s) 442, 610
CviAII CATG 9 cut(s) 184, 247, 264, 316, 445, 498, 667, 740, 783
CviJI RGCY 9 cut(s) 98, 222, 477, 616, 647, 653, 664, 710, 721
CviKI_1 RGCY 9 cut(s) 98, 222, 477, 616, 647, 653, 664, 710, 721
CviQI GTAC 2 cut(s) 442, 610
DdeI CTNAG 1 cut(s) 310
DpnI GATC 5 cut(s) 217, 378, 455, 461, 729
DpnII GATC 5 cut(s) 215, 376, 453, 459, 727
Eam1104I CTCTTC 4 cut(s) 38, 245, 307, 600
EarI CTCTTC 4 cut(s) 38, 245, 307, 600
Eco130I CCWWGG 2 cut(s) 263, 618
Eco24I GRGCYC 1 cut(s) 224
Eco47I GGWCC 1 cut(s) 580
EcoO109I RGGNCCY 1 cut(s) 615
EcoT14I CCWWGG 2 cut(s) 263, 618
EcoT38I GRGCYC 1 cut(s) 224
ErhI CCWWGG 2 cut(s) 263, 618
FaeI CATG 9 cut(s) 187, 250, 267, 319, 448, 501, 670, 743, 786
FaqI GGGAC 1 cut(s) 593
FatI CATG 9 cut(s) 183, 246, 263, 315, 444, 497, 666, 739, 782
FbaI TGATCA 1 cut(s) 376
Fnu4HI GCNGC 1 cut(s) 194
FokI GGATG 7 cut(s) 151, 184, 281, 385, 514, 604, 621
FriOI GRGCYC 1 cut(s) 224
Fsp4HI GCNGC 1 cut(s) 194
GlaI GCGC 1 cut(s) 468
GluI GCNGC 1 cut(s) 194
GsaI CCCAGC 1 cut(s) 467
HaeIII GGCC 2 cut(s) 98, 616
HapII CCGG 1 cut(s) 682
HgaI GACGC 1 cut(s) 424
HhaI GCGC 1 cut(s) 469
Hin1II CATG 9 cut(s) 187, 250, 267, 319, 448, 501, 670, 743, 786
Hin6I GCGC 1 cut(s) 467
HinP1I GCGC 1 cut(s) 467
HincII GTYRAC 1 cut(s) 357
HindII GTYRAC 1 cut(s) 357
HinfI GANTC 3 cut(s) 299, 338, 752
HpaI GTTAAC 1 cut(s) 357
HpaII CCGG 1 cut(s) 682
HphI GGTGA 2 cut(s) 484, 547
Hpy166II GTNNAC 2 cut(s) 357, 679
Hpy188I TCNGA 8 cut(s) 87, 295, 313, 343, 376, 403, 727, 732
Hpy188III TCNNGA 3 cut(s) 437, 457, 783
Hpy8I GTNNAC 2 cut(s) 357, 679
HpyAV CCTTC 3 cut(s) 29, 398, 414
HpyCH4III ACNGT 3 cut(s) 236, 473, 576
HpyCH4V TGCA 4 cut(s) 142, 166, 547, 736
HpyF10VI GCNNNNNNNGC 2 cut(s) 139, 207
HpyF3I CTNAG 1 cut(s) 310
Hsp92II CATG 9 cut(s) 187, 250, 267, 319, 448, 501, 670, 743, 786
HspAI GCGC 1 cut(s) 467
Ksp22I TGATCA 1 cut(s) 376
KspAI GTTAAC 1 cut(s) 357
Kzo9I GATC 5 cut(s) 215, 376, 453, 459, 727
LpnPI CCDG 8 cut(s) 260, 396, 422, 477, 598, 646, 695, 703
Lsp1109I GCAGC 1 cut(s) 205
LweI GCATC 2 cut(s) 129, 723
MaeIII GTNAC 1 cut(s) 230
MalI GATC 5 cut(s) 217, 378, 455, 461, 729
MboI GATC 5 cut(s) 215, 376, 453, 459, 727
MboII GAAGA 7 cut(s) 44, 55, 262, 294, 297, 617, 683
MfeI CAATTG 1 cut(s) 584
MflI RGATCY 2 cut(s) 453, 727
MhlI GDGCHC 1 cut(s) 224
MluCI AATT 3 cut(s) 143, 584, 630
MlyI GAGTC 2 cut(s) 293, 347
MmeI TCCRAC 1 cut(s) 105
MroXI GAANNNNTTC 1 cut(s) 179
MseI TTAA 3 cut(s) 356, 522, 770
MslI CAYNNNNRTG 2 cut(s) 262, 320
MspI CCGG 1 cut(s) 682
MunI CAATTG 1 cut(s) 584
MvnI CGCG 1 cut(s) 418
MwoI GCNNNNNNNGC 2 cut(s) 139, 207
NcoI CCATGG 1 cut(s) 263
NdeII GATC 5 cut(s) 215, 376, 453, 459, 727
NlaIII CATG 9 cut(s) 187, 250, 267, 319, 448, 501, 670, 743, 786
NlaIV GGNNCC 1 cut(s) 581
NmeAIII GCCGAG 1 cut(s) 124
PagI TCATGA 1 cut(s) 782
PdmI GAANNNNTTC 1 cut(s) 179
PfeI GAWTC 1 cut(s) 752
PflMI CCANNNNNTGG 2 cut(s) 660, 717
PkrI GCNGC 1 cut(s) 195
Ple19I CGATCG 1 cut(s) 218
PleI GAGTC 2 cut(s) 293, 346
PpsI GAGTC 2 cut(s) 293, 346
PspFI CCCAGC 1 cut(s) 463
PspN4I GGNNCC 1 cut(s) 581
PspPI GGNCC 2 cut(s) 580, 615
PsuI RGATCY 2 cut(s) 453, 727
PvuI CGATCG 1 cut(s) 218
RsaI GTAC 2 cut(s) 443, 611
RsaNI GTAC 2 cut(s) 442, 610
RseI CAYNNNNRTG 2 cut(s) 262, 320
SaqAI TTAA 3 cut(s) 356, 522, 770
SatI GCNGC 1 cut(s) 194
Sau3AI GATC 5 cut(s) 215, 376, 453, 459, 727
Sau96I GGNCC 2 cut(s) 580, 615
SchI GAGTC 2 cut(s) 293, 347
SduI GDGCHC 1 cut(s) 224
SfaNI GCATC 2 cut(s) 129, 723
SinI GGWCC 1 cut(s) 580
SmiMI CAYNNNNRTG 2 cut(s) 262, 320
Sse9I AATT 3 cut(s) 143, 584, 630
SsiI CCGC 2 cut(s) 21, 764
SspI AATATT 2 cut(s) 334, 562
StyI CCWWGG 2 cut(s) 263, 618
TaaI ACNGT 3 cut(s) 236, 473, 576
TasI AATT 3 cut(s) 143, 584, 630
TatI WGTACW 2 cut(s) 441, 609
TfiI GAWTC 1 cut(s) 752
Tru1I TTAA 3 cut(s) 356, 522, 770
Tru9I TTAA 3 cut(s) 356, 522, 770
TscAI CASTG 2 cut(s) 581, 604
TseI GCWGC 1 cut(s) 193
TspDTI ATGAA 5 cut(s) 172, 188, 263, 461, 623
TspGWI ACGGA 1 cut(s) 627
TspRI CASTG 2 cut(s) 581, 604
Van91I CCANNNNNTGG 2 cut(s) 660, 717
VpaK11BI GGWCC 1 cut(s) 580
XcmI CCANNNNNNNNNTGG 2 cut(s) 495, 664
XmnI GAANNNNTTC 1 cut(s) 179
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.