RchiOBHm_Chr1g0367131

RNA-directed DNA methylation 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
1
OG0017745
Physical Location & Seq
Forward (+)
57503615 .. 57504652
1038 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 591 bp
ATGCTAAGACGTCGTTGTCCTTTAAGCTACCAGCATCTACTTATGTCGGATTCAGAGACGGATTCCGATGATCTAAGTGAAATGTGTAATGCTCGAGTTGGATTGAGCAAAAAGAGGGGAAAATCCACCGTAAATGAAGGAAGGAAAGTAAAGATAAATAAGAAGAAAAAAAGCAATGAAGGACCGGGGATTGCAAAGGAAGATCAGCCAGAATTGCATGTAGTGAAGGTTGCGGAAGAGTATCAAGAACACATGAAGAAGATACCGATCCCAATGATTCGCCGATCGGATGCTATGTTTATCACTTGGCATTCATTAGCTAATTCCATGAAGCAATTTTATGGCCAACCATTGCACTACCTGACTCATGTTCTTGTGAAGCAGTGGGATCAGTCAAGAATAGGTAATGTGGATGAAGAGAAGCCAATGGACAACATTATTCATTCAAGGAAAGCTGAATCTACCATATGGGGTGTTGAGGAAGTCCACAGGCGTTGTACTTCTCACATTCATTTGGCTAAGCTGTGGCTTTCTGACCCGGATTACAGTGCTGTTGTTGGTGACGTCATCACCTCTAAATTGGTTGCATGA
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

196

Amino Acids

22.54

Weight (kDa)

9.05

Isoelectric Point (pI)

55.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RdDM_RDM1 PF09187 75 - 190 4.1e-49 RNA-directed DNA methylation 1
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: OG0017745)

Species Orthologous Gene IDs
prunus_persica Prupe.2G235500_v2.0.a1
rosa_chinensis RchiOBHm_Chr1g0367131
rosa_laevigata RLG00000027295
rosa_multiflora Rmu_sc0007844.1_g000004 Rmu_sc0017251.1_g000001
rosa_roxburghii Rroxscaffold_4G00289590
rosa_rugosa Rorug01G0334900
rosa_samantha Rh1AG341600 Rh1BG302100 Rh1CG318500 Rh1DG334600
rosa_wichuraiana Rw1G030360

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 15
AatII GACGTC 2 cut(s) 13, 567
AciI CCGC 1 cut(s) 233
AclWI GGATC 2 cut(s) 262, 396
AcoI YGGCCR 1 cut(s) 343
AcyI GRCGYC 2 cut(s) 10, 564
AfaI GTAC 1 cut(s) 499
AgsI TTSAA 1 cut(s) 447
AluBI AGCT 4 cut(s) 27, 320, 455, 523
AluI AGCT 4 cut(s) 27, 320, 455, 523
Alw26I GTCTC 1 cut(s) 50
AlwI GGATC 2 cut(s) 262, 396
Ama87I CYCGRG 1 cut(s) 93
AoxI GGCC 1 cut(s) 343
AspS9I GGNCC 1 cut(s) 182
AsuC2I CCSGG 2 cut(s) 186, 539
AsuHPI GGTGA 2 cut(s) 562, 572
AvaI CYCGRG 1 cut(s) 93
AvaII GGWCC 1 cut(s) 182
BalI TGGCCA 1 cut(s) 345
BcnI CCSGG 2 cut(s) 186, 539
BcoDI GTCTC 1 cut(s) 50
BlpI GCTNAGC 1 cut(s) 519
Bme1390I CCNGG 2 cut(s) 186, 539
Bme18I GGWCC 1 cut(s) 182
BmeT110I CYCGRG 1 cut(s) 93
BmgT120I GGNCC 1 cut(s) 182
BmrFI CCNGG 2 cut(s) 186, 539
BmsI GCATC 2 cut(s) 43, 280
Bpu1102I GCTNAGC 1 cut(s) 519
BpuMI CCSGG 2 cut(s) 186, 539
BsaBI GATNNNNATC 1 cut(s) 266
BsaHI GRCGYC 2 cut(s) 10, 564
BsaJI CCNNGG 1 cut(s) 185
Bse3DI GCAATG 2 cut(s) 181, 350
Bse8I GATNNNNATC 1 cut(s) 266
BseDI CCNNGG 1 cut(s) 185
BseGI GGATG 2 cut(s) 295, 418
BseJI GATNNNNATC 1 cut(s) 266
BseMI GCAATG 2 cut(s) 181, 350
Bsh1285I CGRYCG 1 cut(s) 287
BshFI GGCC 1 cut(s) 345
BsiEI CGRYCG 1 cut(s) 287
BsiHKCI CYCGRG 1 cut(s) 93
BsiSI CCGG 2 cut(s) 185, 539
BsmAI GTCTC 1 cut(s) 50
BsmBI CGTCTC 1 cut(s) 50
BsmI GAATGC 1 cut(s) 310
BsnI GGCC 1 cut(s) 345
BsoBI CYCGRG 1 cut(s) 93
Bsp143I GATC 5 cut(s) 70, 202, 267, 284, 388
Bsp1720I GCTNAGC 1 cut(s) 519
BspACI CCGC 1 cut(s) 233
BspANI GGCC 1 cut(s) 345
BspPI GGATC 2 cut(s) 262, 396
BsrDI GCAATG 2 cut(s) 181, 350
BssECI CCNNGG 1 cut(s) 185
BssMI GATC 5 cut(s) 70, 202, 267, 284, 388
BssNI GRCGYC 2 cut(s) 10, 564
Bst4CI ACNGT 2 cut(s) 130, 548
Bst6I CTCTTC 2 cut(s) 231, 411
BstACI GRCGYC 2 cut(s) 10, 564
BstDEI CTNAG 3 cut(s) 5, 74, 519
BstF5I GGATG 2 cut(s) 295, 418
BstKTI GATC 5 cut(s) 73, 205, 270, 287, 391
BstMAI GTCTC 1 cut(s) 50
BstMBI GATC 5 cut(s) 70, 202, 267, 284, 388
BstMCI CGRYCG 1 cut(s) 287
BstMWI GCNNNNNNNGC 1 cut(s) 214
BstNSI RCATGY 1 cut(s) 221
BstSCI CCNGG 2 cut(s) 184, 537
BsuRI GGCC 1 cut(s) 345
BtsCI GGATG 2 cut(s) 295, 418
BtsI GCAGTG 1 cut(s) 389
BtsIMutI CAGTG 2 cut(s) 389, 553
Cfr13I GGNCC 1 cut(s) 182
Csp6I GTAC 1 cut(s) 498
CspCI CAANNNNNGTGG 2 cut(s) 476, 511
CviAII CATG 5 cut(s) 218, 253, 328, 368, 588
CviJI RGCY 9 cut(s) 27, 208, 320, 345, 424, 455, 518, 523, 529
CviKI_1 RGCY 9 cut(s) 27, 208, 320, 345, 424, 455, 518, 523, 529
CviQI GTAC 1 cut(s) 498
DdeI CTNAG 3 cut(s) 5, 74, 519
DpnI GATC 5 cut(s) 72, 204, 269, 286, 390
DpnII GATC 5 cut(s) 70, 202, 267, 284, 388
DrdI GACNNNNNNGTC 1 cut(s) 15
DseDI GACNNNNNNGTC 1 cut(s) 15
EaeI YGGCCR 1 cut(s) 343
Eam1104I CTCTTC 2 cut(s) 231, 411
EarI CTCTTC 2 cut(s) 231, 411
Eco47I GGWCC 1 cut(s) 182
Eco88I CYCGRG 1 cut(s) 93
Esp3I CGTCTC 1 cut(s) 50
FaeI CATG 5 cut(s) 221, 256, 331, 371, 591
FatI CATG 5 cut(s) 217, 252, 327, 367, 587
FauNDI CATATG 1 cut(s) 467
FokI GGATG 2 cut(s) 302, 425
HaeIII GGCC 1 cut(s) 345
HapII CCGG 2 cut(s) 185, 539
Hin1I GRCGYC 2 cut(s) 10, 564
Hin1II CATG 5 cut(s) 221, 256, 331, 371, 591
HinfI GANTC 5 cut(s) 50, 62, 277, 364, 458
HpaII CCGG 2 cut(s) 185, 539
HphI GGTGA 2 cut(s) 562, 572
Hpy166II GTNNAC 1 cut(s) 487
Hpy188I TCNGA 5 cut(s) 49, 55, 67, 289, 535
Hpy188III TCNNGA 2 cut(s) 245, 396
Hpy8I GTNNAC 1 cut(s) 487
Hpy99I CGWCG 1 cut(s) 15
HpyAV CCTTC 4 cut(s) 131, 135, 173, 220
HpyCH4III ACNGT 2 cut(s) 130, 548
HpyCH4IV ACGT 2 cut(s) 10, 564
HpyCH4V TGCA 4 cut(s) 194, 217, 355, 587
HpyF10VI GCNNNNNNNGC 1 cut(s) 214
HpyF3I CTNAG 3 cut(s) 5, 74, 519
HpySE526I ACGT 2 cut(s) 10, 564
Hsp92I GRCGYC 2 cut(s) 10, 564
Hsp92II CATG 5 cut(s) 221, 256, 331, 371, 591
Kzo9I GATC 5 cut(s) 70, 202, 267, 284, 388
LpnPI CCDG 6 cut(s) 44, 198, 222, 374, 475, 552
LweI GCATC 2 cut(s) 43, 280
MaeII ACGT 2 cut(s) 10, 564
MaeIII GTNAC 1 cut(s) 560
MalI GATC 5 cut(s) 72, 204, 269, 286, 390
MboI GATC 5 cut(s) 70, 202, 267, 284, 388
MboII GAAGA 6 cut(s) 175, 212, 248, 268, 271, 428
MlsI TGGCCA 1 cut(s) 345
MluCI AATT 4 cut(s) 212, 322, 335, 578
MluNI TGGCCA 1 cut(s) 345
MlyI GAGTC 1 cut(s) 358
MmeI TCCRAC 2 cut(s) 27, 79
MnlI CCTC 3 cut(s) 108, 472, 583
Mox20I TGGCCA 1 cut(s) 345
MscI TGGCCA 1 cut(s) 345
MseI TTAA 1 cut(s) 23
Msp20I TGGCCA 1 cut(s) 345
MspI CCGG 2 cut(s) 185, 539
MspR9I CCNGG 2 cut(s) 186, 539
Mva1269I GAATGC 1 cut(s) 310
MwoI GCNNNNNNNGC 1 cut(s) 214
NciI CCSGG 2 cut(s) 186, 539
NdeI CATATG 1 cut(s) 467
NdeII GATC 5 cut(s) 70, 202, 267, 284, 388
NlaIII CATG 5 cut(s) 221, 256, 331, 371, 591
NmuCI GTSAC 1 cut(s) 560
NspI RCATGY 1 cut(s) 221
PaeR7I CTCGAG 1 cut(s) 93
PctI GAATGC 1 cut(s) 310
PfeI GAWTC 4 cut(s) 50, 62, 277, 458
Ple19I CGATCG 1 cut(s) 287
PleI GAGTC 1 cut(s) 358
PpsI GAGTC 1 cut(s) 358
PspPI GGNCC 1 cut(s) 182
PspXI VCTCGAGB 1 cut(s) 93
PvuI CGATCG 1 cut(s) 287
RsaI GTAC 1 cut(s) 499
RsaNI GTAC 1 cut(s) 498
SaqAI TTAA 1 cut(s) 23
Sau3AI GATC 5 cut(s) 70, 202, 267, 284, 388
Sau96I GGNCC 1 cut(s) 182
SchI GAGTC 1 cut(s) 358
ScrFI CCNGG 2 cut(s) 186, 539
SfaNI GCATC 2 cut(s) 43, 280
Sfr274I CTCGAG 1 cut(s) 93
SinI GGWCC 1 cut(s) 182
SlaI CTCGAG 1 cut(s) 93
SmlI CTYRAG 1 cut(s) 93
SmoI CTYRAG 1 cut(s) 93
Sse9I AATT 4 cut(s) 212, 322, 335, 578
SsiI CCGC 1 cut(s) 233
StyD4I CCNGG 2 cut(s) 184, 537
TaaI ACNGT 2 cut(s) 130, 548
TaiI ACGT 2 cut(s) 13, 567
TaqI TCGA 1 cut(s) 94
TasI AATT 4 cut(s) 212, 322, 335, 578
TatI WGTACW 1 cut(s) 497
TfiI GAWTC 4 cut(s) 50, 62, 277, 458
Tru1I TTAA 1 cut(s) 23
Tru9I TTAA 1 cut(s) 23
TscAI CASTG 2 cut(s) 389, 553
TseFI GTSAC 1 cut(s) 560
Tsp45I GTSAC 1 cut(s) 560
TspDTI ATGAA 8 cut(s) 150, 192, 269, 303, 344, 429, 431, 500
TspGWI ACGGA 1 cut(s) 74
TspRI CASTG 2 cut(s) 389, 553
VpaK11BI GGWCC 1 cut(s) 182
XceI RCATGY 1 cut(s) 221
XhoI CTCGAG 1 cut(s) 93
ZraI GACGTC 2 cut(s) 11, 565
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.