Rh1BG302100

RNA-directed DNA methylation 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1B
OG0017745
Physical Location & Seq
Forward (+)
43883648 .. 43884484
837 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1BG302100.1

Sequence Viewer

Length: 246 bp
ATGAAGGACCGGGGATTGCAAAGGGAGATTAGCCAGCAGTGGGATCAGTCAAGAATAGGTAATGTGGATGAAGAGAATCCAATGGACAACATTATTCATTCAAGGAAAGCTGAATCTACCATATGGGGTGTTGAGGAAGTCCACAGGCGTTGTACTTCTCACATTCATTTGGCTAAGCTGTGGCTTTCTGACCCGGATTACGGTGCTGTTGTTGGTGACGTTATCACCTCTAAATTGGTTGCATGA
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

81

Amino Acids

9.27

Weight (kDa)

5.72

Isoelectric Point (pI)

57.46

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RdDM_RDM1 PF09187 11 - 75 4.7e-24 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)
AclWI GGATC 1 cut(s) 51
AfaI GTAC 1 cut(s) 154
AfiI CCNNNNNNNGG 2 cut(s) 40, 200
AgsI TTSAA 1 cut(s) 102
AluBI AGCT 2 cut(s) 110, 178
AluI AGCT 2 cut(s) 110, 178
AlwI GGATC 1 cut(s) 51
AspS9I GGNCC 1 cut(s) 7
AsuC2I CCSGG 2 cut(s) 11, 194
AsuHPI GGTGA 2 cut(s) 217, 227
AvaII GGWCC 1 cut(s) 7
BcnI CCSGG 2 cut(s) 11, 194
BlpI GCTNAGC 1 cut(s) 174
Bme1390I CCNGG 2 cut(s) 11, 194
Bme18I GGWCC 1 cut(s) 7
BmgT120I GGNCC 1 cut(s) 7
BmrFI CCNGG 2 cut(s) 11, 194
Bpu1102I GCTNAGC 1 cut(s) 174
BpuMI CCSGG 2 cut(s) 11, 194
BsaJI CCNNGG 1 cut(s) 10
Bsc4I CCNNNNNNNGG 2 cut(s) 40, 200
BseDI CCNNGG 1 cut(s) 10
BseGI GGATG 1 cut(s) 73
BseLI CCNNNNNNNGG 2 cut(s) 40, 200
BsiSI CCGG 2 cut(s) 10, 194
BslI CCNNNNNNNGG 2 cut(s) 40, 200
Bsp143I GATC 1 cut(s) 43
Bsp1720I GCTNAGC 1 cut(s) 174
BspPI GGATC 1 cut(s) 51
BssECI CCNNGG 1 cut(s) 10
BssMI GATC 1 cut(s) 43
Bst4CI ACNGT 1 cut(s) 203
Bst6I CTCTTC 1 cut(s) 66
BstC8I GCNNGC 1 cut(s) 35
BstDEI CTNAG 1 cut(s) 174
BstF5I GGATG 1 cut(s) 73
BstKTI GATC 1 cut(s) 46
BstMBI GATC 1 cut(s) 43
BstSCI CCNGG 2 cut(s) 9, 192
BtsCI GGATG 1 cut(s) 73
BtsI GCAGTG 1 cut(s) 44
BtsIMutI CAGTG 1 cut(s) 44
Cac8I GCNNGC 1 cut(s) 35
Cfr13I GGNCC 1 cut(s) 7
Csp6I GTAC 1 cut(s) 153
CspCI CAANNNNNGTGG 2 cut(s) 131, 166
CviAII CATG 1 cut(s) 243
CviJI RGCY 5 cut(s) 33, 110, 173, 178, 184
CviKI_1 RGCY 5 cut(s) 33, 110, 173, 178, 184
CviQI GTAC 1 cut(s) 153
DdeI CTNAG 1 cut(s) 174
DpnI GATC 1 cut(s) 45
DpnII GATC 1 cut(s) 43
Eam1104I CTCTTC 1 cut(s) 66
EarI CTCTTC 1 cut(s) 66
Eco47I GGWCC 1 cut(s) 7
FaeI CATG 1 cut(s) 246
FaiI YATR 3 cut(s) 122, 124, 244
FatI CATG 1 cut(s) 242
FauNDI CATATG 1 cut(s) 122
FokI GGATG 1 cut(s) 80
HapII CCGG 2 cut(s) 10, 194
Hin1II CATG 1 cut(s) 246
HinfI GANTC 2 cut(s) 76, 113
HpaII CCGG 2 cut(s) 10, 194
HphI GGTGA 2 cut(s) 217, 227
Hpy166II GTNNAC 1 cut(s) 142
Hpy188I TCNGA 1 cut(s) 190
Hpy188III TCNNGA 1 cut(s) 51
Hpy8I GTNNAC 1 cut(s) 142
HpyCH4III ACNGT 1 cut(s) 203
HpyCH4IV ACGT 1 cut(s) 219
HpyCH4V TGCA 2 cut(s) 19, 242
HpyF3I CTNAG 1 cut(s) 174
HpySE526I ACGT 1 cut(s) 219
Hsp92II CATG 1 cut(s) 246
Kzo9I GATC 1 cut(s) 43
LpnPI CCDG 4 cut(s) 23, 47, 130, 207
MaeII ACGT 1 cut(s) 219
MaeIII GTNAC 1 cut(s) 215
MalI GATC 1 cut(s) 45
MboI GATC 1 cut(s) 43
MboII GAAGA 1 cut(s) 83
MluCI AATT 1 cut(s) 233
MnlI CCTC 2 cut(s) 127, 238
MspI CCGG 2 cut(s) 10, 194
MspR9I CCNGG 2 cut(s) 11, 194
NciI CCSGG 2 cut(s) 11, 194
NdeI CATATG 1 cut(s) 122
NdeII GATC 1 cut(s) 43
NlaIII CATG 1 cut(s) 246
NmuCI GTSAC 1 cut(s) 215
PfeI GAWTC 2 cut(s) 76, 113
PspPI GGNCC 1 cut(s) 7
RsaI GTAC 1 cut(s) 154
RsaNI GTAC 1 cut(s) 153
Sau3AI GATC 1 cut(s) 43
Sau96I GGNCC 1 cut(s) 7
ScrFI CCNGG 2 cut(s) 11, 194
SetI ASST 5 cut(s) 61, 112, 180, 222, 230
SgeI CNNG 8 cut(s) 22, 23, 46, 63, 114, 157, 205, 206
SinI GGWCC 1 cut(s) 7
Sse9I AATT 1 cut(s) 233
StyD4I CCNGG 2 cut(s) 9, 192
TaaI ACNGT 1 cut(s) 203
TaiI ACGT 1 cut(s) 222
TasI AATT 1 cut(s) 233
TatI WGTACW 1 cut(s) 152
TfiI GAWTC 2 cut(s) 76, 113
TscAI CASTG 1 cut(s) 44
TseFI GTSAC 1 cut(s) 215
Tsp45I GTSAC 1 cut(s) 215
TspDTI ATGAA 4 cut(s) 17, 84, 86, 155
TspRI CASTG 1 cut(s) 44
VpaK11BI GGWCC 1 cut(s) 7
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.