Rroxscaffold_4G00289590

Pfam:DUF1950

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0017745
Physical Location & Seq
Reverse (-)
10189930 .. 10190268
339 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00289590.1

Sequence Viewer

Length: 339 bp
ATGAAGAAGATACCGATCCCAATGATTCGCCGATCGGATGCTATGTTTATCACTTGGCATTCATTAGCTAATTCCATGAAGCAATTTTATGGCCAACCATTGCACTACCTGACTCATGTTCTTGTGAAGCAGTGGGATCAGTCAAGAATAGGTAATTTGGATGAAGAGAAGCCAATGGACAACATTATTCATTCAAGGAAAGCTGAATCTACCATATGGGGTGTTGAGGAAGTCCACAGGCGTTGTACTTCTCACATTCATTTGGCTAAGCTGTGGCTTTCTGACCCGGATTACAGTGCTGTTGTTGGTGACGTTATCACCTCTAAATTGGTTGCATGA
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

112

Amino Acids

12.99

Weight (kDa)

8.79

Isoelectric Point (pI)

59.08

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RdDM_RDM1 PF09187 1 - 106 3e-45 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 2 cut(s) 10, 144
AcoI YGGCCR 1 cut(s) 91
AfaI GTAC 1 cut(s) 247
AgsI TTSAA 1 cut(s) 195
AluBI AGCT 3 cut(s) 68, 203, 271
AluI AGCT 3 cut(s) 68, 203, 271
AlwI GGATC 2 cut(s) 10, 144
AoxI GGCC 1 cut(s) 91
AsuC2I CCSGG 1 cut(s) 287
AsuHPI GGTGA 2 cut(s) 310, 320
BalI TGGCCA 1 cut(s) 93
BcnI CCSGG 1 cut(s) 287
BlpI GCTNAGC 1 cut(s) 267
Bme1390I CCNGG 1 cut(s) 287
BmrFI CCNGG 1 cut(s) 287
BmsI GCATC 1 cut(s) 28
Bpu1102I GCTNAGC 1 cut(s) 267
BpuMI CCSGG 1 cut(s) 287
BsaBI GATNNNNATC 1 cut(s) 14
Bse3DI GCAATG 1 cut(s) 98
Bse8I GATNNNNATC 1 cut(s) 14
BseGI GGATG 2 cut(s) 43, 166
BseJI GATNNNNATC 1 cut(s) 14
BseMI GCAATG 1 cut(s) 98
Bsh1285I CGRYCG 1 cut(s) 35
BshFI GGCC 1 cut(s) 93
BsiEI CGRYCG 1 cut(s) 35
BsiSI CCGG 1 cut(s) 287
BsmI GAATGC 1 cut(s) 58
BsnI GGCC 1 cut(s) 93
Bsp143I GATC 3 cut(s) 15, 32, 136
Bsp1720I GCTNAGC 1 cut(s) 267
BspANI GGCC 1 cut(s) 93
BspPI GGATC 2 cut(s) 10, 144
BsrDI GCAATG 1 cut(s) 98
BssMI GATC 3 cut(s) 15, 32, 136
Bst4CI ACNGT 1 cut(s) 296
Bst6I CTCTTC 1 cut(s) 159
BstDEI CTNAG 1 cut(s) 267
BstF5I GGATG 2 cut(s) 43, 166
BstKTI GATC 3 cut(s) 18, 35, 139
BstMBI GATC 3 cut(s) 15, 32, 136
BstMCI CGRYCG 1 cut(s) 35
BstSCI CCNGG 1 cut(s) 285
BsuRI GGCC 1 cut(s) 93
BtsCI GGATG 2 cut(s) 43, 166
BtsI GCAGTG 1 cut(s) 137
BtsIMutI CAGTG 2 cut(s) 137, 301
Csp6I GTAC 1 cut(s) 246
CspCI CAANNNNNGTGG 2 cut(s) 224, 259
CviAII CATG 3 cut(s) 76, 116, 336
CviJI RGCY 7 cut(s) 68, 93, 172, 203, 266, 271, 277
CviKI_1 RGCY 7 cut(s) 68, 93, 172, 203, 266, 271, 277
CviQI GTAC 1 cut(s) 246
DdeI CTNAG 1 cut(s) 267
DpnI GATC 3 cut(s) 17, 34, 138
DpnII GATC 3 cut(s) 15, 32, 136
EaeI YGGCCR 1 cut(s) 91
Eam1104I CTCTTC 1 cut(s) 159
EarI CTCTTC 1 cut(s) 159
FaeI CATG 3 cut(s) 79, 119, 339
FaiI YATR 7 cut(s) 44, 77, 90, 117, 215, 217, 337
FatI CATG 3 cut(s) 75, 115, 335
FauNDI CATATG 1 cut(s) 215
FokI GGATG 2 cut(s) 50, 173
HaeIII GGCC 1 cut(s) 93
HapII CCGG 1 cut(s) 287
Hin1II CATG 3 cut(s) 79, 119, 339
HinfI GANTC 3 cut(s) 25, 112, 206
HpaII CCGG 1 cut(s) 287
HphI GGTGA 2 cut(s) 310, 320
Hpy166II GTNNAC 1 cut(s) 235
Hpy188I TCNGA 2 cut(s) 37, 283
Hpy188III TCNNGA 1 cut(s) 144
Hpy8I GTNNAC 1 cut(s) 235
HpyCH4III ACNGT 1 cut(s) 296
HpyCH4IV ACGT 1 cut(s) 312
HpyCH4V TGCA 2 cut(s) 103, 335
HpyF3I CTNAG 1 cut(s) 267
HpySE526I ACGT 1 cut(s) 312
Hsp92II CATG 3 cut(s) 79, 119, 339
Kzo9I GATC 3 cut(s) 15, 32, 136
LpnPI CCDG 3 cut(s) 122, 223, 300
LweI GCATC 1 cut(s) 28
MaeII ACGT 1 cut(s) 312
MaeIII GTNAC 1 cut(s) 308
MalI GATC 3 cut(s) 17, 34, 138
MboI GATC 3 cut(s) 15, 32, 136
MboII GAAGA 3 cut(s) 16, 19, 176
MlsI TGGCCA 1 cut(s) 93
MluCI AATT 4 cut(s) 70, 83, 154, 326
MluNI TGGCCA 1 cut(s) 93
MlyI GAGTC 1 cut(s) 106
MnlI CCTC 2 cut(s) 220, 331
Mox20I TGGCCA 1 cut(s) 93
MscI TGGCCA 1 cut(s) 93
Msp20I TGGCCA 1 cut(s) 93
MspI CCGG 1 cut(s) 287
MspR9I CCNGG 1 cut(s) 287
Mva1269I GAATGC 1 cut(s) 58
NciI CCSGG 1 cut(s) 287
NdeI CATATG 1 cut(s) 215
NdeII GATC 3 cut(s) 15, 32, 136
NlaIII CATG 3 cut(s) 79, 119, 339
NmuCI GTSAC 1 cut(s) 308
PctI GAATGC 1 cut(s) 58
PfeI GAWTC 2 cut(s) 25, 206
Ple19I CGATCG 1 cut(s) 35
PleI GAGTC 1 cut(s) 106
PpsI GAGTC 1 cut(s) 106
PvuI CGATCG 1 cut(s) 35
RsaI GTAC 1 cut(s) 247
RsaNI GTAC 1 cut(s) 246
Sau3AI GATC 3 cut(s) 15, 32, 136
SchI GAGTC 1 cut(s) 106
ScrFI CCNGG 1 cut(s) 287
SetI ASST 7 cut(s) 70, 111, 154, 205, 273, 315, 323
SfaNI GCATC 1 cut(s) 28
Sse9I AATT 4 cut(s) 70, 83, 154, 326
StyD4I CCNGG 1 cut(s) 285
TaaI ACNGT 1 cut(s) 296
TaiI ACGT 1 cut(s) 315
TasI AATT 4 cut(s) 70, 83, 154, 326
TatI WGTACW 1 cut(s) 245
TfiI GAWTC 2 cut(s) 25, 206
TscAI CASTG 2 cut(s) 137, 301
TseFI GTSAC 1 cut(s) 308
Tsp45I GTSAC 1 cut(s) 308
TspDTI ATGAA 6 cut(s) 17, 51, 92, 177, 179, 248
TspRI CASTG 2 cut(s) 137, 301
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.