Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr2

Orthogroup ID

OG0012911

Physical Location & Seq

Genomic Coordinates Reverse (-)

63633790 .. 63634550

Gene Structure 761 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000010156

Sequence Viewer

CDS Protein Promoter (2k)

Length: 492 bp

ATGGCCACTTCCTTACTATGTCGACTGAGCAAGTACTCTTTCTCCATCTCATCAACATCAAGCAGGACATTAATTGTCCAAATCAGCAGGAATGTGACCAGCATCTCTGAGTCTGCTGTTTATTTCTTGCAACATCAACGCAATGCGGCTCTTCTCTTCTCTGTGTGTATCAGTATCACCACCGGGGGTAAGCCCATGAATCACTCCATTAACTTCAATGGAACAGGATCCGGGAACAAGTTGAAGGCTTTCCGGGCAAAGTCTAACTTCAAGGAACATGTGCCTATGAAGCGCATCCCAATCCCAACACACCGTGGCTCTGCTATTCCATTTACCTCATGGATGGGTTTAGGTAAATCCATTAAGCAGCTTTACGGACAACCTCTGCATTATCTCACCAATATTCAGCTAAAACAGTGGGACCAACTGAGGATCGGTAGTGAGGATGCATACAGGCCCTTGGATGCCATCATTCACCATCTGGCTCATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000419 GO:0000428 GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006259 GO:0006304 GO:0006305 GO:0006306 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010629 GO:0014070 GO:0016070 GO:0016458 GO:0019219 GO:0019222 GO:0030880 GO:0031047 GO:0031050 GO:0031323 GO:0032259 GO:0032991 GO:0034641 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043331 GO:0043412 GO:0043414 GO:0043621 GO:0044030 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0044728 GO:0046483 GO:0048519 GO:0050789 GO:0050794 GO:0050896 GO:0051052 GO:0051171 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0080090 GO:0090304 GO:1901360 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RdDM_RDM1

Protein Analysis

164

Amino Acids

18.23

Weight (kDa)

10.29

Isoelectric Point (pI)

27.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RdDM_RDM1	PF09187	95 - 160	2.3e-31	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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Align Labels (Cladogram)

Image

Tree File

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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)
AccI	GTMKAC	1 cut(s)	22
AciI	CCGC	1 cut(s)	146
AclWI	GGATC	3 cut(s)	222, 235, 440
AcoI	YGGCCR	1 cut(s)	3
AdeI	CACNNNGTG	1 cut(s)	314
AfaI	GTAC	1 cut(s)	35
AflIII	ACRYGT	1 cut(s)	277
AgsI	TTSAA	3 cut(s)	217, 244, 271
AluBI	AGCT	2 cut(s)	370, 409
AluI	AGCT	2 cut(s)	370, 409
AlwI	GGATC	3 cut(s)	222, 235, 440
AoxI	GGCC	2 cut(s)	3, 455
ApeKI	GCWGC	1 cut(s)	367
AseI	ATTAAT	1 cut(s)	71
Asp700I	GAANNNNTTC	1 cut(s)	248
AspLEI	GCGC	1 cut(s)	294
AspS9I	GGNCC	2 cut(s)	421, 456
AsuC2I	CCSGG	3 cut(s)	184, 232, 254
AsuHPI	GGTGA	3 cut(s)	169, 388, 467
AvaII	GGWCC	1 cut(s)	421
BalI	TGGCCA	1 cut(s)	5
BamHI	GGATCC	1 cut(s)	227
BbvI	GCAGC	1 cut(s)	379
BccI	CCATC	4 cut(s)	53, 337, 476, 486
BcnI	CCSGG	3 cut(s)	184, 232, 254
BisI	GCNGC	2 cut(s)	147, 368
BlsI	GCNGC	2 cut(s)	148, 369
BmcAI	AGTACT	1 cut(s)	35
Bme1390I	CCNGG	3 cut(s)	184, 232, 254
Bme18I	GGWCC	1 cut(s)	421
BmgT120I	GGNCC	2 cut(s)	421, 456
BmiI	GGNNCC	2 cut(s)	229, 422
BmrFI	CCNGG	3 cut(s)	184, 232, 254
BmsI	GCATC	4 cut(s)	111, 303, 436, 454
BpuMI	CCSGG	3 cut(s)	184, 232, 254
BsaJI	CCNNGG	3 cut(s)	183, 313, 459
BsaXI	ACNNNNNCTCC	2 cut(s)	26, 56
Bse3DI	GCAATG	1 cut(s)	148
BseDI	CCNNGG	3 cut(s)	183, 313, 459
BseGI	GGATG	4 cut(s)	294, 348, 451, 469
BseMI	GCAATG	1 cut(s)	148
BseMII	CTCAG	3 cut(s)	17, 99, 419
BseXI	GCAGC	1 cut(s)	379
BshFI	GGCC	2 cut(s)	5, 457
BsiSI	CCGG	3 cut(s)	183, 231, 253
BslFI	GGGAC	1 cut(s)	434
BsmFI	GGGAC	1 cut(s)	434
BsnI	GGCC	2 cut(s)	5, 457
Bsp143I	GATC	2 cut(s)	227, 432
BspACI	CCGC	1 cut(s)	146
BspANI	GGCC	2 cut(s)	5, 457
BspCNI	CTCAG	3 cut(s)	18, 100, 420
BspLI	GGNNCC	2 cut(s)	229, 422
BspPI	GGATC	3 cut(s)	222, 235, 440
BspQI	GCTCTTC	1 cut(s)	156
BsrDI	GCAATG	1 cut(s)	148
BssECI	CCNNGG	3 cut(s)	183, 313, 459
BssMI	GATC	2 cut(s)	227, 432
BssT1I	CCWWGG	1 cut(s)	459
Bst4CI	ACNGT	2 cut(s)	314, 417
Bst6I	CTCTTC	2 cut(s)	156, 161
BstDEI	CTNAG	3 cut(s)	26, 108, 428
BstDSI	CCRYGG	1 cut(s)	313
BstF5I	GGATG	4 cut(s)	294, 348, 451, 469
BstHHI	GCGC	1 cut(s)	294
BstKTI	GATC	2 cut(s)	230, 435
BstMBI	GATC	2 cut(s)	227, 432
BstMWI	GCNNNNNNNGC	2 cut(s)	254, 289
BstNSI	RCATGY	1 cut(s)	281
BstSCI	CCNGG	3 cut(s)	182, 230, 252
BstV1I	GCAGC	1 cut(s)	379
BstX2I	RGATCY	1 cut(s)	227
BstYI	RGATCY	1 cut(s)	227
BsuRI	GGCC	2 cut(s)	5, 457
BtgI	CCRYGG	1 cut(s)	313
BtsCI	GGATG	4 cut(s)	294, 348, 451, 469
BtsIMutI	CAGTG	1 cut(s)	422
CfoI	GCGC	1 cut(s)	294
Cfr13I	GGNCC	2 cut(s)	421, 456
Csp6I	GTAC	1 cut(s)	34
CviAII	CATG	3 cut(s)	196, 278, 339
CviJI	RGCY	9 cut(s)	5, 149, 193, 248, 318, 370, 409, 457, 485
CviKI_1	RGCY	9 cut(s)	5, 149, 193, 248, 318, 370, 409, 457, 485
CviQI	GTAC	1 cut(s)	34
DdeI	CTNAG	3 cut(s)	26, 108, 428
DpnI	GATC	2 cut(s)	229, 434
DpnII	GATC	2 cut(s)	227, 432
DraIII	CACNNNGTG	1 cut(s)	314
EaeI	YGGCCR	1 cut(s)	3
Eam1104I	CTCTTC	2 cut(s)	156, 161
EarI	CTCTTC	2 cut(s)	156, 161
Eco130I	CCWWGG	1 cut(s)	459
Eco47I	GGWCC	1 cut(s)	421
EcoO109I	RGGNCCY	1 cut(s)	456
EcoT14I	CCWWGG	1 cut(s)	459
EcoT22I	ATGCAT	1 cut(s)	451
ErhI	CCWWGG	1 cut(s)	459
FaeI	CATG	3 cut(s)	199, 281, 342
FaiI	YATR	6 cut(s)	19, 197, 279, 287, 340, 451
FalI	AAGNNNNNCTT	2 cut(s)	251, 283
FaqI	GGGAC	1 cut(s)	434
FatI	CATG	3 cut(s)	195, 277, 338
FblI	GTMKAC	1 cut(s)	22
Fnu4HI	GCNGC	2 cut(s)	147, 368
FokI	GGATG	4 cut(s)	281, 355, 458, 476
Fsp4HI	GCNGC	2 cut(s)	147, 368
GlaI	GCGC	1 cut(s)	293
GluI	GCNGC	2 cut(s)	147, 368
HaeIII	GGCC	2 cut(s)	5, 457
HapII	CCGG	3 cut(s)	183, 231, 253
HhaI	GCGC	1 cut(s)	294
Hin1II	CATG	3 cut(s)	199, 281, 342
Hin6I	GCGC	1 cut(s)	292
HinP1I	GCGC	1 cut(s)	292
HincII	GTYRAC	1 cut(s)	23
HindII	GTYRAC	1 cut(s)	23
HinfI	GANTC	2 cut(s)	110, 199
HpaII	CCGG	3 cut(s)	183, 231, 253
HphI	GGTGA	3 cut(s)	169, 388, 467
Hpy166II	GTNNAC	1 cut(s)	23
Hpy188I	TCNGA	1 cut(s)	109
Hpy8I	GTNNAC	1 cut(s)	23
HpyAV	CCTTC	1 cut(s)	238
HpyCH4III	ACNGT	2 cut(s)	314, 417
HpyCH4V	TGCA	3 cut(s)	130, 388, 449
HpyF10VI	GCNNNNNNNGC	2 cut(s)	254, 289
HpyF3I	CTNAG	3 cut(s)	26, 108, 428
Hsp92II	CATG	3 cut(s)	199, 281, 342
HspAI	GCGC	1 cut(s)	292
Kzo9I	GATC	2 cut(s)	227, 432
LguI	GCTCTTC	1 cut(s)	156
LpnPI	CCDG	9 cut(s)	49, 73, 112, 196, 210, 244, 266, 439, 467
Lsp1109I	GCAGC	1 cut(s)	379
LweI	GCATC	4 cut(s)	111, 303, 436, 454
MaeIII	GTNAC	1 cut(s)	94
MalI	GATC	2 cut(s)	229, 434
MboI	GATC	2 cut(s)	227, 432
MboII	GAAGA	2 cut(s)	143, 148
MflI	RGATCY	1 cut(s)	227
MlsI	TGGCCA	1 cut(s)	5
MluCI	AATT	1 cut(s)	72
MluNI	TGGCCA	1 cut(s)	5
MlyI	GAGTC	1 cut(s)	119
MnlI	CCTC	4 cut(s)	346, 393, 423, 436
Mox20I	TGGCCA	1 cut(s)	5
Mph1103I	ATGCAT	1 cut(s)	451
MroXI	GAANNNNTTC	1 cut(s)	248
MscI	TGGCCA	1 cut(s)	5
MseI	TTAA	3 cut(s)	71, 210, 363
Msp20I	TGGCCA	1 cut(s)	5
MspI	CCGG	3 cut(s)	183, 231, 253
MspR9I	CCNGG	3 cut(s)	184, 232, 254
MwoI	GCNNNNNNNGC	2 cut(s)	254, 289
NciI	CCSGG	3 cut(s)	184, 232, 254
NdeII	GATC	2 cut(s)	227, 432
NlaIII	CATG	3 cut(s)	199, 281, 342
NlaIV	GGNNCC	2 cut(s)	229, 422
NmuCI	GTSAC	1 cut(s)	94
NsiI	ATGCAT	1 cut(s)	451
NspI	RCATGY	1 cut(s)	281
PciI	ACATGT	1 cut(s)	277
PciSI	GCTCTTC	1 cut(s)	156
PdmI	GAANNNNTTC	1 cut(s)	248
PfeI	GAWTC	1 cut(s)	199
PfoI	TCCNGGA	1 cut(s)	230
PkrI	GCNGC	2 cut(s)	148, 369
PleI	GAGTC	1 cut(s)	118
PpsI	GAGTC	1 cut(s)	118
PscI	ACATGT	1 cut(s)	277
PshBI	ATTAAT	1 cut(s)	71
PspN4I	GGNNCC	2 cut(s)	229, 422
PspPI	GGNCC	2 cut(s)	421, 456
PsuI	RGATCY	1 cut(s)	227
RsaI	GTAC	1 cut(s)	35
RsaNI	GTAC	1 cut(s)	34
SalI	GTCGAC	1 cut(s)	21
SapI	GCTCTTC	1 cut(s)	156
SaqAI	TTAA	3 cut(s)	71, 210, 363
SatI	GCNGC	2 cut(s)	147, 368
Sau3AI	GATC	2 cut(s)	227, 432
Sau96I	GGNCC	2 cut(s)	421, 456
ScaI	AGTACT	1 cut(s)	35
SchI	GAGTC	1 cut(s)	119
ScrFI	CCNGG	3 cut(s)	184, 232, 254
SetI	ASST	5 cut(s)	338, 355, 372, 385, 411
SfaNI	GCATC	4 cut(s)	111, 303, 436, 454
SinI	GGWCC	1 cut(s)	421
Sse9I	AATT	1 cut(s)	72
SsiI	CCGC	1 cut(s)	146
SspI	AATATT	1 cut(s)	403
StyD4I	CCNGG	3 cut(s)	182, 230, 252
StyI	CCWWGG	1 cut(s)	459
TaaI	ACNGT	2 cut(s)	314, 417
TaqI	TCGA	1 cut(s)	22
TasI	AATT	1 cut(s)	72
TatI	WGTACW	1 cut(s)	33
TauI	GCSGC	1 cut(s)	149
TfiI	GAWTC	1 cut(s)	199
Tru1I	TTAA	3 cut(s)	71, 210, 363
Tru9I	TTAA	3 cut(s)	71, 210, 363
TscAI	CASTG	1 cut(s)	422
TseFI	GTSAC	1 cut(s)	94
TseI	GCWGC	1 cut(s)	367
Tsp45I	GTSAC	1 cut(s)	94
TspDTI	ATGAA	2 cut(s)	212, 302
TspGWI	ACGGA	1 cut(s)	390
TspRI	CASTG	1 cut(s)	422
VpaK11BI	GGWCC	1 cut(s)	421
VspI	ATTAAT	1 cut(s)	71
XceI	RCATGY	1 cut(s)	281
XcmI	CCANNNNNNNNNTGG	1 cut(s)	336
XmiI	GTMKAC	1 cut(s)	22
XmnI	GAANNNNTTC	1 cut(s)	248
ZrmI	AGTACT	1 cut(s)	35
Zsp2I	ATGCAT	1 cut(s)	451

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.