Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0012911

Physical Location & Seq

Genomic Coordinates Forward (+)

36815832 .. 36818303

Gene Structure 2472 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG145400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 372 bp

ATGAGAAGGGCAGAGATGTATCAGGAGTACATGAAGCACATCCCAATCCCAACACACCGTGGCTCAGTTATTCCATTTACCTCATGGATGGGTTTAGGTAAATCCATTAAGCAGCTTTATGGACAACCTCTGCATTATCTCACCAATATTCAGCTAAAACAGTGGGACCAATTGAGGATCGGCAGTGAAGACGAATACAGGCCCTTGGATGCCATTATTCATCCCTGTAAAGCCGAAGCCACCATCTGGCTCATTGAAGAAGTTCACCGAAACACCTCATCTCATCATCATGTAGCCAATCTGTGGCTATCAGATCCGATGCACCATGCTTTTGTTGATTCCATCTTTCCCCAATTAGACAGCCGCTCGTGA

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

123

Amino Acids

14.47

Weight (kDa)

6.79

Isoelectric Point (pI)

66.57

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RdDM_RDM1	PF09187	1 - 118	1.3e-68	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: 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)
AccB7I	CCANNNNNTGG	2 cut(s)	246, 303
AccBSI	CCGCTC	1 cut(s)	366
AciI	CCGC	1 cut(s)	364
AclWI	GGATC	2 cut(s)	185, 308
AdeI	CACNNNGTG	1 cut(s)	59
AfaI	GTAC	1 cut(s)	29
AfiI	CCNNNNNNNGG	2 cut(s)	246, 303
AgsI	TTSAA	1 cut(s)	257
AluBI	AGCT	2 cut(s)	115, 154
AluI	AGCT	2 cut(s)	115, 154
AlwI	GGATC	2 cut(s)	185, 308
AoxI	GGCC	1 cut(s)	200
ApeKI	GCWGC	1 cut(s)	112
Asp700I	GAANNNNTTC	1 cut(s)	261
AspS9I	GGNCC	2 cut(s)	166, 201
AsuHPI	GGTGA	2 cut(s)	133, 257
AvaII	GGWCC	1 cut(s)	166
BauI	CACGAG	1 cut(s)	367
BbsI	GAAGAC	1 cut(s)	195
BbvI	GCAGC	1 cut(s)	124
BccI	CCATC	3 cut(s)	82, 251, 350
BisI	GCNGC	2 cut(s)	113, 364
BlsI	GCNGC	2 cut(s)	114, 365
Bme18I	GGWCC	1 cut(s)	166
BmgT120I	GGNCC	2 cut(s)	166, 201
BmiI	GGNNCC	1 cut(s)	167
BmsI	GCATC	2 cut(s)	199, 309
BpiI	GAAGAC	1 cut(s)	195
BsaJI	CCNNGG	2 cut(s)	58, 204
Bsc4I	CCNNNNNNNGG	2 cut(s)	246, 303
BseDI	CCNNGG	2 cut(s)	58, 204
BseGI	GGATG	4 cut(s)	39, 93, 214, 220
BseLI	CCNNNNNNNGG	2 cut(s)	246, 303
BseMII	CTCAG	1 cut(s)	78
BseXI	GCAGC	1 cut(s)	124
BshFI	GGCC	1 cut(s)	202
BslFI	GGGAC	1 cut(s)	179
BslI	CCNNNNNNNGG	2 cut(s)	246, 303
BsmFI	GGGAC	1 cut(s)	179
BsnI	GGCC	1 cut(s)	202
Bsp143I	GATC	2 cut(s)	177, 313
BspACI	CCGC	1 cut(s)	364
BspANI	GGCC	1 cut(s)	202
BspCNI	CTCAG	1 cut(s)	77
BspLI	GGNNCC	1 cut(s)	167
BspPI	GGATC	2 cut(s)	185, 308
BsrBI	CCGCTC	1 cut(s)	366
BssECI	CCNNGG	2 cut(s)	58, 204
BssMI	GATC	2 cut(s)	177, 313
BssSI	CACGAG	1 cut(s)	367
BssT1I	CCWWGG	1 cut(s)	204
Bst2BI	CACGAG	1 cut(s)	367
Bst4CI	ACNGT	2 cut(s)	59, 162
BstDEI	CTNAG	1 cut(s)	64
BstDSI	CCRYGG	1 cut(s)	58
BstF5I	GGATG	4 cut(s)	39, 93, 214, 220
BstKTI	GATC	2 cut(s)	180, 316
BstMBI	GATC	2 cut(s)	177, 313
BstV1I	GCAGC	1 cut(s)	124
BstV2I	GAAGAC	1 cut(s)	195
BstX2I	RGATCY	1 cut(s)	313
BstYI	RGATCY	1 cut(s)	313
BsuRI	GGCC	1 cut(s)	202
BtgI	CCRYGG	1 cut(s)	58
BtsCI	GGATG	4 cut(s)	39, 93, 214, 220
BtsI	GCAGTG	1 cut(s)	190
BtsIMutI	CAGTG	2 cut(s)	167, 190
Cfr13I	GGNCC	2 cut(s)	166, 201
Csp6I	GTAC	1 cut(s)	28
CviAII	CATG	4 cut(s)	31, 84, 290, 326
CviQI	GTAC	1 cut(s)	28
DdeI	CTNAG	1 cut(s)	64
DpnI	GATC	2 cut(s)	179, 315
DpnII	GATC	2 cut(s)	177, 313
DraIII	CACNNNGTG	1 cut(s)	59
Eco130I	CCWWGG	1 cut(s)	204
Eco47I	GGWCC	1 cut(s)	166
EcoO109I	RGGNCCY	1 cut(s)	201
EcoT14I	CCWWGG	1 cut(s)	204
ErhI	CCWWGG	1 cut(s)	204
FaeI	CATG	4 cut(s)	34, 87, 293, 329
FaiI	YATR	5 cut(s)	32, 85, 120, 291, 327
FaqI	GGGAC	1 cut(s)	179
FatI	CATG	4 cut(s)	30, 83, 289, 325
Fnu4HI	GCNGC	2 cut(s)	113, 364
FokI	GGATG	4 cut(s)	26, 100, 207, 221
Fsp4HI	GCNGC	2 cut(s)	113, 364
GluI	GCNGC	2 cut(s)	113, 364
HaeIII	GGCC	1 cut(s)	202
Hin1II	CATG	4 cut(s)	34, 87, 293, 329
HinfI	GANTC	1 cut(s)	338
HphI	GGTGA	2 cut(s)	133, 257
Hpy166II	GTNNAC	1 cut(s)	265
Hpy188I	TCNGA	2 cut(s)	313, 318
Hpy188III	TCNNGA	2 cut(s)	23, 369
Hpy8I	GTNNAC	1 cut(s)	265
HpyCH4III	ACNGT	2 cut(s)	59, 162
HpyCH4V	TGCA	2 cut(s)	133, 322
HpyF3I	CTNAG	1 cut(s)	64
Hsp92II	CATG	4 cut(s)	34, 87, 293, 329
Kzo9I	GATC	2 cut(s)	177, 313
LpnPI	CCDG	4 cut(s)	8, 184, 232, 238
Lsp1109I	GCAGC	1 cut(s)	124
LweI	GCATC	2 cut(s)	199, 309
MalI	GATC	2 cut(s)	179, 315
MbiI	CCGCTC	1 cut(s)	366
MboI	GATC	2 cut(s)	177, 313
MboII	GAAGA	2 cut(s)	200, 269
MfeI	CAATTG	1 cut(s)	170
MflI	RGATCY	1 cut(s)	313
MluCI	AATT	2 cut(s)	170, 353
MnlI	CCTC	4 cut(s)	91, 138, 168, 286
MroXI	GAANNNNTTC	1 cut(s)	261
MseI	TTAA	1 cut(s)	108
MslI	CAYNNNNRTG	1 cut(s)	288
MunI	CAATTG	1 cut(s)	170
NdeII	GATC	2 cut(s)	177, 313
NlaIII	CATG	4 cut(s)	34, 87, 293, 329
NlaIV	GGNNCC	1 cut(s)	167
PdmI	GAANNNNTTC	1 cut(s)	261
PfeI	GAWTC	1 cut(s)	338
PflMI	CCANNNNNTGG	2 cut(s)	246, 303
PkrI	GCNGC	2 cut(s)	114, 365
PspN4I	GGNNCC	1 cut(s)	167
PspPI	GGNCC	2 cut(s)	166, 201
PsuI	RGATCY	1 cut(s)	313
RsaI	GTAC	1 cut(s)	29
RsaNI	GTAC	1 cut(s)	28
RseI	CAYNNNNRTG	1 cut(s)	288
SaqAI	TTAA	1 cut(s)	108
SatI	GCNGC	2 cut(s)	113, 364
Sau3AI	GATC	2 cut(s)	177, 313
Sau96I	GGNCC	2 cut(s)	166, 201
SetI	ASST	6 cut(s)	83, 100, 117, 130, 156, 278
SfaNI	GCATC	2 cut(s)	199, 309
SinI	GGWCC	1 cut(s)	166
SmiMI	CAYNNNNRTG	1 cut(s)	288
Sse9I	AATT	2 cut(s)	170, 353
SsiI	CCGC	1 cut(s)	364
SspI	AATATT	1 cut(s)	148
StyI	CCWWGG	1 cut(s)	204
TaaI	ACNGT	2 cut(s)	59, 162
TasI	AATT	2 cut(s)	170, 353
TatI	WGTACW	1 cut(s)	27
TauI	GCSGC	1 cut(s)	366
TfiI	GAWTC	1 cut(s)	338
Tru1I	TTAA	1 cut(s)	108
Tru9I	TTAA	1 cut(s)	108
TscAI	CASTG	2 cut(s)	167, 190
TseI	GCWGC	1 cut(s)	112
TspDTI	ATGAA	2 cut(s)	47, 209
TspRI	CASTG	2 cut(s)	167, 190
Van91I	CCANNNNNTGG	2 cut(s)	246, 303
VpaK11BI	GGWCC	1 cut(s)	166
XcmI	CCANNNNNNNNNTGG	1 cut(s)	81
XmnI	GAANNNNTTC	1 cut(s)	261

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