Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr16

Orthogroup ID

OG0012911

Physical Location & Seq

Genomic Coordinates Forward (+)

17679460 .. 17684766

Gene Structure 5307 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD16G1197500.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 540 bp

ATGAAGAGGGCAGCTCCCTGGGATGAGCAGGTGGATGTTATTTCATCAGATGACTCTTCTTCCCCGGACATGGAGATGGAATCCGTTAATGAGTGCGATAGCAAGCAGTCAGACACTAATATCACATTTGATCAGCCTGACAAAGAAATAACACCAGAAGGTGCTTTGGCACGAAGGGCAGAGATGTATCAGGACTACATGAAGCAGATCCCGATCCCATCAAACCGTGGCTCTGTTATTCCATTTACCTCATGGACGGGTTTAGGCAAGTCCATTAAGCAATTGTATGGACAACCGTTGCATTACCTCACCAATCTTCTCCTAAAACAGTGGGATCAGCTGAGGATCGGCAGTGAGGAGGAGTACAGGCCCTTGGATACCATCATTCATCCTTGTAAAGCTGAAGCCACCATCTGGCTCGTTGAAGAAGTCCACCGGCAGACCTCATCTCATCATCATGTAGCAAATCTCTGGCTCAAAGATCCGATGCACCATGCCTCCATTGACGCCATGTTTCCCCAGCTACGAAGCAAATCGTGA

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

180

Amino Acids

20.56

Weight (kDa)

5.3

Isoelectric Point (pI)

64.74

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RdDM_RDM1	PF09187	56 - 174	1.4e-66	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)
AarI	CACCTGC	1 cut(s)	19
Acc36I	ACCTGC	1 cut(s)	19
AccB7I	CCANNNNNTGG	1 cut(s)	414
AclWI	GGATC	5 cut(s)	202, 208, 342, 353, 476
AcuI	CTGAAG	1 cut(s)	423
AcyI	GRCGYC	1 cut(s)	507
AfaI	GTAC	1 cut(s)	365
AfiI	CCNNNNNNNGG	2 cut(s)	70, 414
AgsI	TTSAA	1 cut(s)	425
AjnI	CCWGG	1 cut(s)	17
AluBI	AGCT	4 cut(s)	14, 340, 401, 523
AluI	AGCT	4 cut(s)	14, 340, 401, 523
AlwI	GGATC	5 cut(s)	202, 208, 342, 353, 476
AoxI	GGCC	1 cut(s)	368
ApeKI	GCWGC	1 cut(s)	11
AspS9I	GGNCC	1 cut(s)	369
AsuC2I	CCSGG	1 cut(s)	65
AsuHPI	GGTGA	1 cut(s)	301
BbvCI	CCTCAGC	1 cut(s)	341
BbvI	GCAGC	1 cut(s)	23
BccI	CCATC	4 cut(s)	70, 226, 389, 419
BciT130I	CCWGG	1 cut(s)	19
BciVI	GTATCC	1 cut(s)	370
BclI	TGATCA	1 cut(s)	130
BcnI	CCSGG	1 cut(s)	65
BfuAI	ACCTGC	1 cut(s)	19
BfuI	GTATCC	1 cut(s)	370
BisI	GCNGC	1 cut(s)	12
BlsI	GCNGC	1 cut(s)	13
Bme1390I	CCNGG	2 cut(s)	19, 65
BmgT120I	GGNCC	1 cut(s)	369
BmrFI	CCNGG	2 cut(s)	19, 65
BmsI	GCATC	1 cut(s)	477
BplI	GAGNNNNNCTC	1 cut(s)	30
Bpu10I	CCTNAGC	1 cut(s)	341
BpuMI	CCSGG	1 cut(s)	65
BsaBI	GATNNNNATC	1 cut(s)	212
BsaHI	GRCGYC	1 cut(s)	507
BsaJI	CCNNGG	5 cut(s)	17, 18, 63, 226, 372
BsaXI	ACNNNNNCTCC	2 cut(s)	482, 512
Bsc4I	CCNNNNNNNGG	2 cut(s)	70, 414
Bse118I	RCCGGY	1 cut(s)	435
Bse8I	GATNNNNATC	1 cut(s)	212
BseBI	CCWGG	1 cut(s)	19
BseDI	CCNNGG	5 cut(s)	17, 18, 63, 226, 372
BseGI	GGATG	3 cut(s)	28, 40, 388
BseJI	GATNNNNATC	1 cut(s)	212
BseLI	CCNNNNNNNGG	2 cut(s)	70, 414
BseMII	CTCAG	1 cut(s)	332
BseRI	GAGGAG	2 cut(s)	371, 374
BseXI	GCAGC	1 cut(s)	23
BseYI	CCCAGC	1 cut(s)	519
BshFI	GGCC	1 cut(s)	370
BsiSI	CCGG	2 cut(s)	65, 436
BslI	CCNNNNNNNGG	2 cut(s)	70, 414
BsnI	GGCC	1 cut(s)	370
Bsp143I	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
BspANI	GGCC	1 cut(s)	370
BspCNI	CTCAG	1 cut(s)	333
BspMI	ACCTGC	1 cut(s)	19
BspPI	GGATC	5 cut(s)	202, 208, 342, 353, 476
BsrFI	RCCGGY	1 cut(s)	435
BssAI	RCCGGY	1 cut(s)	435
BssECI	CCNNGG	5 cut(s)	17, 18, 63, 226, 372
BssMI	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
BssNI	GRCGYC	1 cut(s)	507
BssT1I	CCWWGG	1 cut(s)	372
Bst2UI	CCWGG	1 cut(s)	19
Bst4CI	ACNGT	3 cut(s)	227, 297, 330
Bst6I	CTCTTC	1 cut(s)	61
BstACI	GRCGYC	1 cut(s)	507
BstC8I	GCNNGC	1 cut(s)	104
BstDEI	CTNAG	1 cut(s)	341
BstDSI	CCRYGG	1 cut(s)	226
BstF5I	GGATG	3 cut(s)	28, 40, 388
BstKTI	GATC	6 cut(s)	133, 210, 216, 337, 348, 484
BstMBI	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
BstMWI	GCNNNNNNNGC	1 cut(s)	176
BstNI	CCWGG	1 cut(s)	19
BstSCI	CCNGG	2 cut(s)	17, 63
BstV1I	GCAGC	1 cut(s)	23
BstX2I	RGATCY	2 cut(s)	207, 481
BstYI	RGATCY	2 cut(s)	207, 481
BsuI	GTATCC	1 cut(s)	370
BsuRI	GGCC	1 cut(s)	370
BtgI	CCRYGG	1 cut(s)	226
BtsCI	GGATG	3 cut(s)	28, 40, 388
BtsI	GCAGTG	1 cut(s)	358
BtsIMutI	CAGTG	2 cut(s)	335, 358
BveI	ACCTGC	1 cut(s)	19
Cac8I	GCNNGC	1 cut(s)	104
Cfr10I	RCCGGY	1 cut(s)	435
Cfr13I	GGNCC	1 cut(s)	369
CseI	GACGC	1 cut(s)	515
Csp6I	GTAC	1 cut(s)	364
CviAII	CATG	6 cut(s)	70, 199, 252, 458, 494, 511
CviQI	GTAC	1 cut(s)	364
DdeI	CTNAG	1 cut(s)	341
DpnI	GATC	6 cut(s)	132, 209, 215, 336, 347, 483
DpnII	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
Eam1104I	CTCTTC	1 cut(s)	61
EarI	CTCTTC	1 cut(s)	61
Eco130I	CCWWGG	1 cut(s)	372
Eco57I	CTGAAG	1 cut(s)	423
EcoO109I	RGGNCCY	1 cut(s)	369
EcoRII	CCWGG	1 cut(s)	17
EcoT14I	CCWWGG	1 cut(s)	372
ErhI	CCWWGG	1 cut(s)	372
FaeI	CATG	6 cut(s)	73, 202, 255, 461, 497, 514
FaiI	YATR	7 cut(s)	71, 200, 253, 288, 459, 495, 512
FatI	CATG	6 cut(s)	69, 198, 251, 457, 493, 510
FbaI	TGATCA	1 cut(s)	130
Fnu4HI	GCNGC	1 cut(s)	12
FokI	GGATG	3 cut(s)	35, 47, 375
Fsp4HI	GCNGC	1 cut(s)	12
GluI	GCNGC	1 cut(s)	12
GsaI	CCCAGC	1 cut(s)	523
HaeIII	GGCC	1 cut(s)	370
HapII	CCGG	2 cut(s)	65, 436
HgaI	GACGC	1 cut(s)	515
Hin1I	GRCGYC	1 cut(s)	507
Hin1II	CATG	6 cut(s)	73, 202, 255, 461, 497, 514
HinfI	GANTC	2 cut(s)	53, 80
HpaII	CCGG	2 cut(s)	65, 436
HphI	GGTGA	1 cut(s)	301
Hpy166II	GTNNAC	1 cut(s)	433
Hpy188I	TCNGA	3 cut(s)	49, 112, 486
Hpy188III	TCNNGA	3 cut(s)	191, 211, 537
Hpy8I	GTNNAC	1 cut(s)	433
HpyAV	CCTTC	2 cut(s)	152, 168
HpyCH4III	ACNGT	3 cut(s)	227, 297, 330
HpyCH4V	TGCA	2 cut(s)	301, 490
HpyF10VI	GCNNNNNNNGC	1 cut(s)	176
HpyF3I	CTNAG	1 cut(s)	341
Hsp92I	GRCGYC	1 cut(s)	507
Hsp92II	CATG	6 cut(s)	73, 202, 255, 461, 497, 514
Ksp22I	TGATCA	1 cut(s)	130
Kzo9I	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
LmnI	GCTCC	1 cut(s)	19
Lsp1109I	GCAGC	1 cut(s)	23
LweI	GCATC	1 cut(s)	477
MalI	GATC	6 cut(s)	132, 209, 215, 336, 347, 483
MboI	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
MboII	GAAGA	5 cut(s)	16, 48, 51, 308, 437
MfeI	CAATTG	1 cut(s)	281
MflI	RGATCY	2 cut(s)	207, 481
MluCI	AATT	1 cut(s)	281
MlyI	GAGTC	1 cut(s)	47
MnlI	CCTC	7 cut(s)	259, 317, 336, 349, 352, 454, 508
MseI	TTAA	2 cut(s)	87, 276
MslI	CAYNNNNRTG	2 cut(s)	74, 456
MspA1I	CMGCKG	1 cut(s)	340
MspI	CCGG	2 cut(s)	65, 436
MspR9I	CCNGG	2 cut(s)	19, 65
MunI	CAATTG	1 cut(s)	281
MvaI	CCWGG	1 cut(s)	19
MwoI	GCNNNNNNNGC	1 cut(s)	176
NciI	CCSGG	1 cut(s)	65
NdeII	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
NlaIII	CATG	6 cut(s)	73, 202, 255, 461, 497, 514
PaqCI	CACCTGC	1 cut(s)	19
PasI	CCCWGGG	1 cut(s)	18
PfeI	GAWTC	1 cut(s)	80
PflMI	CCANNNNNTGG	1 cut(s)	414
PkrI	GCNGC	1 cut(s)	13
PleI	GAGTC	1 cut(s)	47
PpsI	GAGTC	1 cut(s)	47
Psp6I	CCWGG	1 cut(s)	17
PspFI	CCCAGC	1 cut(s)	519
PspGI	CCWGG	1 cut(s)	17
PspPI	GGNCC	1 cut(s)	369
PsuI	RGATCY	2 cut(s)	207, 481
PvuII	CAGCTG	1 cut(s)	340
RsaI	GTAC	1 cut(s)	365
RsaNI	GTAC	1 cut(s)	364
RseI	CAYNNNNRTG	2 cut(s)	74, 456
SaqAI	TTAA	2 cut(s)	87, 276
SatI	GCNGC	1 cut(s)	12
Sau3AI	GATC	6 cut(s)	130, 207, 213, 334, 345, 481
Sau96I	GGNCC	1 cut(s)	369
SchI	GAGTC	1 cut(s)	47
ScrFI	CCNGG	2 cut(s)	19, 65
SetI	ASST	9 cut(s)	16, 33, 163, 251, 309, 342, 403, 446, 525
SfaNI	GCATC	1 cut(s)	477
SmiMI	CAYNNNNRTG	2 cut(s)	74, 456
Sse9I	AATT	1 cut(s)	281
StyD4I	CCNGG	2 cut(s)	17, 63
StyI	CCWWGG	1 cut(s)	372
TaaI	ACNGT	3 cut(s)	227, 297, 330
TasI	AATT	1 cut(s)	281
TatI	WGTACW	1 cut(s)	363
TfiI	GAWTC	1 cut(s)	80
Tru1I	TTAA	2 cut(s)	87, 276
Tru9I	TTAA	2 cut(s)	87, 276
TscAI	CASTG	2 cut(s)	335, 358
TseI	GCWGC	1 cut(s)	11
TspDTI	ATGAA	4 cut(s)	17, 33, 215, 377
TspGWI	ACGGA	1 cut(s)	73
TspRI	CASTG	2 cut(s)	335, 358
Van91I	CCANNNNNTGG	1 cut(s)	414
XcmI	CCANNNNNNNNNTGG	1 cut(s)	249

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