Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0003605

Physical Location & Seq

Genomic Coordinates Reverse (-)

66661592 .. 66662131

Gene Structure 540 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG423600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 540 bp

ATGGGGAAGACAATAAACTTACATGGATTCCCTTCAGGTGAATCTGCCGAAAAAATTAAGGTATTTTTGGAGAAACATACAGGAGAAGGAAGTGTTTTTGCTGTTAAATTACGGCCTGCCCAAAGGGGTGGAAGATTCTATGCTTATATACAGTTTGAGTCCACCAGTCAGGCTGATTTTATCACCTCTTTGGCTAACGCTAGGGGTGGGCTGTGGTATGGGAGATCCTATTTGAAAGCTCATCCAGCGGACCATGATATTGTACCAAAGCCAAGAACTGTAATGCATAGCATGCAAAATTTAGTATTGCATGTTGGCTGCCAGGTTGCAAATGATAAGTTGTCTGTTTTTTGGAGAACAGCTGAAGTTTCAGTGGAGTTTGGGACTGGAACGCGGACATTCCAATTTCGGCTGTTATATCATCAGAAGGTATACAGACTTCAGCTTTCGTATGAGAACATCTGGCAAATTGAGTTGCATCGTCCACGTGGTCGTACTGCGAAGTATCTTGTGATTCAGGTCTGTCACCTTCTTAATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001101 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009605 GO:0009607 GO:0009615 GO:0009719 GO:0009725 GO:0009751 GO:0009892 GO:0009987 GO:0010025 GO:0010033 GO:0010166 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0019222 GO:0030422 GO:0031047 GO:0031050 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0042493 GO:0043170 GO:0043207 GO:0043331 GO:0044237 GO:0044238 GO:0046483 GO:0046677 GO:0048518 GO:0048519 GO:0048522 GO:0050789 GO:0050794 GO:0050896 GO:0051704 GO:0051707 GO:0051716 GO:0060147 GO:0060148 GO:0060255 GO:0060968 GO:0065007 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:1901360 GO:1901568 GO:1901570 GO:1901576 GO:1901698 GO:1901699 GO:1901700

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RdRP

Protein Analysis

179

Amino Acids

20.51

Weight (kDa)

9.82

Isoelectric Point (pI)

24.61

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RRM_RdRP1_2	PF26250	4 - 85	1.9e-15	RdRP1/2, RRM domain
PH_RDR2	PF24823	103 - 175	1.6e-14	RDR2 PH-like domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Publication-ready

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Orthologous Genes (Group: OG0003605)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G14790
fragaria_vesca	FvH4_4g33391 FvH4_4g33391 FvH4_4g33391 FvH4_4g33391 FvH4_4g33391 FvH4_4g33391
malus_domestica	MD13G1019300.v1.1 MD13G1041300.v1.1 MD16G1017200.v1.1
prunus_persica	Prupe.1G334600_v2.0.a1 Prupe.1G334600_v2.0.a1
pyrus_communis	pycom13g01640 pycom13g03560 pycom13g03580 pycom16g01590
rosa_chinensis	RchiOBHm_Chr4g0442681 RchiOBHm_Chr4g0442701
rosa_laevigata	RLG00000005990 RLG00000005992
rosa_multiflora	Rmu_ssc0000204.1_g000024 Rmu_ssc0000204.1_g000026
rosa_roxburghii	Rroxscaffold_5G00383490 Rroxscaffold_5G00383510
rosa_rugosa	Rorug04G0342200 Rorug04G0342300
rosa_samantha	Rh4AG394700 Rh4AG394900 Rh4BG407600 Rh4CG423000 Rh4CG423600 Rh4DG401700 Rh4DG401900
rosa_wichuraiana	Rw4G034110 Rw4G034130

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	432
AccII	CGCG	1 cut(s)	394
AciI	CCGC	2 cut(s)	248, 394
AclWI	GGATC	1 cut(s)	219
AcsI	RAATTY	1 cut(s)	298
AcuI	CTGAAG	3 cut(s)	18, 384, 425
AcvI	CACGTG	1 cut(s)	488
AfaI	GTAC	2 cut(s)	264, 496
AgsI	TTSAA	1 cut(s)	235
AjnI	CCWGG	1 cut(s)	321
AluBI	AGCT	3 cut(s)	239, 362, 445
AluI	AGCT	3 cut(s)	239, 362, 445
AlwI	GGATC	1 cut(s)	219
AoxI	GGCC	1 cut(s)	113
ApeKI	GCWGC	1 cut(s)	318
ApoI	RAATTY	1 cut(s)	298
AspS9I	GGNCC	1 cut(s)	250
AsuHPI	GGTGA	3 cut(s)	50, 175, 518
AvaII	GGWCC	1 cut(s)	250
BarI	GAAGNNNNNNTAC	2 cut(s)	423, 455
BbrPI	CACGTG	1 cut(s)	488
BbsI	GAAGAC	1 cut(s)	14
BbvI	GCAGC	1 cut(s)	305
BceAI	ACGGC	1 cut(s)	128
BciT130I	CCWGG	1 cut(s)	323
BfaI	CTAG	1 cut(s)	201
BisI	GCNGC	1 cut(s)	319
BlsI	GCNGC	1 cut(s)	320
Bme1390I	CCNGG	1 cut(s)	323
Bme18I	GGWCC	1 cut(s)	250
BmgT120I	GGNCC	1 cut(s)	250
BmrFI	CCNGG	1 cut(s)	323
BmsI	GCATC	1 cut(s)	487
BpiI	GAAGAC	1 cut(s)	14
BsaAI	YACGTR	1 cut(s)	488
Bse1I	ACTGG	2 cut(s)	165, 391
BseBI	CCWGG	1 cut(s)	323
BseGI	GGATG	1 cut(s)	241
BseNI	ACTGG	2 cut(s)	165, 391
BseXI	GCAGC	1 cut(s)	305
Bsh1236I	CGCG	1 cut(s)	394
BshFI	GGCC	1 cut(s)	115
BslFI	GGGAC	1 cut(s)	397
BsmFI	GGGAC	1 cut(s)	397
BsnI	GGCC	1 cut(s)	115
Bsp143I	GATC	1 cut(s)	224
BspACI	CCGC	2 cut(s)	248, 394
BspANI	GGCC	1 cut(s)	115
BspFNI	CGCG	1 cut(s)	394
BspPI	GGATC	1 cut(s)	219
BsrI	ACTGG	2 cut(s)	165, 391
BssMI	GATC	1 cut(s)	224
BssNAI	GTATAC	1 cut(s)	433
Bst1107I	GTATAC	1 cut(s)	433
Bst2UI	CCWGG	1 cut(s)	323
Bst4CI	ACNGT	2 cut(s)	153, 280
BstAPI	GCANNNNNTGC	1 cut(s)	292
BstBAI	YACGTR	1 cut(s)	488
BstC8I	GCNNGC	2 cut(s)	117, 293
BstF5I	GGATG	1 cut(s)	241
BstFNI	CGCG	1 cut(s)	394
BstKTI	GATC	1 cut(s)	227
BstMBI	GATC	1 cut(s)	224
BstMWI	GCNNNNNNNGC	2 cut(s)	245, 292
BstNI	CCWGG	1 cut(s)	323
BstNSI	RCATGY	2 cut(s)	295, 314
BstSCI	CCNGG	1 cut(s)	321
BstUI	CGCG	1 cut(s)	394
BstV1I	GCAGC	1 cut(s)	305
BstV2I	GAAGAC	1 cut(s)	14
BstX2I	RGATCY	1 cut(s)	224
BstXI	CCANNNNNNTGG	1 cut(s)	128
BstYI	RGATCY	1 cut(s)	224
BstZ17I	GTATAC	1 cut(s)	433
BsuRI	GGCC	1 cut(s)	115
BtsCI	GGATG	1 cut(s)	241
BtsIMutI	CAGTG	1 cut(s)	378
Cac8I	GCNNGC	2 cut(s)	117, 293
Cfr13I	GGNCC	1 cut(s)	250
Csp6I	GTAC	2 cut(s)	263, 495
CviAII	CATG	4 cut(s)	23, 254, 292, 311
CviQI	GTAC	2 cut(s)	263, 495
DpnI	GATC	1 cut(s)	226
DpnII	GATC	1 cut(s)	224
Eco47I	GGWCC	1 cut(s)	250
Eco57I	CTGAAG	3 cut(s)	18, 384, 425
Eco72I	CACGTG	1 cut(s)	488
EcoRII	CCWGG	1 cut(s)	321
EcoT22I	ATGCAT	1 cut(s)	288
FaeI	CATG	4 cut(s)	26, 257, 295, 314
FaqI	GGGAC	1 cut(s)	397
FatI	CATG	4 cut(s)	22, 253, 291, 310
FblI	GTMKAC	1 cut(s)	432
Fnu4HI	GCNGC	1 cut(s)	319
FokI	GGATG	1 cut(s)	228
Fsp4HI	GCNGC	1 cut(s)	319
FspBI	CTAG	1 cut(s)	201
GluI	GCNGC	1 cut(s)	319
HaeIII	GGCC	1 cut(s)	115
Hin1II	CATG	4 cut(s)	26, 257, 295, 314
HinfI	GANTC	5 cut(s)	27, 41, 135, 158, 514
HphI	GGTGA	3 cut(s)	50, 175, 518
Hpy166II	GTNNAC	3 cut(s)	162, 433, 485
Hpy188I	TCNGA	1 cut(s)	426
Hpy8I	GTNNAC	3 cut(s)	162, 433, 485
HpyAV	CCTTC	4 cut(s)	42, 80, 421, 539
HpyCH4III	ACNGT	2 cut(s)	153, 280
HpyCH4IV	ACGT	1 cut(s)	487
HpyCH4V	TGCA	5 cut(s)	286, 295, 310, 329, 478
HpyF10VI	GCNNNNNNNGC	2 cut(s)	245, 292
HpySE526I	ACGT	1 cut(s)	487
Hsp92II	CATG	4 cut(s)	26, 257, 295, 314
Kzo9I	GATC	1 cut(s)	224
Lsp1109I	GCAGC	1 cut(s)	305
LweI	GCATC	1 cut(s)	487
MaeI	CTAG	1 cut(s)	201
MaeII	ACGT	1 cut(s)	487
MaeIII	GTNAC	1 cut(s)	524
MalI	GATC	1 cut(s)	226
MboI	GATC	1 cut(s)	224
MboII	GAAGA	2 cut(s)	19, 144
MflI	RGATCY	1 cut(s)	224
MluCI	AATT	6 cut(s)	54, 107, 298, 404, 468, 535
MlyI	GAGTC	1 cut(s)	167
MnlI	CCTC	1 cut(s)	196
Mph1103I	ATGCAT	1 cut(s)	288
MseI	TTAA	4 cut(s)	57, 105, 534, 538
MspA1I	CMGCKG	2 cut(s)	248, 362
MspR9I	CCNGG	1 cut(s)	323
MvaI	CCWGG	1 cut(s)	323
MvnI	CGCG	1 cut(s)	394
MwoI	GCNNNNNNNGC	2 cut(s)	245, 292
NdeII	GATC	1 cut(s)	224
NlaIII	CATG	4 cut(s)	26, 257, 295, 314
NmuCI	GTSAC	1 cut(s)	524
NsiI	ATGCAT	1 cut(s)	288
NspI	RCATGY	2 cut(s)	295, 314
PacI	TTAATTAA	1 cut(s)	538
PaeI	GCATGC	1 cut(s)	295
PfeI	GAWTC	4 cut(s)	27, 41, 135, 514
PkrI	GCNGC	1 cut(s)	320
PleI	GAGTC	1 cut(s)	166
PmaCI	CACGTG	1 cut(s)	488
PmlI	CACGTG	1 cut(s)	488
PpsI	GAGTC	1 cut(s)	166
Ppu21I	YACGTR	1 cut(s)	488
Psp6I	CCWGG	1 cut(s)	321
PspCI	CACGTG	1 cut(s)	488
PspGI	CCWGG	1 cut(s)	321
PspPI	GGNCC	1 cut(s)	250
PsuI	RGATCY	1 cut(s)	224
PvuII	CAGCTG	1 cut(s)	362
RsaI	GTAC	2 cut(s)	264, 496
RsaNI	GTAC	2 cut(s)	263, 495
SaqAI	TTAA	4 cut(s)	57, 105, 534, 538
SatI	GCNGC	1 cut(s)	319
Sau3AI	GATC	1 cut(s)	224
Sau96I	GGNCC	1 cut(s)	250
SchI	GAGTC	1 cut(s)	167
ScrFI	CCNGG	1 cut(s)	323
SfaNI	GCATC	1 cut(s)	487
SinI	GGWCC	1 cut(s)	250
SphI	GCATGC	1 cut(s)	295
Sse9I	AATT	6 cut(s)	54, 107, 298, 404, 468, 535
SsiI	CCGC	2 cut(s)	248, 394
SspMI	CTAG	1 cut(s)	201
StyD4I	CCNGG	1 cut(s)	321
TaaI	ACNGT	2 cut(s)	153, 280
TaiI	ACGT	1 cut(s)	490
TasI	AATT	6 cut(s)	54, 107, 298, 404, 468, 535
TfiI	GAWTC	4 cut(s)	27, 41, 135, 514
Tru1I	TTAA	4 cut(s)	57, 105, 534, 538
Tru9I	TTAA	4 cut(s)	57, 105, 534, 538
TscAI	CASTG	1 cut(s)	378
TseFI	GTSAC	1 cut(s)	524
TseI	GCWGC	1 cut(s)	318
Tsp45I	GTSAC	1 cut(s)	524
TspRI	CASTG	1 cut(s)	378
VpaK11BI	GGWCC	1 cut(s)	250
XapI	RAATTY	1 cut(s)	298
XceI	RCATGY	2 cut(s)	295, 314
XmiI	GTMKAC	1 cut(s)	432
XspI	CTAG	1 cut(s)	201
Zsp2I	ATGCAT	1 cut(s)	288

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