Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000005

Orthogroup ID

OG0001845

Physical Location & Seq

Genomic Coordinates Reverse (-)

63135697 .. 63138907

Gene Structure 3211 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_5G00383530.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1029 bp

ATGGTCAAGAAAGTTTACCTGTATGGATTTCCCACTGTGGAGTCTCCAGAAGCAGTGACGAAATTTCTGGAGGAGTATACCGGAGAAGGAACTGTTCTCTCATCAAGATCATCTGCCACAGTTCAATTCACAATTGCAGAATGTGCTGAAATACTACTTCTATTAGCCGAAAAAAAAGGCCTGTGGTACGGAGAGTCTTATCTGAAAGCTCGAGAATGGAAGCATGACATGGCACCGAGATCAAAAGTCTTGGAGGAACTTGTGACACTTCACTTTGGATTCAAGATATATGAGGAGAAGTTTTCGGTGCTTTGGACAAAATCAGATGTTTCTGTGACATTTGGGATGGAACGGAAAAATTTGCACTTGTCTTTCTCCTATGATTTCGTTGAATACAAGCTTGAGCTCCCATCTGACACTATTTTCCGGATTGAGCTGTATTGTCCACGTGATCAGTTTAGAAAGTTTCTTCTCATCCAGCTATGTGGTGCCCCTCGGATCTATAAGAAAGATGTAAATTTGGCTTCTGACAACCACTGGGTTCGAGAAGTTGATTTCACTCCATCATGCTGCATCGAGCAATCCTCTTCTTTATGTTTGGAACTTCCATTAAGAAATTCAGCTCTTGTTCCTACTCTGGCTCCACCCCTAGGGATTGACTTGCCATATAAAATCATGTTCAAGATAAATTCATTGGTTCAGCATGGTTATATTCCCGGCCAAGCTCTTGATGTCCATTTTTATAATCTAGTGGATCATAAAAGAATAAAAATTGAATATATAGAGTGTGCCCTGGACAAACTGTTCAACTCCAAGGAGTGCTGCTATGAACCTGTAAGGTGGCTTCTTAAGCAGTACATGGCATGCAAGCGGATTCCTCAGTCACCAGCTATATCTTTAGATGATGACTTGAGGAAGATTCACTCTATCTTTGAGAATCTGTTTCCCTCATCCACCCGAGGCATTCTTCTGCAGTTCCTAAGAGATGAGCAAGCTGCCATGCAATTAGCTTTTCTTATTGCCAAGTAA

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

342

Amino Acids

39.62

Weight (kDa)

6.72

Isoelectric Point (pI)

49.81

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RRM_RdRP1_2	PF26250	7 - 74	4.5e-06	RdRP1/2, RRM domain
PH_RDR2	PF24823	90 - 205	4.8e-25	RDR2 PH-like domain
RdRP_helical	PF26252	213 - 293	9.8e-13	RNA dependent RNA polymerase, helical domain

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: OG0001845)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_4g13760 FvH4_4g33441 FvH4_4g33445
malus_domestica	MD13G1019400.v1.1 MD13G1041200.v1.1 MD16G1017600.v1.1
prunus_persica	Prupe.1G132100_v2.0.a1 Prupe.1G132200_v2.0.a1 Prupe.1G132200_v2.0.a1 Prupe.1G332600_v2.0.a1 Prupe.1G332600_v2.0.a1 Prupe.1G332600_v2.0.a1 Prupe.1G334500_v2.0.a1 Prupe.1G334500_v2.0.a1 Prupe.1G334500_v2.0.a1
pyrus_communis	pycom13g01650 pycom13g03550
rosa_chinensis	RchiOBHm_Chr2g0166231 RchiOBHm_Chr4g0442711 RchiOBHm_Chr4g0442751
rosa_laevigata	RLG00000005987 RLG00000005988 RLG00000005989 RLG00000021600
rosa_multiflora	Rmu_co8517261.1_g000001 Rmu_sc0018648.1_g000004 Rmu_sc0035717.1_g000001 Rmu_ssc0000204.1_g000023
rosa_roxburghii	Rroxscaffold_2G00085060 Rroxscaffold_5G00383520 Rroxscaffold_5G00383530 Rroxscaffold_5G00383540
rosa_rugosa	Rorug02G0521500 Rorug02G0521600
rosa_samantha	Rh2AG587500 Rh2BG599400 Rh2CG569900 Rh2DG609500 Rh4AG395000 Rh4AG395300 Rh4BG408000 Rh4CG423700 Rh4DG402000 Rh4DG402200
rosa_wichuraiana	Rw2G048970 Rw4G034140 Rw4G034160

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	744
AccB1I	GGYRCC	2 cut(s)	232, 488
AccI	GTMKAC	1 cut(s)	77
AccIII	TCCGGA	1 cut(s)	426
AciI	CCGC	1 cut(s)	871
AclWI	GGATC	2 cut(s)	506, 762
AcoI	YGGCCR	1 cut(s)	718
AcsI	RAATTY	5 cut(s)	62, 358, 517, 616, 688
AcvI	CACGTG	1 cut(s)	449
AfaI	GTAC	2 cut(s)	188, 857
AfiI	CCNNNNNNNGG	1 cut(s)	650
AflII	CTTAAG	1 cut(s)	848
AgsI	TTSAA	6 cut(s)	125, 283, 392, 682, 776, 808
AjnI	CCWGG	1 cut(s)	792
AloI	GAACNNNNNNTCC	2 cut(s)	788, 820
Alw21I	GWGCWC	1 cut(s)	408
Alw26I	GTCTC	1 cut(s)	48
AlwI	GGATC	2 cut(s)	506, 762
Ama87I	CYCGRG	2 cut(s)	210, 957
Aor13HI	TCCGGA	1 cut(s)	426
AoxI	GGCC	2 cut(s)	178, 718
ApeKI	GCWGC	3 cut(s)	570, 822, 995
ApoI	RAATTY	5 cut(s)	62, 358, 517, 616, 688
AspA2I	CCTAGG	1 cut(s)	649
AsuC2I	CCSGG	1 cut(s)	717
AsuHPI	GGTGA	1 cut(s)	876
AvaI	CYCGRG	2 cut(s)	210, 957
AvrII	CCTAGG	1 cut(s)	649
BaeGI	GKGCMC	2 cut(s)	493, 793
BanI	GGYRCC	2 cut(s)	232, 488
BanII	GRGCYC	1 cut(s)	408
BarI	GAAGNNNNNNTAC	2 cut(s)	828, 860
BbrPI	CACGTG	1 cut(s)	449
Bbv12I	GWGCWC	1 cut(s)	408
BbvI	GCAGC	3 cut(s)	557, 809, 982
BccI	CCATC	3 cut(s)	340, 418, 571
BciT130I	CCWGG	1 cut(s)	794
BclI	TGATCA	1 cut(s)	451
BcnI	CCSGG	1 cut(s)	717
BcoDI	GTCTC	1 cut(s)	48
BfaI	CTAG	2 cut(s)	650, 749
BfmI	CTRYAG	1 cut(s)	971
BfrI	CTTAAG	1 cut(s)	848
BisI	GCNGC	3 cut(s)	571, 823, 996
BlnI	CCTAGG	1 cut(s)	649
BlsI	GCNGC	3 cut(s)	572, 824, 997
Bme1390I	CCNGG	2 cut(s)	717, 794
BmeT110I	CYCGRG	2 cut(s)	210, 957
BmiI	GGNNCC	3 cut(s)	234, 490, 642
BmrFI	CCNGG	2 cut(s)	717, 794
BmrI	ACTGGG	1 cut(s)	547
BmsI	GCATC	1 cut(s)	582
BmuI	ACTGGG	1 cut(s)	547
BplI	GAGNNNNNCTC	2 cut(s)	569, 601
BpmI	CTGGAG	2 cut(s)	30, 89
BpuEI	CTTGAG	2 cut(s)	422, 931
BpuMI	CCSGG	1 cut(s)	717
BsaAI	YACGTR	1 cut(s)	449
BsaJI	CCNNGG	5 cut(s)	494, 649, 792, 813, 958
BsaWI	WCCGGW	2 cut(s)	80, 426
BsaXI	ACNNNNNCTCC	2 cut(s)	625, 655
Bsc4I	CCNNNNNNNGG	1 cut(s)	650
Bse1I	ACTGG	1 cut(s)	542
BseAI	TCCGGA	1 cut(s)	426
BseBI	CCWGG	1 cut(s)	794
BseDI	CCNNGG	5 cut(s)	494, 649, 792, 813, 958
BseGI	GGATG	3 cut(s)	351, 474, 950
BseLI	CCNNNNNNNGG	1 cut(s)	650
BseMII	CTCAG	1 cut(s)	893
BseNI	ACTGG	1 cut(s)	542
BseRI	GAGGAG	2 cut(s)	86, 308
BseSI	GKGCMC	2 cut(s)	493, 793
BseXI	GCAGC	3 cut(s)	557, 809, 982
BshFI	GGCC	2 cut(s)	180, 720
BshNI	GGYRCC	2 cut(s)	232, 488
BsiHKAI	GWGCWC	1 cut(s)	408
BsiHKCI	CYCGRG	2 cut(s)	210, 957
BsiSI	CCGG	3 cut(s)	81, 427, 717
BslI	CCNNNNNNNGG	1 cut(s)	650
BsmAI	GTCTC	1 cut(s)	48
BsmI	GAATGC	1 cut(s)	963
BsnI	GGCC	2 cut(s)	180, 720
BsoBI	CYCGRG	2 cut(s)	210, 957
Bsp1286I	GDGCHC	3 cut(s)	408, 493, 793
Bsp13I	TCCGGA	1 cut(s)	426
Bsp143I	GATC	5 cut(s)	107, 239, 451, 498, 754
BspACI	CCGC	1 cut(s)	871
BspANI	GGCC	2 cut(s)	180, 720
BspCNI	CTCAG	1 cut(s)	892
BspEI	TCCGGA	1 cut(s)	426
BspLI	GGNNCC	3 cut(s)	234, 490, 642
BspMAI	CTGCAG	1 cut(s)	975
BspPI	GGATC	2 cut(s)	506, 762
BspT107I	GGYRCC	2 cut(s)	232, 488
BspTI	CTTAAG	1 cut(s)	848
BsrI	ACTGG	1 cut(s)	542
BssECI	CCNNGG	5 cut(s)	494, 649, 792, 813, 958
BssMI	GATC	5 cut(s)	107, 239, 451, 498, 754
BssNAI	GTATAC	1 cut(s)	78
BssT1I	CCWWGG	2 cut(s)	649, 813
Bst1107I	GTATAC	1 cut(s)	78
Bst2UI	CCWGG	1 cut(s)	794
Bst4CI	ACNGT	4 cut(s)	37, 94, 121, 804
Bst6I	CTCTTC	1 cut(s)	592
BstAFI	CTTAAG	1 cut(s)	848
BstAPI	GCANNNNNTGC	1 cut(s)	143
BstBAI	YACGTR	1 cut(s)	449
BstC8I	GCNNGC	3 cut(s)	865, 869, 993
BstDEI	CTNAG	2 cut(s)	879, 980
BstF5I	GGATG	3 cut(s)	351, 474, 950
BstKTI	GATC	5 cut(s)	110, 242, 454, 501, 757
BstMAI	GTCTC	1 cut(s)	48
BstMBI	GATC	5 cut(s)	107, 239, 451, 498, 754
BstMWI	GCNNNNNNNGC	2 cut(s)	143, 850
BstNI	CCWGG	1 cut(s)	794
BstNSI	RCATGY	1 cut(s)	867
BstSCI	CCNGG	2 cut(s)	715, 792
BstSFI	CTRYAG	1 cut(s)	971
BstSLI	GKGCMC	2 cut(s)	493, 793
BstV1I	GCAGC	3 cut(s)	557, 809, 982
BstX2I	RGATCY	1 cut(s)	498
BstXI	CCANNNNNNTGG	1 cut(s)	485
BstYI	RGATCY	1 cut(s)	498
BstZ17I	GTATAC	1 cut(s)	78
BsuRI	GGCC	2 cut(s)	180, 720
BtsCI	GGATG	3 cut(s)	351, 474, 950
BtsI	GCAGTG	1 cut(s)	60
BtsIMutI	CAGTG	3 cut(s)	33, 60, 535
Cac8I	GCNNGC	3 cut(s)	865, 869, 993
Csp6I	GTAC	2 cut(s)	187, 856
CviAII	CATG	8 cut(s)	224, 229, 567, 676, 704, 859, 864, 1000
CviQI	GTAC	2 cut(s)	187, 856
DdeI	CTNAG	2 cut(s)	879, 980
DpnI	GATC	5 cut(s)	109, 241, 453, 500, 756
DpnII	GATC	5 cut(s)	107, 239, 451, 498, 754
EaeI	YGGCCR	1 cut(s)	718
Eam1104I	CTCTTC	1 cut(s)	592
EarI	CTCTTC	1 cut(s)	592
Ecl136II	GAGCTC	1 cut(s)	406
Eco130I	CCWWGG	2 cut(s)	649, 813
Eco147I	AGGCCT	1 cut(s)	180
Eco24I	GRGCYC	1 cut(s)	408
Eco53kI	GAGCTC	1 cut(s)	406
Eco72I	CACGTG	1 cut(s)	449
Eco88I	CYCGRG	2 cut(s)	210, 957
EcoICRI	GAGCTC	1 cut(s)	406
EcoRII	CCWGG	1 cut(s)	792
EcoT14I	CCWWGG	2 cut(s)	649, 813
EcoT38I	GRGCYC	1 cut(s)	408
ErhI	CCWWGG	2 cut(s)	649, 813
FaeI	CATG	8 cut(s)	227, 232, 570, 679, 707, 862, 867, 1003
FatI	CATG	8 cut(s)	223, 228, 566, 675, 703, 858, 863, 999
FbaI	TGATCA	1 cut(s)	451
FblI	GTMKAC	1 cut(s)	77
Fnu4HI	GCNGC	3 cut(s)	571, 823, 996
FokI	GGATG	3 cut(s)	358, 461, 937
FriOI	GRGCYC	1 cut(s)	408
Fsp4HI	GCNGC	3 cut(s)	571, 823, 996
FspBI	CTAG	2 cut(s)	650, 749
GluI	GCNGC	3 cut(s)	571, 823, 996
GsuI	CTGGAG	2 cut(s)	30, 89
HaeIII	GGCC	2 cut(s)	180, 720
HapII	CCGG	3 cut(s)	81, 427, 717
Hin1II	CATG	8 cut(s)	227, 232, 570, 679, 707, 862, 867, 1003
HindIII	AAGCTT	1 cut(s)	398
HinfI	GANTC	6 cut(s)	41, 194, 279, 874, 919, 937
HpaII	CCGG	3 cut(s)	81, 427, 717
HphI	GGTGA	1 cut(s)	876
Hpy166II	GTNNAC	3 cut(s)	16, 78, 446
Hpy188I	TCNGA	5 cut(s)	204, 325, 415, 498, 529
Hpy8I	GTNNAC	3 cut(s)	16, 78, 446
HpyAV	CCTTC	1 cut(s)	80
HpyCH4III	ACNGT	4 cut(s)	37, 94, 121, 804
HpyCH4IV	ACGT	1 cut(s)	448
HpyCH4V	TGCA	6 cut(s)	137, 364, 573, 867, 973, 1003
HpyF10VI	GCNNNNNNNGC	2 cut(s)	143, 850
HpyF3I	CTNAG	2 cut(s)	879, 980
HpySE526I	ACGT	1 cut(s)	448
Hsp92II	CATG	8 cut(s)	227, 232, 570, 679, 707, 862, 867, 1003
Kpn2I	TCCGGA	1 cut(s)	426
Ksp22I	TGATCA	1 cut(s)	451
Kzo9I	GATC	5 cut(s)	107, 239, 451, 498, 754
LmnI	GCTCC	2 cut(s)	411, 646
Lsp1109I	GCAGC	3 cut(s)	557, 809, 982
LweI	GCATC	1 cut(s)	582
MaeI	CTAG	2 cut(s)	650, 749
MaeII	ACGT	1 cut(s)	448
MaeIII	GTNAC	4 cut(s)	55, 262, 334, 882
MalI	GATC	5 cut(s)	109, 241, 453, 500, 756
MboI	GATC	5 cut(s)	107, 239, 451, 498, 754
MboII	GAAGA	4 cut(s)	461, 579, 928, 959
MfeI	CAATTG	1 cut(s)	132
MflI	RGATCY	1 cut(s)	498
MhlI	GDGCHC	3 cut(s)	408, 493, 793
MluCI	AATT	9 cut(s)	62, 125, 132, 358, 517, 616, 688, 771, 1004
MlyI	GAGTC	2 cut(s)	50, 203
MnlI	CCTC	9 cut(s)	64, 247, 286, 504, 595, 888, 906, 953, 958
MroI	TCCGGA	1 cut(s)	426
MseI	TTAA	2 cut(s)	611, 849
MspCI	CTTAAG	1 cut(s)	848
MspI	CCGG	3 cut(s)	81, 427, 717
MspR9I	CCNGG	2 cut(s)	717, 794
MunI	CAATTG	1 cut(s)	132
Mva1269I	GAATGC	1 cut(s)	963
MvaI	CCWGG	1 cut(s)	794
MwoI	GCNNNNNNNGC	2 cut(s)	143, 850
NciI	CCSGG	1 cut(s)	717
NdeII	GATC	5 cut(s)	107, 239, 451, 498, 754
NlaIII	CATG	8 cut(s)	227, 232, 570, 679, 707, 862, 867, 1003
NlaIV	GGNNCC	3 cut(s)	234, 490, 642
NmuCI	GTSAC	4 cut(s)	55, 262, 334, 882
NspI	RCATGY	1 cut(s)	867
PaeI	GCATGC	1 cut(s)	867
PaeR7I	CTCGAG	1 cut(s)	210
PceI	AGGCCT	1 cut(s)	180
PctI	GAATGC	1 cut(s)	963
PfeI	GAWTC	4 cut(s)	279, 874, 919, 937
PkrI	GCNGC	3 cut(s)	572, 824, 997
PleI	GAGTC	2 cut(s)	49, 202
PmaCI	CACGTG	1 cut(s)	449
PmlI	CACGTG	1 cut(s)	449
PpsI	GAGTC	2 cut(s)	49, 202
Ppu21I	YACGTR	1 cut(s)	449
PsiI	TTATAA	1 cut(s)	744
Psp124BI	GAGCTC	1 cut(s)	408
Psp6I	CCWGG	1 cut(s)	792
PspCI	CACGTG	1 cut(s)	449
PspGI	CCWGG	1 cut(s)	792
PspN4I	GGNNCC	3 cut(s)	234, 490, 642
PstI	CTGCAG	1 cut(s)	975
PsuI	RGATCY	1 cut(s)	498
RsaI	GTAC	2 cut(s)	188, 857
RsaNI	GTAC	2 cut(s)	187, 856
SacI	GAGCTC	1 cut(s)	408
SaqAI	TTAA	2 cut(s)	611, 849
SatI	GCNGC	3 cut(s)	571, 823, 996
Sau3AI	GATC	5 cut(s)	107, 239, 451, 498, 754
SchI	GAGTC	2 cut(s)	50, 203
ScrFI	CCNGG	2 cut(s)	717, 794
SduI	GDGCHC	3 cut(s)	408, 493, 793
SfaNI	GCATC	1 cut(s)	582
SfcI	CTRYAG	1 cut(s)	971
Sfr274I	CTCGAG	1 cut(s)	210
SlaI	CTCGAG	1 cut(s)	210
SmlI	CTYRAG	4 cut(s)	210, 401, 848, 910
SmoI	CTYRAG	4 cut(s)	210, 401, 848, 910
SphI	GCATGC	1 cut(s)	867
Sse9I	AATT	9 cut(s)	62, 125, 132, 358, 517, 616, 688, 771, 1004
SseBI	AGGCCT	1 cut(s)	180
SsiI	CCGC	1 cut(s)	871
SspMI	CTAG	2 cut(s)	650, 749
SstI	GAGCTC	1 cut(s)	408
StuI	AGGCCT	1 cut(s)	180
StyD4I	CCNGG	2 cut(s)	715, 792
StyI	CCWWGG	2 cut(s)	649, 813
TaaI	ACNGT	4 cut(s)	37, 94, 121, 804
TaiI	ACGT	1 cut(s)	451
TaqI	TCGA	3 cut(s)	211, 544, 576
TasI	AATT	9 cut(s)	62, 125, 132, 358, 517, 616, 688, 771, 1004
TatI	WGTACW	1 cut(s)	855
TfiI	GAWTC	4 cut(s)	279, 874, 919, 937
Tru1I	TTAA	2 cut(s)	611, 849
Tru9I	TTAA	2 cut(s)	611, 849
TscAI	CASTG	3 cut(s)	40, 60, 542
TseFI	GTSAC	4 cut(s)	55, 262, 334, 882
TseI	GCWGC	3 cut(s)	570, 822, 995
Tsp45I	GTSAC	4 cut(s)	55, 262, 334, 882
TspDTI	ATGAA	2 cut(s)	681, 843
TspGWI	ACGGA	2 cut(s)	204, 367
TspRI	CASTG	3 cut(s)	40, 60, 542
Vha464I	CTTAAG	1 cut(s)	848
XapI	RAATTY	5 cut(s)	62, 358, 517, 616, 688
XceI	RCATGY	1 cut(s)	867
XhoI	CTCGAG	1 cut(s)	210
XmaJI	CCTAGG	1 cut(s)	649
XmiI	GTMKAC	1 cut(s)	77
XspI	CTAG	2 cut(s)	650, 749

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