Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0001141

Physical Location & Seq

Genomic Coordinates Reverse (-)

34858534 .. 34869363

Gene Structure 10830 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG276400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1161 bp

ATGAACCCCCGATCGAACGAGAAAATTACCACCGTGGCACCACTCCGCCTGCCAGAAATGAAAAAATCGGTGGACGCCGTGGAGCGGATCCTAGACTATGACTTCAAGAACAAGATGCTTCTAGAGGAAGCTCTCATCCACCCCTCCTGCCGAATAAGCGACGCCGTTTGGTATCAGCGGCTCGCGTTCCTCGGCGACACCGTTCTTGACCTCGCTGTAAGTAAAGACCTCTTCCTTGCTTACCCTGTAATTGACCAAGGCGACCTCACTCGGCTACGCTCCGCTAACGTCAGCAACGAGAAGTTCGCACGTGTGGCTGTGAGACATGGGCTTTATAACTACCTTCGCTGCACTGCAACTCGTCCTCTCGATGATCAGGTTAGGGAGTTTACTGAAGCTATAAGACGAGAAGAGGAGAAGACGCCTGTATTTGGACGGTCTGTAGAAGCCCCTAAAGTTCTTGCAGATATTGTGGAGTCTGTGGCTGGTGCTATTTATTTTGACTTGAATTTTGATCTGGAACTACTTTGGATGAAATTTAAGCATGTTTTGGAGCCTATAGTTACTCTTGAAGAGTTGCAGCAACAAACTCATCCTGTGACAGAGTTGCAGCAACAACCTCGTCCTGTAACAGAGTTGCAGCAACAACCTCGTCCTCAACAACCTTATCCTGTTCAACAACCTCATCCTGTGACAGAGTTGCATCAACTTTGCCAGAAGCAGGGGAAGAATGTCAGTATCGAGTACGGGAGAGGTAAGATGAAGAGTAATATTGATGGGAAGTGTGTTGCCTTGGGTTCGGCTGAACAGAAAGGAAGTGCTATAGTCAATGCTGCTGAGATGGCTCTGAGGAAGTTGATTTATGATGCGCTGGTTGAAGTTATTGCTGAAATCGATCAGCCATTTTCTGTTAAAAAAGCAAAAGATGAGTTGCATAAGATTTGTGTCGAGAAGAGGTGGCCTCAACCAATTTACACCATTGAGCATGAAGAAGGTCCTCCACATGATAAGATGTTTAAATCGATGGTAACTATAGGTCTGGTATATATGATTGGAAATGCAAAGTCAAGAGTAAAAGATGCGGAGAACTCTGCAGCTTTTCTAATGATCCGCTCATTGCAAGACCCTAAAAATGTACGTATGAAACACCTCTGTGCCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0004521 GO:0004525 GO:0004540 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016442 GO:0016458 GO:0016787 GO:0016788 GO:0016891 GO:0016893 GO:0019222 GO:0030422 GO:0031047 GO:0031050 GO:0031332 GO:0032296 GO:0032991 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043331 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0060255 GO:0065007 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:0090305 GO:0090501 GO:0090502 GO:0097159 GO:0140098 GO:1901360 GO:1901363 GO:1901698 GO:1901699 GO:1990904

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DND1_DSRM Ribonuclease_3 dsrm

Protein Analysis

386

Amino Acids

44.02

Weight (kDa)

7.14

Isoelectric Point (pI)

54.77

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ribonucleas_3_3	PF14622	37 - 169	2.9e-16	Ribonuclease-III-like
Ribonuclease_3	PF00636	59 - 168	3.9e-23	Ribonuclease III domain
DND1_DSRM	PF14709	306 - 373	1.1e-07	double strand RNA binding domain from DEAD END PROTEIN 1
dsrm	PF00035	307 - 373	6.7e-13	Double-stranded RNA binding motif

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

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Publication-ready

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Orthologous Genes (Group: OG0001141)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G20420
fragaria_vesca	FvH4_3g23250
malus_domestica	MD03G1196200.v1.1 MD11G1212500.v1.1
prunus_persica	Prupe.4G219200_v2.0.a1 Prupe.4G219200_v2.0.a1 Prupe.4G219400_v2.0.a1 Prupe.4G219400_v2.0.a1
pyrus_communis	pycom03g14830 pycom11g18750
rosa_chinensis	RchiOBHm_Chr5g0040511 RchiOBHm_Chr5g0040931 RchiOBHm_Chr5g0040941
rosa_laevigata	RLG00000033986 RLG00000034014 RLG00000034016 RLG00000034026
rosa_multiflora	Rmu_co8051550.1_g000001 Rmu_co8392905.1_g000001 Rmu_sc0002475.1_g000019 Rmu_sc0002848.1_g000007 Rmu_sc0006651.1_g000007 Rmu_sc0006651.1_g000008 Rmu_sc0008620.1_g000001
rosa_roxburghii	Rroxscaffold_1G00039580 Rroxscaffold_1G00039750 Rroxscaffold_1G00039760 Rroxscaffold_1G00040130 Rroxscaffold_1G00040850
rosa_rugosa	Rorug02G0350900 Rorug02G0350900 Rorug02G0351000 Rorug05G0185500 Rorug05G0188700 Rorug05G0188900 Rorug05G0188900
rosa_samantha	Rh2AG398700 Rh2BG409100 Rh2CG385500 Rh2CG540800 Rh2DG418900 Rh5AG272400 Rh5AG274300 Rh5AG274400 Rh5AG344200 Rh5BG276400 Rh5BG279300 Rh5BG279400 Rh5CG308900 Rh5CG311400 Rh5CG311600 Rh5DG284900 Rh5DG287500
rosa_wichuraiana	Rw2G032480 Rw5G025510 Rw5G025770 Rw5G025780 Rw5G025790

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	336
AccB1I	GGYRCC	1 cut(s)	37
AccBSI	CCGCTC	2 cut(s)	85, 1113
AccII	CGCG	1 cut(s)	185
AciI	CCGC	6 cut(s)	46, 85, 178, 282, 1082, 1111
AclWI	GGATC	3 cut(s)	82, 95, 1102
AcsI	RAATTY	2 cut(s)	508, 536
AcuI	CTGAAG	1 cut(s)	414
AcvI	CACGTG	1 cut(s)	311
AcyI	GRCGYC	3 cut(s)	75, 162, 422
AfaI	GTAC	2 cut(s)	746, 1137
AfiI	CCNNNNNNNGG	3 cut(s)	84, 431, 721
AflIII	ACRYGT	1 cut(s)	310
AgsI	TTSAA	5 cut(s)	106, 508, 572, 677, 878
AleI	CACNNNNGTG	1 cut(s)	1152
AluBI	AGCT	3 cut(s)	131, 398, 1097
AluI	AGCT	3 cut(s)	131, 398, 1097
Alw26I	GTCTC	1 cut(s)	316
AlwI	GGATC	3 cut(s)	82, 95, 1102
AoxI	GGCC	1 cut(s)	959
ApeKI	GCWGC	6 cut(s)	348, 580, 610, 640, 833, 1094
ApoI	RAATTY	2 cut(s)	508, 536
ArsI	GACNNNNNNTTYG	2 cut(s)	494, 526
AspLEI	GCGC	1 cut(s)	871
AspS9I	GGNCC	1 cut(s)	995
AvaII	GGWCC	1 cut(s)	995
BamHI	GGATCC	1 cut(s)	87
BanI	GGYRCC	1 cut(s)	37
BbrPI	CACGTG	1 cut(s)	311
BbsI	GAAGAC	1 cut(s)	425
BbvI	GCAGC	6 cut(s)	335, 592, 622, 652, 820, 1106
BccI	CCATC	3 cut(s)	770, 835, 1018
BceAI	ACGGC	2 cut(s)	62, 149
BcgI	CGANNNNNNTGC	4 cut(s)	602, 632, 636, 666
BclI	TGATCA	1 cut(s)	373
BcoDI	GTCTC	1 cut(s)	316
BfaI	CTAG	2 cut(s)	92, 122
BfmI	CTRYAG	5 cut(s)	441, 558, 822, 1032, 1092
BisI	GCNGC	7 cut(s)	179, 349, 581, 611, 641, 834, 1095
BlsI	GCNGC	7 cut(s)	180, 350, 582, 612, 642, 835, 1096
Bme18I	GGWCC	1 cut(s)	995
BmgT120I	GGNCC	1 cut(s)	995
BmiI	GGNNCC	3 cut(s)	39, 89, 555
BmsI	GCATC	4 cut(s)	105, 712, 856, 1069
BpiI	GAAGAC	1 cut(s)	425
BplI	GAGNNNNNCTC	2 cut(s)	946, 978
Bsa29I	ATCGAT	2 cut(s)	894, 1022
BsaAI	YACGTR	2 cut(s)	311, 1139
BsaHI	GRCGYC	3 cut(s)	75, 162, 422
BsaJI	CCNNGG	5 cut(s)	33, 78, 190, 256, 792
Bsc4I	CCNNNNNNNGG	3 cut(s)	84, 431, 721
Bse3DI	GCAATG	1 cut(s)	1115
BseCI	ATCGAT	2 cut(s)	894, 1022
BseDI	CCNNGG	5 cut(s)	33, 78, 190, 256, 792
BseGI	GGATG	4 cut(s)	135, 537, 592, 685
BseLI	CCNNNNNNNGG	3 cut(s)	84, 431, 721
BseMI	GCAATG	1 cut(s)	1115
BseMII	CTCAG	2 cut(s)	828, 839
BseRI	GAGGAG	1 cut(s)	428
BseXI	GCAGC	6 cut(s)	335, 592, 622, 652, 820, 1106
BsgI	GTGCAG	1 cut(s)	334
Bsh1236I	CGCG	1 cut(s)	185
Bsh1285I	CGRYCG	1 cut(s)	14
BshFI	GGCC	1 cut(s)	961
BshNI	GGYRCC	1 cut(s)	37
BshVI	ATCGAT	2 cut(s)	894, 1022
BsiEI	CGRYCG	1 cut(s)	14
BslI	CCNNNNNNNGG	3 cut(s)	84, 431, 721
BsmAI	GTCTC	1 cut(s)	316
BsnI	GGCC	1 cut(s)	961
Bsp143I	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
BspACI	CCGC	6 cut(s)	46, 85, 178, 282, 1082, 1111
BspANI	GGCC	1 cut(s)	961
BspCNI	CTCAG	2 cut(s)	829, 840
BspDI	ATCGAT	2 cut(s)	894, 1022
BspFNI	CGCG	1 cut(s)	185
BspLI	GGNNCC	3 cut(s)	39, 89, 555
BspMAI	CTGCAG	1 cut(s)	1096
BspPI	GGATC	3 cut(s)	82, 95, 1102
BspT107I	GGYRCC	1 cut(s)	37
BsrBI	CCGCTC	2 cut(s)	85, 1113
BsrDI	GCAATG	1 cut(s)	1115
BssECI	CCNNGG	5 cut(s)	33, 78, 190, 256, 792
BssMI	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
BssNI	GRCGYC	3 cut(s)	75, 162, 422
BssT1I	CCWWGG	2 cut(s)	256, 792
Bst4CI	ACNGT	3 cut(s)	34, 202, 438
Bst6I	CTCTTC	5 cut(s)	236, 405, 567, 758, 947
BstACI	GRCGYC	3 cut(s)	75, 162, 422
BstBAI	YACGTR	2 cut(s)	311, 1139
BstC8I	GCNNGC	2 cut(s)	50, 183
BstDEI	CTNAG	2 cut(s)	837, 848
BstDSI	CCRYGG	2 cut(s)	33, 78
BstF5I	GGATG	4 cut(s)	135, 537, 592, 685
BstFNI	CGCG	1 cut(s)	185
BstHHI	GCGC	1 cut(s)	871
BstKTI	GATC	6 cut(s)	14, 90, 376, 517, 898, 1110
BstMAI	GTCTC	1 cut(s)	316
BstMBI	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
BstMCI	CGRYCG	1 cut(s)	14
BstMWI	GCNNNNNNNGC	3 cut(s)	156, 314, 842
BstNSI	RCATGY	1 cut(s)	548
BstSFI	CTRYAG	5 cut(s)	441, 558, 822, 1032, 1092
BstSNI	TACGTA	1 cut(s)	1139
BstUI	CGCG	1 cut(s)	185
BstV1I	GCAGC	6 cut(s)	335, 592, 622, 652, 820, 1106
BstV2I	GAAGAC	1 cut(s)	425
BstX2I	RGATCY	1 cut(s)	87
BstYI	RGATCY	1 cut(s)	87
Bsu15I	ATCGAT	2 cut(s)	894, 1022
BsuRI	GGCC	1 cut(s)	961
BsuTUI	ATCGAT	2 cut(s)	894, 1022
BtgI	CCRYGG	2 cut(s)	33, 78
BtsCI	GGATG	4 cut(s)	135, 537, 592, 685
BtsI	GCAGTG	1 cut(s)	351
BtsIMutI	CAGTG	1 cut(s)	351
Cac8I	GCNNGC	2 cut(s)	50, 183
CfoI	GCGC	1 cut(s)	871
Cfr13I	GGNCC	1 cut(s)	995
ClaI	ATCGAT	2 cut(s)	894, 1022
CseI	GACGC	3 cut(s)	83, 170, 430
Csp6I	GTAC	2 cut(s)	745, 1136
CviAII	CATG	4 cut(s)	326, 545, 986, 1004
CviQI	GTAC	2 cut(s)	745, 1136
DdeI	CTNAG	2 cut(s)	837, 848
DpnI	GATC	6 cut(s)	13, 89, 375, 516, 897, 1109
DpnII	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
DraI	TTTAAA	1 cut(s)	1018
Eam1104I	CTCTTC	5 cut(s)	236, 405, 567, 758, 947
EarI	CTCTTC	5 cut(s)	236, 405, 567, 758, 947
EciI	GGCGGA	1 cut(s)	35
Eco105I	TACGTA	1 cut(s)	1139
Eco130I	CCWWGG	2 cut(s)	256, 792
Eco47I	GGWCC	1 cut(s)	995
Eco57I	CTGAAG	1 cut(s)	414
Eco72I	CACGTG	1 cut(s)	311
EcoO109I	RGGNCCY	1 cut(s)	995
EcoT14I	CCWWGG	2 cut(s)	256, 792
ErhI	CCWWGG	2 cut(s)	256, 792
FaeI	CATG	4 cut(s)	329, 548, 989, 1007
FatI	CATG	4 cut(s)	325, 544, 985, 1003
FbaI	TGATCA	1 cut(s)	373
Fnu4HI	GCNGC	7 cut(s)	179, 349, 581, 611, 641, 834, 1095
FokI	GGATG	4 cut(s)	122, 544, 579, 672
Fsp4HI	GCNGC	7 cut(s)	179, 349, 581, 611, 641, 834, 1095
FspBI	CTAG	2 cut(s)	92, 122
GlaI	GCGC	1 cut(s)	870
GluI	GCNGC	7 cut(s)	179, 349, 581, 611, 641, 834, 1095
HaeIII	GGCC	1 cut(s)	961
HgaI	GACGC	3 cut(s)	83, 170, 430
HhaI	GCGC	1 cut(s)	871
Hin1I	GRCGYC	3 cut(s)	75, 162, 422
Hin1II	CATG	4 cut(s)	329, 548, 989, 1007
Hin6I	GCGC	1 cut(s)	869
HinP1I	GCGC	1 cut(s)	869
HinfI	GANTC	1 cut(s)	476
Hpy166II	GTNNAC	2 cut(s)	73, 390
Hpy188I	TCNGA	1 cut(s)	849
Hpy188III	TCNNGA	8 cut(s)	106, 122, 206, 368, 518, 569, 949, 1068
Hpy8I	GTNNAC	2 cut(s)	73, 390
Hpy99I	CGWCG	1 cut(s)	164
HpyAV	CCTTC	2 cut(s)	353, 986
HpyCH4III	ACNGT	3 cut(s)	34, 202, 438
HpyCH4IV	ACGT	3 cut(s)	288, 310, 1138
HpyF10VI	GCNNNNNNNGC	3 cut(s)	156, 314, 842
HpyF3I	CTNAG	2 cut(s)	837, 848
HpySE526I	ACGT	3 cut(s)	288, 310, 1138
Hsp92I	GRCGYC	3 cut(s)	75, 162, 422
Hsp92II	CATG	4 cut(s)	329, 548, 989, 1007
HspAI	GCGC	1 cut(s)	869
Ksp22I	TGATCA	1 cut(s)	373
Kzo9I	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
LmnI	GCTCC	3 cut(s)	82, 284, 553
Lsp1109I	GCAGC	6 cut(s)	335, 592, 622, 652, 820, 1106
LweI	GCATC	4 cut(s)	105, 712, 856, 1069
MaeI	CTAG	2 cut(s)	92, 122
MaeII	ACGT	3 cut(s)	288, 310, 1138
MaeIII	GTNAC	5 cut(s)	562, 598, 628, 691, 1027
MalI	GATC	6 cut(s)	13, 89, 375, 516, 897, 1109
MbiI	CCGCTC	2 cut(s)	85, 1113
MboI	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
MboII	GAAGA	8 cut(s)	223, 422, 430, 584, 739, 775, 964, 1001
MflI	RGATCY	1 cut(s)	87
MluCI	AATT	5 cut(s)	24, 249, 508, 536, 969
MlyI	GAGTC	1 cut(s)	485
MseI	TTAA	3 cut(s)	540, 912, 1017
MslI	CAYNNNNRTG	1 cut(s)	1152
MspA1I	CMGCKG	1 cut(s)	178
MvnI	CGCG	1 cut(s)	185
MwoI	GCNNNNNNNGC	3 cut(s)	156, 314, 842
NdeII	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
NlaIII	CATG	4 cut(s)	329, 548, 989, 1007
NlaIV	GGNNCC	3 cut(s)	39, 89, 555
NmeAIII	GCCGAG	2 cut(s)	171, 250
NmuCI	GTSAC	2 cut(s)	598, 691
NspI	RCATGY	1 cut(s)	548
OliI	CACNNNNGTG	1 cut(s)	1152
PcsI	WCGNNNNNNNCGW	2 cut(s)	198, 294
PkrI	GCNGC	7 cut(s)	180, 350, 582, 612, 642, 835, 1096
Ple19I	CGATCG	1 cut(s)	14
PleI	GAGTC	1 cut(s)	484
PmaCI	CACGTG	1 cut(s)	311
PmlI	CACGTG	1 cut(s)	311
PpsI	GAGTC	1 cut(s)	484
Ppu21I	YACGTR	2 cut(s)	311, 1139
PpuMI	RGGWCCY	1 cut(s)	995
PsiI	TTATAA	1 cut(s)	336
Psp5II	RGGWCCY	1 cut(s)	995
PspCI	CACGTG	1 cut(s)	311
PspN4I	GGNNCC	3 cut(s)	39, 89, 555
PspPI	GGNCC	1 cut(s)	995
PspPPI	RGGWCCY	1 cut(s)	995
PstI	CTGCAG	1 cut(s)	1096
PsuI	RGATCY	1 cut(s)	87
PvuI	CGATCG	1 cut(s)	14
RsaI	GTAC	2 cut(s)	746, 1137
RsaNI	GTAC	2 cut(s)	745, 1136
RseI	CAYNNNNRTG	1 cut(s)	1152
SaqAI	TTAA	3 cut(s)	540, 912, 1017
SatI	GCNGC	7 cut(s)	179, 349, 581, 611, 641, 834, 1095
Sau3AI	GATC	6 cut(s)	11, 87, 373, 514, 895, 1107
Sau96I	GGNCC	1 cut(s)	995
SchI	GAGTC	1 cut(s)	485
SfaNI	GCATC	4 cut(s)	105, 712, 856, 1069
SfcI	CTRYAG	5 cut(s)	441, 558, 822, 1032, 1092
SinI	GGWCC	1 cut(s)	995
SmiMI	CAYNNNNRTG	1 cut(s)	1152
SnaBI	TACGTA	1 cut(s)	1139
Sse9I	AATT	5 cut(s)	24, 249, 508, 536, 969
SsiI	CCGC	6 cut(s)	46, 85, 178, 282, 1082, 1111
SspI	AATATT	1 cut(s)	772
SspMI	CTAG	2 cut(s)	92, 122
StyI	CCWWGG	2 cut(s)	256, 792
TaaI	ACNGT	3 cut(s)	34, 202, 438
TaiI	ACGT	3 cut(s)	291, 313, 1141
TaqI	TCGA	6 cut(s)	14, 369, 741, 894, 948, 1022
TasI	AATT	5 cut(s)	24, 249, 508, 536, 969
TauI	GCSGC	1 cut(s)	181
Tru1I	TTAA	3 cut(s)	540, 912, 1017
Tru9I	TTAA	3 cut(s)	540, 912, 1017
TscAI	CASTG	1 cut(s)	358
TseFI	GTSAC	2 cut(s)	598, 691
TseI	GCWGC	6 cut(s)	348, 580, 610, 640, 833, 1094
Tsp45I	GTSAC	2 cut(s)	598, 691
TspDTI	ATGAA	6 cut(s)	17, 74, 548, 776, 1002, 1157
TspRI	CASTG	1 cut(s)	358
VpaK11BI	GGWCC	1 cut(s)	995
XapI	RAATTY	2 cut(s)	508, 536
XbaI	TCTAGA	1 cut(s)	121
XceI	RCATGY	1 cut(s)	548
XspI	CTAG	2 cut(s)	92, 122

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