Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0001141

Physical Location & Seq

Genomic Coordinates Forward (+)

36729120 .. 36731282

Gene Structure 2163 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG274300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1098 bp

ATGAACCCTTACTTGAACATGAAAATCTTCACCCAAACACCACGCGACCTCCACGCACCACCACCACCCTCGCCGGAAATGAAACAAGCCGTGGCAGCCGTGGAGATGATCGTAAGCTACGCATTCAAGAACAAGAGGCTTCTAGAGGAGGCTCTCACCCACCCCTCCCATTCCGACGCTGTGTCGTATCAGCGGCTCGAGTTCGTCGGCGATGCCGTTCTTAGCCTCGCTGTAAGCAACTACCTTTTTCTTGCTTACCCTAGAATTGACCAAGGCAACCTCTCTATGCTACGCTCCGCTAACGTCAGTACCGAGAAGCTCGCACGTGTTTCCGTACGACACGGGCTTTTTCGCTTCCTTCGCCACTCTGCACCTGTTCTCGATGATAAGGTTAGGGAGTTTACTGAAGTTGTCAGTGGAGAAGAAGAGATGCCACTTGTATATAGAGGGTCTGTAAAAGCCCCAAAAGTTCTTGCAGATATTGTGGAGTCTGTTGCTGCTGCTATTTATGTTGATTTGAATTTCGATCTGGAAAAACTTTGGATGATCTTTAGGCATGTTTTGGAGCCTATAGTGACGCTCGAAGACTTGCAGCAACAACCTCAACCCGTGACAAAGTTGTTTGAGGTTTGCCAAAAGCATGGGAAGCATGTCGACATTAAGTATTGGAGGGATGAGACGAAAAGCATTGCGAGTGTGTATGTTGATGGCAAGTTTGTTGCCTCGGGTTCTTCTGAACAGAAAGAAGTTGCCAAGGTCAATGCTGCTGAGATAGCTCTATATAAGTTGTCGAAATTGATGCTCATAGATGATGTGTCGATTGAAGTTATTGCTGGAATTGATGGGTCATTTCATATTGAAGGAGCAAAACATAAGTTGCATGAGCTATGTGGAAAGAAGAAGTGGCCTAAACCAATCTACAACATCAAGCAAGACAAAGGTTTTTCACATGAGAAGAAGTTTGTATCGACAGTTCAAATTGCAACTATTGATGGTGTGCTTTGTATGACGGGAGATGAAATGTCGAGAGTAAAGGATGCAGAGAATTCTGCAGCATCTTTAATGATCCGTGCTTTGCAAGAGTCTGATTATGTATGA

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

365

Amino Acids

41.02

Weight (kDa)

6.47

Isoelectric Point (pI)

36.56

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ribonucleas_3_3	PF14622	44 - 175	4.6e-17	Ribonuclease-III-like
Ribonuclease_3	PF00636	64 - 172	1e-21	Ribonuclease III domain
dsrm	PF00035	203 - 263	1.4e-08	Double-stranded RNA binding motif
DND1_DSRM	PF14709	288 - 360	3.5e-13	double strand RNA binding domain from DEAD END PROTEIN 1
dsrm	PF00035	289 - 359	5.8e-12	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

Tree File

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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)
AccI	GTMKAC	1 cut(s)	654
AccII	CGCG	1 cut(s)	45
AciI	CCGC	2 cut(s)	193, 297
AclWI	GGATC	1 cut(s)	1060
AcsI	RAATTY	2 cut(s)	520, 1045
AcuI	CTGAAG	1 cut(s)	426
AcvI	CACGTG	1 cut(s)	326
AfaI	GTAC	2 cut(s)	310, 336
AflIII	ACRYGT	1 cut(s)	325
AgsI	TTSAA	6 cut(s)	16, 127, 520, 824, 860, 977
AhdI	GACNNNNNGTC	1 cut(s)	181
AluBI	AGCT	4 cut(s)	117, 319, 776, 886
AluI	AGCT	4 cut(s)	117, 319, 776, 886
Alw26I	GTCTC	1 cut(s)	671
AlwI	GGATC	1 cut(s)	1060
Ama87I	CYCGRG	2 cut(s)	197, 724
AoxI	GGCC	1 cut(s)	905
ApeKI	GCWGC	6 cut(s)	95, 497, 500, 592, 764, 1052
ApoI	RAATTY	2 cut(s)	520, 1045
Asp700I	GAANNNNTTC	1 cut(s)	26
AsuHPI	GGTGA	2 cut(s)	22, 148
AvaI	CYCGRG	2 cut(s)	197, 724
BaeI	ACNNNNGTAYC	2 cut(s)	292, 325
BbrPI	CACGTG	1 cut(s)	326
BbsI	GAAGAC	1 cut(s)	591
BbvI	GCAGC	6 cut(s)	107, 484, 487, 604, 751, 1064
BccI	CCATC	3 cut(s)	701, 836, 986
BceAI	ACGGC	3 cut(s)	74, 83, 200
BcgI	CGANNNNNNTGC	2 cut(s)	781, 815
BcoDI	GTCTC	1 cut(s)	671
BfaI	CTAG	2 cut(s)	143, 261
BfmI	CTRYAG	2 cut(s)	570, 1050
BisI	GCNGC	7 cut(s)	96, 194, 498, 501, 593, 765, 1053
BlsI	GCNGC	7 cut(s)	97, 195, 499, 502, 594, 766, 1054
BmeRI	GACNNNNNGTC	1 cut(s)	181
BmeT110I	CYCGRG	2 cut(s)	197, 724
BmiI	GGNNCC	1 cut(s)	567
BmsI	GCATC	5 cut(s)	202, 420, 789, 1027, 1064
BpiI	GAAGAC	1 cut(s)	591
BsaAI	YACGTR	1 cut(s)	326
BsaJI	CCNNGG	5 cut(s)	90, 99, 271, 723, 753
BsaXI	ACNNNNNCTCC	2 cut(s)	33, 63
Bse3DI	GCAATG	1 cut(s)	687
BseDI	CCNNGG	5 cut(s)	90, 99, 271, 723, 753
BseGI	GGATG	3 cut(s)	549, 679, 1042
BseMI	GCAATG	1 cut(s)	687
BseMII	CTCAG	1 cut(s)	759
BseRI	GAGGAG	1 cut(s)	161
BseXI	GCAGC	6 cut(s)	107, 484, 487, 604, 751, 1064
BsgI	GTGCAG	1 cut(s)	354
Bsh1236I	CGCG	1 cut(s)	45
BshFI	GGCC	1 cut(s)	907
BsiHKCI	CYCGRG	2 cut(s)	197, 724
BsiSI	CCGG	1 cut(s)	74
BsiWI	CGTACG	1 cut(s)	334
BsmAI	GTCTC	1 cut(s)	671
BsmBI	CGTCTC	1 cut(s)	671
BsmI	GAATGC	1 cut(s)	122
BsnI	GGCC	1 cut(s)	907
BsoBI	CYCGRG	2 cut(s)	197, 724
Bsp143I	GATC	4 cut(s)	108, 526, 546, 1065
BspACI	CCGC	2 cut(s)	193, 297
BspANI	GGCC	1 cut(s)	907
BspCNI	CTCAG	1 cut(s)	760
BspFNI	CGCG	1 cut(s)	45
BspLI	GGNNCC	1 cut(s)	567
BspMAI	CTGCAG	1 cut(s)	1054
BspPI	GGATC	1 cut(s)	1060
BsrDI	GCAATG	1 cut(s)	687
BssECI	CCNNGG	5 cut(s)	90, 99, 271, 723, 753
BssMI	GATC	4 cut(s)	108, 526, 546, 1065
BssT1I	CCWWGG	2 cut(s)	271, 753
Bst4CI	ACNGT	1 cut(s)	973
Bst6I	CTCTTC	1 cut(s)	420
BstBAI	YACGTR	1 cut(s)	326
BstC8I	GCNNGC	1 cut(s)	321
BstDEI	CTNAG	2 cut(s)	221, 768
BstDSI	CCRYGG	2 cut(s)	90, 99
BstF5I	GGATG	3 cut(s)	549, 679, 1042
BstFNI	CGCG	1 cut(s)	45
BstKTI	GATC	4 cut(s)	111, 529, 549, 1068
BstMAI	GTCTC	1 cut(s)	671
BstMBI	GATC	4 cut(s)	108, 526, 546, 1065
BstMWI	GCNNNNNNNGC	4 cut(s)	95, 360, 646, 773
BstNSI	RCATGY	2 cut(s)	560, 653
BstSFI	CTRYAG	2 cut(s)	570, 1050
BstUI	CGCG	1 cut(s)	45
BstV1I	GCAGC	6 cut(s)	107, 484, 487, 604, 751, 1064
BstV2I	GAAGAC	1 cut(s)	591
BstXI	CCANNNNNNTGG	1 cut(s)	641
BsuRI	GGCC	1 cut(s)	907
BtgI	CCRYGG	2 cut(s)	90, 99
BtgZI	GCGATG	1 cut(s)	225
BtsCI	GGATG	3 cut(s)	549, 679, 1042
BtsIMutI	CAGTG	1 cut(s)	421
Cac8I	GCNNGC	1 cut(s)	321
CseI	GACGC	2 cut(s)	185, 586
Csp6I	GTAC	2 cut(s)	309, 335
CviAII	CATG	6 cut(s)	19, 557, 641, 650, 881, 950
CviQI	GTAC	2 cut(s)	309, 335
DdeI	CTNAG	2 cut(s)	221, 768
DpnI	GATC	4 cut(s)	110, 528, 548, 1067
DpnII	GATC	4 cut(s)	108, 526, 546, 1065
DriI	GACNNNNNGTC	1 cut(s)	181
Eam1104I	CTCTTC	1 cut(s)	420
Eam1105I	GACNNNNNGTC	1 cut(s)	181
EarI	CTCTTC	1 cut(s)	420
Eco130I	CCWWGG	2 cut(s)	271, 753
Eco57I	CTGAAG	1 cut(s)	426
Eco72I	CACGTG	1 cut(s)	326
Eco88I	CYCGRG	2 cut(s)	197, 724
EcoRI	GAATTC	1 cut(s)	1045
EcoT14I	CCWWGG	2 cut(s)	271, 753
ErhI	CCWWGG	2 cut(s)	271, 753
Esp3I	CGTCTC	1 cut(s)	671
FaeI	CATG	6 cut(s)	22, 560, 644, 653, 884, 953
FatI	CATG	6 cut(s)	18, 556, 640, 649, 880, 949
FblI	GTMKAC	1 cut(s)	654
Fnu4HI	GCNGC	7 cut(s)	96, 194, 498, 501, 593, 765, 1053
FokI	GGATG	3 cut(s)	556, 686, 1049
Fsp4HI	GCNGC	7 cut(s)	96, 194, 498, 501, 593, 765, 1053
FspBI	CTAG	2 cut(s)	143, 261
GluI	GCNGC	7 cut(s)	96, 194, 498, 501, 593, 765, 1053
HaeIII	GGCC	1 cut(s)	907
HapII	CCGG	1 cut(s)	74
HgaI	GACGC	2 cut(s)	185, 586
Hin1II	CATG	6 cut(s)	22, 560, 644, 653, 884, 953
HincII	GTYRAC	1 cut(s)	655
HindII	GTYRAC	1 cut(s)	655
HinfI	GANTC	2 cut(s)	488, 1082
HpaII	CCGG	1 cut(s)	74
HphI	GGTGA	2 cut(s)	22, 148
Hpy166II	GTNNAC	2 cut(s)	402, 655
Hpy188I	TCNGA	3 cut(s)	175, 736, 1087
Hpy188III	TCNNGA	5 cut(s)	127, 143, 380, 530, 1026
Hpy8I	GTNNAC	2 cut(s)	402, 655
Hpy99I	CGWCG	2 cut(s)	179, 209
HpyAV	CCTTC	2 cut(s)	368, 854
HpyCH4III	ACNGT	1 cut(s)	973
HpyCH4IV	ACGT	2 cut(s)	303, 325
HpyCH4V	TGCA	8 cut(s)	371, 476, 592, 880, 983, 1040, 1052, 1078
HpyF10VI	GCNNNNNNNGC	4 cut(s)	95, 360, 646, 773
HpyF3I	CTNAG	2 cut(s)	221, 768
HpySE526I	ACGT	2 cut(s)	303, 325
Hsp92II	CATG	6 cut(s)	22, 560, 644, 653, 884, 953
Kzo9I	GATC	4 cut(s)	108, 526, 546, 1065
LmnI	GCTCC	3 cut(s)	299, 565, 863
LpnPI	CCDG	4 cut(s)	87, 387, 515, 819
Lsp1109I	GCAGC	6 cut(s)	107, 484, 487, 604, 751, 1064
LweI	GCATC	5 cut(s)	202, 420, 789, 1027, 1064
MaeI	CTAG	2 cut(s)	143, 261
MaeII	ACGT	2 cut(s)	303, 325
MaeIII	GTNAC	2 cut(s)	574, 610
MalI	GATC	4 cut(s)	110, 528, 548, 1067
MboI	GATC	4 cut(s)	108, 526, 546, 1065
MboII	GAAGA	7 cut(s)	19, 434, 437, 596, 723, 910, 967
MluCI	AATT	6 cut(s)	264, 520, 794, 837, 978, 1045
MlyI	GAGTC	2 cut(s)	497, 1091
MmeI	TCCRAC	1 cut(s)	198
MroXI	GAANNNNTTC	1 cut(s)	26
MseI	TTAA	2 cut(s)	660, 1061
MspA1I	CMGCKG	1 cut(s)	193
MspI	CCGG	1 cut(s)	74
Mva1269I	GAATGC	1 cut(s)	122
MvnI	CGCG	1 cut(s)	45
MwoI	GCNNNNNNNGC	4 cut(s)	95, 360, 646, 773
NdeII	GATC	4 cut(s)	108, 526, 546, 1065
NlaIII	CATG	6 cut(s)	22, 560, 644, 653, 884, 953
NlaIV	GGNNCC	1 cut(s)	567
NmuCI	GTSAC	2 cut(s)	574, 610
NspI	RCATGY	2 cut(s)	560, 653
PaeR7I	CTCGAG	1 cut(s)	197
PcsI	WCGNNNNNNNCGW	2 cut(s)	213, 309
PctI	GAATGC	1 cut(s)	122
PdmI	GAANNNNTTC	1 cut(s)	26
Pfl23II	CGTACG	1 cut(s)	334
PkrI	GCNGC	7 cut(s)	97, 195, 499, 502, 594, 766, 1054
PleI	GAGTC	2 cut(s)	496, 1090
PmaCI	CACGTG	1 cut(s)	326
PmlI	CACGTG	1 cut(s)	326
PpsI	GAGTC	2 cut(s)	496, 1090
Ppu21I	YACGTR	1 cut(s)	326
PspCI	CACGTG	1 cut(s)	326
PspLI	CGTACG	1 cut(s)	334
PspN4I	GGNNCC	1 cut(s)	567
PspXI	VCTCGAGB	1 cut(s)	197
PsrI	GAACNNNNNNTAC	2 cut(s)	957, 989
PstI	CTGCAG	1 cut(s)	1054
RsaI	GTAC	2 cut(s)	310, 336
RsaNI	GTAC	2 cut(s)	309, 335
SalI	GTCGAC	1 cut(s)	653
SaqAI	TTAA	2 cut(s)	660, 1061
SatI	GCNGC	7 cut(s)	96, 194, 498, 501, 593, 765, 1053
Sau3AI	GATC	4 cut(s)	108, 526, 546, 1065
SchI	GAGTC	2 cut(s)	497, 1091
SfaNI	GCATC	5 cut(s)	202, 420, 789, 1027, 1064
SfcI	CTRYAG	2 cut(s)	570, 1050
Sfr274I	CTCGAG	1 cut(s)	197
SlaI	CTCGAG	1 cut(s)	197
SmlI	CTYRAG	1 cut(s)	197
SmoI	CTYRAG	1 cut(s)	197
Sse9I	AATT	6 cut(s)	264, 520, 794, 837, 978, 1045
SsiI	CCGC	2 cut(s)	193, 297
SspMI	CTAG	2 cut(s)	143, 261
StyI	CCWWGG	2 cut(s)	271, 753
TaaI	ACNGT	1 cut(s)	973
TaiI	ACGT	2 cut(s)	306, 328
TaqI	TCGA	9 cut(s)	198, 381, 525, 582, 654, 791, 818, 968, 1025
TasI	AATT	6 cut(s)	264, 520, 794, 837, 978, 1045
TauI	GCSGC	1 cut(s)	196
Tru1I	TTAA	2 cut(s)	660, 1061
Tru9I	TTAA	2 cut(s)	660, 1061
TscAI	CASTG	1 cut(s)	421
TseFI	GTSAC	2 cut(s)	574, 610
TseI	GCWGC	6 cut(s)	95, 497, 500, 592, 764, 1052
Tsp45I	GTSAC	2 cut(s)	574, 610
TspDTI	ATGAA	5 cut(s)	17, 35, 95, 842, 1032
TspGWI	ACGGA	2 cut(s)	322, 1058
TspRI	CASTG	1 cut(s)	421
XapI	RAATTY	2 cut(s)	520, 1045
XbaI	TCTAGA	1 cut(s)	142
XceI	RCATGY	2 cut(s)	560, 653
XhoI	CTCGAG	1 cut(s)	197
XmiI	GTMKAC	1 cut(s)	654
XmnI	GAANNNNTTC	1 cut(s)	26
XspI	CTAG	2 cut(s)	143, 261

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