Rh5DG050100

S1/P1 Nuclease

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0012928
Physical Location & Seq
Forward (+)
4218053 .. 4220142
2090 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG050100.1

Sequence Viewer

Length: 993 bp
ATGTCAATTAACCAGAGAAATTTCTTCCAGATGGATAGTTACAGAGGCTTTGGAAGATTTGCCAATTACTTTCGTGAATTTGTTTTGTTGCTTGCATTTGTTTGCATTTTAGTCCCGAGAGCTCAGGGATGGAGCAAAGAGGGTCACACCATGACGTGCCGGATTGCACAGGCACTCCTAGAGCCTGAAGCTGCAGAAGCTGTTAAAAATTTACTACCTCATGATGTCAATGGCGATCTGTCGGCTCTGTGTGTGTGGCCTGACCAGATCAGGCACTGGTACAGATACCGGTGGACTAGCCCTCTTCACTTCATTGACACCCCTGATAATGTTTGCAACTTTGAATACTCAAGAGATTGCCATGATGAACATGGTTCCAAGGACATGTGTGTTGCTGGTGCAGTCCAGAATTTCACATCGCAGCTTTCACACTACACAGAAGGAACATCTGACCGTCGATATAATATGACCGAGGCCTTGCTTTTCTTGTCACACTTTATGGGTGATCTCCATCAGCCAATGCATATTGGATTCACGACAGATAGAGGAGGAAACACAATAGACTTGCGGTGGTACAGGCACAAATCCAATCTCCACCATGTATGGGATCGAGAGATTTTACTTCAAGCTCTGCATGATTATTATGACAAGGACATGGAACTCCTCCTGCAAGACATACAGGGAAACATCACAGATGGAGTCTGGTCTGATGATGTTACATCATGGGGACATTGTGATGATATCAGTTCTTGTATAAACAAGTATGCTACAGAAAGTATAAACATAGCTTGCAAATGGGGTTACAAGGGCGTTGAGTCCGGTGATACTCTAACAGAGGATTACTTCCTTCCTCGGCTGCCTATTGTGGAGAAGAGGATTGCCCAAGGTGGAGTCCGGTTGGCTGCTATCCTCAATCGTGCCTTCTCCTCTGAATCTGAAGCACAACCTGCTGATCATCACAAAAACAAAAGAGCATCACATTCACCCACTTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
S1-P1_nuclease

Protein Analysis

330

Amino Acids

38.02

Weight (kDa)

5.88

Isoelectric Point (pI)

44.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
S1-P1_nuclease PF02265 44 - 308 2.1e-87 S1/P1 Nuclease
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0012928)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G11190
fragaria_vesca FvH4_3g04360 FvH4_3g04360
malus_domestica MD05G1323600.v1.1 MD10G1079400.v1.1 MD10G1301500.v1.1
prunus_persica Prupe.4G038900_v2.0.a1
pyrus_communis pycom10g25420
rosa_chinensis RchiOBHm_Chr5g0006751
rosa_laevigata RLG00000031425
rosa_multiflora Rmu_sc0001044.1_g000042
rosa_roxburghii Rroxscaffold_1G00069290
rosa_rugosa Rorug04G0424200
rosa_samantha Rh5AG052100 Rh5BG051000 Rh5CG059600 Rh5DG050100
rosa_wichuraiana Rw5G005240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 955
AciI CCGC 1 cut(s) 568
AclWI GGATC 1 cut(s) 615
AcsI RAATTY 4 cut(s) 19, 77, 208, 409
AcuI CTGAAG 2 cut(s) 207, 957
AfaI GTAC 2 cut(s) 281, 575
AfiI CCNNNNNNNGG 1 cut(s) 604
AflIII ACRYGT 1 cut(s) 384
AgeI ACCGGT 1 cut(s) 288
AgsI TTSAA 2 cut(s) 344, 626
AjiI CACGTC 1 cut(s) 156
AluBI AGCT 6 cut(s) 122, 191, 200, 424, 629, 788
AluI AGCT 6 cut(s) 122, 191, 200, 424, 629, 788
Alw21I GWGCWC 1 cut(s) 124
AlwI GGATC 1 cut(s) 615
AlwNI CAGNNNCTG 2 cut(s) 200, 276
Ama87I CYCGRG 1 cut(s) 115
AoxI GGCC 2 cut(s) 257, 474
ApeKI GCWGC 4 cut(s) 191, 421, 856, 902
ApoI RAATTY 4 cut(s) 19, 77, 208, 409
AsiGI ACCGGT 1 cut(s) 288
AsuHPI GGTGA 3 cut(s) 515, 833, 975
AvaI CYCGRG 1 cut(s) 115
BanII GRGCYC 1 cut(s) 124
Bbv12I GWGCWC 1 cut(s) 124
BbvI GCAGC 4 cut(s) 178, 433, 843, 889
BccI CCATC 4 cut(s) 25, 123, 519, 689
BclI TGATCA 1 cut(s) 952
BfaI CTAG 2 cut(s) 179, 297
BfmI CTRYAG 2 cut(s) 192, 768
BfuAI ACCTGC 1 cut(s) 955
BisI GCNGC 4 cut(s) 192, 422, 857, 903
BlsI GCNGC 4 cut(s) 193, 423, 858, 904
BmeT110I CYCGRG 1 cut(s) 115
BmgBI CACGTC 1 cut(s) 156
BmiI GGNNCC 1 cut(s) 376
BmsI GCATC 1 cut(s) 983
Bpu10I CCTNAGC 1 cut(s) 123
BpuEI CTTGAG 1 cut(s) 334
BsaBI GATNNNNATC 1 cut(s) 510
BsaJI CCNNGG 4 cut(s) 378, 471, 851, 883
BsaWI WCCGGW 3 cut(s) 288, 818, 894
BsaXI ACNNNNNCTCC 2 cut(s) 159, 189
Bsc4I CCNNNNNNNGG 1 cut(s) 604
Bse118I RCCGGY 1 cut(s) 288
Bse1I ACTGG 1 cut(s) 281
Bse8I GATNNNNATC 1 cut(s) 510
BseDI CCNNGG 4 cut(s) 378, 471, 851, 883
BseGI GGATG 1 cut(s) 134
BseJI GATNNNNATC 1 cut(s) 510
BseLI CCNNNNNNNGG 1 cut(s) 604
BseMII CTCAG 1 cut(s) 137
BseNI ACTGG 1 cut(s) 281
BseRI GAGGAG 3 cut(s) 561, 653, 916
BseXI GCAGC 4 cut(s) 178, 433, 843, 889
BsgI GTGCAG 1 cut(s) 420
BshFI GGCC 2 cut(s) 259, 476
BshTI ACCGGT 1 cut(s) 288
BsiHKAI GWGCWC 1 cut(s) 124
BsiHKCI CYCGRG 1 cut(s) 115
BsiSI CCGG 4 cut(s) 160, 289, 819, 895
BslFI GGGAC 2 cut(s) 98, 741
BslI CCNNNNNNNGG 1 cut(s) 604
BsmFI GGGAC 2 cut(s) 98, 741
BsnI GGCC 2 cut(s) 259, 476
BsoBI CYCGRG 1 cut(s) 115
Bsp1286I GDGCHC 1 cut(s) 124
Bsp143I GATC 5 cut(s) 235, 267, 505, 607, 952
BspACI CCGC 1 cut(s) 568
BspANI GGCC 2 cut(s) 259, 476
BspCNI CTCAG 1 cut(s) 136
BspHI TCATGA 1 cut(s) 220
BspLI GGNNCC 1 cut(s) 376
BspMAI CTGCAG 1 cut(s) 196
BspMI ACCTGC 1 cut(s) 955
BspPI GGATC 1 cut(s) 615
BsrFI RCCGGY 1 cut(s) 288
BsrI ACTGG 1 cut(s) 281
BssAI RCCGGY 1 cut(s) 288
BssECI CCNNGG 4 cut(s) 378, 471, 851, 883
BssMI GATC 5 cut(s) 235, 267, 505, 607, 952
BssT1I CCWWGG 2 cut(s) 378, 883
Bst4CI ACNGT 1 cut(s) 455
Bst6I CTCTTC 2 cut(s) 309, 866
BstAPI GCANNNNNTGC 1 cut(s) 947
BstC8I GCNNGC 2 cut(s) 93, 790
BstDEI CTNAG 2 cut(s) 123, 990
BstF5I GGATG 1 cut(s) 134
BstKTI GATC 5 cut(s) 238, 270, 508, 610, 955
BstMBI GATC 5 cut(s) 235, 267, 505, 607, 952
BstMWI GCNNNNNNNGC 2 cut(s) 197, 947
BstNSI RCATGY 1 cut(s) 388
BstSFI CTRYAG 2 cut(s) 192, 768
BstV1I GCAGC 4 cut(s) 178, 433, 843, 889
BsuRI GGCC 2 cut(s) 259, 476
BtgZI GCGATG 1 cut(s) 402
BtrI CACGTC 1 cut(s) 156
BtsCI GGATG 1 cut(s) 134
BtsIMutI CAGTG 1 cut(s) 274
BveI ACCTGC 1 cut(s) 955
Cac8I GCNNGC 2 cut(s) 93, 790
CaiI CAGNNNCTG 2 cut(s) 200, 276
CciI TCATGA 1 cut(s) 220
Cfr10I RCCGGY 1 cut(s) 288
Csp6I GTAC 2 cut(s) 280, 574
CspAI ACCGGT 1 cut(s) 288
CviAII CATG 9 cut(s) 151, 221, 362, 371, 385, 599, 635, 655, 723
CviQI GTAC 2 cut(s) 280, 574
DdeI CTNAG 2 cut(s) 123, 990
DpnI GATC 5 cut(s) 237, 269, 507, 609, 954
DpnII GATC 5 cut(s) 235, 267, 505, 607, 952
Eam1104I CTCTTC 2 cut(s) 309, 866
EarI CTCTTC 2 cut(s) 309, 866
Ecl136II GAGCTC 1 cut(s) 122
Eco130I CCWWGG 2 cut(s) 378, 883
Eco147I AGGCCT 1 cut(s) 476
Eco24I GRGCYC 1 cut(s) 124
Eco32I GATATC 1 cut(s) 742
Eco53kI GAGCTC 1 cut(s) 122
Eco57I CTGAAG 2 cut(s) 207, 957
Eco88I CYCGRG 1 cut(s) 115
EcoICRI GAGCTC 1 cut(s) 122
EcoRV GATATC 1 cut(s) 742
EcoT14I CCWWGG 2 cut(s) 378, 883
EcoT22I ATGCAT 1 cut(s) 525
EcoT38I GRGCYC 1 cut(s) 124
ErhI CCWWGG 2 cut(s) 378, 883
FaeI CATG 9 cut(s) 154, 224, 365, 374, 388, 602, 638, 658, 726
FaqI GGGAC 2 cut(s) 98, 741
FatI CATG 9 cut(s) 150, 220, 361, 370, 384, 598, 634, 654, 722
FbaI TGATCA 1 cut(s) 952
Fnu4HI GCNGC 4 cut(s) 192, 422, 857, 903
FokI GGATG 1 cut(s) 141
FriOI GRGCYC 1 cut(s) 124
Fsp4HI GCNGC 4 cut(s) 192, 422, 857, 903
FspBI CTAG 2 cut(s) 179, 297
GluI GCNGC 4 cut(s) 192, 422, 857, 903
HaeIII GGCC 2 cut(s) 259, 476
HapII CCGG 4 cut(s) 160, 289, 819, 895
Hin1II CATG 9 cut(s) 154, 224, 365, 374, 388, 602, 638, 658, 726
HinfI GANTC 5 cut(s) 531, 699, 815, 891, 932
HpaII CCGG 4 cut(s) 160, 289, 819, 895
HphI GGTGA 3 cut(s) 515, 833, 975
Hpy166II GTNNAC 1 cut(s) 294
Hpy188I TCNGA 4 cut(s) 451, 709, 931, 937
Hpy188III TCNNGA 8 cut(s) 28, 74, 115, 221, 351, 406, 535, 611
Hpy8I GTNNAC 1 cut(s) 294
Hpy99I CGWCG 1 cut(s) 459
HpyAV CCTTC 3 cut(s) 434, 857, 931
HpyCH4III ACNGT 1 cut(s) 455
HpyCH4IV ACGT 1 cut(s) 155
HpyF10VI GCNNNNNNNGC 2 cut(s) 197, 947
HpyF3I CTNAG 2 cut(s) 123, 990
HpySE526I ACGT 1 cut(s) 155
Hsp92II CATG 9 cut(s) 154, 224, 365, 374, 388, 602, 638, 658, 726
Ksp22I TGATCA 1 cut(s) 952
Kzo9I GATC 5 cut(s) 235, 267, 505, 607, 952
LmnI GCTCC 1 cut(s) 132
Lsp1109I GCAGC 4 cut(s) 178, 433, 843, 889
LweI GCATC 1 cut(s) 983
MaeI CTAG 2 cut(s) 179, 297
MaeII ACGT 1 cut(s) 155
MaeIII GTNAC 5 cut(s) 38, 143, 489, 715, 800
MalI GATC 5 cut(s) 237, 269, 507, 609, 954
MboI GATC 5 cut(s) 235, 267, 505, 607, 952
MboII GAAGA 4 cut(s) 16, 66, 296, 883
MhlI GDGCHC 1 cut(s) 124
MluCI AATT 6 cut(s) 6, 19, 64, 77, 208, 409
MlyI GAGTC 3 cut(s) 708, 824, 900
Mph1103I ATGCAT 1 cut(s) 525
MseI TTAA 2 cut(s) 9, 204
MslI CAYNNNNRTG 1 cut(s) 735
MspI CCGG 4 cut(s) 160, 289, 819, 895
MwoI GCNNNNNNNGC 2 cut(s) 197, 947
NdeII GATC 5 cut(s) 235, 267, 505, 607, 952
NlaIII CATG 9 cut(s) 154, 224, 365, 374, 388, 602, 638, 658, 726
NlaIV GGNNCC 1 cut(s) 376
NmeAIII GCCGAG 1 cut(s) 832
NmuCI GTSAC 2 cut(s) 143, 489
NsiI ATGCAT 1 cut(s) 525
NspI RCATGY 1 cut(s) 388
PagI TCATGA 1 cut(s) 220
PceI AGGCCT 1 cut(s) 476
PciI ACATGT 1 cut(s) 384
PfeI GAWTC 2 cut(s) 531, 932
PinAI ACCGGT 1 cut(s) 288
PkrI GCNGC 4 cut(s) 193, 423, 858, 904
PleI GAGTC 3 cut(s) 707, 823, 899
PpsI GAGTC 3 cut(s) 707, 823, 899
PscI ACATGT 1 cut(s) 384
Psp124BI GAGCTC 1 cut(s) 124
PspN4I GGNNCC 1 cut(s) 376
PstI CTGCAG 1 cut(s) 196
PstNI CAGNNNCTG 2 cut(s) 200, 276
RsaI GTAC 2 cut(s) 281, 575
RsaNI GTAC 2 cut(s) 280, 574
RseI CAYNNNNRTG 1 cut(s) 735
SacI GAGCTC 1 cut(s) 124
SaqAI TTAA 2 cut(s) 9, 204
SatI GCNGC 4 cut(s) 192, 422, 857, 903
Sau3AI GATC 5 cut(s) 235, 267, 505, 607, 952
SchI GAGTC 3 cut(s) 708, 824, 900
SduI GDGCHC 1 cut(s) 124
SfaNI GCATC 1 cut(s) 983
SfcI CTRYAG 2 cut(s) 192, 768
SmiMI CAYNNNNRTG 1 cut(s) 735
SmlI CTYRAG 1 cut(s) 349
SmoI CTYRAG 1 cut(s) 349
Sse9I AATT 6 cut(s) 6, 19, 64, 77, 208, 409
SseBI AGGCCT 1 cut(s) 476
SsiI CCGC 1 cut(s) 568
SspMI CTAG 2 cut(s) 179, 297
SstI GAGCTC 1 cut(s) 124
StuI AGGCCT 1 cut(s) 476
StyI CCWWGG 2 cut(s) 378, 883
TaaI ACNGT 1 cut(s) 455
TaiI ACGT 1 cut(s) 158
TaqI TCGA 2 cut(s) 457, 610
TaqII GACCGA 1 cut(s) 485
TasI AATT 6 cut(s) 6, 19, 64, 77, 208, 409
TfiI GAWTC 2 cut(s) 531, 932
Tru1I TTAA 2 cut(s) 9, 204
Tru9I TTAA 2 cut(s) 9, 204
TscAI CASTG 1 cut(s) 281
TseFI GTSAC 2 cut(s) 143, 489
TseI GCWGC 4 cut(s) 191, 421, 856, 902
Tsp45I GTSAC 2 cut(s) 143, 489
TspDTI ATGAA 2 cut(s) 301, 381
TspRI CASTG 1 cut(s) 281
XapI RAATTY 4 cut(s) 19, 77, 208, 409
XceI RCATGY 1 cut(s) 388
XcmI CCANNNNNNNNNTGG 1 cut(s) 368
XspI CTAG 2 cut(s) 179, 297
Zsp2I ATGCAT 1 cut(s) 525
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.