Rroxscaffold_1G00034500

HNH endonuclease

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0012307
Physical Location & Seq
Reverse (-)
50107606 .. 50112638
5033 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00034500.1

Sequence Viewer

Length: 888 bp
ATGGCACGGTTAGCTGCACGAGCAAATGTGAAGTCACTCTTCAATGGTGAGGGAGTCCCATCATCAGGATCCGGGTTGGACCCAAAAGACCCATTGAGCTGCATGTTCTCTTTCTCTTCATCGATCAAACCCCAAAACCGCAGGCTTCGCTCATTTGACTCCACTAGGCTTTACTCTTCATCCAACTCTTCTTCCAACAAGACCAAGCGTCTCAAGGCCGAGGTTCGTTTGTTTTTCGGGGATGAGGAGGATGTTAAGGGTGACAACAAGGTTGGTGAGCATGCCCATCATGGTGGTGATGATGATGATGATGATGAGTTTGAGAGGGATGAGCTGTCCTGTTTCAGAGGTCTGGTTTTGGATATCTCATACAGGCCAATTAATGTGGTCTGCTGGAAACGTGCTATTTGTTTGGAATTCATGGATAAGGCGGATGTCCTAGAATACTATGATCAGACTGTTAATTCCCCAAGTGGATCCTTCTACATACCGGCTGTTTTAAGGATTCCCCATTTACTGCAAGTTGTAAAGAGAAGAAGAATTAAGTGCAATCTTAGTCGTAAAAATATACTTTGTCGGGACAGTTTCACTTGTCAGTACTGTTCTTCACGTGAAAACTTGACCATTGACCATGTTATACCAATTGCACGAGGTGGAGAATGGAAGTGGGAAAATCTGGTTACGGCATGTGCAAAATGCAACTCGAAGAAAGGGCAGAAGACATTGGAGGAAGCATGTATGAAGCTGATGAAAATTCCCAAGACTCCAAAAGACTATGACATACTTGCCATACCCCTAACAAGTGCGGCAGTAAAGATGCTGAAAATGAGAAAGGGAACTCCAGAAGAGTGGCTCCAATATCTATCGAAGCCTTCTTCAATGCCATGA
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
HNH_5

Protein Analysis

295

Amino Acids

33.42

Weight (kDa)

8.95

Isoelectric Point (pI)

54.07

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HNH_5 PF14279 198 - 249 4.1e-17 HNH endonuclease
HNH PF01844 198 - 239 1.9e-14 HNH endonuclease
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: OG0012307)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G23840
fragaria_vesca FvH4_3g25250 FvH4_3g25250
malus_domestica MD12G1002500.v1.1
prunus_persica Prupe.7G002400_v2.0.a1 Prupe.7G002400_v2.0.a1 Prupe.7G002400_v2.0.a1 Prupe.7G002400_v2.0.a1
pyrus_communis pycom12g00220
rosa_chinensis RchiOBHm_Chr5g0046891
rosa_laevigata RLG00000034453
rosa_multiflora Rmu_sc0005233.1_g000003
rosa_roxburghii Rroxscaffold_1G00034500
rosa_rugosa Rorug05G0232400
rosa_samantha Rh5AG311900 Rh5BG320900 Rh5CG347100 Rh5DG331600
rosa_wichuraiana Rw5G029150

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 3 cut(s) 139, 431, 806
AclWI GGATC 4 cut(s) 63, 76, 471, 484
AcsI RAATTY 2 cut(s) 416, 753
AcvI CACGTG 1 cut(s) 611
AdeI CACNNNGTG 1 cut(s) 653
AfaI GTAC 1 cut(s) 599
AfiI CCNNNNNNNGG 1 cut(s) 65
AgsI TTSAA 2 cut(s) 43, 879
AhdI GACNNNNNGTC 1 cut(s) 207
AluBI AGCT 4 cut(s) 14, 99, 334, 745
AluI AGCT 4 cut(s) 14, 99, 334, 745
Alw26I GTCTC 1 cut(s) 215
AlwI GGATC 4 cut(s) 63, 76, 471, 484
AoxI GGCC 2 cut(s) 216, 374
ApeKI GCWGC 2 cut(s) 14, 99
ApoI RAATTY 2 cut(s) 416, 753
ArsI GACNNNNNNTTYG 2 cut(s) 17, 49
AseI ATTAAT 1 cut(s) 381
AspS9I GGNCC 1 cut(s) 79
AsuC2I CCSGG 1 cut(s) 73
AsuHPI GGTGA 4 cut(s) 59, 272, 287, 308
AvaII GGWCC 1 cut(s) 79
BamHI GGATCC 2 cut(s) 68, 476
BauI CACGAG 2 cut(s) 18, 648
BbrPI CACGTG 1 cut(s) 611
BbsI GAAGAC 1 cut(s) 725
BbvI GCAGC 1 cut(s) 86
BccI CCATC 2 cut(s) 67, 294
BceAI ACGGC 1 cut(s) 699
BclI TGATCA 1 cut(s) 451
BcnI CCSGG 1 cut(s) 73
BcoDI GTCTC 1 cut(s) 215
BfaI CTAG 2 cut(s) 165, 440
BisI GCNGC 3 cut(s) 15, 100, 807
BlsI GCNGC 3 cut(s) 16, 101, 808
BmcAI AGTACT 1 cut(s) 599
Bme1390I CCNGG 1 cut(s) 73
Bme18I GGWCC 1 cut(s) 79
BmeRI GACNNNNNGTC 1 cut(s) 207
BmgT120I GGNCC 1 cut(s) 79
BmiI GGNNCC 4 cut(s) 70, 81, 478, 854
BmrFI CCNGG 1 cut(s) 73
BmsI GCATC 1 cut(s) 807
BpiI GAAGAC 1 cut(s) 725
BpmI CTGGAG 1 cut(s) 825
BpuEI CTTGAG 1 cut(s) 197
BpuMI CCSGG 1 cut(s) 73
Bsa29I ATCGAT 1 cut(s) 122
BsaAI YACGTR 1 cut(s) 611
BsaJI CCNNGG 1 cut(s) 219
Bsc4I CCNNNNNNNGG 1 cut(s) 65
Bse118I RCCGGY 1 cut(s) 490
BseCI ATCGAT 1 cut(s) 122
BseDI CCNNGG 1 cut(s) 219
BseGI GGATG 5 cut(s) 179, 247, 256, 334, 439
BseLI CCNNNNNNNGG 1 cut(s) 65
BseRI GAGGAG 1 cut(s) 260
BseXI GCAGC 1 cut(s) 86
BshFI GGCC 2 cut(s) 218, 376
BshVI ATCGAT 1 cut(s) 122
BsiSI CCGG 2 cut(s) 72, 491
BslFI GGGAC 2 cut(s) 41, 593
BslI CCNNNNNNNGG 1 cut(s) 65
BsmAI GTCTC 1 cut(s) 215
BsmBI CGTCTC 1 cut(s) 215
BsmFI GGGAC 2 cut(s) 41, 593
BsnI GGCC 2 cut(s) 218, 376
Bsp143I GATC 4 cut(s) 68, 123, 451, 476
BspACI CCGC 3 cut(s) 139, 431, 806
BspANI GGCC 2 cut(s) 218, 376
BspDI ATCGAT 1 cut(s) 122
BspLI GGNNCC 4 cut(s) 70, 81, 478, 854
BspPI GGATC 4 cut(s) 63, 76, 471, 484
BsrFI RCCGGY 1 cut(s) 490
BssAI RCCGGY 1 cut(s) 490
BssECI CCNNGG 1 cut(s) 219
BssMI GATC 4 cut(s) 68, 123, 451, 476
BssSI CACGAG 2 cut(s) 18, 648
Bst2BI CACGAG 2 cut(s) 18, 648
Bst4CI ACNGT 4 cut(s) 9, 460, 584, 602
Bst6I CTCTTC 5 cut(s) 44, 121, 181, 193, 840
BstBAI YACGTR 1 cut(s) 611
BstC8I GCNNGC 2 cut(s) 143, 282
BstDEI CTNAG 1 cut(s) 554
BstF5I GGATG 5 cut(s) 179, 247, 256, 334, 439
BstKTI GATC 4 cut(s) 71, 126, 454, 479
BstMAI GTCTC 1 cut(s) 215
BstMBI GATC 4 cut(s) 68, 123, 451, 476
BstMWI GCNNNNNNNGC 3 cut(s) 11, 20, 147
BstNSI RCATGY 4 cut(s) 106, 284, 690, 738
BstSCI CCNGG 1 cut(s) 71
BstV1I GCAGC 1 cut(s) 86
BstV2I GAAGAC 1 cut(s) 725
BstX2I RGATCY 2 cut(s) 68, 476
BstXI CCANNNNNNTGG 2 cut(s) 293, 849
BstYI RGATCY 2 cut(s) 68, 476
Bsu15I ATCGAT 1 cut(s) 122
BsuRI GGCC 2 cut(s) 218, 376
BsuTUI ATCGAT 1 cut(s) 122
BtsCI GGATG 5 cut(s) 179, 247, 256, 334, 439
Cac8I GCNNGC 2 cut(s) 143, 282
Cfr10I RCCGGY 1 cut(s) 490
Cfr13I GGNCC 1 cut(s) 79
ClaI ATCGAT 1 cut(s) 122
CseI GACGC 1 cut(s) 197
Csp6I GTAC 1 cut(s) 598
CspCI CAANNNNNGTGG 2 cut(s) 366, 401
CviAII CATG 8 cut(s) 103, 281, 290, 421, 632, 687, 735, 885
CviQI GTAC 1 cut(s) 598
DdeI CTNAG 1 cut(s) 554
DpnI GATC 4 cut(s) 70, 125, 453, 478
DpnII GATC 4 cut(s) 68, 123, 451, 476
DraIII CACNNNGTG 1 cut(s) 653
DriI GACNNNNNGTC 1 cut(s) 207
Eam1104I CTCTTC 5 cut(s) 44, 121, 181, 193, 840
Eam1105I GACNNNNNGTC 1 cut(s) 207
EarI CTCTTC 5 cut(s) 44, 121, 181, 193, 840
EciI GGCGGA 1 cut(s) 446
Eco32I GATATC 1 cut(s) 364
Eco47I GGWCC 1 cut(s) 79
Eco72I CACGTG 1 cut(s) 611
EcoRI GAATTC 1 cut(s) 416
EcoRV GATATC 1 cut(s) 364
Esp3I CGTCTC 1 cut(s) 215
FaeI CATG 8 cut(s) 106, 284, 293, 424, 635, 690, 738, 888
FalI AAGNNNNNCTT 2 cut(s) 23, 55
FaqI GGGAC 2 cut(s) 41, 593
FatI CATG 8 cut(s) 102, 280, 289, 420, 631, 686, 734, 884
FbaI TGATCA 1 cut(s) 451
Fnu4HI GCNGC 3 cut(s) 15, 100, 807
FokI GGATG 5 cut(s) 166, 254, 263, 341, 446
Fsp4HI GCNGC 3 cut(s) 15, 100, 807
FspBI CTAG 2 cut(s) 165, 440
GluI GCNGC 3 cut(s) 15, 100, 807
GsuI CTGGAG 1 cut(s) 825
HaeIII GGCC 2 cut(s) 218, 376
HapII CCGG 2 cut(s) 72, 491
HgaI GACGC 1 cut(s) 197
Hin1II CATG 8 cut(s) 106, 284, 293, 424, 635, 690, 738, 888
HinfI GANTC 4 cut(s) 54, 158, 505, 763
HpaII CCGG 2 cut(s) 72, 491
HphI GGTGA 4 cut(s) 59, 272, 287, 308
Hpy188I TCNGA 2 cut(s) 347, 456
Hpy188III TCNNGA 3 cut(s) 66, 578, 842
HpyAV CCTTC 2 cut(s) 490, 882
HpyCH4III ACNGT 4 cut(s) 9, 460, 584, 602
HpyCH4IV ACGT 2 cut(s) 400, 610
HpyCH4V TGCA 7 cut(s) 17, 102, 520, 549, 647, 692, 699
HpyF10VI GCNNNNNNNGC 3 cut(s) 11, 20, 147
HpyF3I CTNAG 1 cut(s) 554
HpySE526I ACGT 2 cut(s) 400, 610
Hsp92II CATG 8 cut(s) 106, 284, 293, 424, 635, 690, 738, 888
Ksp22I TGATCA 1 cut(s) 451
Kzo9I GATC 4 cut(s) 68, 123, 451, 476
LmnI GCTCC 1 cut(s) 858
Lsp1109I GCAGC 1 cut(s) 86
LweI GCATC 1 cut(s) 807
MaeI CTAG 2 cut(s) 165, 440
MaeII ACGT 2 cut(s) 400, 610
MaeIII GTNAC 3 cut(s) 33, 260, 679
MalI GATC 4 cut(s) 70, 125, 453, 478
MboI GATC 4 cut(s) 68, 123, 451, 476
MfeI CAATTG 1 cut(s) 642
MflI RGATCY 2 cut(s) 68, 476
MluCI AATT 6 cut(s) 378, 416, 463, 540, 642, 753
MlyI GAGTC 3 cut(s) 63, 152, 757
MmeI TCCRAC 3 cut(s) 57, 207, 219
MnlI CCTC 8 cut(s) 43, 214, 238, 241, 318, 341, 644, 721
MseI TTAA 5 cut(s) 255, 381, 462, 500, 543
MslI CAYNNNNRTG 2 cut(s) 291, 294
MspI CCGG 2 cut(s) 72, 491
MspR9I CCNGG 1 cut(s) 73
MunI CAATTG 1 cut(s) 642
MwoI GCNNNNNNNGC 3 cut(s) 11, 20, 147
NciI CCSGG 1 cut(s) 73
NdeII GATC 4 cut(s) 68, 123, 451, 476
NlaIII CATG 8 cut(s) 106, 284, 293, 424, 635, 690, 738, 888
NlaIV GGNNCC 4 cut(s) 70, 81, 478, 854
NmeAIII GCCGAG 1 cut(s) 244
NmuCI GTSAC 2 cut(s) 33, 260
NspI RCATGY 4 cut(s) 106, 284, 690, 738
PaeI GCATGC 1 cut(s) 284
PfeI GAWTC 1 cut(s) 505
PkrI GCNGC 3 cut(s) 16, 101, 808
PleI GAGTC 3 cut(s) 62, 152, 757
PmaCI CACGTG 1 cut(s) 611
PmlI CACGTG 1 cut(s) 611
PpsI GAGTC 3 cut(s) 62, 152, 757
Ppu21I YACGTR 1 cut(s) 611
PshBI ATTAAT 1 cut(s) 381
PspCI CACGTG 1 cut(s) 611
PspN4I GGNNCC 4 cut(s) 70, 81, 478, 854
PspPI GGNCC 1 cut(s) 79
PsuI RGATCY 2 cut(s) 68, 476
RsaI GTAC 1 cut(s) 599
RsaNI GTAC 1 cut(s) 598
RseI CAYNNNNRTG 2 cut(s) 291, 294
SaqAI TTAA 5 cut(s) 255, 381, 462, 500, 543
SatI GCNGC 3 cut(s) 15, 100, 807
Sau3AI GATC 4 cut(s) 68, 123, 451, 476
Sau96I GGNCC 1 cut(s) 79
ScaI AGTACT 1 cut(s) 599
SchI GAGTC 3 cut(s) 63, 152, 757
ScrFI CCNGG 1 cut(s) 73
SfaNI GCATC 1 cut(s) 807
SinI GGWCC 1 cut(s) 79
SmiMI CAYNNNNRTG 2 cut(s) 291, 294
SmlI CTYRAG 1 cut(s) 212
SmoI CTYRAG 1 cut(s) 212
SphI GCATGC 1 cut(s) 284
Sse9I AATT 6 cut(s) 378, 416, 463, 540, 642, 753
SsiI CCGC 3 cut(s) 139, 431, 806
SspMI CTAG 2 cut(s) 165, 440
StyD4I CCNGG 1 cut(s) 71
TaaI ACNGT 4 cut(s) 9, 460, 584, 602
TaiI ACGT 2 cut(s) 403, 613
TaqI TCGA 3 cut(s) 122, 704, 866
TasI AATT 6 cut(s) 378, 416, 463, 540, 642, 753
TatI WGTACW 1 cut(s) 597
TauI GCSGC 1 cut(s) 809
TfiI GAWTC 1 cut(s) 505
Tru1I TTAA 5 cut(s) 255, 381, 462, 500, 543
Tru9I TTAA 5 cut(s) 255, 381, 462, 500, 543
TseFI GTSAC 2 cut(s) 33, 260
TseI GCWGC 2 cut(s) 14, 99
Tsp45I GTSAC 2 cut(s) 33, 260
TspDTI ATGAA 5 cut(s) 108, 168, 409, 755, 764
VpaK11BI GGWCC 1 cut(s) 79
VspI ATTAAT 1 cut(s) 381
XapI RAATTY 2 cut(s) 416, 753
XceI RCATGY 4 cut(s) 106, 284, 690, 738
XspI CTAG 2 cut(s) 165, 440
ZrmI AGTACT 1 cut(s) 599
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.