Rw5G003940

NPH3 family

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0015568
Physical Location & Seq
Forward (+)
3919954 .. 3922214
2261 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G003940.1

Sequence Viewer

Length: 1521 bp
ATGGCAATGTTCTGTGATCTCCAAGTCGATGTCAATGGCGAAGAAGTCTTCATGGTGAACAAGAAAACTTTGGCGTCTTTCTCTTGTCGATTAAGCAAACTATTTGGTAAATCAATGGGTACAACGAGCCTCAAAGTGATATTCCATGACTTTCCTGGAGGTGCAGAGGGTTTTGAGCTCATGACAAGGTTTTGTTACAACAATGGAACAACCGAAATAACTCCTTCCAACTTAGTCCTTGTATATTGCATTGCCGATTTCATGGAGATGGATGGTGATATACTATTGCAAGCTCAAAACACTCTTGATGGTATCAGCTCTTGGACGTGGTCTGAGCTTCTAGTAGCTCTGAAGCAGTGCCAAGATTTACTTGCCCCCTCAAATTCTTCATTGATATTGCAGATAGTCATGGACTGCATCATAGGTAAGCTTTCTTGTCCATTTTTTCCAACCCCCAATGATACTACTTCATCAGAGAACGTGAGTAGTTTCCAGTTTTCTAGTGGTTCGAGGAGCAGTTATAATCTGAAAAGCAATTGCTCTATGAAAACATGGTGGTTTGAAGACTTGATGTTCTTAAATACCAAATCGATCGAAATGGTTATAAGAAGCCTGATATCCAAGGAGATTGAACAGTCTACAGTTTTCAAGTTTCTCCTTTGTTATCATCAGTCAAAGTGTTTTGGTGCCAAACCAGAAGAGAAGTATAAGATCACAGAGGTTGTTATCGGTCTACTTTCTCTGCTTGATAGGAGCTCCCTTTCTTTCAAGGGATTATTCAATATATATCAAGCGGCTTTGAACATGAAAGTAGGCAAGAAATACAAAAACAAGTTGGAGATTATGATAGGTTCACAGCTGGATCAAGCAACAATCGATTATTTACTTGTTCCATCTCCCTGTGGGAAAAAGTATGTTTATGATGTGAATTTGATTTTGAGGTTAGGGAAATCATTTCTTCTTCAAGAAGGGGGTCATTTATTCCGGAAGAGTCGCTTCACAAAGGTCGCCAAGTTGATGGATTTATACCTTGCAGAAGTGGCTCCAGATTTTCATTTGAAACCTTCAAAGTTTGCAGCATTAGTTATGATGTTACCAGAGTCTGTGCGAGAATCTCATGACAGACTTTACGAGGCCATTGCTGTATATTTTAAGTGCCACACTGGTCTATCTGAACAAGAGAAGCTGACAATCTGTTGTGCACTGAACTATAAGAAGCTCTCAGCAGGACCTTTGAAACAAGCCTCTCGCACAAAGTTCCCTTCCAGAAGAGCAGTTGAAGCTTTCAAGAAACAGCGAACAAAGGATAGGAAAGAGGAAATTGAGTCAGTCCTACTTGACGCAAAGAGTCTTGATCTCCCAACAGAGGCTCAGAAGCTCAGTGCAGATTTGATGCATTTGAAGGCATTGGAATTGGGGAAGGTTTTCGGGACAATGCAGATACGAGTGACAAGTGTAATCAAATCAAGATTGCCCTTTCAGGCAACCAATACTCGATACTTGCCAAAACTCTTTCCATAA
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
NPH3

Protein Analysis

506

Amino Acids

57.19

Weight (kDa)

8.97

Isoelectric Point (pI)

39.09

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
NPH3 PF03000 184 - 409 9e-54 NPH3 family
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: OG0015568)

Species Orthologous Gene IDs
fragaria_vesca FvH4_3g03040
malus_domestica MD05G1335300.v1.1
prunus_persica Prupe.4G030100_v2.0.a1 Prupe.4G030100_v2.0.a1 Prupe.4G030100_v2.0.a1 Prupe.4G030100_v2.0.a1
pyrus_communis pycom05g30670
rosa_chinensis RchiOBHm_Chr5g0004691
rosa_laevigata RLG00000031252
rosa_roxburghii Rroxscaffold_1G00070870
rosa_rugosa Rorug04G0413300
rosa_samantha Rh5AG040900 Rh5BG040600 Rh5CG044400 Rh5DG040600
rosa_wichuraiana Rw5G003940

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 2 cut(s) 522, 605
AccB1I GGYRCC 1 cut(s) 686
AccI GTMKAC 2 cut(s) 638, 733
AccIII TCCGGA 1 cut(s) 984
AciI CCGC 1 cut(s) 794
AclWI GGATC 1 cut(s) 870
AcsI RAATTY 2 cut(s) 382, 928
AcuI CTGAAG 1 cut(s) 371
AcyI GRCGYC 1 cut(s) 74
AfaI GTAC 1 cut(s) 121
AfiI CCNNNNNNNGG 1 cut(s) 1366
AjiI CACGTC 1 cut(s) 327
AjnI CCWGG 1 cut(s) 154
Alw21I GWGCWC 3 cut(s) 180, 758, 1204
Alw44I GTGCAC 1 cut(s) 1200
AlwI GGATC 1 cut(s) 870
AlwNI CAGNNNCTG 1 cut(s) 1103
Aor13HI TCCGGA 1 cut(s) 984
AoxI GGCC 1 cut(s) 1134
ApaLI GTGCAC 1 cut(s) 1200
ApeKI GCWGC 1 cut(s) 1076
ApoI RAATTY 2 cut(s) 382, 928
Asp700I GAANNNNTTC 1 cut(s) 1424
AspS9I GGNCC 1 cut(s) 1229
AsuHPI GGTGA 2 cut(s) 67, 287
AvaII GGWCC 1 cut(s) 1229
BaeGI GKGCMC 1 cut(s) 1204
BanI GGYRCC 1 cut(s) 686
BanII GRGCYC 2 cut(s) 180, 758
BbsI GAAGAC 2 cut(s) 40, 570
Bbv12I GWGCWC 3 cut(s) 180, 758, 1204
BbvI GCAGC 1 cut(s) 1088
BccI CCATC 5 cut(s) 262, 266, 302, 901, 1012
BcgI CGANNNNNNTGC 2 cut(s) 1121, 1155
BciT130I CCWGG 1 cut(s) 156
BfaI CTAG 2 cut(s) 341, 501
BfmI CTRYAG 1 cut(s) 639
BisI GCNGC 2 cut(s) 795, 1077
BlsI GCNGC 2 cut(s) 796, 1078
Bme1390I CCNGG 1 cut(s) 156
Bme18I GGWCC 1 cut(s) 1229
BmgBI CACGTC 1 cut(s) 327
BmgT120I GGNCC 1 cut(s) 1229
BmiI GGNNCC 2 cut(s) 688, 1044
BmrFI CCNGG 1 cut(s) 156
BmsI GCATC 2 cut(s) 426, 1383
BpiI GAAGAC 2 cut(s) 40, 570
BpmI CTGGAG 2 cut(s) 177, 1029
Bsa29I ATCGAT 2 cut(s) 590, 876
BsaHI GRCGYC 1 cut(s) 74
BsaJI CCNNGG 1 cut(s) 621
BsaWI WCCGGW 1 cut(s) 984
Bsc4I CCNNNNNNNGG 1 cut(s) 1366
Bse1I ACTGG 2 cut(s) 493, 1168
Bse3DI GCAATG 3 cut(s) 12, 249, 1137
BseAI TCCGGA 1 cut(s) 984
BseBI CCWGG 1 cut(s) 156
BseCI ATCGAT 2 cut(s) 590, 876
BseDI CCNNGG 1 cut(s) 621
BseGI GGATG 1 cut(s) 277
BseLI CCNNNNNNNGG 1 cut(s) 1366
BseMI GCAATG 3 cut(s) 12, 249, 1137
BseMII CTCAG 4 cut(s) 324, 1236, 1385, 1393
BseNI ACTGG 2 cut(s) 493, 1168
BseRI GAGGAG 1 cut(s) 526
BseSI GKGCMC 1 cut(s) 1204
BseXI GCAGC 1 cut(s) 1088
BsgI GTGCAG 2 cut(s) 183, 1404
Bsh1285I CGRYCG 1 cut(s) 594
BshFI GGCC 1 cut(s) 1136
BshNI GGYRCC 1 cut(s) 686
BshVI ATCGAT 2 cut(s) 590, 876
BsiEI CGRYCG 1 cut(s) 594
BsiHKAI GWGCWC 3 cut(s) 180, 758, 1204
BsiSI CCGG 1 cut(s) 985
BslFI GGGAC 1 cut(s) 1444
BslI CCNNNNNNNGG 1 cut(s) 1366
BsmFI GGGAC 1 cut(s) 1444
BsnI GGCC 1 cut(s) 1136
Bsp1286I GDGCHC 3 cut(s) 180, 758, 1204
Bsp13I TCCGGA 1 cut(s) 984
Bsp143I GATC 5 cut(s) 16, 591, 711, 862, 1354
BspACI CCGC 1 cut(s) 794
BspANI GGCC 1 cut(s) 1136
BspCNI CTCAG 4 cut(s) 325, 1235, 1384, 1392
BspDI ATCGAT 2 cut(s) 590, 876
BspEI TCCGGA 1 cut(s) 984
BspHI TCATGA 2 cut(s) 180, 1117
BspLI GGNNCC 2 cut(s) 688, 1044
BspPI GGATC 1 cut(s) 870
BspQI GCTCTTC 1 cut(s) 1264
BspT107I GGYRCC 1 cut(s) 686
BsrDI GCAATG 3 cut(s) 12, 249, 1137
BsrI ACTGG 2 cut(s) 493, 1168
BssECI CCNNGG 1 cut(s) 621
BssMI GATC 5 cut(s) 16, 591, 711, 862, 1354
BssNI GRCGYC 1 cut(s) 74
BssT1I CCWWGG 1 cut(s) 621
Bst2UI CCWGG 1 cut(s) 156
Bst4CI ACNGT 2 cut(s) 636, 643
Bst6I CTCTTC 3 cut(s) 693, 983, 1264
BstACI GRCGYC 1 cut(s) 74
BstC8I GCNNGC 1 cut(s) 291
BstDEI CTNAG 5 cut(s) 232, 333, 1222, 1371, 1379
BstF5I GGATG 1 cut(s) 277
BstKTI GATC 5 cut(s) 19, 594, 714, 865, 1357
BstMBI GATC 5 cut(s) 16, 591, 711, 862, 1354
BstMCI CGRYCG 1 cut(s) 594
BstMWI GCNNNNNNNGC 2 cut(s) 1040, 1280
BstNI CCWGG 1 cut(s) 156
BstSCI CCNGG 1 cut(s) 154
BstSFI CTRYAG 1 cut(s) 639
BstSLI GKGCMC 1 cut(s) 1204
BstV1I GCAGC 1 cut(s) 1088
BstV2I GAAGAC 2 cut(s) 40, 570
BstXI CCANNNNNNTGG 1 cut(s) 1018
Bsu15I ATCGAT 2 cut(s) 590, 876
BsuRI GGCC 1 cut(s) 1136
BsuTUI ATCGAT 2 cut(s) 590, 876
BtrI CACGTC 1 cut(s) 327
BtsCI GGATG 1 cut(s) 277
BtsI GCAGTG 1 cut(s) 362
BtsIMutI CAGTG 4 cut(s) 362, 1161, 1202, 1387
Cac8I GCNNGC 1 cut(s) 291
CaiI CAGNNNCTG 1 cut(s) 1103
CciI TCATGA 2 cut(s) 180, 1117
Cfr13I GGNCC 1 cut(s) 1229
ClaI ATCGAT 2 cut(s) 590, 876
CseI GACGC 2 cut(s) 63, 1349
Csp6I GTAC 1 cut(s) 120
CviAII CATG 8 cut(s) 52, 146, 181, 262, 409, 552, 805, 1118
CviQI GTAC 1 cut(s) 120
DdeI CTNAG 5 cut(s) 232, 333, 1222, 1371, 1379
DpnI GATC 5 cut(s) 18, 593, 713, 864, 1356
DpnII GATC 5 cut(s) 16, 591, 711, 862, 1354
Eam1104I CTCTTC 3 cut(s) 693, 983, 1264
EarI CTCTTC 3 cut(s) 693, 983, 1264
Ecl136II GAGCTC 2 cut(s) 178, 756
Eco130I CCWWGG 1 cut(s) 621
Eco24I GRGCYC 2 cut(s) 180, 758
Eco32I GATATC 1 cut(s) 618
Eco47I GGWCC 1 cut(s) 1229
Eco53kI GAGCTC 2 cut(s) 178, 756
Eco57I CTGAAG 1 cut(s) 371
EcoICRI GAGCTC 2 cut(s) 178, 756
EcoO109I RGGNCCY 1 cut(s) 1229
EcoRII CCWGG 1 cut(s) 154
EcoRV GATATC 1 cut(s) 618
EcoT14I CCWWGG 1 cut(s) 621
EcoT22I ATGCAT 1 cut(s) 1398
EcoT38I GRGCYC 2 cut(s) 180, 758
ErhI CCWWGG 1 cut(s) 621
FaeI CATG 8 cut(s) 55, 149, 184, 265, 412, 555, 808, 1121
FalI AAGNNNNNCTT 4 cut(s) 354, 386, 980, 1012
FaqI GGGAC 1 cut(s) 1444
FatI CATG 8 cut(s) 51, 145, 180, 261, 408, 551, 804, 1117
FblI GTMKAC 2 cut(s) 638, 733
Fnu4HI GCNGC 2 cut(s) 795, 1077
FokI GGATG 1 cut(s) 284
FriOI GRGCYC 2 cut(s) 180, 758
Fsp4HI GCNGC 2 cut(s) 795, 1077
FspBI CTAG 2 cut(s) 341, 501
GluI GCNGC 2 cut(s) 795, 1077
GsuI CTGGAG 2 cut(s) 177, 1029
HaeIII GGCC 1 cut(s) 1136
HapII CCGG 1 cut(s) 985
HgaI GACGC 2 cut(s) 63, 1349
Hin1I GRCGYC 1 cut(s) 74
Hin1II CATG 8 cut(s) 55, 149, 184, 265, 412, 555, 808, 1121
HindIII AAGCTT 2 cut(s) 428, 1281
HinfI GANTC 5 cut(s) 991, 1100, 1112, 1325, 1348
HpaII CCGG 1 cut(s) 985
HphI GGTGA 2 cut(s) 67, 287
Hpy166II GTNNAC 5 cut(s) 58, 639, 734, 854, 1202
Hpy188I TCNGA 6 cut(s) 334, 351, 475, 528, 1174, 1374
Hpy8I GTNNAC 5 cut(s) 58, 639, 734, 854, 1202
HpyAV CCTTC 6 cut(s) 234, 962, 1074, 1272, 1396, 1414
HpyCH4III ACNGT 2 cut(s) 636, 643
HpyCH4IV ACGT 2 cut(s) 326, 480
HpyF10VI GCNNNNNNNGC 2 cut(s) 1040, 1280
HpyF3I CTNAG 5 cut(s) 232, 333, 1222, 1371, 1379
HpySE526I ACGT 2 cut(s) 326, 480
Hsp92I GRCGYC 1 cut(s) 74
Hsp92II CATG 8 cut(s) 55, 149, 184, 265, 412, 555, 808, 1121
Kpn2I TCCGGA 1 cut(s) 984
Kzo9I GATC 5 cut(s) 16, 591, 711, 862, 1354
LguI GCTCTTC 1 cut(s) 1264
LmnI GCTCC 4 cut(s) 513, 753, 761, 1048
Lsp1109I GCAGC 1 cut(s) 1088
LweI GCATC 2 cut(s) 426, 1383
MaeI CTAG 2 cut(s) 341, 501
MaeII ACGT 2 cut(s) 326, 480
MaeIII GTNAC 3 cut(s) 194, 1092, 1447
MalI GATC 5 cut(s) 18, 593, 713, 864, 1356
MboI GATC 5 cut(s) 16, 591, 711, 862, 1354
MboII GAAGA 9 cut(s) 40, 53, 378, 575, 710, 950, 953, 1000, 1281
MfeI CAATTG 1 cut(s) 535
MhlI GDGCHC 3 cut(s) 180, 758, 1204
MluCI AATT 5 cut(s) 382, 535, 928, 1320, 1412
MlyI GAGTC 4 cut(s) 1000, 1109, 1334, 1357
MmeI TCCRAC 3 cut(s) 252, 473, 816
Mph1103I ATGCAT 1 cut(s) 1398
MroI TCCGGA 1 cut(s) 984
MroXI GAANNNNTTC 1 cut(s) 1424
MseI TTAA 3 cut(s) 92, 578, 1152
MslI CAYNNNNRTG 1 cut(s) 266
MspA1I CMGCKG 1 cut(s) 859
MspI CCGG 1 cut(s) 985
MspR9I CCNGG 1 cut(s) 156
MunI CAATTG 1 cut(s) 535
MvaI CCWGG 1 cut(s) 156
MwoI GCNNNNNNNGC 2 cut(s) 1040, 1280
NdeII GATC 5 cut(s) 16, 591, 711, 862, 1354
NlaIII CATG 8 cut(s) 55, 149, 184, 265, 412, 555, 808, 1121
NlaIV GGNNCC 2 cut(s) 688, 1044
NmuCI GTSAC 1 cut(s) 1447
NsiI ATGCAT 1 cut(s) 1398
PagI TCATGA 2 cut(s) 180, 1117
PciSI GCTCTTC 1 cut(s) 1264
PdmI GAANNNNTTC 1 cut(s) 1424
PfeI GAWTC 1 cut(s) 1112
PflFI GACNNNGTC 1 cut(s) 328
PfoI TCCNGGA 1 cut(s) 154
PkrI GCNGC 2 cut(s) 796, 1078
Ple19I CGATCG 1 cut(s) 594
PleI GAGTC 4 cut(s) 999, 1108, 1333, 1356
PpsI GAGTC 4 cut(s) 999, 1108, 1333, 1356
PpuMI RGGWCCY 1 cut(s) 1229
PsiI TTATAA 2 cut(s) 522, 605
Psp124BI GAGCTC 2 cut(s) 180, 758
Psp5II RGGWCCY 1 cut(s) 1229
Psp6I CCWGG 1 cut(s) 154
PspGI CCWGG 1 cut(s) 154
PspN4I GGNNCC 2 cut(s) 688, 1044
PspPI GGNCC 1 cut(s) 1229
PspPPI RGGWCCY 1 cut(s) 1229
PstNI CAGNNNCTG 1 cut(s) 1103
PsyI GACNNNGTC 1 cut(s) 328
PvuI CGATCG 1 cut(s) 594
PvuII CAGCTG 1 cut(s) 859
RsaI GTAC 1 cut(s) 121
RsaNI GTAC 1 cut(s) 120
RseI CAYNNNNRTG 1 cut(s) 266
SacI GAGCTC 2 cut(s) 180, 758
SapI GCTCTTC 1 cut(s) 1264
SaqAI TTAA 3 cut(s) 92, 578, 1152
SatI GCNGC 2 cut(s) 795, 1077
Sau3AI GATC 5 cut(s) 16, 591, 711, 862, 1354
Sau96I GGNCC 1 cut(s) 1229
SchI GAGTC 4 cut(s) 1000, 1109, 1334, 1357
ScrFI CCNGG 1 cut(s) 156
SduI GDGCHC 3 cut(s) 180, 758, 1204
SfaNI GCATC 2 cut(s) 426, 1383
SfcI CTRYAG 1 cut(s) 639
SinI GGWCC 1 cut(s) 1229
SmiMI CAYNNNNRTG 1 cut(s) 266
Sse9I AATT 5 cut(s) 382, 535, 928, 1320, 1412
SsiI CCGC 1 cut(s) 794
SspMI CTAG 2 cut(s) 341, 501
SstI GAGCTC 2 cut(s) 180, 758
StyD4I CCNGG 1 cut(s) 154
StyI CCWWGG 1 cut(s) 621
TaaI ACNGT 2 cut(s) 636, 643
TaiI ACGT 2 cut(s) 329, 483
TaqI TCGA 7 cut(s) 27, 88, 509, 590, 594, 876, 1495
TaqII GACCGA 1 cut(s) 719
TasI AATT 5 cut(s) 382, 535, 928, 1320, 1412
TauI GCSGC 1 cut(s) 797
TfiI GAWTC 1 cut(s) 1112
Tru1I TTAA 3 cut(s) 92, 578, 1152
Tru9I TTAA 3 cut(s) 92, 578, 1152
TscAI CASTG 4 cut(s) 362, 1168, 1209, 1387
TseFI GTSAC 1 cut(s) 1447
TseI GCWGC 1 cut(s) 1076
Tsp45I GTSAC 1 cut(s) 1447
TspDTI ATGAA 7 cut(s) 40, 250, 378, 459, 560, 821, 1043
TspRI CASTG 4 cut(s) 362, 1168, 1209, 1387
Tth111I GACNNNGTC 1 cut(s) 328
VneI GTGCAC 1 cut(s) 1200
VpaK11BI GGWCC 1 cut(s) 1229
XapI RAATTY 2 cut(s) 382, 928
XcmI CCANNNNNNNNNTGG 2 cut(s) 152, 500
XmiI GTMKAC 2 cut(s) 638, 733
XmnI GAANNNNTTC 1 cut(s) 1424
XspI CTAG 2 cut(s) 341, 501
Zsp2I ATGCAT 1 cut(s) 1398
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.