Rh5BG401100

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0002778
Physical Location & Seq
Forward (+)
65089629 .. 65091137
1509 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5BG401100.1

Sequence Viewer

Length: 1308 bp
ATGGCTAAAGTTAGAGGGTCATATATTTTGTTGGCTCTCTTTGTGGTGCTCATTTCGATGGAAGCCTCTGTTGTTTTTGGTCAAGCCAACGGCAATGGAAATGCGAATGGAAACGGCAACACTGGCAGTGGCAACGGAAATGCCAACGGCAATGGCAACACCGGCAGTGGCAACGGAAATGGGAACGGCAATGGCAACACTGGCAGTGGCAACGGCAATGGGAATGGGAACGGCGACACTGGCAGTGGCAATGGCAACGGGAATGGGAACGGCAATACTGGCAGTGGCAACGGAAACGGCAACGGGAATGGCAATGGCAATGGAAACGGAAACGGGAATGGGAACGGAAATCAAGTTTATGCTGATGTTACAAACTACCAGGTATTGTCACCACTAGCAACCGGACAAGAGAGATGCATGTGCAAAGCTCAGGGCACCTGTTTCTACAAGACCCTTGTCTGTCCACCGGAGTGCCCTCAGAGAAAGCCTAAGCAGAACAAGAAACACAAGGGCTGCTTCGTCAACTGCGGCAGCAAGTGTGAAGTCACCTGCAAGTTTAGAAGAGCCAACTGTAATGGGTATGGTTCTCTCTGCTATGATCCTCGATTTGTTGGTGGAGATGGTGTTATGTTCTACTTCCATGGAGCCAAGGGAGTAAACTTTGCCATTGTTTCAGATGATAACCTCCAGATCAATGCACACTTCATTGGGACTCGACCACTTGGAAGGACTCGCGACTTCACATGGGTTCAAGCCCTCTCAATCATGTTCGACAATCACAACCTTGTCATTGCAGCGAAGAAAGTCTCAAAGTGGGCTGACAAAGTTGATGCTCTCATCGTAAGGTGGGATGGCGAGTCGGTTAGCATTCCTACTGATGGAGAAGCCGATTGGAGGACTAATGGTGATCAAGAACGACAGGTAATAGTGGAAAGAACCGATGATACTAACAACGTAAGAGTTACAGTTGCAGGGCTACTGGAAATGGACATAAAGATTAGGCCTATTGGAGAAGAAGAAAACAAGGTTCATAAGTATCAAATACCAGCTGATGATACTTTTGCTCACTTGGAAACACAGTTCAGATTTTCGAACTTATCTGATCTTGTCGAAGGAGTTTTGGGCAAGACTTATAGGCCAGGTTATGTTAGTCCAGTCAAGGTTGGAGTTCCAATGCCGATGATGGGTGGGGAGGACAAGTACAGAACTCCTTCACTGTTCTCACCTCTCTGCAAGGTTTGCAGGTTCCAAACTACTAGTCAATCTTCAGGGTTTGATATCACAAGTGGAGGAGTGACATCATACTGA
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
Root_cap

Protein Analysis

435

Amino Acids

46.14

Weight (kDa)

8.34

Isoelectric Point (pI)

4.31

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 360 - 416 1.8e-29 Root cap
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 557
Acc36I ACCTGC 2 cut(s) 557, 1233
AccB1I GGYRCC 1 cut(s) 434
AccII CGCG 1 cut(s) 735
AciI CCGC 1 cut(s) 528
AclWI GGATC 1 cut(s) 593
AcuI CTGAAG 1 cut(s) 1251
AfaI GTAC 1 cut(s) 1202
AfiI CCNNNNNNNGG 3 cut(s) 878, 894, 1184
AgsI TTSAA 1 cut(s) 752
AhlI ACTAGT 1 cut(s) 1256
AjnI CCWGG 2 cut(s) 378, 1138
AleI CACNNNNGTG 1 cut(s) 469
AloI GAACNNNNNNTCC 2 cut(s) 1064, 1096
AluBI AGCT 2 cut(s) 428, 1049
AluI AGCT 2 cut(s) 428, 1049
Alw21I GWGCWC 1 cut(s) 51
Alw26I GTCTC 1 cut(s) 811
AlwI GGATC 1 cut(s) 593
AoxI GGCC 2 cut(s) 1001, 1136
ApeKI GCWGC 3 cut(s) 513, 531, 794
ArsI GACNNNNNNTTYG 2 cut(s) 1243, 1275
Asp700I GAANNNNTTC 1 cut(s) 1210
AsuHPI GGTGA 4 cut(s) 381, 538, 917, 1215
AsuII TTCGAA 1 cut(s) 1091
BaeGI GKGCMC 2 cut(s) 437, 476
BanI GGYRCC 1 cut(s) 434
Bbv12I GWGCWC 1 cut(s) 51
BbvI GCAGC 3 cut(s) 500, 543, 806
BccI CCATC 5 cut(s) 52, 614, 845, 872, 1177
BceAI ACGGC 8 cut(s) 106, 130, 163, 202, 229, 247, 286, 313
BciT130I CCWGG 2 cut(s) 380, 1140
BclI TGATCA 1 cut(s) 907
BcoDI GTCTC 1 cut(s) 811
BcuI ACTAGT 1 cut(s) 1256
BfaI CTAG 2 cut(s) 395, 1257
BfuAI ACCTGC 2 cut(s) 557, 1233
BisI GCNGC 4 cut(s) 514, 529, 532, 795
BlsI GCNGC 4 cut(s) 515, 530, 533, 796
Bme1390I CCNGG 2 cut(s) 380, 1140
BmiI GGNNCC 3 cut(s) 436, 646, 1247
BmrFI CCNGG 2 cut(s) 380, 1140
BmsI GCATC 2 cut(s) 404, 820
BoxI GACNNNNGTC 1 cut(s) 455
BpmI CTGGAG 1 cut(s) 671
Bpu10I CCTNAGC 2 cut(s) 429, 489
Bpu14I TTCGAA 1 cut(s) 1091
BsaJI CCNNGG 2 cut(s) 640, 648
BsaWI WCCGGW 2 cut(s) 401, 466
BsaXI ACNNNNNCTCC 4 cut(s) 609, 639, 1184, 1214
Bsc4I CCNNNNNNNGG 3 cut(s) 878, 894, 1184
Bse118I RCCGGY 1 cut(s) 161
Bse1I ACTGG 6 cut(s) 127, 205, 244, 283, 984, 1154
Bse3DI GCAATG 8 cut(s) 100, 157, 196, 223, 256, 319, 325, 789
BseBI CCWGG 2 cut(s) 380, 1140
BseDI CCNNGG 2 cut(s) 640, 648
BseGI GGATG 1 cut(s) 856
BseLI CCNNNNNNNGG 3 cut(s) 878, 894, 1184
BseMI GCAATG 8 cut(s) 100, 157, 196, 223, 256, 319, 325, 789
BseMII CTCAG 2 cut(s) 443, 491
BseNI ACTGG 6 cut(s) 127, 205, 244, 283, 984, 1154
BseRI GAGGAG 1 cut(s) 1305
BseSI GKGCMC 2 cut(s) 437, 476
BseXI GCAGC 3 cut(s) 500, 543, 806
Bsh1236I CGCG 1 cut(s) 735
BshFI GGCC 2 cut(s) 1003, 1138
BshNI GGYRCC 1 cut(s) 434
BsiHKAI GWGCWC 1 cut(s) 51
BsiSI CCGG 3 cut(s) 162, 402, 467
BslFI GGGAC 1 cut(s) 724
BslI CCNNNNNNNGG 3 cut(s) 878, 894, 1184
BsmAI GTCTC 1 cut(s) 811
BsmFI GGGAC 1 cut(s) 724
BsmI GAATGC 1 cut(s) 867
BsnI GGCC 2 cut(s) 1003, 1138
Bsp119I TTCGAA 1 cut(s) 1091
Bsp1286I GDGCHC 3 cut(s) 51, 437, 476
Bsp143I GATC 4 cut(s) 598, 690, 907, 1102
Bsp19I CCATGG 1 cut(s) 640
Bsp68I TCGCGA 1 cut(s) 735
BspACI CCGC 1 cut(s) 528
BspANI GGCC 2 cut(s) 1003, 1138
BspCNI CTCAG 2 cut(s) 442, 490
BspFNI CGCG 1 cut(s) 735
BspLI GGNNCC 3 cut(s) 436, 646, 1247
BspMI ACCTGC 2 cut(s) 557, 1233
BspPI GGATC 1 cut(s) 593
BspQI GCTCTTC 1 cut(s) 556
BspT104I TTCGAA 1 cut(s) 1091
BspT107I GGYRCC 1 cut(s) 434
BsrDI GCAATG 8 cut(s) 100, 157, 196, 223, 256, 319, 325, 789
BsrFI RCCGGY 1 cut(s) 161
BsrI ACTGG 6 cut(s) 127, 205, 244, 283, 984, 1154
BssAI RCCGGY 1 cut(s) 161
BssECI CCNNGG 2 cut(s) 640, 648
BssMI GATC 4 cut(s) 598, 690, 907, 1102
BssT1I CCWWGG 2 cut(s) 640, 648
Bst2UI CCWGG 2 cut(s) 380, 1140
Bst4CI ACNGT 4 cut(s) 572, 967, 1080, 1218
Bst6I CTCTTC 1 cut(s) 556
BstAPI GCANNNNNTGC 1 cut(s) 1239
BstBI TTCGAA 1 cut(s) 1091
BstDEI CTNAG 3 cut(s) 429, 477, 489
BstDSI CCRYGG 1 cut(s) 640
BstF5I GGATG 1 cut(s) 856
BstFNI CGCG 1 cut(s) 735
BstKTI GATC 4 cut(s) 601, 693, 910, 1105
BstMAI GTCTC 1 cut(s) 811
BstMBI GATC 4 cut(s) 598, 690, 907, 1102
BstMWI GCNNNNNNNGC 6 cut(s) 123, 162, 201, 240, 279, 1239
BstNI CCWGG 2 cut(s) 380, 1140
BstNSI RCATGY 1 cut(s) 421
BstPAI GACNNNNGTC 1 cut(s) 455
BstSCI CCNGG 2 cut(s) 378, 1138
BstSLI GKGCMC 2 cut(s) 437, 476
BstUI CGCG 1 cut(s) 735
BstV1I GCAGC 3 cut(s) 500, 543, 806
BsuRI GGCC 2 cut(s) 1003, 1138
BtgI CCRYGG 1 cut(s) 640
BtsCI GGATG 1 cut(s) 856
BtsI GCAGTG 5 cut(s) 133, 172, 211, 250, 289
BtsIMutI CAGTG 9 cut(s) 120, 133, 172, 198, 211, 237, 250, 289, 1214
BtuMI TCGCGA 1 cut(s) 735
BveI ACCTGC 2 cut(s) 557, 1233
Cfr10I RCCGGY 1 cut(s) 161
CsiI ACCWGGT 1 cut(s) 378
Csp6I GTAC 1 cut(s) 1201
CviAII CATG 4 cut(s) 418, 641, 744, 766
CviQI GTAC 1 cut(s) 1201
DdeI CTNAG 3 cut(s) 429, 477, 489
DpnI GATC 4 cut(s) 600, 692, 909, 1104
DpnII GATC 4 cut(s) 598, 690, 907, 1102
Eam1104I CTCTTC 1 cut(s) 556
EarI CTCTTC 1 cut(s) 556
Eco130I CCWWGG 2 cut(s) 640, 648
Eco147I AGGCCT 1 cut(s) 1003
Eco32I GATATC 1 cut(s) 1279
Eco57I CTGAAG 1 cut(s) 1251
EcoRII CCWGG 2 cut(s) 378, 1138
EcoRV GATATC 1 cut(s) 1279
EcoT14I CCWWGG 2 cut(s) 640, 648
EcoT22I ATGCAT 1 cut(s) 419
ErhI CCWWGG 2 cut(s) 640, 648
FaeI CATG 4 cut(s) 421, 644, 747, 769
FalI AAGNNNNNCTT 2 cut(s) 500, 532
FaqI GGGAC 1 cut(s) 724
FatI CATG 4 cut(s) 417, 640, 743, 765
FbaI TGATCA 1 cut(s) 907
Fnu4HI GCNGC 4 cut(s) 514, 529, 532, 795
FokI GGATG 1 cut(s) 863
Fsp4HI GCNGC 4 cut(s) 514, 529, 532, 795
FspBI CTAG 2 cut(s) 395, 1257
GluI GCNGC 4 cut(s) 514, 529, 532, 795
GsuI CTGGAG 1 cut(s) 671
HaeIII GGCC 2 cut(s) 1003, 1138
HapII CCGG 3 cut(s) 162, 402, 467
Hin1II CATG 4 cut(s) 421, 644, 747, 769
HincII GTYRAC 1 cut(s) 523
HindII GTYRAC 1 cut(s) 523
HinfI GANTC 3 cut(s) 712, 730, 857
HpaII CCGG 3 cut(s) 162, 402, 467
HphI GGTGA 4 cut(s) 381, 538, 917, 1215
Hpy166II GTNNAC 3 cut(s) 464, 523, 658
Hpy188I TCNGA 4 cut(s) 480, 676, 1085, 1102
Hpy188III TCNNGA 3 cut(s) 688, 734, 911
Hpy8I GTNNAC 3 cut(s) 464, 523, 658
HpyAV CCTTC 3 cut(s) 720, 1106, 1221
HpyCH4III ACNGT 4 cut(s) 572, 967, 1080, 1218
HpyCH4IV ACGT 1 cut(s) 954
HpyCH4V TGCA 8 cut(s) 417, 423, 552, 698, 794, 971, 1233, 1242
HpyF10VI GCNNNNNNNGC 6 cut(s) 123, 162, 201, 240, 279, 1239
HpyF3I CTNAG 3 cut(s) 429, 477, 489
HpySE526I ACGT 1 cut(s) 954
Hsp92II CATG 4 cut(s) 421, 644, 747, 769
Ksp22I TGATCA 1 cut(s) 907
Kzo9I GATC 4 cut(s) 598, 690, 907, 1102
LguI GCTCTTC 1 cut(s) 556
LmnI GCTCC 1 cut(s) 644
Lsp1109I GCAGC 3 cut(s) 500, 543, 806
LweI GCATC 2 cut(s) 404, 820
MabI ACCWGGT 1 cut(s) 378
MaeI CTAG 2 cut(s) 395, 1257
MaeII ACGT 1 cut(s) 954
MaeIII GTNAC 5 cut(s) 367, 387, 544, 961, 1294
MalI GATC 4 cut(s) 600, 692, 909, 1104
MboI GATC 4 cut(s) 598, 690, 907, 1102
MboII GAAGA 5 cut(s) 573, 811, 1025, 1028, 1257
MhlI GDGCHC 3 cut(s) 51, 437, 476
MlyI GAGTC 3 cut(s) 706, 724, 866
MmeI TCCRAC 1 cut(s) 1144
Mph1103I ATGCAT 1 cut(s) 419
MroXI GAANNNNTTC 1 cut(s) 1210
MslI CAYNNNNRTG 2 cut(s) 56, 469
MspA1I CMGCKG 1 cut(s) 1049
MspI CCGG 3 cut(s) 162, 402, 467
MspR9I CCNGG 2 cut(s) 380, 1140
Mva1269I GAATGC 1 cut(s) 867
MvaI CCWGG 2 cut(s) 380, 1140
MvnI CGCG 1 cut(s) 735
MwoI GCNNNNNNNGC 6 cut(s) 123, 162, 201, 240, 279, 1239
NcoI CCATGG 1 cut(s) 640
NdeII GATC 4 cut(s) 598, 690, 907, 1102
NlaIII CATG 4 cut(s) 421, 644, 747, 769
NlaIV GGNNCC 3 cut(s) 436, 646, 1247
NmuCI GTSAC 3 cut(s) 387, 544, 1294
NruI TCGCGA 1 cut(s) 735
NsiI ATGCAT 1 cut(s) 419
NspI RCATGY 1 cut(s) 421
NspV TTCGAA 1 cut(s) 1091
OliI CACNNNNGTG 1 cut(s) 469
PaqCI CACCTGC 1 cut(s) 557
PceI AGGCCT 1 cut(s) 1003
PciSI GCTCTTC 1 cut(s) 556
PctI GAATGC 1 cut(s) 867
PdmI GAANNNNTTC 1 cut(s) 1210
PkrI GCNGC 4 cut(s) 515, 530, 533, 796
PleI GAGTC 3 cut(s) 706, 724, 865
PpsI GAGTC 3 cut(s) 706, 724, 865
PshAI GACNNNNGTC 1 cut(s) 455
Psp6I CCWGG 2 cut(s) 378, 1138
PspGI CCWGG 2 cut(s) 378, 1138
PspN4I GGNNCC 3 cut(s) 436, 646, 1247
PsrI GAACNNNNNNTAC 2 cut(s) 928, 960
PvuII CAGCTG 1 cut(s) 1049
RruI TCGCGA 1 cut(s) 735
RsaI GTAC 1 cut(s) 1202
RsaNI GTAC 1 cut(s) 1201
RseI CAYNNNNRTG 2 cut(s) 56, 469
SapI GCTCTTC 1 cut(s) 556
SatI GCNGC 4 cut(s) 514, 529, 532, 795
Sau3AI GATC 4 cut(s) 598, 690, 907, 1102
SchI GAGTC 3 cut(s) 706, 724, 866
ScrFI CCNGG 2 cut(s) 380, 1140
SduI GDGCHC 3 cut(s) 51, 437, 476
SexAI ACCWGGT 1 cut(s) 378
SfaNI GCATC 2 cut(s) 404, 820
SfuI TTCGAA 1 cut(s) 1091
SmiMI CAYNNNNRTG 2 cut(s) 56, 469
SpeI ACTAGT 1 cut(s) 1256
SseBI AGGCCT 1 cut(s) 1003
SsiI CCGC 1 cut(s) 528
SspMI CTAG 2 cut(s) 395, 1257
StuI AGGCCT 1 cut(s) 1003
StyD4I CCNGG 2 cut(s) 378, 1138
StyI CCWWGG 2 cut(s) 640, 648
TaaI ACNGT 4 cut(s) 572, 967, 1080, 1218
TaiI ACGT 1 cut(s) 957
TaqI TCGA 6 cut(s) 56, 604, 715, 771, 1091, 1110
TatI WGTACW 1 cut(s) 1200
TauI GCSGC 1 cut(s) 531
TscAI CASTG 9 cut(s) 127, 133, 172, 205, 211, 244, 250, 289, 1221
TseFI GTSAC 3 cut(s) 387, 544, 1294
TseI GCWGC 3 cut(s) 513, 531, 794
Tsp45I GTSAC 3 cut(s) 387, 544, 1294
TspDTI ATGAA 2 cut(s) 694, 1019
TspGWI ACGGA 5 cut(s) 150, 189, 306, 342, 360
TspRI CASTG 9 cut(s) 127, 133, 172, 205, 211, 244, 250, 289, 1221
XceI RCATGY 1 cut(s) 421
XmnI GAANNNNTTC 1 cut(s) 1210
XspI CTAG 2 cut(s) 395, 1257
Zsp2I ATGCAT 1 cut(s) 419
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.