Rh5AG359400

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0002618
Physical Location & Seq
Forward (+)
60476619 .. 60509415
32797 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG359400.1

Sequence Viewer

Length: 1608 bp
ATGCAGGCCCTTGAAGTCCCTGTGGTGGGCTTCACCAAGACTAGAGATGAGCGTGATGAGGATGTTGTTGATTGCATTAGAGAAGGGGAGTCCATGGCATTGGATTCGGGGAGTGAAGTGGAGGCTATAGCAGGAGGTCAATTGGTGAAAAGAAGACGGGTTTTGAGTGAGTTTTCTGAGCTTTCTACTGCTGAGGGATCTCCTAAACCAAAGGCTAAGAAAGTCAAGTGCCAAGACAAGAAGTTCTACAAGTGTTACCATAAAGATCTCTACTGCCCAGCAGCATGCCTCCGCACTTGTGTTGTGGATTGTAAGAAATGCAAAGCTGTTTGTAAGGCGCCGCCTCCACCACCACCACCTCCTCCACCGCCGCCACCCAGACGAAAGTGGCGCCACCCACCCCCTCCTCCCCCAAAGAGTTATCACCACTCACCGCCTCCTCCTCCCAAGACTTATCCTTCACCACCACCTGCCCCTTCAGTTGTTCCTACTCCCCCTCCTCCAGCTACAACTCCACCTCCGTCACCCCCCATCTCTACCCCGTCGTCACAACCGATGCCTCCTGCTACTACCCCATCACCACCGCCATCCCCTATTACTACTCCATCACCACCTTTGTCCACACCATCATCACCGCCACCCCCTACTCCTACTCCATCACCACCGCTGCCCCCTACTTCTACACCACCTTCTTTCTATCCTCCACCACCGCCTTCATCAGAGGCCGCGGGTGAAAAGAGAGTCAAATGCAAGAATAAGAACTACCCTCATTGCTATGGTCTGGAGCTAAGTTGTCCTAGTGGGTGCCCTGAGCAATGTGAAGTTGACTGCGTCACATGCAGTCCCGTTTGTAACTGCAACAAACCAGGTGCTGTTTGCCAAGACCCTAGATTTATTGGTGGTGATGGTATAACCTTCTACTTCCATGGCAAGCGAGACCAAGACTTCTGTCTCGTATCTGATTCCAACATCCACATCAACGCCCATTTCATCGGAAAAAGAGACCAAAATATGAAGAGGGACTTCACTTGGGTCCAATCTGTAGGTATCCTCTTTGACAATCGCAAGCTCTTCATAGGTGCCAAACCAACCTCCACTTGGGATGACACCGTCGACCGCCTAACCCTAGCCATTGACGACGAAACCATTAGCCTTGCCGACAACGAAGGCGCATATTGGCAATCACAAGGACTCAAGATCACAAGGAGCAAGAACACAAATGCTGTAGAAATTGAAGCTGAAGGGAACTTCAAGATCAAAGCAGTGGTGGTGCCGATAACGGAGAAGGAGTCGGTGATACACAGGTATGGGATTACACAGGAGGATTGCTTTGCTCACCTTGACTTGAGCTTCAAGTTTTATGCCCTAAGTGGGGAAGTTAATGGCGTGCTAGGACAGACATACGGTGAGAACTATGTTAGTAGGGTCAAGATGGGTGTCGTGATGCCTGTTTTGGGTGGCGATAGAGAATTTTCATCGTCTAGCATCTTTGCCTCGGATTGTGCTGTTGCTAGGTTTAGCGGTGAGTCTAGTGGAAAGTCCAAGTATGCTAGTACTATGAATTGCGCTAGTGGGATGGATGGCCGTGGAGTTTTTTGTAAGAGGTAA
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

535

Amino Acids

58.01

Weight (kDa)

8.4

Isoelectric Point (pI)

67.27

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 450 - 506 4.7e-27 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) 478
Acc36I ACCTGC 1 cut(s) 478
AccB1I GGYRCC 5 cut(s) 337, 390, 804, 1079, 1270
AccI GTMKAC 1 cut(s) 1113
AccII CGCG 1 cut(s) 728
AclWI GGATC 1 cut(s) 205
AcoI YGGCCR 1 cut(s) 1582
AcsI RAATTY 1 cut(s) 1469
AcuI CTGAAG 2 cut(s) 462, 1260
AcyI GRCGYC 2 cut(s) 338, 391
AfaI GTAC 1 cut(s) 1555
AfiI CCNNNNNNNGG 6 cut(s) 25, 26, 1098, 1371, 1372, 1454
AgsI TTSAA 4 cut(s) 14, 1235, 1252, 1354
AjnI CCWGG 1 cut(s) 865
AluBI AGCT 7 cut(s) 181, 326, 506, 787, 1069, 1238, 1350
AluI AGCT 7 cut(s) 181, 326, 506, 787, 1069, 1238, 1350
Alw26I GTCTC 3 cut(s) 930, 956, 996
AlwI GGATC 1 cut(s) 205
AlwNI CAGNNNCTG 1 cut(s) 872
AoxI GGCC 3 cut(s) 6, 723, 1582
ApeKI GCWGC 2 cut(s) 281, 667
ApoI RAATTY 1 cut(s) 1469
AspLEI GCGC 4 cut(s) 340, 393, 1172, 1568
AspS9I GGNCC 2 cut(s) 7, 1033
AvaII GGWCC 1 cut(s) 1033
BaeGI GKGCMC 1 cut(s) 809
BaeI ACNNNNGTAYC 2 cut(s) 1289, 1322
BanI GGYRCC 5 cut(s) 337, 390, 804, 1079, 1270
BbsI GAAGAC 1 cut(s) 160
BbvCI CCTCAGC 1 cut(s) 192
BbvI GCAGC 2 cut(s) 293, 654
BceAI ACGGC 1 cut(s) 1569
BcgI CGANNNNNNTGC 2 cut(s) 87, 121
BciT130I CCWGG 1 cut(s) 867
BciVI GTATCC 1 cut(s) 1058
BcoDI GTCTC 3 cut(s) 930, 956, 996
BfmI CTRYAG 3 cut(s) 126, 1041, 1224
BfoI RGCGCY 2 cut(s) 341, 394
BfuAI ACCTGC 1 cut(s) 478
BfuI GTATCC 1 cut(s) 1058
BglII AGATCT 1 cut(s) 265
BisI GCNGC 5 cut(s) 282, 341, 371, 668, 726
BlsI GCNGC 5 cut(s) 283, 342, 372, 669, 727
BmcAI AGTACT 1 cut(s) 1555
Bme1390I CCNGG 1 cut(s) 867
Bme18I GGWCC 1 cut(s) 1033
BmgT120I GGNCC 2 cut(s) 7, 1033
BmiI GGNNCC 6 cut(s) 339, 392, 806, 1034, 1081, 1272
BmrFI CCNGG 1 cut(s) 867
BmsI GCATC 3 cut(s) 546, 1434, 1494
BoxI GACNNNNGTC 1 cut(s) 948
BpiI GAAGAC 1 cut(s) 160
BpmI CTGGAG 2 cut(s) 486, 803
Bpu10I CCTNAGC 2 cut(s) 192, 810
BpuEI CTTGAG 2 cut(s) 1178, 1366
BsaHI GRCGYC 2 cut(s) 338, 391
BsaI GGTCTC 2 cut(s) 930, 996
BsaJI CCNNGG 5 cut(s) 93, 726, 925, 1494, 1585
BsaXI ACNNNNNCTCC 8 cut(s) 481, 502, 511, 532, 637, 667, 1274, 1304
Bsc4I CCNNNNNNNGG 6 cut(s) 25, 26, 1098, 1371, 1372, 1454
Bse3DI GCAATG 2 cut(s) 769, 821
BseBI CCWGG 1 cut(s) 867
BseDI CCNNGG 5 cut(s) 93, 726, 925, 1494, 1585
BseGI GGATG 6 cut(s) 67, 587, 969, 1108, 1581, 1585
BseLI CCNNNNNNNGG 6 cut(s) 25, 26, 1098, 1371, 1372, 1454
BseMI GCAATG 2 cut(s) 769, 821
BseMII CTCAG 3 cut(s) 168, 183, 801
BseRI GAGGAG 5 cut(s) 351, 396, 429, 432, 489
BseSI GKGCMC 1 cut(s) 809
BseXI GCAGC 2 cut(s) 293, 654
BseYI CCCAGC 1 cut(s) 277
Bsh1236I CGCG 1 cut(s) 728
Bsh1285I CGRYCG 1 cut(s) 1117
BshFI GGCC 3 cut(s) 8, 725, 1584
BshNI GGYRCC 5 cut(s) 337, 390, 804, 1079, 1270
BsiEI CGRYCG 1 cut(s) 1117
BslFI GGGAC 3 cut(s) 2, 828, 1034
BslI CCNNNNNNNGG 6 cut(s) 25, 26, 1098, 1371, 1372, 1454
BsmAI GTCTC 3 cut(s) 930, 956, 996
BsmFI GGGAC 3 cut(s) 2, 828, 1034
BsnI GGCC 3 cut(s) 8, 725, 1584
Bso31I GGTCTC 2 cut(s) 930, 996
Bsp1286I GDGCHC 1 cut(s) 809
Bsp143I GATC 4 cut(s) 197, 265, 1197, 1254
Bsp19I CCATGG 2 cut(s) 93, 925
BspANI GGCC 3 cut(s) 8, 725, 1584
BspCNI CTCAG 3 cut(s) 169, 184, 802
BspFNI CGCG 1 cut(s) 728
BspLI GGNNCC 6 cut(s) 339, 392, 806, 1034, 1081, 1272
BspMI ACCTGC 1 cut(s) 478
BspPI GGATC 1 cut(s) 205
BspQI GCTCTTC 1 cut(s) 1076
BspT107I GGYRCC 5 cut(s) 337, 390, 804, 1079, 1270
BspTNI GGTCTC 2 cut(s) 930, 996
BsrDI GCAATG 2 cut(s) 769, 821
BssECI CCNNGG 5 cut(s) 93, 726, 925, 1494, 1585
BssMI GATC 4 cut(s) 197, 265, 1197, 1254
BssNI GRCGYC 2 cut(s) 338, 391
BssT1I CCWWGG 2 cut(s) 93, 925
Bst2UI CCWGG 1 cut(s) 867
Bst4CI ACNGT 2 cut(s) 1111, 1406
Bst6I CTCTTC 2 cut(s) 1010, 1076
BstACI GRCGYC 2 cut(s) 338, 391
BstC8I GCNNGC 5 cut(s) 6, 286, 932, 1067, 1388
BstDEI CTNAG 6 cut(s) 177, 192, 216, 788, 810, 1367
BstDSI CCRYGG 4 cut(s) 93, 726, 925, 1585
BstF5I GGATG 6 cut(s) 67, 587, 969, 1108, 1581, 1585
BstFNI CGCG 1 cut(s) 728
BstH2I RGCGCY 2 cut(s) 341, 394
BstHHI GCGC 4 cut(s) 340, 393, 1172, 1568
BstKTI GATC 4 cut(s) 200, 268, 1200, 1257
BstMAI GTCTC 3 cut(s) 930, 956, 996
BstMBI GATC 4 cut(s) 197, 265, 1197, 1254
BstMCI CGRYCG 1 cut(s) 1117
BstMWI GCNNNNNNNGC 1 cut(s) 837
BstNI CCWGG 1 cut(s) 867
BstNSI RCATGY 2 cut(s) 288, 840
BstPAI GACNNNNGTC 1 cut(s) 948
BstSCI CCNGG 1 cut(s) 865
BstSFI CTRYAG 3 cut(s) 126, 1041, 1224
BstSLI GKGCMC 1 cut(s) 809
BstUI CGCG 1 cut(s) 728
BstV1I GCAGC 2 cut(s) 293, 654
BstV2I GAAGAC 1 cut(s) 160
BstX2I RGATCY 2 cut(s) 197, 265
BstXI CCANNNNNNTGG 1 cut(s) 100
BstYI RGATCY 2 cut(s) 197, 265
BsuI GTATCC 1 cut(s) 1058
BsuRI GGCC 3 cut(s) 8, 725, 1584
BtgI CCRYGG 4 cut(s) 93, 726, 925, 1585
BtsCI GGATG 6 cut(s) 67, 587, 969, 1108, 1581, 1585
BtsI GCAGTG 1 cut(s) 1269
BtsIMutI CAGTG 1 cut(s) 1269
BveI ACCTGC 1 cut(s) 478
Cac8I GCNNGC 5 cut(s) 6, 286, 932, 1067, 1388
CaiI CAGNNNCTG 1 cut(s) 872
CfoI GCGC 4 cut(s) 340, 393, 1172, 1568
Cfr13I GGNCC 2 cut(s) 7, 1033
Cfr42I CCGCGG 1 cut(s) 729
CseI GACGC 1 cut(s) 820
CsiI ACCWGGT 1 cut(s) 865
Csp6I GTAC 1 cut(s) 1554
CviAII CATG 4 cut(s) 94, 285, 837, 926
CviQI GTAC 1 cut(s) 1554
DdeI CTNAG 6 cut(s) 177, 192, 216, 788, 810, 1367
DinI GGCGCC 2 cut(s) 339, 392
DpnI GATC 4 cut(s) 199, 267, 1199, 1256
DpnII GATC 4 cut(s) 197, 265, 1197, 1254
EaeI YGGCCR 1 cut(s) 1582
Eam1104I CTCTTC 2 cut(s) 1010, 1076
EarI CTCTTC 2 cut(s) 1010, 1076
Eco130I CCWWGG 2 cut(s) 93, 925
Eco31I GGTCTC 2 cut(s) 930, 996
Eco47I GGWCC 1 cut(s) 1033
Eco57I CTGAAG 2 cut(s) 462, 1260
EcoO109I RGGNCCY 1 cut(s) 7
EcoRII CCWGG 1 cut(s) 865
EcoT14I CCWWGG 2 cut(s) 93, 925
EgeI GGCGCC 2 cut(s) 339, 392
EheI GGCGCC 2 cut(s) 339, 392
ErhI CCWWGG 2 cut(s) 93, 925
FaeI CATG 4 cut(s) 97, 288, 840, 929
FalI AAGNNNNNCTT 2 cut(s) 1007, 1039
FaqI GGGAC 3 cut(s) 2, 828, 1034
FatI CATG 4 cut(s) 93, 284, 836, 925
FauI CCCGC 1 cut(s) 721
FblI GTMKAC 1 cut(s) 1113
Fnu4HI GCNGC 5 cut(s) 282, 341, 371, 668, 726
FokI GGATG 6 cut(s) 74, 574, 956, 1115, 1588, 1592
Fsp4HI GCNGC 5 cut(s) 282, 341, 371, 668, 726
GlaI GCGC 4 cut(s) 339, 392, 1171, 1567
GluI GCNGC 5 cut(s) 282, 341, 371, 668, 726
GsaI CCCAGC 1 cut(s) 281
GsuI CTGGAG 2 cut(s) 486, 803
HaeII RGCGCY 2 cut(s) 341, 394
HaeIII GGCC 3 cut(s) 8, 725, 1584
HgaI GACGC 1 cut(s) 820
HhaI GCGC 4 cut(s) 340, 393, 1172, 1568
Hin1I GRCGYC 2 cut(s) 338, 391
Hin1II CATG 4 cut(s) 97, 288, 840, 929
Hin6I GCGC 4 cut(s) 338, 391, 1170, 1566
HinP1I GCGC 4 cut(s) 338, 391, 1170, 1566
HincII GTYRAC 2 cut(s) 826, 1114
HindII GTYRAC 2 cut(s) 826, 1114
HinfI GANTC 7 cut(s) 89, 104, 741, 962, 1191, 1289, 1526
Hpy166II GTNNAC 3 cut(s) 621, 826, 1114
Hpy188I TCNGA 5 cut(s) 178, 721, 961, 995, 1498
Hpy188III TCNNGA 5 cut(s) 782, 1195, 1252, 1429, 1441
Hpy8I GTNNAC 3 cut(s) 621, 826, 1114
Hpy99I CGWCG 3 cut(s) 547, 1115, 1142
HpyAV CCTTC 9 cut(s) 77, 468, 486, 699, 723, 925, 1160, 1235, 1279
HpyCH4III ACNGT 2 cut(s) 1111, 1406
HpyCH4V TGCA 6 cut(s) 4, 75, 321, 750, 840, 858
HpyF10VI GCNNNNNNNGC 1 cut(s) 837
HpyF3I CTNAG 6 cut(s) 177, 192, 216, 788, 810, 1367
Hsp92I GRCGYC 2 cut(s) 338, 391
Hsp92II CATG 4 cut(s) 97, 288, 840, 929
HspAI GCGC 4 cut(s) 338, 391, 1170, 1566
KasI GGCGCC 2 cut(s) 337, 390
KspI CCGCGG 1 cut(s) 729
Kzo9I GATC 4 cut(s) 197, 265, 1197, 1254
LguI GCTCTTC 1 cut(s) 1076
LmnI GCTCC 2 cut(s) 784, 1206
Lsp1109I GCAGC 2 cut(s) 293, 654
LweI GCATC 3 cut(s) 546, 1434, 1494
MabI ACCWGGT 1 cut(s) 865
MaeIII GTNAC 5 cut(s) 254, 522, 546, 832, 851
MalI GATC 4 cut(s) 199, 267, 1199, 1256
MboI GATC 4 cut(s) 197, 265, 1197, 1254
MboII GAAGA 3 cut(s) 165, 1027, 1063
MfeI CAATTG 1 cut(s) 140
MflI RGATCY 2 cut(s) 197, 265
MhlI GDGCHC 1 cut(s) 809
MluCI AATT 4 cut(s) 140, 1230, 1469, 1561
Mly113I GGCGCC 2 cut(s) 338, 391
MlyI GAGTC 5 cut(s) 98, 750, 1185, 1298, 1535
MmeI TCCRAC 1 cut(s) 990
MseI TTAA 1 cut(s) 1380
MslI CAYNNNNRTG 2 cut(s) 774, 1305
MspA1I CMGCKG 2 cut(s) 667, 728
MspR9I CCNGG 1 cut(s) 867
MunI CAATTG 1 cut(s) 140
MvaI CCWGG 1 cut(s) 867
MvnI CGCG 1 cut(s) 728
MwoI GCNNNNNNNGC 1 cut(s) 837
NarI GGCGCC 2 cut(s) 338, 391
NcoI CCATGG 2 cut(s) 93, 925
NdeII GATC 4 cut(s) 197, 265, 1197, 1254
NlaIII CATG 4 cut(s) 97, 288, 840, 929
NlaIV GGNNCC 6 cut(s) 339, 392, 806, 1034, 1081, 1272
NmuCI GTSAC 3 cut(s) 522, 546, 832
NspI RCATGY 2 cut(s) 288, 840
PaeI GCATGC 1 cut(s) 288
PaqCI CACCTGC 1 cut(s) 478
PciSI GCTCTTC 1 cut(s) 1076
PcsI WCGNNNNNNNCGW 1 cut(s) 551
PfeI GAWTC 2 cut(s) 104, 962
PflFI GACNNNGTC 2 cut(s) 830, 1109
PkrI GCNGC 5 cut(s) 283, 342, 372, 669, 727
PleI GAGTC 5 cut(s) 97, 749, 1185, 1297, 1534
PluTI GGCGCC 2 cut(s) 341, 394
PpsI GAGTC 5 cut(s) 97, 749, 1185, 1297, 1534
PshAI GACNNNNGTC 1 cut(s) 948
Psp6I CCWGG 1 cut(s) 865
PspFI CCCAGC 1 cut(s) 277
PspGI CCWGG 1 cut(s) 865
PspN4I GGNNCC 6 cut(s) 339, 392, 806, 1034, 1081, 1272
PspPI GGNCC 2 cut(s) 7, 1033
PstNI CAGNNNCTG 1 cut(s) 872
PsuI RGATCY 2 cut(s) 197, 265
PsyI GACNNNGTC 2 cut(s) 830, 1109
RsaI GTAC 1 cut(s) 1555
RsaNI GTAC 1 cut(s) 1554
RseI CAYNNNNRTG 2 cut(s) 774, 1305
SacII CCGCGG 1 cut(s) 729
SalI GTCGAC 1 cut(s) 1112
SapI GCTCTTC 1 cut(s) 1076
SaqAI TTAA 1 cut(s) 1380
SatI GCNGC 5 cut(s) 282, 341, 371, 668, 726
Sau3AI GATC 4 cut(s) 197, 265, 1197, 1254
Sau96I GGNCC 2 cut(s) 7, 1033
ScaI AGTACT 1 cut(s) 1555
SchI GAGTC 5 cut(s) 98, 750, 1185, 1298, 1535
ScrFI CCNGG 1 cut(s) 867
SduI GDGCHC 1 cut(s) 809
SexAI ACCWGGT 1 cut(s) 865
SfaNI GCATC 3 cut(s) 546, 1434, 1494
SfcI CTRYAG 3 cut(s) 126, 1041, 1224
SfoI GGCGCC 2 cut(s) 339, 392
Sfr303I CCGCGG 1 cut(s) 729
SgrBI CCGCGG 1 cut(s) 729
SinI GGWCC 1 cut(s) 1033
SmiMI CAYNNNNRTG 2 cut(s) 774, 1305
SmlI CTYRAG 2 cut(s) 1193, 1345
SmoI CTYRAG 2 cut(s) 1193, 1345
SphI GCATGC 1 cut(s) 288
Sse9I AATT 4 cut(s) 140, 1230, 1469, 1561
SspDI GGCGCC 2 cut(s) 337, 390
StyD4I CCNGG 1 cut(s) 865
StyI CCWWGG 2 cut(s) 93, 925
TaaI ACNGT 2 cut(s) 1111, 1406
TaqI TCGA 1 cut(s) 1113
TasI AATT 4 cut(s) 140, 1230, 1469, 1561
TatI WGTACW 1 cut(s) 1553
TauI GCSGC 3 cut(s) 343, 373, 728
TfiI GAWTC 2 cut(s) 104, 962
Tru1I TTAA 1 cut(s) 1380
Tru9I TTAA 1 cut(s) 1380
TscAI CASTG 1 cut(s) 1269
TseFI GTSAC 3 cut(s) 522, 546, 832
TseI GCWGC 2 cut(s) 281, 667
Tsp45I GTSAC 3 cut(s) 522, 546, 832
TspDTI ATGAA 6 cut(s) 705, 979, 1028, 1063, 1464, 1574
TspGWI ACGGA 2 cut(s) 510, 1295
TspRI CASTG 1 cut(s) 1269
Tth111I GACNNNGTC 2 cut(s) 830, 1109
VpaK11BI GGWCC 1 cut(s) 1033
XapI RAATTY 1 cut(s) 1469
XceI RCATGY 2 cut(s) 288, 840
XcmI CCANNNNNNNNNTGG 1 cut(s) 1095
XmiI GTMKAC 1 cut(s) 1113
ZrmI AGTACT 1 cut(s) 1555
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.