Rh5DG250900

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0006038
Physical Location & Seq
Reverse (-)
29008577 .. 29010176
1600 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG250900.1

Sequence Viewer

Length: 1020 bp
ATGGAGTTCTTAGCAGGTAGCTACAAAACCTTGTTGATCATTCTGCTATTCTTTGTTTCTGCCATACTACAAAGTCGAGCAGAAACTAAAGTTTGCTTCAGCAAGGGCAGTCCATGTTTTCTCAAGAAGCTACAGTGCCCTGCACAATGCCCATCCTCTTCACCAACCGACCCAAAAGTAACCAAGGTGTGCGTTGTCAACTGTAACTCCCCCATATGCAAAGCTGAGTGCAGAAATCGCAAACCTAATTGCAATGGTCCTGGATCAGCATGCCTGGACCCTCGCTTCATCGGTGGAGATGGCATTGTCTTTTACTTCCACGGCAAGAAAAACGAGCATTTCACCTTGGTTTCCGATCCAAACCTCCAAATCAATGCCCGGTTCATTGGTCTCCGCCCTGAAGGAAGAACCAGGGACTATACATGGATTCAAGCCCTTGGACTTCTCTTTAACTCTAACAGCTTCACACTTGAGGCCACCCCATCAGCAACATGGGATGATGAAGTTGACCACTTGAAATTCTCTTATAATGGTGAGGAGCTAATCATCCCAGGATCAGATCTCTCCGTTTGGAAATCTCAGGAATCTTCTATTAGAGTGGAAAGAACATCAACCAAGAACAGTGTCCTAGTCACTCTCCCAGAAGTTGCTGAAATTTCGGTAAATGTGGTGCCTGTGACAAAGGAAGATGATAAGATCCACAATTATCAGATACCATCAGATGACTGTTTTGCTCACCTTGAAGTGCAGTTCAGATTCTATGGCCTGTCTTCAAATGTTGAAGGAGTTCTTGGGAGGACTTACCAGCCAGATTTCAAGAACCCAGCAAAGCCAGGAGTAGCCATGCCGGTAGTTGGAGGTGAACACAAGTACAAAACAACGTCACTTGTTTCTGCCGATTGCATGGCTTGTGTGTTCACTCAGGCCGGTAATCAAAAGGATTCAAGGGTGATGGACTACAGCAAGCTGGACTGCACCGGCAATACCTTCAGTGGGAACGGAATTGTTTGCAGGAAATAA
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

339

Amino Acids

37.43

Weight (kDa)

7.85

Isoelectric Point (pI)

34.18

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 250 - 306 1.7e-26 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)
AanI TTATAA 1 cut(s) 528
Acc36I ACCTGC 1 cut(s) 5
AccB1I GGYRCC 1 cut(s) 670
AciI CCGC 1 cut(s) 394
AclWI GGATC 4 cut(s) 271, 350, 562, 691
AcsI RAATTY 2 cut(s) 518, 654
AcuI CTGAAG 3 cut(s) 82, 420, 973
AfaI GTAC 1 cut(s) 872
AfiI CCNNNNNNNGG 2 cut(s) 854, 993
AgsI TTSAA 7 cut(s) 431, 517, 743, 774, 782, 817, 945
AjnI CCWGG 5 cut(s) 259, 273, 410, 550, 832
AjuI GAANNNNNNNTTGG 2 cut(s) 774, 806
AluBI AGCT 6 cut(s) 21, 130, 224, 462, 541, 967
AluI AGCT 6 cut(s) 21, 130, 224, 462, 541, 967
Alw26I GTCTC 1 cut(s) 395
AlwI GGATC 4 cut(s) 271, 350, 562, 691
AoxI GGCC 3 cut(s) 474, 763, 924
ApoI RAATTY 2 cut(s) 518, 654
Asp700I GAANNNNTTC 1 cut(s) 786
AspS9I GGNCC 2 cut(s) 257, 277
AsuC2I CCSGG 1 cut(s) 379
AsuHPI GGTGA 6 cut(s) 153, 334, 545, 728, 872, 961
AvaII GGWCC 2 cut(s) 257, 277
BaeGI GKGCMC 1 cut(s) 140
BanI GGYRCC 1 cut(s) 670
BbsI GAAGAC 1 cut(s) 762
BccI CCATC 5 cut(s) 160, 293, 490, 724, 946
BceAI ACGGC 1 cut(s) 337
BciT130I CCWGG 5 cut(s) 261, 275, 412, 552, 834
BclI TGATCA 1 cut(s) 36
BcnI CCSGG 1 cut(s) 379
BcoDI GTCTC 1 cut(s) 395
BfaI CTAG 1 cut(s) 629
BfmI CTRYAG 2 cut(s) 131, 958
BfuAI ACCTGC 1 cut(s) 5
BglII AGATCT 1 cut(s) 559
Bme1390I CCNGG 6 cut(s) 261, 275, 379, 412, 552, 834
Bme18I GGWCC 2 cut(s) 257, 277
BmgT120I GGNCC 2 cut(s) 257, 277
BmiI GGNNCC 2 cut(s) 279, 672
BmrFI CCNGG 6 cut(s) 261, 275, 379, 412, 552, 834
BpiI GAAGAC 1 cut(s) 762
BpuEI CTTGAG 2 cut(s) 107, 491
BpuMI CCSGG 1 cut(s) 379
BsaI GGTCTC 1 cut(s) 395
BsaJI CCNNGG 6 cut(s) 183, 319, 345, 411, 436, 550
BsaXI ACNNNNNCTCC 2 cut(s) 191, 221
Bsc4I CCNNNNNNNGG 2 cut(s) 854, 993
Bse118I RCCGGY 3 cut(s) 847, 926, 977
Bse3DI GCAATG 1 cut(s) 259
BseBI CCWGG 5 cut(s) 261, 275, 412, 552, 834
BseDI CCNNGG 6 cut(s) 183, 319, 345, 411, 436, 550
BseGI GGATG 3 cut(s) 152, 502, 546
BseLI CCNNNNNNNGG 2 cut(s) 854, 993
BseMI GCAATG 1 cut(s) 259
BseMII CTCAG 3 cut(s) 216, 593, 935
BseRI GAGGAG 1 cut(s) 551
BseSI GKGCMC 1 cut(s) 140
BseYI CCCAGC 1 cut(s) 823
BsgI GTGCAG 4 cut(s) 126, 250, 767, 958
BshFI GGCC 3 cut(s) 476, 765, 926
BshNI GGYRCC 1 cut(s) 670
BsiSI CCGG 4 cut(s) 379, 848, 927, 978
BslFI GGGAC 1 cut(s) 428
BslI CCNNNNNNNGG 2 cut(s) 854, 993
BsmAI GTCTC 1 cut(s) 395
BsmFI GGGAC 1 cut(s) 428
BsnI GGCC 3 cut(s) 476, 765, 926
Bso31I GGTCTC 1 cut(s) 395
Bsp1286I GDGCHC 1 cut(s) 140
Bsp143I GATC 6 cut(s) 36, 263, 355, 554, 559, 696
BspACI CCGC 1 cut(s) 394
BspANI GGCC 3 cut(s) 476, 765, 926
BspCNI CTCAG 3 cut(s) 217, 592, 934
BspLI GGNNCC 2 cut(s) 279, 672
BspMI ACCTGC 1 cut(s) 5
BspPI GGATC 4 cut(s) 271, 350, 562, 691
BspT107I GGYRCC 1 cut(s) 670
BspTNI GGTCTC 1 cut(s) 395
BsrDI GCAATG 1 cut(s) 259
BsrFI RCCGGY 3 cut(s) 847, 926, 977
BssAI RCCGGY 3 cut(s) 847, 926, 977
BssECI CCNNGG 6 cut(s) 183, 319, 345, 411, 436, 550
BssMI GATC 6 cut(s) 36, 263, 355, 554, 559, 696
BssT1I CCWWGG 3 cut(s) 183, 345, 436
Bst2UI CCWGG 5 cut(s) 261, 275, 412, 552, 834
Bst4CI ACNGT 4 cut(s) 135, 203, 623, 728
Bst6I CTCTTC 1 cut(s) 163
BstC8I GCNNGC 2 cut(s) 271, 965
BstDEI CTNAG 4 cut(s) 10, 225, 579, 921
BstDSI CCRYGG 1 cut(s) 319
BstF5I GGATG 3 cut(s) 152, 502, 546
BstKTI GATC 6 cut(s) 39, 266, 358, 557, 562, 699
BstMAI GTCTC 1 cut(s) 395
BstMBI GATC 6 cut(s) 36, 263, 355, 554, 559, 696
BstMWI GCNNNNNNNGC 1 cut(s) 237
BstNI CCWGG 5 cut(s) 261, 275, 412, 552, 834
BstNSI RCATGY 1 cut(s) 273
BstSCI CCNGG 6 cut(s) 259, 273, 377, 410, 550, 832
BstSFI CTRYAG 2 cut(s) 131, 958
BstSLI GKGCMC 1 cut(s) 140
BstV2I GAAGAC 1 cut(s) 762
BstX2I RGATCY 2 cut(s) 559, 696
BstYI RGATCY 2 cut(s) 559, 696
BsuRI GGCC 3 cut(s) 476, 765, 926
BtgI CCRYGG 1 cut(s) 319
BtsCI GGATG 3 cut(s) 152, 502, 546
BtsIMutI CAGTG 3 cut(s) 140, 628, 997
BveI ACCTGC 1 cut(s) 5
Cac8I GCNNGC 2 cut(s) 271, 965
Cfr10I RCCGGY 3 cut(s) 847, 926, 977
Cfr13I GGNCC 2 cut(s) 257, 277
Csp6I GTAC 1 cut(s) 871
CviAII CATG 6 cut(s) 114, 270, 423, 492, 844, 904
CviQI GTAC 1 cut(s) 871
DdeI CTNAG 4 cut(s) 10, 225, 579, 921
DpnI GATC 6 cut(s) 38, 265, 357, 556, 561, 698
DpnII GATC 6 cut(s) 36, 263, 355, 554, 559, 696
Eam1104I CTCTTC 1 cut(s) 163
EarI CTCTTC 1 cut(s) 163
EciI GGCGGA 1 cut(s) 383
Eco130I CCWWGG 3 cut(s) 183, 345, 436
Eco31I GGTCTC 1 cut(s) 395
Eco47I GGWCC 2 cut(s) 257, 277
Eco57I CTGAAG 3 cut(s) 82, 420, 973
EcoRII CCWGG 5 cut(s) 259, 273, 410, 550, 832
EcoT14I CCWWGG 3 cut(s) 183, 345, 436
ErhI CCWWGG 3 cut(s) 183, 345, 436
FaeI CATG 6 cut(s) 117, 273, 426, 495, 847, 907
FalI AAGNNNNNCTT 2 cut(s) 774, 806
FaqI GGGAC 1 cut(s) 428
FatI CATG 6 cut(s) 113, 269, 422, 491, 843, 903
FauNDI CATATG 1 cut(s) 215
FbaI TGATCA 1 cut(s) 36
FokI GGATG 3 cut(s) 139, 509, 533
FspBI CTAG 1 cut(s) 629
GsaI CCCAGC 1 cut(s) 827
HaeIII GGCC 3 cut(s) 476, 765, 926
HapII CCGG 4 cut(s) 379, 848, 927, 978
Hin1II CATG 6 cut(s) 117, 273, 426, 495, 847, 907
HincII GTYRAC 2 cut(s) 199, 508
HindII GTYRAC 2 cut(s) 199, 508
HinfI GANTC 4 cut(s) 427, 584, 756, 941
HpaII CCGG 4 cut(s) 379, 848, 927, 978
HphI GGTGA 6 cut(s) 153, 334, 545, 728, 872, 961
Hpy166II GTNNAC 4 cut(s) 199, 508, 863, 918
Hpy188I TCNGA 5 cut(s) 355, 559, 711, 721, 755
Hpy188III TCNNGA 3 cut(s) 124, 581, 817
Hpy8I GTNNAC 4 cut(s) 199, 508, 863, 918
HpyAV CCTTC 3 cut(s) 395, 776, 997
HpyCH4III ACNGT 4 cut(s) 135, 203, 623, 728
HpyCH4IV ACGT 1 cut(s) 881
HpyCH4V TGCA 8 cut(s) 143, 219, 231, 252, 748, 903, 975, 1011
HpyF10VI GCNNNNNNNGC 1 cut(s) 237
HpyF3I CTNAG 4 cut(s) 10, 225, 579, 921
HpySE526I ACGT 1 cut(s) 881
Hsp92II CATG 6 cut(s) 117, 273, 426, 495, 847, 907
Ksp22I TGATCA 1 cut(s) 36
Kzo9I GATC 6 cut(s) 36, 263, 355, 554, 559, 696
LmnI GCTCC 1 cut(s) 538
MaeI CTAG 1 cut(s) 629
MaeII ACGT 1 cut(s) 881
MaeIII GTNAC 5 cut(s) 178, 203, 631, 676, 882
MalI GATC 6 cut(s) 38, 265, 357, 556, 561, 698
MboI GATC 6 cut(s) 36, 263, 355, 554, 559, 696
MboII GAAGA 5 cut(s) 150, 417, 579, 698, 762
MflI RGATCY 2 cut(s) 559, 696
MhlI GDGCHC 1 cut(s) 140
MluCI AATT 5 cut(s) 247, 518, 654, 703, 1002
MmeI TCCRAC 1 cut(s) 835
MnlI CCTC 7 cut(s) 166, 291, 374, 466, 529, 789, 851
MroXI GAANNNNTTC 1 cut(s) 786
MseI TTAA 1 cut(s) 450
MspI CCGG 4 cut(s) 379, 848, 927, 978
MspR9I CCNGG 6 cut(s) 261, 275, 379, 412, 552, 834
MvaI CCWGG 5 cut(s) 261, 275, 412, 552, 834
MwoI GCNNNNNNNGC 1 cut(s) 237
NciI CCSGG 1 cut(s) 379
NdeI CATATG 1 cut(s) 215
NdeII GATC 6 cut(s) 36, 263, 355, 554, 559, 696
NlaIII CATG 6 cut(s) 117, 273, 426, 495, 847, 907
NlaIV GGNNCC 2 cut(s) 279, 672
NmuCI GTSAC 3 cut(s) 631, 676, 882
NspI RCATGY 1 cut(s) 273
PaeI GCATGC 1 cut(s) 273
PdmI GAANNNNTTC 1 cut(s) 786
PfeI GAWTC 4 cut(s) 427, 584, 756, 941
PfoI TCCNGGA 1 cut(s) 259
PsiI TTATAA 1 cut(s) 528
Psp6I CCWGG 5 cut(s) 259, 273, 410, 550, 832
PspFI CCCAGC 1 cut(s) 823
PspGI CCWGG 5 cut(s) 259, 273, 410, 550, 832
PspN4I GGNNCC 2 cut(s) 279, 672
PspPI GGNCC 2 cut(s) 257, 277
PsuI RGATCY 2 cut(s) 559, 696
RsaI GTAC 1 cut(s) 872
RsaNI GTAC 1 cut(s) 871
SaqAI TTAA 1 cut(s) 450
Sau3AI GATC 6 cut(s) 36, 263, 355, 554, 559, 696
Sau96I GGNCC 2 cut(s) 257, 277
ScrFI CCNGG 6 cut(s) 261, 275, 379, 412, 552, 834
SduI GDGCHC 1 cut(s) 140
SfcI CTRYAG 2 cut(s) 131, 958
SinI GGWCC 2 cut(s) 257, 277
SmlI CTYRAG 2 cut(s) 122, 470
SmoI CTYRAG 2 cut(s) 122, 470
SphI GCATGC 1 cut(s) 273
Sse9I AATT 5 cut(s) 247, 518, 654, 703, 1002
SsiI CCGC 1 cut(s) 394
SspMI CTAG 1 cut(s) 629
StyD4I CCNGG 6 cut(s) 259, 273, 377, 410, 550, 832
StyI CCWWGG 3 cut(s) 183, 345, 436
TaaI ACNGT 4 cut(s) 135, 203, 623, 728
TaiI ACGT 1 cut(s) 884
TaqI TCGA 1 cut(s) 76
TasI AATT 5 cut(s) 247, 518, 654, 703, 1002
TatI WGTACW 1 cut(s) 870
TfiI GAWTC 4 cut(s) 427, 584, 756, 941
Tru1I TTAA 1 cut(s) 450
Tru9I TTAA 1 cut(s) 450
TscAI CASTG 3 cut(s) 140, 628, 997
TseFI GTSAC 3 cut(s) 631, 676, 882
Tsp45I GTSAC 3 cut(s) 631, 676, 882
TspDTI ATGAA 3 cut(s) 277, 373, 516
TspGWI ACGGA 2 cut(s) 556, 1014
TspRI CASTG 3 cut(s) 140, 628, 997
VpaK11BI GGWCC 2 cut(s) 257, 277
XapI RAATTY 2 cut(s) 518, 654
XceI RCATGY 1 cut(s) 273
XcmI CCANNNNNNNNNTGG 1 cut(s) 489
XmnI GAANNNNTTC 1 cut(s) 786
XspI CTAG 1 cut(s) 629
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.