Rh5DG417500

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0002778
Physical Location & Seq
Forward (+)
66335996 .. 66337044
1049 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG417500.1

Sequence Viewer

Length: 891 bp
ATGTGCAAAGCTCAGGGTACCTGTTTCTACAAGACCCTTGTCTGTCCACCGGAGTGCCCTCAGAGAAAGCCTAAGCAGAACAAGAAACACAAGGGCTGCTTCGTCAACTGCGGCAGCAAGTGTGAAGTCACCTGCAAGTTTAGAAGAGCCAACTGTAATGGGTATGGTTCTCTCTGCTATGATCCTCGATTTGTTGGTGGAGATGGTGTTATGTTCTACTTCCATGGAGCCAAGGGAGTAAACTTTGCCATTGTTTCAGATGATAACCTCCAGATCAATGCACACTTCATTGGGACTCGACCACTAGGAAGGACTCGCGACTTCACATGGGTTCAAGCCCTCTCAATCATGTTCGACAATCACAACCTTGTCATTGCAGCGAAGAAAGTCTCAAAGTGGGCTGACAAAGTTGATGCTCTCATCGTAAGGTGGGATGGCGAGTCAGTTAGCATTCCTACTGATGGAGAAGCCGAATGGAGGACTAATGGTGATCAACAACGACAGGTAATAGTGGAAAGAACCGATGATACTAACAACGTAAGAGTTACAGTTGCAGGGCTACTGGAAATGGACATAAAGATTAGGCCTATTGGAGAAGAAGAAAACAAGGTTCATAAGTATCAAATACCAGCTGATGATACTTTTGCTCACTTGGAAACACAGTTCAGATTTTCGAATTTATCTGATCTTGTCGAAGGAGTTTTGGGCAAGACTTATAGGCCAGGTTATGTTAGTCCAGTCAAGGTTGGAGTTCCAATGCCGACAATGGGTGGGGAGGACAAGTACAGAACTCCTTCACTGTTCTCACCTCTCTGCAAGGTTTGCAGGTTCCAAACTACTAGTCAATCTTCAGGGTTTGATATCACAAGTGGAGGAGTGGCATCATACTGA
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

296

Amino Acids

33.03

Weight (kDa)

8.65

Isoelectric Point (pI)

27.19

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 221 - 277 6.5e-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) 140
Acc36I ACCTGC 2 cut(s) 140, 816
Acc65I GGTACC 1 cut(s) 17
AccB1I GGYRCC 1 cut(s) 17
AccII CGCG 1 cut(s) 318
AciI CCGC 1 cut(s) 111
AclWI GGATC 1 cut(s) 176
AcsI RAATTY 1 cut(s) 676
AcuI CTGAAG 1 cut(s) 834
AfaI GTAC 2 cut(s) 19, 785
AfiI CCNNNNNNNGG 3 cut(s) 461, 477, 767
AgsI TTSAA 1 cut(s) 335
AhlI ACTAGT 1 cut(s) 839
AjnI CCWGG 1 cut(s) 721
AleI CACNNNNGTG 1 cut(s) 52
AloI GAACNNNNNNTCC 2 cut(s) 647, 679
AluBI AGCT 2 cut(s) 11, 632
AluI AGCT 2 cut(s) 11, 632
Alw26I GTCTC 1 cut(s) 394
AlwI GGATC 1 cut(s) 176
AoxI GGCC 2 cut(s) 584, 719
ApeKI GCWGC 3 cut(s) 96, 114, 377
ApoI RAATTY 1 cut(s) 676
ArsI GACNNNNNNTTYG 2 cut(s) 826, 858
Asp700I GAANNNNTTC 1 cut(s) 793
Asp718I GGTACC 1 cut(s) 17
AsuHPI GGTGA 3 cut(s) 121, 500, 798
AsuII TTCGAA 1 cut(s) 674
BaeGI GKGCMC 1 cut(s) 59
BanI GGYRCC 1 cut(s) 17
BbvI GCAGC 3 cut(s) 83, 126, 389
BccI CCATC 3 cut(s) 197, 428, 455
BciT130I CCWGG 1 cut(s) 723
BclI TGATCA 1 cut(s) 490
BcoDI GTCTC 1 cut(s) 394
BcuI ACTAGT 1 cut(s) 839
BfaI CTAG 2 cut(s) 305, 840
BfuAI ACCTGC 2 cut(s) 140, 816
BisI GCNGC 4 cut(s) 97, 112, 115, 378
BlsI GCNGC 4 cut(s) 98, 113, 116, 379
Bme1390I CCNGG 1 cut(s) 723
BmiI GGNNCC 3 cut(s) 19, 229, 830
BmrFI CCNGG 1 cut(s) 723
BmsI GCATC 1 cut(s) 403
BoxI GACNNNNGTC 1 cut(s) 38
BpmI CTGGAG 1 cut(s) 254
Bpu10I CCTNAGC 2 cut(s) 12, 72
Bpu14I TTCGAA 1 cut(s) 674
BsaJI CCNNGG 2 cut(s) 223, 231
BsaWI WCCGGW 1 cut(s) 49
BsaXI ACNNNNNCTCC 4 cut(s) 192, 222, 767, 797
Bsc4I CCNNNNNNNGG 3 cut(s) 461, 477, 767
Bse1I ACTGG 2 cut(s) 567, 737
Bse3DI GCAATG 1 cut(s) 372
BseBI CCWGG 1 cut(s) 723
BseDI CCNNGG 2 cut(s) 223, 231
BseGI GGATG 1 cut(s) 439
BseLI CCNNNNNNNGG 3 cut(s) 461, 477, 767
BseMI GCAATG 1 cut(s) 372
BseMII CTCAG 2 cut(s) 26, 74
BseNI ACTGG 2 cut(s) 567, 737
BseRI GAGGAG 1 cut(s) 888
BseSI GKGCMC 1 cut(s) 59
BseXI GCAGC 3 cut(s) 83, 126, 389
Bsh1236I CGCG 1 cut(s) 318
BshFI GGCC 2 cut(s) 586, 721
BshNI GGYRCC 1 cut(s) 17
BsiSI CCGG 1 cut(s) 50
BslFI GGGAC 1 cut(s) 307
BslI CCNNNNNNNGG 3 cut(s) 461, 477, 767
BsmAI GTCTC 1 cut(s) 394
BsmFI GGGAC 1 cut(s) 307
BsmI GAATGC 1 cut(s) 450
BsnI GGCC 2 cut(s) 586, 721
Bsp119I TTCGAA 1 cut(s) 674
Bsp1286I GDGCHC 1 cut(s) 59
Bsp143I GATC 4 cut(s) 181, 273, 490, 685
Bsp19I CCATGG 1 cut(s) 223
Bsp68I TCGCGA 1 cut(s) 318
BspACI CCGC 1 cut(s) 111
BspANI GGCC 2 cut(s) 586, 721
BspCNI CTCAG 2 cut(s) 25, 73
BspFNI CGCG 1 cut(s) 318
BspLI GGNNCC 3 cut(s) 19, 229, 830
BspMI ACCTGC 2 cut(s) 140, 816
BspPI GGATC 1 cut(s) 176
BspQI GCTCTTC 1 cut(s) 139
BspT104I TTCGAA 1 cut(s) 674
BspT107I GGYRCC 1 cut(s) 17
BsrDI GCAATG 1 cut(s) 372
BsrI ACTGG 2 cut(s) 567, 737
BssECI CCNNGG 2 cut(s) 223, 231
BssMI GATC 4 cut(s) 181, 273, 490, 685
BssT1I CCWWGG 2 cut(s) 223, 231
Bst2UI CCWGG 1 cut(s) 723
Bst4CI ACNGT 4 cut(s) 155, 550, 663, 801
Bst6I CTCTTC 1 cut(s) 139
BstAPI GCANNNNNTGC 1 cut(s) 822
BstBI TTCGAA 1 cut(s) 674
BstDEI CTNAG 3 cut(s) 12, 60, 72
BstDSI CCRYGG 1 cut(s) 223
BstF5I GGATG 1 cut(s) 439
BstFNI CGCG 1 cut(s) 318
BstKTI GATC 4 cut(s) 184, 276, 493, 688
BstMAI GTCTC 1 cut(s) 394
BstMBI GATC 4 cut(s) 181, 273, 490, 685
BstMWI GCNNNNNNNGC 1 cut(s) 822
BstNI CCWGG 1 cut(s) 723
BstPAI GACNNNNGTC 1 cut(s) 38
BstSCI CCNGG 1 cut(s) 721
BstSLI GKGCMC 1 cut(s) 59
BstUI CGCG 1 cut(s) 318
BstV1I GCAGC 3 cut(s) 83, 126, 389
BsuRI GGCC 2 cut(s) 586, 721
BtgI CCRYGG 1 cut(s) 223
BtsCI GGATG 1 cut(s) 439
BtsIMutI CAGTG 1 cut(s) 797
BtuMI TCGCGA 1 cut(s) 318
BveI ACCTGC 2 cut(s) 140, 816
Csp6I GTAC 2 cut(s) 18, 784
CviAII CATG 3 cut(s) 224, 327, 349
CviQI GTAC 2 cut(s) 18, 784
DdeI CTNAG 3 cut(s) 12, 60, 72
DpnI GATC 4 cut(s) 183, 275, 492, 687
DpnII GATC 4 cut(s) 181, 273, 490, 685
Eam1104I CTCTTC 1 cut(s) 139
EarI CTCTTC 1 cut(s) 139
Eco130I CCWWGG 2 cut(s) 223, 231
Eco147I AGGCCT 1 cut(s) 586
Eco32I GATATC 1 cut(s) 862
Eco57I CTGAAG 1 cut(s) 834
EcoRII CCWGG 1 cut(s) 721
EcoRV GATATC 1 cut(s) 862
EcoT14I CCWWGG 2 cut(s) 223, 231
ErhI CCWWGG 2 cut(s) 223, 231
FaeI CATG 3 cut(s) 227, 330, 352
FalI AAGNNNNNCTT 2 cut(s) 83, 115
FaqI GGGAC 1 cut(s) 307
FatI CATG 3 cut(s) 223, 326, 348
FbaI TGATCA 1 cut(s) 490
Fnu4HI GCNGC 4 cut(s) 97, 112, 115, 378
FokI GGATG 1 cut(s) 446
Fsp4HI GCNGC 4 cut(s) 97, 112, 115, 378
FspBI CTAG 2 cut(s) 305, 840
GluI GCNGC 4 cut(s) 97, 112, 115, 378
GsuI CTGGAG 1 cut(s) 254
HaeIII GGCC 2 cut(s) 586, 721
HapII CCGG 1 cut(s) 50
Hin1II CATG 3 cut(s) 227, 330, 352
HincII GTYRAC 1 cut(s) 106
HindII GTYRAC 1 cut(s) 106
HinfI GANTC 3 cut(s) 295, 313, 440
HpaII CCGG 1 cut(s) 50
HphI GGTGA 3 cut(s) 121, 500, 798
Hpy166II GTNNAC 3 cut(s) 47, 106, 241
Hpy188I TCNGA 4 cut(s) 63, 259, 668, 685
Hpy188III TCNNGA 2 cut(s) 271, 317
Hpy8I GTNNAC 3 cut(s) 47, 106, 241
HpyAV CCTTC 3 cut(s) 303, 689, 804
HpyCH4III ACNGT 4 cut(s) 155, 550, 663, 801
HpyCH4IV ACGT 1 cut(s) 537
HpyCH4V TGCA 7 cut(s) 6, 135, 281, 377, 554, 816, 825
HpyF10VI GCNNNNNNNGC 1 cut(s) 822
HpyF3I CTNAG 3 cut(s) 12, 60, 72
HpySE526I ACGT 1 cut(s) 537
Hsp92II CATG 3 cut(s) 227, 330, 352
KpnI GGTACC 1 cut(s) 21
Ksp22I TGATCA 1 cut(s) 490
Kzo9I GATC 4 cut(s) 181, 273, 490, 685
LguI GCTCTTC 1 cut(s) 139
LmnI GCTCC 1 cut(s) 227
Lsp1109I GCAGC 3 cut(s) 83, 126, 389
LweI GCATC 1 cut(s) 403
MaeI CTAG 2 cut(s) 305, 840
MaeII ACGT 1 cut(s) 537
MaeIII GTNAC 2 cut(s) 127, 544
MalI GATC 4 cut(s) 183, 275, 492, 687
MboI GATC 4 cut(s) 181, 273, 490, 685
MboII GAAGA 5 cut(s) 156, 394, 608, 611, 840
MhlI GDGCHC 1 cut(s) 59
MluCI AATT 1 cut(s) 676
MlyI GAGTC 3 cut(s) 289, 307, 449
MmeI TCCRAC 1 cut(s) 727
MnlI CCTC 8 cut(s) 69, 195, 278, 350, 471, 769, 819, 866
MroXI GAANNNNTTC 1 cut(s) 793
MslI CAYNNNNRTG 1 cut(s) 52
MspA1I CMGCKG 1 cut(s) 632
MspI CCGG 1 cut(s) 50
MspR9I CCNGG 1 cut(s) 723
Mva1269I GAATGC 1 cut(s) 450
MvaI CCWGG 1 cut(s) 723
MvnI CGCG 1 cut(s) 318
MwoI GCNNNNNNNGC 1 cut(s) 822
NcoI CCATGG 1 cut(s) 223
NdeII GATC 4 cut(s) 181, 273, 490, 685
NlaIII CATG 3 cut(s) 227, 330, 352
NlaIV GGNNCC 3 cut(s) 19, 229, 830
NmuCI GTSAC 1 cut(s) 127
NruI TCGCGA 1 cut(s) 318
NspV TTCGAA 1 cut(s) 674
OliI CACNNNNGTG 1 cut(s) 52
PaqCI CACCTGC 1 cut(s) 140
PceI AGGCCT 1 cut(s) 586
PciSI GCTCTTC 1 cut(s) 139
PctI GAATGC 1 cut(s) 450
PdmI GAANNNNTTC 1 cut(s) 793
PkrI GCNGC 4 cut(s) 98, 113, 116, 379
PleI GAGTC 3 cut(s) 289, 307, 448
PpsI GAGTC 3 cut(s) 289, 307, 448
PshAI GACNNNNGTC 1 cut(s) 38
Psp6I CCWGG 1 cut(s) 721
PspGI CCWGG 1 cut(s) 721
PspN4I GGNNCC 3 cut(s) 19, 229, 830
PsrI GAACNNNNNNTAC 2 cut(s) 511, 543
PvuII CAGCTG 1 cut(s) 632
RruI TCGCGA 1 cut(s) 318
RsaI GTAC 2 cut(s) 19, 785
RsaNI GTAC 2 cut(s) 18, 784
RseI CAYNNNNRTG 1 cut(s) 52
SapI GCTCTTC 1 cut(s) 139
SatI GCNGC 4 cut(s) 97, 112, 115, 378
Sau3AI GATC 4 cut(s) 181, 273, 490, 685
SchI GAGTC 3 cut(s) 289, 307, 449
ScrFI CCNGG 1 cut(s) 723
SduI GDGCHC 1 cut(s) 59
SfaNI GCATC 1 cut(s) 403
SfuI TTCGAA 1 cut(s) 674
SmiMI CAYNNNNRTG 1 cut(s) 52
SpeI ACTAGT 1 cut(s) 839
Sse9I AATT 1 cut(s) 676
SseBI AGGCCT 1 cut(s) 586
SsiI CCGC 1 cut(s) 111
SspMI CTAG 2 cut(s) 305, 840
StuI AGGCCT 1 cut(s) 586
StyD4I CCNGG 1 cut(s) 721
StyI CCWWGG 2 cut(s) 223, 231
TaaI ACNGT 4 cut(s) 155, 550, 663, 801
TaiI ACGT 1 cut(s) 540
TaqI TCGA 5 cut(s) 187, 298, 354, 674, 693
TasI AATT 1 cut(s) 676
TatI WGTACW 1 cut(s) 783
TauI GCSGC 1 cut(s) 114
TscAI CASTG 1 cut(s) 804
TseFI GTSAC 1 cut(s) 127
TseI GCWGC 3 cut(s) 96, 114, 377
Tsp45I GTSAC 1 cut(s) 127
TspDTI ATGAA 2 cut(s) 277, 602
TspRI CASTG 1 cut(s) 804
XapI RAATTY 1 cut(s) 676
XmnI GAANNNNTTC 1 cut(s) 793
XspI CTAG 2 cut(s) 305, 840
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.