Rh5BG242600

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0017497
Physical Location & Seq
Reverse (-)
29318210 .. 29319402
1193 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5BG242600.1

Sequence Viewer

Length: 879 bp
ATGGCTCTTGTGACACTGTCGGCCTTATTGACTGTCAATGTGAAAGTGAATTTTTGTTTAAATATCTCAAGATTATCGATTCAGCGCAAACCAAACTGCAATAGCCCTGGATCAGCATGCTATGATCCACGTTTCATCGGTGGTGATGGCATTGTTTTCTATTTCCACGGCAAGAGCAACGAGCAGTTCAGCTTAGTCTCAGACAAAAACCTCCAGATCAATGGCCGCTTCATTGGCCACAGACCAGCCGGCTGTGCTCGTGACTATACCTGGATTCAGGCCCTTGGAGTCCTTCTGAACTCCCAGAGTTTCTCTGTGGAAGCCACCAAAGTGGCTACATGGAACAACCAAATTGACCATCTGAGATTCACTCACAATGGAAATGATGTAGTTCTGGAAGAAGGGTATCTTTCCACTTGGTACTCACCAGATAAAGATATCAAAGTTGAGAGAATAGCAAGCAAGAACAGTGTGATAGTGTCGCTCAAGGATGTAGCTGAGATTATGATCAATGTTGTACCAGTGACCAAAGAAGATGATAGGATTCACAACTACCAAGTACCTGAAAATGACTGCTTTGCCCATTTGGAAGCCCAGTTCAAGTTCTTTGCTCTGTCCCCAAAAGTTGTGGGAGTTCTTGGAAGGACTTACAGGCCCGATTTTGAGAACCCGGCAAAGCCTGGAGTGGCAATGCCAGTTATTGGAGGTGAAGAGAAGTACAGAACCACATCACTTCTCTCTGCTGATTGTGCTACTTGTGATTTGTTCTCAAAGGAAATTAGTGAGTCCGAGAAAGAAACTTCAGCAATTGTGGACTATGGTACACTAGACTGTACCAGAAGATCCTCAGGAGGGTATGGGATTGTTTGCAAGAAATGA
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

292

Amino Acids

32.39

Weight (kDa)

6.6

Isoelectric Point (pI)

32.09

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 199 - 253 1.5e-25 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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Orthologous Genes (Group: OG0017497)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G27400 AT5G54370
malus_domestica MD11G1238300.v1.1
prunus_persica Prupe.4G188500_v2.0.a1
rosa_chinensis RchiOBHm_Chr5g0035121
rosa_multiflora Rmu_sc0000879.1_g000008 Rmu_sc0005362.1_g000004
rosa_rugosa Rorug05G0150200
rosa_samantha Rh5AG243000 Rh5BG242600 Rh5CG274200 Rh5DG251300

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 701
AciI CCGC 1 cut(s) 226
AclWI GGATC 3 cut(s) 118, 119, 837
AcoI YGGCCR 2 cut(s) 223, 235
AcsI RAATTY 1 cut(s) 49
AcuI CTGAAG 1 cut(s) 786
AfaI GTAC 6 cut(s) 422, 519, 561, 719, 823, 835
AfiI CCNNNNNNNGG 2 cut(s) 701, 852
AgsI TTSAA 1 cut(s) 601
AjnI CCWGG 3 cut(s) 106, 269, 679
AleI CACNNNNGTG 1 cut(s) 329
AloI GAACNNNNNNTCC 2 cut(s) 581, 613
AluBI AGCT 2 cut(s) 192, 497
AluI AGCT 2 cut(s) 192, 497
Alw21I GWGCWC 1 cut(s) 259
Alw26I GTCTC 1 cut(s) 202
AlwI GGATC 3 cut(s) 118, 119, 837
AoxI GGCC 5 cut(s) 21, 223, 235, 279, 653
ApoI RAATTY 1 cut(s) 49
AspLEI GCGC 1 cut(s) 87
AspS9I GGNCC 2 cut(s) 280, 654
AsuC2I CCSGG 1 cut(s) 671
AsuHPI GGTGA 3 cut(s) 155, 417, 719
AxyI CCTNAGG 1 cut(s) 847
BalI TGGCCA 1 cut(s) 237
BauI CACGAG 1 cut(s) 258
Bbv12I GWGCWC 1 cut(s) 259
BccI CCATC 2 cut(s) 140, 366
BceAI ACGGC 1 cut(s) 184
BciT130I CCWGG 3 cut(s) 108, 271, 681
BclI TGATCA 1 cut(s) 507
BcnI CCSGG 1 cut(s) 671
BcoDI GTCTC 1 cut(s) 202
BfaI CTAG 1 cut(s) 827
BisI GCNGC 1 cut(s) 226
BlsI GCNGC 1 cut(s) 227
Bme1390I CCNGG 4 cut(s) 108, 271, 671, 681
BmgT120I GGNCC 2 cut(s) 280, 654
BmrFI CCNGG 4 cut(s) 108, 271, 671, 681
BmrI ACTGGG 1 cut(s) 589
BmuI ACTGGG 1 cut(s) 589
BplI GAGNNNNNCTC 2 cut(s) 355, 387
BpmI CTGGAG 2 cut(s) 197, 702
BpuEI CTTGAG 2 cut(s) 52, 470
BpuMI CCSGG 1 cut(s) 671
Bsa29I ATCGAT 1 cut(s) 77
BsaBI GATNNNNATC 1 cut(s) 506
BsaJI CCNNGG 3 cut(s) 106, 166, 283
Bsc4I CCNNNNNNNGG 2 cut(s) 701, 852
Bse118I RCCGGY 1 cut(s) 248
Bse1I ACTGG 3 cut(s) 521, 595, 695
Bse21I CCTNAGG 1 cut(s) 847
Bse3DI GCAATG 1 cut(s) 696
Bse8I GATNNNNATC 1 cut(s) 506
BseBI CCWGG 3 cut(s) 108, 271, 681
BseCI ATCGAT 1 cut(s) 77
BseDI CCNNGG 3 cut(s) 106, 166, 283
BseGI GGATG 1 cut(s) 496
BseJI GATNNNNATC 1 cut(s) 506
BseLI CCNNNNNNNGG 2 cut(s) 701, 852
BseMI GCAATG 1 cut(s) 696
BseMII CTCAG 4 cut(s) 213, 353, 489, 861
BseNI ACTGG 3 cut(s) 521, 595, 695
BshFI GGCC 5 cut(s) 23, 225, 237, 281, 655
BshVI ATCGAT 1 cut(s) 77
BsiHKAI GWGCWC 1 cut(s) 259
BsiSI CCGG 2 cut(s) 249, 671
BslFI GGGAC 1 cut(s) 601
BslI CCNNNNNNNGG 2 cut(s) 701, 852
BsmAI GTCTC 1 cut(s) 202
BsmFI GGGAC 1 cut(s) 601
BsnI GGCC 5 cut(s) 23, 225, 237, 281, 655
Bsp1286I GDGCHC 1 cut(s) 259
Bsp143I GATC 5 cut(s) 110, 124, 216, 507, 842
BspACI CCGC 1 cut(s) 226
BspANI GGCC 5 cut(s) 23, 225, 237, 281, 655
BspCNI CTCAG 4 cut(s) 212, 354, 490, 860
BspDI ATCGAT 1 cut(s) 77
BspPI GGATC 3 cut(s) 118, 119, 837
BsrDI GCAATG 1 cut(s) 696
BsrFI RCCGGY 1 cut(s) 248
BsrI ACTGG 3 cut(s) 521, 595, 695
BssAI RCCGGY 1 cut(s) 248
BssECI CCNNGG 3 cut(s) 106, 166, 283
BssMI GATC 5 cut(s) 110, 124, 216, 507, 842
BssSI CACGAG 1 cut(s) 258
BssT1I CCWWGG 1 cut(s) 283
Bst2BI CACGAG 1 cut(s) 258
Bst2UI CCWGG 3 cut(s) 108, 271, 681
Bst4CI ACNGT 4 cut(s) 18, 34, 470, 833
Bst6I CTCTTC 1 cut(s) 705
BstC8I GCNNGC 3 cut(s) 118, 250, 460
BstDEI CTNAG 5 cut(s) 193, 199, 362, 498, 847
BstDSI CCRYGG 1 cut(s) 166
BstF5I GGATG 1 cut(s) 496
BstHHI GCGC 1 cut(s) 87
BstKTI GATC 5 cut(s) 113, 127, 219, 510, 845
BstMAI GTCTC 1 cut(s) 202
BstMBI GATC 5 cut(s) 110, 124, 216, 507, 842
BstMWI GCNNNNNNNGC 3 cut(s) 234, 254, 749
BstNI CCWGG 3 cut(s) 108, 271, 681
BstNSI RCATGY 1 cut(s) 120
BstSCI CCNGG 4 cut(s) 106, 269, 669, 679
BstX2I RGATCY 1 cut(s) 842
BstXI CCANNNNNNTGG 2 cut(s) 221, 331
BstYI RGATCY 1 cut(s) 842
Bsu15I ATCGAT 1 cut(s) 77
Bsu36I CCTNAGG 1 cut(s) 847
BsuRI GGCC 5 cut(s) 23, 225, 237, 281, 655
BsuTUI ATCGAT 1 cut(s) 77
BtgI CCRYGG 1 cut(s) 166
BtsCI GGATG 1 cut(s) 496
BtsIMutI CAGTG 3 cut(s) 14, 475, 528
Cac8I GCNNGC 3 cut(s) 118, 250, 460
CfoI GCGC 1 cut(s) 87
Cfr10I RCCGGY 1 cut(s) 248
Cfr13I GGNCC 2 cut(s) 280, 654
ClaI ATCGAT 1 cut(s) 77
Csp6I GTAC 6 cut(s) 421, 518, 560, 718, 822, 834
CspCI CAANNNNNGTGG 2 cut(s) 609, 644
CviAII CATG 2 cut(s) 117, 339
CviQI GTAC 6 cut(s) 421, 518, 560, 718, 822, 834
DdeI CTNAG 5 cut(s) 193, 199, 362, 498, 847
DpnI GATC 5 cut(s) 112, 126, 218, 509, 844
DpnII GATC 5 cut(s) 110, 124, 216, 507, 842
DraI TTTAAA 1 cut(s) 60
EaeI YGGCCR 2 cut(s) 223, 235
Eam1104I CTCTTC 1 cut(s) 705
EarI CTCTTC 1 cut(s) 705
Eco130I CCWWGG 1 cut(s) 283
Eco32I GATATC 1 cut(s) 439
Eco57I CTGAAG 1 cut(s) 786
Eco81I CCTNAGG 1 cut(s) 847
EcoO109I RGGNCCY 1 cut(s) 280
EcoRII CCWGG 3 cut(s) 106, 269, 679
EcoRV GATATC 1 cut(s) 439
EcoT14I CCWWGG 1 cut(s) 283
ErhI CCWWGG 1 cut(s) 283
FaeI CATG 2 cut(s) 120, 342
FaiI YATR 7 cut(s) 118, 123, 267, 340, 506, 819, 858
FalI AAGNNNNNCTT 2 cut(s) 393, 425
FaqI GGGAC 1 cut(s) 601
FatI CATG 2 cut(s) 116, 338
FbaI TGATCA 1 cut(s) 507
Fnu4HI GCNGC 1 cut(s) 226
FokI GGATG 1 cut(s) 503
Fsp4HI GCNGC 1 cut(s) 226
FspBI CTAG 1 cut(s) 827
GlaI GCGC 1 cut(s) 86
GluI GCNGC 1 cut(s) 226
GsuI CTGGAG 2 cut(s) 197, 702
HaeIII GGCC 5 cut(s) 23, 225, 237, 281, 655
HapII CCGG 2 cut(s) 249, 671
HhaI GCGC 1 cut(s) 87
Hin1II CATG 2 cut(s) 120, 342
Hin6I GCGC 1 cut(s) 85
HinP1I GCGC 1 cut(s) 85
HinfI GANTC 6 cut(s) 79, 274, 288, 366, 544, 785
HpaII CCGG 2 cut(s) 249, 671
HphI GGTGA 3 cut(s) 155, 417, 719
Hpy166II GTNNAC 2 cut(s) 814, 824
Hpy188I TCNGA 4 cut(s) 202, 297, 363, 790
Hpy188III TCNNGA 5 cut(s) 69, 214, 260, 395, 849
Hpy8I GTNNAC 2 cut(s) 814, 824
HpyAV CCTTC 3 cut(s) 302, 395, 636
HpyCH4III ACNGT 4 cut(s) 18, 34, 470, 833
HpyCH4IV ACGT 1 cut(s) 130
HpyCH4V TGCA 2 cut(s) 99, 870
HpyF10VI GCNNNNNNNGC 3 cut(s) 234, 254, 749
HpyF3I CTNAG 5 cut(s) 193, 199, 362, 498, 847
HpySE526I ACGT 1 cut(s) 130
Hsp92II CATG 2 cut(s) 120, 342
HspAI GCGC 1 cut(s) 85
KroI GCCGGC 1 cut(s) 248
KroNI GCCGGC 1 cut(s) 250
Ksp22I TGATCA 1 cut(s) 507
Kzo9I GATC 5 cut(s) 110, 124, 216, 507, 842
MaeI CTAG 1 cut(s) 827
MaeII ACGT 1 cut(s) 130
MaeIII GTNAC 3 cut(s) 10, 260, 523
MalI GATC 5 cut(s) 112, 126, 218, 509, 844
MboI GATC 5 cut(s) 110, 124, 216, 507, 842
MboII GAAGA 4 cut(s) 410, 545, 722, 852
MfeI CAATTG 1 cut(s) 807
MflI RGATCY 1 cut(s) 842
MhlI GDGCHC 1 cut(s) 259
MlsI TGGCCA 1 cut(s) 237
MluCI AATT 4 cut(s) 49, 351, 777, 807
MluNI TGGCCA 1 cut(s) 237
MlyI GAGTC 2 cut(s) 297, 794
MnlI CCTC 4 cut(s) 221, 698, 845, 856
Mox20I TGGCCA 1 cut(s) 237
MroNI GCCGGC 1 cut(s) 248
MscI TGGCCA 1 cut(s) 237
MseI TTAA 1 cut(s) 59
MslI CAYNNNNRTG 1 cut(s) 329
Msp20I TGGCCA 1 cut(s) 237
MspI CCGG 2 cut(s) 249, 671
MspR9I CCNGG 4 cut(s) 108, 271, 671, 681
MunI CAATTG 1 cut(s) 807
MvaI CCWGG 3 cut(s) 108, 271, 681
MwoI GCNNNNNNNGC 3 cut(s) 234, 254, 749
NaeI GCCGGC 1 cut(s) 250
NciI CCSGG 1 cut(s) 671
NdeII GATC 5 cut(s) 110, 124, 216, 507, 842
NgoMIV GCCGGC 1 cut(s) 248
NlaIII CATG 2 cut(s) 120, 342
NmuCI GTSAC 3 cut(s) 10, 260, 523
NspI RCATGY 1 cut(s) 120
OliI CACNNNNGTG 1 cut(s) 329
PaeI GCATGC 1 cut(s) 120
PdiI GCCGGC 1 cut(s) 250
PfeI GAWTC 4 cut(s) 79, 274, 366, 544
PflFI GACNNNGTC 1 cut(s) 16
PflMI CCANNNNNTGG 1 cut(s) 701
PkrI GCNGC 1 cut(s) 227
PleI GAGTC 2 cut(s) 296, 793
PpsI GAGTC 2 cut(s) 296, 793
Psp6I CCWGG 3 cut(s) 106, 269, 679
PspGI CCWGG 3 cut(s) 106, 269, 679
PspPI GGNCC 2 cut(s) 280, 654
PsuI RGATCY 1 cut(s) 842
PsyI GACNNNGTC 1 cut(s) 16
RsaI GTAC 6 cut(s) 422, 519, 561, 719, 823, 835
RsaNI GTAC 6 cut(s) 421, 518, 560, 718, 822, 834
RseI CAYNNNNRTG 1 cut(s) 329
SaqAI TTAA 1 cut(s) 59
SatI GCNGC 1 cut(s) 226
Sau3AI GATC 5 cut(s) 110, 124, 216, 507, 842
Sau96I GGNCC 2 cut(s) 280, 654
SchI GAGTC 2 cut(s) 297, 794
ScrFI CCNGG 4 cut(s) 108, 271, 671, 681
SduI GDGCHC 1 cut(s) 259
SetI ASST 7 cut(s) 133, 194, 213, 272, 499, 565, 709
SmiMI CAYNNNNRTG 1 cut(s) 329
SmlI CTYRAG 2 cut(s) 67, 485
SmoI CTYRAG 2 cut(s) 67, 485
SphI GCATGC 1 cut(s) 120
Sse9I AATT 4 cut(s) 49, 351, 777, 807
SsiI CCGC 1 cut(s) 226
SspMI CTAG 1 cut(s) 827
StyD4I CCNGG 4 cut(s) 106, 269, 669, 679
StyI CCWWGG 1 cut(s) 283
TaaI ACNGT 4 cut(s) 18, 34, 470, 833
TaiI ACGT 1 cut(s) 133
TaqI TCGA 1 cut(s) 77
TasI AATT 4 cut(s) 49, 351, 777, 807
TatI WGTACW 1 cut(s) 717
TauI GCSGC 1 cut(s) 228
TfiI GAWTC 4 cut(s) 79, 274, 366, 544
Tru1I TTAA 1 cut(s) 59
Tru9I TTAA 1 cut(s) 59
TscAI CASTG 3 cut(s) 21, 475, 528
TseFI GTSAC 3 cut(s) 10, 260, 523
Tsp45I GTSAC 3 cut(s) 10, 260, 523
TspDTI ATGAA 2 cut(s) 124, 220
TspRI CASTG 3 cut(s) 21, 475, 528
Tth111I GACNNNGTC 1 cut(s) 16
Van91I CCANNNNNTGG 1 cut(s) 701
XapI RAATTY 1 cut(s) 49
XceI RCATGY 1 cut(s) 120
XspI CTAG 1 cut(s) 827
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.