RchiOBHm_Chr5g0053851

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0014977
Physical Location & Seq
Forward (+)
56181566 .. 56182982
1417 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ33110

Sequence Viewer

Length: 765 bp
ATGGATTCTTCCTCTGCAAAAATGGTTAGACGGCTCGAATACCTTATCAGTGGTTTTATTGAGAATCAAAGTGGTGCATCAATATTAGCTTCGCTAAGTGGTTCTAACCATGAAGGCATCGAAAGACTGCAGTATGAACTTAGCTATCAAATGTGGAACCAGATTCATTCAGATGATTTTGTTCTTTTGCAGACATGTGTTATGAATGCAAATATGGATTGCGAAAAATGTAGGTTAAAAGTCTATGAAGTCGTGATCAATGTCTATGGTGCTTATTCAATAGACATAGATGCAGAACAATCGATGGTAAAAGTTTCAGGCAAAGTAAATCCAAAGATAATTCTACAGGTGCTTGGAGGGAAACATGCCAAGGTAAAAAGTGTCAAGTTTGATAGTGAGGAACCGTCCATGGGGGGCGGTTATCCCCCTCCCCCTCCCCCTCTTCTTCCCCCATACGGAATGGGGCTGGGGCCCCATCCCTATTCCTATCCGAATGGAGGGCCATATGACTACCCCATGATGATGCCACCACTTCTGATGCTGCCACCATCACCACCACCACCACCACCATCAGTGGCAGCACAACCTCAACAAAAACCAACATTACTATTAGAAGCACCACCCCAGAATTCGGGGGCCACAGCACAACCACAAAATTCAGGAACGTCAGCACCACCAACCACTAATGTTGCAGAGGAGGCAGTGATACCCTCAGATAAGAAGTCTAAGCGTTGCGGCATCGTCAAGAATTGCAGCATTATGTGA
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
HMA

Protein Analysis

254

Amino Acids

27.47

Weight (kDa)

6.09

Isoelectric Point (pI)

53.95

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HMA PF00403 70 - 113 6.7e-06 Heavy-metal-associated domain
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: OG0014977)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G13140
fragaria_vesca FvH4_3g29421
malus_domestica MD03G1184600.v1.1 MD03G1184800.v1.1 MD11G1201200.v1.1
prunus_persica Prupe.4G241700_v2.0.a1 Prupe.5G052600_v2.0.a1
pyrus_communis pycom11g17370
rosa_chinensis RchiOBHm_Chr5g0053851
rosa_multiflora Rmu_sc0001759.1_g000008
rosa_roxburghii Rroxscaffold_1G00026750
rosa_samantha Rh5AG353500 Rh5BG365100 Rh5CG390200
rosa_wichuraiana Rw0G002130 Rw0G009540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 2 cut(s) 417, 735
AcsI RAATTY 2 cut(s) 628, 655
AfiI CCNNNNNNNGG 4 cut(s) 410, 455, 497, 631
AflIII ACRYGT 1 cut(s) 194
AgsI TTSAA 1 cut(s) 279
AluBI AGCT 2 cut(s) 89, 144
AluI AGCT 2 cut(s) 89, 144
AoxI GGCC 3 cut(s) 470, 500, 636
ApaI GGGCCC 1 cut(s) 474
ApeKI GCWGC 3 cut(s) 541, 578, 753
ApoI RAATTY 2 cut(s) 628, 655
AspS9I GGNCC 4 cut(s) 470, 471, 500, 636
AsuHPI GGTGA 1 cut(s) 543
BaeGI GKGCMC 1 cut(s) 474
BanII GRGCYC 1 cut(s) 474
BbvI GCAGC 2 cut(s) 528, 590
BccI CCATC 4 cut(s) 298, 483, 556, 577
BceAI ACGGC 1 cut(s) 47
BcgI CGANNNNNNTGC 2 cut(s) 282, 316
BclI TGATCA 1 cut(s) 255
BfmI CTRYAG 2 cut(s) 128, 344
BisI GCNGC 4 cut(s) 542, 579, 736, 754
BlsI GCNGC 4 cut(s) 543, 580, 737, 755
BmgT120I GGNCC 4 cut(s) 470, 471, 500, 636
BmiI GGNNCC 6 cut(s) 158, 402, 471, 472, 473, 637
BmsI GCATC 6 cut(s) 86, 126, 280, 513, 528, 747
Bsa29I ATCGAT 1 cut(s) 302
BsaJI CCNNGG 2 cut(s) 369, 408
Bsc4I CCNNNNNNNGG 4 cut(s) 410, 455, 497, 631
BseCI ATCGAT 1 cut(s) 302
BseDI CCNNGG 2 cut(s) 369, 408
BseGI GGATG 1 cut(s) 475
BseLI CCNNNNNNNGG 4 cut(s) 410, 455, 497, 631
BseMII CTCAG 1 cut(s) 726
BseRI GAGGAG 1 cut(s) 710
BseSI GKGCMC 1 cut(s) 474
BseXI GCAGC 2 cut(s) 528, 590
BseYI CCCAGC 1 cut(s) 466
BshFI GGCC 3 cut(s) 472, 502, 638
BshVI ATCGAT 1 cut(s) 302
BslI CCNNNNNNNGG 4 cut(s) 410, 455, 497, 631
BsmI GAATGC 1 cut(s) 211
BsnI GGCC 3 cut(s) 472, 502, 638
Bsp120I GGGCCC 1 cut(s) 470
Bsp1286I GDGCHC 1 cut(s) 474
Bsp143I GATC 1 cut(s) 255
Bsp19I CCATGG 1 cut(s) 408
BspACI CCGC 2 cut(s) 417, 735
BspANI GGCC 3 cut(s) 472, 502, 638
BspCNI CTCAG 1 cut(s) 725
BspDI ATCGAT 1 cut(s) 302
BspLI GGNNCC 6 cut(s) 158, 402, 471, 472, 473, 637
BspMAI CTGCAG 1 cut(s) 132
BssECI CCNNGG 2 cut(s) 369, 408
BssMI GATC 1 cut(s) 255
BssT1I CCWWGG 2 cut(s) 369, 408
Bst4CI ACNGT 1 cut(s) 405
Bst6I CTCTTC 1 cut(s) 447
BstDEI CTNAG 4 cut(s) 95, 140, 712, 726
BstDSI CCRYGG 1 cut(s) 408
BstF5I GGATG 1 cut(s) 475
BstKTI GATC 1 cut(s) 258
BstMBI GATC 1 cut(s) 255
BstMWI GCNNNNNNNGC 1 cut(s) 698
BstNSI RCATGY 2 cut(s) 198, 368
BstSFI CTRYAG 2 cut(s) 128, 344
BstSLI GKGCMC 1 cut(s) 474
BstV1I GCAGC 2 cut(s) 528, 590
Bsu15I ATCGAT 1 cut(s) 302
BsuRI GGCC 3 cut(s) 472, 502, 638
BsuTUI ATCGAT 1 cut(s) 302
BtgI CCRYGG 1 cut(s) 408
BtsCI GGATG 1 cut(s) 475
BtsI GCAGTG 1 cut(s) 708
BtsIMutI CAGTG 3 cut(s) 55, 579, 708
Cfr13I GGNCC 4 cut(s) 470, 471, 500, 636
ClaI ATCGAT 1 cut(s) 302
CspCI CAANNNNNGTGG 2 cut(s) 670, 705
CviAII CATG 5 cut(s) 110, 195, 365, 409, 517
CviJI RGCY 7 cut(s) 34, 89, 144, 466, 472, 502, 638
CviKI_1 RGCY 7 cut(s) 34, 89, 144, 466, 472, 502, 638
DdeI CTNAG 4 cut(s) 95, 140, 712, 726
DpnI GATC 1 cut(s) 257
DpnII GATC 1 cut(s) 255
Eam1104I CTCTTC 1 cut(s) 447
EarI CTCTTC 1 cut(s) 447
Eco130I CCWWGG 2 cut(s) 369, 408
Eco24I GRGCYC 1 cut(s) 474
EcoO109I RGGNCCY 2 cut(s) 470, 471
EcoRI GAATTC 1 cut(s) 628
EcoT14I CCWWGG 2 cut(s) 369, 408
EcoT38I GRGCYC 1 cut(s) 474
ErhI CCWWGG 2 cut(s) 369, 408
FaeI CATG 5 cut(s) 113, 198, 368, 412, 520
FatI CATG 5 cut(s) 109, 194, 364, 408, 516
FauNDI CATATG 1 cut(s) 505
FbaI TGATCA 1 cut(s) 255
Fnu4HI GCNGC 4 cut(s) 542, 579, 736, 754
FokI GGATG 1 cut(s) 462
FriOI GRGCYC 1 cut(s) 474
Fsp4HI GCNGC 4 cut(s) 542, 579, 736, 754
GluI GCNGC 4 cut(s) 542, 579, 736, 754
GsaI CCCAGC 1 cut(s) 470
HaeIII GGCC 3 cut(s) 472, 502, 638
Hin1II CATG 5 cut(s) 113, 198, 368, 412, 520
HinfI GANTC 3 cut(s) 5, 64, 163
HphI GGTGA 1 cut(s) 543
Hpy188I TCNGA 4 cut(s) 172, 492, 537, 715
Hpy188III TCNNGA 3 cut(s) 253, 660, 745
HpyAV CCTTC 1 cut(s) 107
HpyCH4III ACNGT 1 cut(s) 405
HpyCH4IV ACGT 1 cut(s) 665
HpyCH4V TGCA 8 cut(s) 17, 77, 130, 190, 209, 293, 692, 753
HpyF10VI GCNNNNNNNGC 1 cut(s) 698
HpyF3I CTNAG 4 cut(s) 95, 140, 712, 726
HpySE526I ACGT 1 cut(s) 665
Hsp92II CATG 5 cut(s) 113, 198, 368, 412, 520
Ksp22I TGATCA 1 cut(s) 255
Kzo9I GATC 1 cut(s) 255
LpnPI CCDG 6 cut(s) 173, 303, 332, 452, 638, 645
Lsp1109I GCAGC 2 cut(s) 528, 590
LweI GCATC 6 cut(s) 86, 126, 280, 513, 528, 747
MaeII ACGT 1 cut(s) 665
MalI GATC 1 cut(s) 257
MboI GATC 1 cut(s) 255
MboII GAAGA 2 cut(s) 434, 437
MhlI GDGCHC 1 cut(s) 474
MluCI AATT 4 cut(s) 339, 628, 655, 748
MseI TTAA 1 cut(s) 236
MslI CAYNNNNRTG 2 cut(s) 171, 521
Mva1269I GAATGC 1 cut(s) 211
MwoI GCNNNNNNNGC 1 cut(s) 698
NcoI CCATGG 1 cut(s) 408
NdeI CATATG 1 cut(s) 505
NdeII GATC 1 cut(s) 255
NlaIII CATG 5 cut(s) 113, 198, 368, 412, 520
NlaIV GGNNCC 6 cut(s) 158, 402, 471, 472, 473, 637
NspI RCATGY 2 cut(s) 198, 368
PciI ACATGT 1 cut(s) 194
PctI GAATGC 1 cut(s) 211
PfeI GAWTC 3 cut(s) 5, 64, 163
PkrI GCNGC 4 cut(s) 543, 580, 737, 755
PscI ACATGT 1 cut(s) 194
PspFI CCCAGC 1 cut(s) 466
PspN4I GGNNCC 6 cut(s) 158, 402, 471, 472, 473, 637
PspOMI GGGCCC 1 cut(s) 470
PspPI GGNCC 4 cut(s) 470, 471, 500, 636
PstI CTGCAG 1 cut(s) 132
RseI CAYNNNNRTG 2 cut(s) 171, 521
SaqAI TTAA 1 cut(s) 236
SatI GCNGC 4 cut(s) 542, 579, 736, 754
Sau3AI GATC 1 cut(s) 255
Sau96I GGNCC 4 cut(s) 470, 471, 500, 636
SduI GDGCHC 1 cut(s) 474
SetI ASST 8 cut(s) 45, 91, 146, 236, 351, 375, 589, 668
SfaNI GCATC 6 cut(s) 86, 126, 280, 513, 528, 747
SfcI CTRYAG 2 cut(s) 128, 344
SmiMI CAYNNNNRTG 2 cut(s) 171, 521
Sse9I AATT 4 cut(s) 339, 628, 655, 748
SsiI CCGC 2 cut(s) 417, 735
SspI AATATT 1 cut(s) 84
StyI CCWWGG 2 cut(s) 369, 408
TaaI ACNGT 1 cut(s) 405
TaiI ACGT 1 cut(s) 668
TaqI TCGA 3 cut(s) 36, 120, 302
TasI AATT 4 cut(s) 339, 628, 655, 748
TauI GCSGC 1 cut(s) 738
TfiI GAWTC 3 cut(s) 5, 64, 163
Tru1I TTAA 1 cut(s) 236
Tru9I TTAA 1 cut(s) 236
TscAI CASTG 3 cut(s) 55, 579, 708
TseI GCWGC 3 cut(s) 541, 578, 753
TspDTI ATGAA 5 cut(s) 126, 150, 155, 218, 261
TspGWI ACGGA 1 cut(s) 471
TspRI CASTG 3 cut(s) 55, 579, 708
XapI RAATTY 2 cut(s) 628, 655
XceI RCATGY 2 cut(s) 198, 368
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.