RchiOBHm_Chr4g0436631

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0006436
Physical Location & Seq
Reverse (-)
59904616 .. 59905537
922 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ40495

Sequence Viewer

Length: 486 bp
ATGATGTGTCAGGATCTAGCCACCAAGGAGCAGATTGGTGAAGGTTTTTACCTTAACGGACTATACTACCTCTCAAAGGATTTTAGAGTTCCCAAAGCCTCCCAAGCTAATCTTAGTCTAGCTCAAGAACATCAGCTATGGCACCAGCGTTTGGCTCATCCCTCAGAACATGTTTTGTCTTCTGTATTTCCAAATCTGTGTAAAGAATCTTTTCAATGTGAAATATGCCATCTAGCTAAGTCTACTAGACTTCCTTTTGGTTCATCTGTATCTCGAGCTAGGAAACCTTTTGAAATTGTACACTCTGATATCTGGGGGCCAGCTCCTCTAGATTCCTTTGATGGTTATAAGTACTTTGTTACCTTTGTTGATGATTTTTCTCGTATTTCTATAATCTTGTCACAACTATGTTCTCAACTAAAATCCACACTCTCAGATCAGATAATGGTACCGAATATATGTCCAAAATCATGTCACAATTTCTAA
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
Retrotran_gag_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve

Protein Analysis

161

Amino Acids

18.33

Weight (kDa)

7.03

Isoelectric Point (pI)

48.4

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
gag_pre-integrs PF13976 20 - 81 2.1e-10 GAG-pre-integrase domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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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) 348
Acc65I GGTACC 1 cut(s) 448
AccB1I GGYRCC 2 cut(s) 141, 448
AccB7I CCANNNNNTGG 1 cut(s) 151
AccI GTMKAC 1 cut(s) 242
AclWI GGATC 1 cut(s) 21
AfaI GTAC 3 cut(s) 300, 353, 450
AfiI CCNNNNNNNGG 2 cut(s) 76, 151
AflIII ACRYGT 1 cut(s) 169
AgsI TTSAA 2 cut(s) 215, 293
AluBI AGCT 6 cut(s) 107, 122, 136, 236, 278, 323
AluI AGCT 6 cut(s) 107, 122, 136, 236, 278, 323
AlwI GGATC 1 cut(s) 21
Ama87I CYCGRG 1 cut(s) 273
AoxI GGCC 1 cut(s) 317
Asp700I GAANNNNTTC 1 cut(s) 210
Asp718I GGTACC 1 cut(s) 448
AspS9I GGNCC 1 cut(s) 317
AsuHPI GGTGA 1 cut(s) 50
AvaI CYCGRG 1 cut(s) 273
BanI GGYRCC 2 cut(s) 141, 448
BbsI GAAGAC 1 cut(s) 171
BccI CCATC 2 cut(s) 237, 335
BfaI CTAG 6 cut(s) 17, 119, 233, 246, 279, 329
BmcAI AGTACT 1 cut(s) 353
BmeT110I CYCGRG 1 cut(s) 273
BmgT120I GGNCC 1 cut(s) 317
BmiI GGNNCC 3 cut(s) 143, 318, 450
BpiI GAAGAC 1 cut(s) 171
BpuEI CTTGAG 1 cut(s) 108
BsaJI CCNNGG 1 cut(s) 24
Bsc4I CCNNNNNNNGG 2 cut(s) 76, 151
BseDI CCNNGG 1 cut(s) 24
BseGI GGATG 1 cut(s) 157
BseLI CCNNNNNNNGG 2 cut(s) 76, 151
BseMII CTCAG 2 cut(s) 177, 447
BseRI GAGGAG 1 cut(s) 315
BshFI GGCC 1 cut(s) 319
BshNI GGYRCC 2 cut(s) 141, 448
BsiHKCI CYCGRG 1 cut(s) 273
BslI CCNNNNNNNGG 2 cut(s) 76, 151
BsnI GGCC 1 cut(s) 319
BsoBI CYCGRG 1 cut(s) 273
Bsp1407I TGTACA 1 cut(s) 298
Bsp143I GATC 2 cut(s) 13, 436
BspANI GGCC 1 cut(s) 319
BspCNI CTCAG 2 cut(s) 176, 446
BspLI GGNNCC 3 cut(s) 143, 318, 450
BspPI GGATC 1 cut(s) 21
BspT107I GGYRCC 2 cut(s) 141, 448
BsrGI TGTACA 1 cut(s) 298
BssECI CCNNGG 1 cut(s) 24
BssMI GATC 2 cut(s) 13, 436
BssT1I CCWWGG 1 cut(s) 24
BstAUI TGTACA 1 cut(s) 298
BstC8I GCNNGC 1 cut(s) 321
BstDEI CTNAG 4 cut(s) 113, 163, 237, 433
BstENI CCTNNNNNAGG 1 cut(s) 74
BstF5I GGATG 1 cut(s) 157
BstKTI GATC 2 cut(s) 16, 439
BstMBI GATC 2 cut(s) 13, 436
BstMWI GCNNNNNNNGC 1 cut(s) 104
BstNSI RCATGY 1 cut(s) 173
BstV2I GAAGAC 1 cut(s) 171
BstX2I RGATCY 1 cut(s) 13
BstYI RGATCY 1 cut(s) 13
BsuRI GGCC 1 cut(s) 319
BtsCI GGATG 1 cut(s) 157
Cac8I GCNNGC 1 cut(s) 321
Cfr13I GGNCC 1 cut(s) 317
Csp6I GTAC 3 cut(s) 299, 352, 449
CviAII CATG 2 cut(s) 170, 471
CviQI GTAC 3 cut(s) 299, 352, 449
DdeI CTNAG 4 cut(s) 113, 163, 237, 433
DpnI GATC 2 cut(s) 15, 438
DpnII GATC 2 cut(s) 13, 436
Eco130I CCWWGG 1 cut(s) 24
Eco32I GATATC 1 cut(s) 310
Eco88I CYCGRG 1 cut(s) 273
EcoNI CCTNNNNNAGG 1 cut(s) 74
EcoRV GATATC 1 cut(s) 310
EcoT14I CCWWGG 1 cut(s) 24
ErhI CCWWGG 1 cut(s) 24
FaeI CATG 2 cut(s) 173, 474
FalI AAGNNNNNCTT 2 cut(s) 96, 128
FatI CATG 2 cut(s) 169, 470
FblI GTMKAC 1 cut(s) 242
FokI GGATG 1 cut(s) 144
FspBI CTAG 6 cut(s) 17, 119, 233, 246, 279, 329
HaeIII GGCC 1 cut(s) 319
Hin1II CATG 2 cut(s) 173, 474
HinfI GANTC 2 cut(s) 206, 332
HphI GGTGA 1 cut(s) 50
Hpy166II GTNNAC 2 cut(s) 243, 301
Hpy188I TCNGA 4 cut(s) 166, 307, 436, 441
Hpy188III TCNNGA 4 cut(s) 11, 125, 273, 329
Hpy8I GTNNAC 2 cut(s) 243, 301
HpyAV CCTTC 1 cut(s) 35
HpyF10VI GCNNNNNNNGC 1 cut(s) 104
HpyF3I CTNAG 4 cut(s) 113, 163, 237, 433
Hsp92II CATG 2 cut(s) 173, 474
KpnI GGTACC 1 cut(s) 452
Kzo9I GATC 2 cut(s) 13, 436
LmnI GCTCC 2 cut(s) 28, 328
LpnPI CCDG 3 cut(s) 158, 298, 333
MaeI CTAG 6 cut(s) 17, 119, 233, 246, 279, 329
MaeIII GTNAC 3 cut(s) 358, 399, 473
MalI GATC 2 cut(s) 15, 438
MboI GATC 2 cut(s) 13, 436
MboII GAAGA 1 cut(s) 171
MflI RGATCY 1 cut(s) 13
MluCI AATT 2 cut(s) 294, 478
MnlI CCTC 4 cut(s) 80, 109, 172, 336
MroXI GAANNNNTTC 1 cut(s) 210
MseI TTAA 1 cut(s) 54
MslI CAYNNNNRTG 1 cut(s) 406
MwoI GCNNNNNNNGC 1 cut(s) 104
NdeII GATC 2 cut(s) 13, 436
NlaIII CATG 2 cut(s) 173, 474
NlaIV GGNNCC 3 cut(s) 143, 318, 450
NmuCI GTSAC 2 cut(s) 399, 473
NspI RCATGY 1 cut(s) 173
PaeR7I CTCGAG 1 cut(s) 273
PciI ACATGT 1 cut(s) 169
PdmI GAANNNNTTC 1 cut(s) 210
PfeI GAWTC 2 cut(s) 206, 332
PflMI CCANNNNNTGG 1 cut(s) 151
PscI ACATGT 1 cut(s) 169
PsiI TTATAA 1 cut(s) 348
PspN4I GGNNCC 3 cut(s) 143, 318, 450
PspPI GGNCC 1 cut(s) 317
PsuI RGATCY 1 cut(s) 13
RsaI GTAC 3 cut(s) 300, 353, 450
RsaNI GTAC 3 cut(s) 299, 352, 449
RseI CAYNNNNRTG 1 cut(s) 406
SaqAI TTAA 1 cut(s) 54
Sau3AI GATC 2 cut(s) 13, 436
Sau96I GGNCC 1 cut(s) 317
ScaI AGTACT 1 cut(s) 353
Sfr274I CTCGAG 1 cut(s) 273
SlaI CTCGAG 1 cut(s) 273
SmiMI CAYNNNNRTG 1 cut(s) 406
SmlI CTYRAG 2 cut(s) 123, 273
SmoI CTYRAG 2 cut(s) 123, 273
Sse9I AATT 2 cut(s) 294, 478
SspMI CTAG 6 cut(s) 17, 119, 233, 246, 279, 329
StyI CCWWGG 1 cut(s) 24
TaqI TCGA 1 cut(s) 274
TasI AATT 2 cut(s) 294, 478
TatI WGTACW 2 cut(s) 298, 351
TfiI GAWTC 2 cut(s) 206, 332
Tru1I TTAA 1 cut(s) 54
Tru9I TTAA 1 cut(s) 54
TseFI GTSAC 2 cut(s) 399, 473
Tsp45I GTSAC 2 cut(s) 399, 473
TspDTI ATGAA 1 cut(s) 252
TspGWI ACGGA 1 cut(s) 72
Van91I CCANNNNNTGG 1 cut(s) 151
XagI CCTNNNNNAGG 1 cut(s) 74
XbaI TCTAGA 1 cut(s) 328
XceI RCATGY 1 cut(s) 173
XhoI CTCGAG 1 cut(s) 273
XmiI GTMKAC 1 cut(s) 242
XmnI GAANNNNTTC 1 cut(s) 210
XspI CTAG 6 cut(s) 17, 119, 233, 246, 279, 329
ZrmI AGTACT 1 cut(s) 353
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.