RchiOBHm_Chr4g0394011

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0006436
Physical Location & Seq
Reverse (-)
9704199 .. 9705006
808 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ36654

Sequence Viewer

Length: 777 bp
ATGTCCAATAATATGTCAAATTACTTGAGCACACAAGGCATTGTGCACCAAACCAGCTGTGTTGGTACTCCTCAACAAAACGAGATTGCTGAGAGAAAGAATCGAGACCTCCTTGAAAAAACAAGAGCACTTATGTTTCAAATGAATGTTCCAAAAAAATTTTGGTCTCAAGGTGTTCTCACTGCCACATATCTCATCAACAGACTCCCTAGTAGAGTGCTTGGTTTCAAATCACCTCTTGAAATGTTGAAAGGAAGAAAGATTGATTTGTCTCACTTAAAAGTCTTTGGCTGCACATGTTTTGTTCATATTCAAGCACATCAACGTGATAAACTTGATCCTAGAGCTGATAAGTGTGTTTTCCTGGGATATTCATCTACTCAAAAGGGTTATAAATGTTATAACTATGTTACCAGAAAACTAATTGTTTCCAGAGATGTGAGATTTGATGAAGCTACTCCCTATTTCACTAGAAAATCATGTGATTCTGGTCAGGGGGAGTTTCTATCTGATTTGTTTCCAAGTCCTAATCTTCCTATTGATGAGGAGTGCAACTTGCCTGTCAATCCTGATGTTCATTCTGATCCTCCTATGGATGAGGATTGTGACTTGTCTATCAATCCTGACAGTCCAGTACAAGAAGTTCCAGCTGTAATTTCTGATGCAGAAGTTGATATGCAATCTATTGTTGAGCCTTCCTCTCCACCAGCAGTTATTCTTCGAAGAAACCCTTTGGTATCTCCACCTGCAGTTGTTCTTCGCAGAAATCCTCCATGA
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 rve

Protein Analysis

258

Amino Acids

29.05

Weight (kDa)

6.94

Isoelectric Point (pI)

53.35

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SH3_retrovirus PF25597 98 - 159 7.5e-28 Retroviral polymerase SH3-like domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 2 cut(s) 393, 402
AarI CACCTGC 1 cut(s) 754
Acc36I ACCTGC 1 cut(s) 754
AclWI GGATC 2 cut(s) 332, 578
AcsI RAATTY 1 cut(s) 158
AfaI GTAC 2 cut(s) 67, 636
AflIII ACRYGT 1 cut(s) 296
AgsI TTSAA 6 cut(s) 116, 140, 229, 242, 250, 314
AjnI CCWGG 1 cut(s) 363
AluBI AGCT 4 cut(s) 57, 347, 455, 650
AluI AGCT 4 cut(s) 57, 347, 455, 650
Alw21I GWGCWC 3 cut(s) 32, 48, 130
Alw26I GTCTC 3 cut(s) 99, 171, 276
Alw44I GTGCAC 1 cut(s) 44
AlwI GGATC 2 cut(s) 332, 578
ApaLI GTGCAC 1 cut(s) 44
ApeKI GCWGC 1 cut(s) 291
ApoI RAATTY 1 cut(s) 158
AsuHPI GGTGA 1 cut(s) 225
AsuII TTCGAA 1 cut(s) 721
BaeGI GKGCMC 1 cut(s) 48
Bbv12I GWGCWC 3 cut(s) 32, 48, 130
BbvI GCAGC 1 cut(s) 278
BciT130I CCWGG 1 cut(s) 365
BcoDI GTCTC 3 cut(s) 99, 171, 276
BfaI CTAG 3 cut(s) 210, 342, 471
BfmI CTRYAG 1 cut(s) 747
BfuAI ACCTGC 1 cut(s) 754
BisI GCNGC 1 cut(s) 292
BlsI GCNGC 1 cut(s) 293
Bme1390I CCNGG 1 cut(s) 365
BmrFI CCNGG 1 cut(s) 365
BmsI GCATC 1 cut(s) 652
BplI GAGNNNNNCTC 2 cut(s) 683, 715
Bpu14I TTCGAA 1 cut(s) 721
BpuEI CTTGAG 2 cut(s) 46, 153
BsaBI GATNNNNATC 1 cut(s) 373
BsaI GGTCTC 2 cut(s) 99, 171
BsaJI CCNNGG 1 cut(s) 364
Bse1I ACTGG 1 cut(s) 632
Bse8I GATNNNNATC 1 cut(s) 373
BseBI CCWGG 1 cut(s) 365
BseDI CCNNGG 1 cut(s) 364
BseGI GGATG 1 cut(s) 601
BseJI GATNNNNATC 1 cut(s) 373
BseMII CTCAG 1 cut(s) 81
BseNI ACTGG 1 cut(s) 632
BseRI GAGGAG 2 cut(s) 60, 560
BseSI GKGCMC 1 cut(s) 48
BseXI GCAGC 1 cut(s) 278
BsgI GTGCAG 1 cut(s) 277
BsiHKAI GWGCWC 3 cut(s) 32, 48, 130
BsmAI GTCTC 3 cut(s) 99, 171, 276
Bso31I GGTCTC 2 cut(s) 99, 171
Bsp119I TTCGAA 1 cut(s) 721
Bsp1286I GDGCHC 3 cut(s) 32, 48, 130
Bsp143I GATC 2 cut(s) 337, 583
BspCNI CTCAG 1 cut(s) 82
BspMAI CTGCAG 1 cut(s) 751
BspMI ACCTGC 1 cut(s) 754
BspPI GGATC 2 cut(s) 332, 578
BspT104I TTCGAA 1 cut(s) 721
BspTNI GGTCTC 2 cut(s) 99, 171
BsrI ACTGG 1 cut(s) 632
BssECI CCNNGG 1 cut(s) 364
BssMI GATC 2 cut(s) 337, 583
Bst2UI CCWGG 1 cut(s) 365
Bst4CI ACNGT 1 cut(s) 629
BstBI TTCGAA 1 cut(s) 721
BstDEI CTNAG 1 cut(s) 90
BstF5I GGATG 1 cut(s) 601
BstKTI GATC 2 cut(s) 340, 586
BstMAI GTCTC 3 cut(s) 99, 171, 276
BstMBI GATC 2 cut(s) 337, 583
BstMWI GCNNNNNNNGC 1 cut(s) 36
BstNI CCWGG 1 cut(s) 365
BstNSI RCATGY 1 cut(s) 300
BstSCI CCNGG 1 cut(s) 363
BstSFI CTRYAG 1 cut(s) 747
BstSLI GKGCMC 1 cut(s) 48
BstV1I GCAGC 1 cut(s) 278
BtsCI GGATG 1 cut(s) 601
BtsI GCAGTG 1 cut(s) 180
BtsIMutI CAGTG 1 cut(s) 180
BveI ACCTGC 1 cut(s) 754
Csp6I GTAC 2 cut(s) 66, 635
CviAII CATG 3 cut(s) 297, 480, 774
CviJI RGCY 6 cut(s) 57, 291, 347, 455, 650, 694
CviKI_1 RGCY 6 cut(s) 57, 291, 347, 455, 650, 694
CviQI GTAC 2 cut(s) 66, 635
DdeI CTNAG 1 cut(s) 90
DpnI GATC 2 cut(s) 339, 585
DpnII GATC 2 cut(s) 337, 583
Eco31I GGTCTC 2 cut(s) 99, 171
EcoRII CCWGG 1 cut(s) 363
FaeI CATG 3 cut(s) 300, 483, 777
FalI AAGNNNNNCTT 2 cut(s) 715, 747
FatI CATG 3 cut(s) 296, 479, 773
Fnu4HI GCNGC 1 cut(s) 292
FokI GGATG 1 cut(s) 608
Fsp4HI GCNGC 1 cut(s) 292
FspBI CTAG 3 cut(s) 210, 342, 471
GluI GCNGC 1 cut(s) 292
Hin1II CATG 3 cut(s) 300, 483, 777
HinfI GANTC 3 cut(s) 100, 204, 485
HphI GGTGA 1 cut(s) 225
Hpy166II GTNNAC 1 cut(s) 46
Hpy188I TCNGA 3 cut(s) 511, 583, 661
Hpy188III TCNNGA 5 cut(s) 104, 239, 432, 569, 623
Hpy8I GTNNAC 1 cut(s) 46
HpyAV CCTTC 1 cut(s) 705
HpyCH4III ACNGT 1 cut(s) 629
HpyCH4IV ACGT 1 cut(s) 325
HpyCH4V TGCA 6 cut(s) 46, 294, 552, 665, 679, 749
HpyF10VI GCNNNNNNNGC 1 cut(s) 36
HpyF3I CTNAG 1 cut(s) 90
HpySE526I ACGT 1 cut(s) 325
Hsp92II CATG 3 cut(s) 300, 483, 777
Kzo9I GATC 2 cut(s) 337, 583
Lsp1109I GCAGC 1 cut(s) 278
LweI GCATC 1 cut(s) 652
MaeI CTAG 3 cut(s) 210, 342, 471
MaeII ACGT 1 cut(s) 325
MaeIII GTNAC 2 cut(s) 409, 605
MalI GATC 2 cut(s) 339, 585
MboI GATC 2 cut(s) 337, 583
MboII GAAGA 5 cut(s) 267, 524, 710, 735, 749
MhlI GDGCHC 3 cut(s) 32, 48, 130
MluCI AATT 4 cut(s) 19, 158, 423, 654
MlyI GAGTC 1 cut(s) 198
MnlI CCTC 7 cut(s) 81, 119, 246, 538, 592, 597, 709
MseI TTAA 1 cut(s) 278
MslI CAYNNNNRTG 1 cut(s) 324
MspA1I CMGCKG 2 cut(s) 57, 650
MspR9I CCNGG 1 cut(s) 365
MvaI CCWGG 1 cut(s) 365
MwoI GCNNNNNNNGC 1 cut(s) 36
NdeII GATC 2 cut(s) 337, 583
NlaIII CATG 3 cut(s) 300, 483, 777
NmuCI GTSAC 1 cut(s) 605
NspI RCATGY 1 cut(s) 300
NspV TTCGAA 1 cut(s) 721
PaqCI CACCTGC 1 cut(s) 754
PciI ACATGT 1 cut(s) 296
PfeI GAWTC 2 cut(s) 100, 485
PkrI GCNGC 1 cut(s) 293
PleI GAGTC 1 cut(s) 198
PpsI GAGTC 1 cut(s) 198
PscI ACATGT 1 cut(s) 296
PsiI TTATAA 2 cut(s) 393, 402
Psp6I CCWGG 1 cut(s) 363
PspGI CCWGG 1 cut(s) 363
PsrI GAACNNNNNNTAC 2 cut(s) 627, 659
PstI CTGCAG 1 cut(s) 751
PvuII CAGCTG 2 cut(s) 57, 650
RsaI GTAC 2 cut(s) 67, 636
RsaNI GTAC 2 cut(s) 66, 635
RseI CAYNNNNRTG 1 cut(s) 324
SaqAI TTAA 1 cut(s) 278
SatI GCNGC 1 cut(s) 292
Sau3AI GATC 2 cut(s) 337, 583
SchI GAGTC 1 cut(s) 198
ScrFI CCNGG 1 cut(s) 365
SduI GDGCHC 3 cut(s) 32, 48, 130
SetI ASST 9 cut(s) 59, 111, 175, 238, 328, 349, 457, 652, 748
SfaNI GCATC 1 cut(s) 652
SfcI CTRYAG 1 cut(s) 747
SfuI TTCGAA 1 cut(s) 721
SmiMI CAYNNNNRTG 1 cut(s) 324
SmlI CTYRAG 2 cut(s) 25, 168
SmoI CTYRAG 2 cut(s) 25, 168
Sse9I AATT 4 cut(s) 19, 158, 423, 654
SspMI CTAG 3 cut(s) 210, 342, 471
StyD4I CCNGG 1 cut(s) 363
TaaI ACNGT 1 cut(s) 629
TaiI ACGT 1 cut(s) 328
TaqI TCGA 2 cut(s) 103, 721
TasI AATT 4 cut(s) 19, 158, 423, 654
TatI WGTACW 1 cut(s) 634
TfiI GAWTC 2 cut(s) 100, 485
Tru1I TTAA 1 cut(s) 278
Tru9I TTAA 1 cut(s) 278
TscAI CASTG 1 cut(s) 187
TseFI GTSAC 1 cut(s) 605
TseI GCWGC 1 cut(s) 291
Tsp45I GTSAC 1 cut(s) 605
TspDTI ATGAA 5 cut(s) 158, 296, 363, 465, 566
TspRI CASTG 1 cut(s) 187
VneI GTGCAC 1 cut(s) 44
XapI RAATTY 1 cut(s) 158
XceI RCATGY 1 cut(s) 300
XcmI CCANNNNNNNNNTGG 1 cut(s) 159
XspI CTAG 3 cut(s) 210, 342, 471
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.