Rw2G005400

nuclease HARBI1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000468
Physical Location & Seq
Reverse (-)
5096333 .. 5097080
748 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G005400.1

Sequence Viewer

Length: 663 bp
ATGGTTCCTACCGAAGATAAACCAAGATATCGAAATAGGAAGGGTGACATTAGTACAAATGTTTTAGGTGTTTGTGATGCTAATATGAAGTTCATCTATGTATTACCTGGTTGGGAAGGATCTGCAGCAGATTCTAGAGTTTTACGTGATGCTTTGACTAGGCGCAATGGCTTAAAAATCCAATCAAATAAATACTGTCTTATGGATGCTGGATACACAAATGGACCAGGGTTTCTATCTCCTTATCGTGGAACTAGGTATCATCTTAATTTGTGGAGAGGAAACACCCCAAGGGATCACAAGGAGCTATTCAATCTTCGGCATTCATCGGCAAGAAATACAATTGAAAGAGCATTTGGATTATTGAAGAAGCAATGGGCAATACTACGCACAGCTAGTTTTTTTTATGTGAAAACACAAGTTAGGATTATTAATGCTTGCTGCATCATTCATAATTATCTTCGCGATGAAATGCCCAATGATCAACTATTGGATGATGTGGACCGAGACTTAGAAAATACACTTGAGGTGGAAGATGAAGATGTGGATGATGAGAACATTAGAGTAGTCAAAGTAACTCGAGAGTGGACAACATTTAGAGATGCTTTAGCTATGGAAATGTTTGCAGAATATCAAGCTATTAGAAGAGCTCAAGATTCTTGA
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
DDE_Tnp_4

Protein Analysis

220

Amino Acids

25.64

Weight (kDa)

7.67

Isoelectric Point (pI)

37.32

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DDE_Tnp_4 PF13359 5 - 152 4.8e-22 DDE superfamily endonuclease
DDE_Tnp_1 PF01609 7 - 149 1.2e-10 Transposase DDE domain
Plant_tran PF04827 98 - 154 4.5e-08 Plant transposon protein
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: OG0000468)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g04030 FvH4_2g09411 FvH4_3g15551 FvH4_3g36421 FvH4_4g11701 FvH4_5g36381 FvH4_6g09143 FvH4_6g09144 FvH4_6g21972
malus_domestica MD00G1096500.v1.1 MD00G1122500.v1.1 MD02G1090600.v1.1 MD02G1173300.v1.1 MD05G1202800.v1.1 MD14G1123600.v1.1
prunus_persica Prupe.1G083600_v2.0.a1 Prupe.1G245300_v2.0.a1 Prupe.5G002100_v2.0.a1 Prupe.6G061200_v2.0.a1
pyrus_communis pycom01g07060 pycom02g13920 pycom04g11780 pycom04g13480 pycom04g21940 pycom06g07950 pycom07g03740 pycom07g03980 pycom09g02010 pycom09g02020 pycom09g11510 pycom09g14260 pycom10g02500 pycom10g15690 pycom12g08730 pycom12g08740 pycom14g19840 pycom15g16780 pycom15g24940 pycom15g25660 pycom16g21630 pycom16g26320
rosa_chinensis RchiOBHm_Chr1g0330371 RchiOBHm_Chr1g0331991 RchiOBHm_Chr6g0300321
rosa_laevigata RLG00000013795
rosa_multiflora Rmu_sc0000060.1_g000010 Rmu_sc0000288.1_g000044 Rmu_sc0002219.1_g000002 Rmu_sc0003995.1_g000003
rosa_roxburghii Rroxscaffold_1G00059020 Rroxscaffold_2G00108450 Rroxscaffold_2G00112460 Rroxscaffold_5G00375700 Rroxscaffold_5G00381640 Rroxscaffold_7G00158590
rosa_rugosa Rorug01G0237300 Rorug01G0237400 Rorug01G0237500 Rorug02G0051900 Rorug03G0260600 Rorug03G0285800 Rorug04G0076800 Rorug04G0162600 Rorug07G0264500 Rorug07G0264500
rosa_samantha Rh2DG003500 Rh3CG244800 Rh4CG334200 Rh5AG318300 Rh5BG549000 Rh7AG126400 Rh7CG118500 Rh7CG154500 Rh7DG025400
rosa_wichuraiana Rw1G026390 Rw2G005400 Rw2G034490 Rw3G019530 Rw3G028000 Rw4G010490 Rw5G010830 Rw5G023340 Rw5G026580 Rw5G041150 Rw6G003010 Rw6G003290 Rw6G010630 Rw6G021220 Rw6G035650 Rw7G014310

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 465
AclWI GGATC 2 cut(s) 127, 303
AfaI GTAC 1 cut(s) 55
AfiI CCNNNNNNNGG 1 cut(s) 248
AgsI TTSAA 3 cut(s) 313, 347, 367
AjnI CCWGG 2 cut(s) 106, 226
AjuI GAANNNNNNNTTGG 2 cut(s) 339, 371
AluBI AGCT 5 cut(s) 307, 395, 611, 638, 650
AluI AGCT 5 cut(s) 307, 395, 611, 638, 650
Alw21I GWGCWC 1 cut(s) 652
Alw26I GTCTC 1 cut(s) 501
AlwI GGATC 2 cut(s) 127, 303
Ama87I CYCGRG 1 cut(s) 579
ApeKI GCWGC 2 cut(s) 125, 441
AseI ATTAAT 1 cut(s) 432
AspLEI GCGC 1 cut(s) 165
AspS9I GGNCC 2 cut(s) 224, 502
AsuHPI GGTGA 1 cut(s) 56
AvaI CYCGRG 1 cut(s) 579
AvaII GGWCC 2 cut(s) 224, 502
BanII GRGCYC 1 cut(s) 652
Bbv12I GWGCWC 1 cut(s) 652
BbvI GCAGC 2 cut(s) 137, 428
BciT130I CCWGG 2 cut(s) 108, 228
BciVI GTATCC 1 cut(s) 206
BclI TGATCA 1 cut(s) 481
BcoDI GTCTC 1 cut(s) 501
BfaI CTAG 4 cut(s) 135, 159, 255, 396
BfmI CTRYAG 1 cut(s) 123
BfuI GTATCC 1 cut(s) 206
BisI GCNGC 2 cut(s) 126, 442
BlsI GCNGC 2 cut(s) 127, 443
Bme1390I CCNGG 2 cut(s) 108, 228
Bme18I GGWCC 2 cut(s) 224, 502
BmeT110I CYCGRG 1 cut(s) 579
BmgT120I GGNCC 2 cut(s) 224, 502
BmiI GGNNCC 1 cut(s) 6
BmrFI CCNGG 2 cut(s) 108, 228
BmsI GCATC 5 cut(s) 67, 139, 196, 453, 592
BpuEI CTTGAG 2 cut(s) 545, 636
BsaAI YACGTR 1 cut(s) 146
BsaJI CCNNGG 2 cut(s) 227, 290
Bsc4I CCNNNNNNNGG 1 cut(s) 248
Bse3DI GCAATG 2 cut(s) 172, 380
BseBI CCWGG 2 cut(s) 108, 228
BseDI CCNNGG 2 cut(s) 227, 290
BseGI GGATG 3 cut(s) 211, 499, 553
BseLI CCNNNNNNNGG 1 cut(s) 248
BseMI GCAATG 2 cut(s) 172, 380
BseXI GCAGC 2 cut(s) 137, 428
Bsh1236I CGCG 1 cut(s) 465
BsiHKAI GWGCWC 1 cut(s) 652
BsiHKCI CYCGRG 1 cut(s) 579
BslI CCNNNNNNNGG 1 cut(s) 248
BsmAI GTCTC 1 cut(s) 501
BsmI GAATGC 1 cut(s) 322
BsoBI CYCGRG 1 cut(s) 579
Bsp1286I GDGCHC 1 cut(s) 652
Bsp143I GATC 3 cut(s) 119, 295, 481
Bsp68I TCGCGA 1 cut(s) 465
BspFNI CGCG 1 cut(s) 465
BspLI GGNNCC 1 cut(s) 6
BspMAI CTGCAG 1 cut(s) 127
BspPI GGATC 2 cut(s) 127, 303
BspQI GCTCTTC 1 cut(s) 640
BsrDI GCAATG 2 cut(s) 172, 380
BssECI CCNNGG 2 cut(s) 227, 290
BssMI GATC 3 cut(s) 119, 295, 481
BssT1I CCWWGG 1 cut(s) 290
Bst2UI CCWGG 2 cut(s) 108, 228
Bst4CI ACNGT 1 cut(s) 197
Bst6I CTCTTC 1 cut(s) 640
BstBAI YACGTR 1 cut(s) 146
BstC8I GCNNGC 1 cut(s) 439
BstDEI CTNAG 1 cut(s) 511
BstF5I GGATG 3 cut(s) 211, 499, 553
BstFNI CGCG 1 cut(s) 465
BstHHI GCGC 1 cut(s) 165
BstKTI GATC 3 cut(s) 122, 298, 484
BstMAI GTCTC 1 cut(s) 501
BstMBI GATC 3 cut(s) 119, 295, 481
BstNI CCWGG 2 cut(s) 108, 228
BstSCI CCNGG 2 cut(s) 106, 226
BstSFI CTRYAG 1 cut(s) 123
BstUI CGCG 1 cut(s) 465
BstV1I GCAGC 2 cut(s) 137, 428
BstX2I RGATCY 1 cut(s) 119
BstYI RGATCY 1 cut(s) 119
BsuI GTATCC 1 cut(s) 206
BtgZI GCGATG 1 cut(s) 480
BtsCI GGATG 3 cut(s) 211, 499, 553
BtuMI TCGCGA 1 cut(s) 465
Cac8I GCNNGC 1 cut(s) 439
CfoI GCGC 1 cut(s) 165
Cfr13I GGNCC 2 cut(s) 224, 502
CsiI ACCWGGT 1 cut(s) 106
Csp6I GTAC 1 cut(s) 54
CviJI RGCY 6 cut(s) 171, 307, 395, 611, 638, 650
CviKI_1 RGCY 6 cut(s) 171, 307, 395, 611, 638, 650
CviQI GTAC 1 cut(s) 54
DdeI CTNAG 1 cut(s) 511
DpnI GATC 3 cut(s) 121, 297, 483
DpnII GATC 3 cut(s) 119, 295, 481
Eam1104I CTCTTC 1 cut(s) 640
EarI CTCTTC 1 cut(s) 640
Ecl136II GAGCTC 1 cut(s) 650
Eco130I CCWWGG 1 cut(s) 290
Eco24I GRGCYC 1 cut(s) 652
Eco32I GATATC 1 cut(s) 29
Eco47I GGWCC 2 cut(s) 224, 502
Eco53kI GAGCTC 1 cut(s) 650
Eco88I CYCGRG 1 cut(s) 579
EcoICRI GAGCTC 1 cut(s) 650
EcoRII CCWGG 2 cut(s) 106, 226
EcoRV GATATC 1 cut(s) 29
EcoT14I CCWWGG 1 cut(s) 290
EcoT38I GRGCYC 1 cut(s) 652
ErhI CCWWGG 1 cut(s) 290
FaiI YATR 6 cut(s) 86, 99, 203, 408, 453, 614
FbaI TGATCA 1 cut(s) 481
Fnu4HI GCNGC 2 cut(s) 126, 442
FokI GGATG 3 cut(s) 218, 506, 560
FriOI GRGCYC 1 cut(s) 652
Fsp4HI GCNGC 2 cut(s) 126, 442
FspBI CTAG 4 cut(s) 135, 159, 255, 396
GlaI GCGC 1 cut(s) 164
GluI GCNGC 2 cut(s) 126, 442
HhaI GCGC 1 cut(s) 165
Hin6I GCGC 1 cut(s) 163
HinP1I GCGC 1 cut(s) 163
HinfI GANTC 2 cut(s) 131, 656
HphI GGTGA 1 cut(s) 56
Hpy166II GTNNAC 2 cut(s) 502, 588
Hpy188III TCNNGA 5 cut(s) 135, 464, 581, 653, 660
Hpy8I GTNNAC 2 cut(s) 502, 588
HpyAV CCTTC 2 cut(s) 34, 110
HpyCH4III ACNGT 1 cut(s) 197
HpyCH4IV ACGT 1 cut(s) 145
HpyCH4V TGCA 3 cut(s) 125, 444, 626
HpyF3I CTNAG 1 cut(s) 511
HpySE526I ACGT 1 cut(s) 145
HspAI GCGC 1 cut(s) 163
Ksp22I TGATCA 1 cut(s) 481
Kzo9I GATC 3 cut(s) 119, 295, 481
LguI GCTCTTC 1 cut(s) 640
LmnI GCTCC 1 cut(s) 304
LpnPI CCDG 5 cut(s) 93, 120, 195, 213, 240
Lsp1109I GCAGC 2 cut(s) 137, 428
LweI GCATC 5 cut(s) 67, 139, 196, 453, 592
MabI ACCWGGT 1 cut(s) 106
MaeI CTAG 4 cut(s) 135, 159, 255, 396
MaeII ACGT 1 cut(s) 145
MaeIII GTNAC 2 cut(s) 44, 574
MalI GATC 3 cut(s) 121, 297, 483
MboI GATC 3 cut(s) 119, 295, 481
MboII GAAGA 7 cut(s) 26, 308, 379, 452, 545, 551, 657
MfeI CAATTG 1 cut(s) 342
MflI RGATCY 1 cut(s) 119
MhlI GDGCHC 1 cut(s) 652
MluCI AATT 3 cut(s) 268, 342, 454
MnlI CCTC 2 cut(s) 272, 520
MseI TTAA 3 cut(s) 173, 267, 432
MspR9I CCNGG 2 cut(s) 108, 228
MunI CAATTG 1 cut(s) 342
Mva1269I GAATGC 1 cut(s) 322
MvaI CCWGG 2 cut(s) 108, 228
MvnI CGCG 1 cut(s) 465
NdeII GATC 3 cut(s) 119, 295, 481
NlaIV GGNNCC 1 cut(s) 6
NmuCI GTSAC 1 cut(s) 44
NruI TCGCGA 1 cut(s) 465
PaeR7I CTCGAG 1 cut(s) 579
PciSI GCTCTTC 1 cut(s) 640
PctI GAATGC 1 cut(s) 322
PfeI GAWTC 2 cut(s) 131, 656
PkrI GCNGC 2 cut(s) 127, 443
Ppu21I YACGTR 1 cut(s) 146
PshBI ATTAAT 1 cut(s) 432
Psp124BI GAGCTC 1 cut(s) 652
Psp6I CCWGG 2 cut(s) 106, 226
PspGI CCWGG 2 cut(s) 106, 226
PspN4I GGNNCC 1 cut(s) 6
PspPI GGNCC 2 cut(s) 224, 502
PstI CTGCAG 1 cut(s) 127
PsuI RGATCY 1 cut(s) 119
RruI TCGCGA 1 cut(s) 465
RsaI GTAC 1 cut(s) 55
RsaNI GTAC 1 cut(s) 54
SacI GAGCTC 1 cut(s) 652
SapI GCTCTTC 1 cut(s) 640
SaqAI TTAA 3 cut(s) 173, 267, 432
SatI GCNGC 2 cut(s) 126, 442
Sau3AI GATC 3 cut(s) 119, 295, 481
Sau96I GGNCC 2 cut(s) 224, 502
ScrFI CCNGG 2 cut(s) 108, 228
SduI GDGCHC 1 cut(s) 652
SexAI ACCWGGT 1 cut(s) 106
SfaNI GCATC 5 cut(s) 67, 139, 196, 453, 592
SfcI CTRYAG 1 cut(s) 123
Sfr274I CTCGAG 1 cut(s) 579
SinI GGWCC 2 cut(s) 224, 502
SlaI CTCGAG 1 cut(s) 579
SmlI CTYRAG 3 cut(s) 524, 579, 651
SmoI CTYRAG 3 cut(s) 524, 579, 651
Sse9I AATT 3 cut(s) 268, 342, 454
SspMI CTAG 4 cut(s) 135, 159, 255, 396
SstI GAGCTC 1 cut(s) 652
StyD4I CCNGG 2 cut(s) 106, 226
StyI CCWWGG 1 cut(s) 290
TaaI ACNGT 1 cut(s) 197
TaiI ACGT 1 cut(s) 148
TaqI TCGA 2 cut(s) 31, 580
TaqII GACCGA 1 cut(s) 519
TasI AATT 3 cut(s) 268, 342, 454
TatI WGTACW 1 cut(s) 53
TfiI GAWTC 2 cut(s) 131, 656
Tru1I TTAA 3 cut(s) 173, 267, 432
Tru9I TTAA 3 cut(s) 173, 267, 432
TseFI GTSAC 1 cut(s) 44
TseI GCWGC 2 cut(s) 125, 441
Tsp45I GTSAC 1 cut(s) 44
TspDTI ATGAA 6 cut(s) 82, 101, 315, 440, 483, 552
VpaK11BI GGWCC 2 cut(s) 224, 502
VspI ATTAAT 1 cut(s) 432
XbaI TCTAGA 1 cut(s) 134
XhoI CTCGAG 1 cut(s) 579
XspI CTAG 4 cut(s) 135, 159, 255, 396
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.