Rw3G028000
MYB Family

DDE superfamily endonuclease

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0000468
Physical Location & Seq
Forward (+)
40878144 .. 40879482
1339 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G028000.1

Sequence Viewer

Length: 924 bp
ATGGCTAGTCTAAGTTTGTCCACAAAGGGCACACTACTTGTCGCCATAAATGCATTGTTGCCCTCAGCCATAAGAGTCTATAAACAAGTAGAGTACTTGTATACACTAGTTTATTGGAGTGATGCTATATGTATCGACCAACTACGAATGGTTAGACAATCATTTCATAAGTTGTGTCAAATTCTCATCAGTAAAGGCCAACTAAGACCAACCCAAAATGTGTCTATAGAGGAGATGAAGAATCATAGCATTGCCTTGTATTTTATTAGGTCAGGGCGAACTGTTAGTAAATACTTTCACGAGTGTTTGAAAAAAACACCTGAACCTATACTTGAGGACTCAACAGACAATAGATGGAAGTGGTTTAAGATAGCAACCAATGTTTTAGGAGTTTACTCTCAAGACTTGATGTTTGTATATGTTTTACCAGGATGGGAGGGTTCTACACATGATGCTCGTGTTTTTAGAGATACTTTGAGTATGAGAAATGGATTAAAATTTCCTAACGGTTGTTACTATTTAGTAGATGTTGGGTACATAAATGGAAATGGCTTTCTTGCACCTTTTAGAGGACAACGTTATCATTTCAATGATTGGAGAGATGGATACCGACCTGAGACATCAGAGGATTTTTTCAACATGAAACACTTAAGTGCCCGGAATGCTATTGAGAGGAGTTTTGGTTTACTAAAAATGCGTTGGTCAATTCTTAGGAGTCCATCATTTTATGATATTACAACACAACGTCGTATAATATCTGTGTGTTGCATGCTCCATAGTTTTATTAGAAGAGAGATGGCTGTAGATCCTATAAAAGAAGCATTCGATAATCAGCCAATAGCTGCAGTTGAGAAGTTGGAAGATAATGACTATGTTAATATAGTTGAGATCTCAAATGAGTGGACGATGTGGAGACAAAAATGA
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 Myb_DNA-bind_3

Protein Analysis

307

Amino Acids

35.97

Weight (kDa)

9.02

Isoelectric Point (pI)

44.28

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DUF8040 PF26138 40 - 105 9.9e-09 Domain of unknown function (DUF8040)
DDE_Tnp_4 PF13359 125 - 259 6e-19 DDE superfamily endonuclease
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AccI GTMKAC 1 cut(s) 101
AclI AACGTT 1 cut(s) 577
AclWI GGATC 1 cut(s) 800
AcsI RAATTY 2 cut(s) 180, 497
AfaI GTAC 2 cut(s) 95, 536
AfiI CCNNNNNNNGG 1 cut(s) 569
AflII CTTAAG 1 cut(s) 649
AgsI TTSAA 3 cut(s) 310, 589, 637
AhlI ACTAGT 1 cut(s) 106
AjnI CCWGG 1 cut(s) 427
AleI CACNNNNGTG 1 cut(s) 651
AluBI AGCT 1 cut(s) 842
AluI AGCT 1 cut(s) 842
Alw26I GTCTC 2 cut(s) 611, 907
AlwI GGATC 1 cut(s) 800
AoxI GGCC 1 cut(s) 196
ApeKI GCWGC 1 cut(s) 842
ApoI RAATTY 2 cut(s) 180, 497
ArsI GACNNNNNNTTYG 2 cut(s) 395, 427
AsuC2I CCSGG 1 cut(s) 658
BaeGI GKGCMC 2 cut(s) 32, 658
BauI CACGAG 2 cut(s) 299, 456
BbvCI CCTCAGC 1 cut(s) 64
BbvI GCAGC 1 cut(s) 829
BccI CCATC 5 cut(s) 348, 426, 596, 727, 790
BciT130I CCWGG 1 cut(s) 429
BciVI GTATCC 1 cut(s) 599
BcnI CCSGG 1 cut(s) 658
BcoDI GTCTC 2 cut(s) 611, 907
BcuI ACTAGT 1 cut(s) 106
BfaI CTAG 2 cut(s) 6, 107
BfmI CTRYAG 3 cut(s) 225, 801, 843
BfrI CTTAAG 1 cut(s) 649
BfuI GTATCC 1 cut(s) 599
BglII AGATCT 1 cut(s) 888
BisI GCNGC 1 cut(s) 843
BlsI GCNGC 1 cut(s) 844
BmcAI AGTACT 1 cut(s) 95
Bme1390I CCNGG 2 cut(s) 429, 658
BmrFI CCNGG 2 cut(s) 429, 658
BmsI GCATC 2 cut(s) 112, 442
Bpu10I CCTNAGC 1 cut(s) 64
BpuEI CTTGAG 2 cut(s) 353, 384
BpuMI CCSGG 1 cut(s) 658
BsaXI ACNNNNNCTCC 2 cut(s) 667, 697
Bsc4I CCNNNNNNNGG 1 cut(s) 569
Bse3DI GCAATG 1 cut(s) 249
BseBI CCWGG 1 cut(s) 429
BseGI GGATG 1 cut(s) 437
BseLI CCNNNNNNNGG 1 cut(s) 569
BseMI GCAATG 1 cut(s) 249
BseMII CTCAG 2 cut(s) 78, 606
BseRI GAGGAG 2 cut(s) 245, 688
BseSI GKGCMC 2 cut(s) 32, 658
BseXI GCAGC 1 cut(s) 829
BshFI GGCC 1 cut(s) 198
BsiSI CCGG 1 cut(s) 658
BslI CCNNNNNNNGG 1 cut(s) 569
BsmAI GTCTC 2 cut(s) 611, 907
BsmI GAATGC 2 cut(s) 667, 821
BsnI GGCC 1 cut(s) 198
Bsp1286I GDGCHC 2 cut(s) 32, 658
Bsp143I GATC 2 cut(s) 805, 888
BspANI GGCC 1 cut(s) 198
BspCNI CTCAG 2 cut(s) 77, 607
BspMAI CTGCAG 1 cut(s) 847
BspPI GGATC 1 cut(s) 800
BspTI CTTAAG 1 cut(s) 649
BsrDI GCAATG 1 cut(s) 249
BssMI GATC 2 cut(s) 805, 888
BssNAI GTATAC 1 cut(s) 102
BssSI CACGAG 2 cut(s) 299, 456
Bst1107I GTATAC 1 cut(s) 102
Bst2BI CACGAG 2 cut(s) 299, 456
Bst2UI CCWGG 1 cut(s) 429
Bst4CI ACNGT 2 cut(s) 283, 509
Bst6I CTCTTC 1 cut(s) 784
BstAFI CTTAAG 1 cut(s) 649
BstC8I GCNNGC 1 cut(s) 770
BstDEI CTNAG 5 cut(s) 11, 64, 203, 615, 710
BstENI CCTNNNNNAGG 1 cut(s) 567
BstF5I GGATG 1 cut(s) 437
BstKTI GATC 2 cut(s) 808, 891
BstMAI GTCTC 2 cut(s) 611, 907
BstMBI GATC 2 cut(s) 805, 888
BstMWI GCNNNNNNNGC 2 cut(s) 50, 662
BstNI CCWGG 1 cut(s) 429
BstNSI RCATGY 1 cut(s) 772
BstSCI CCNGG 2 cut(s) 427, 656
BstSFI CTRYAG 3 cut(s) 225, 801, 843
BstSLI GKGCMC 2 cut(s) 32, 658
BstV1I GCAGC 1 cut(s) 829
BstX2I RGATCY 2 cut(s) 805, 888
BstYI RGATCY 2 cut(s) 805, 888
BstZ17I GTATAC 1 cut(s) 102
BsuI GTATCC 1 cut(s) 599
BsuRI GGCC 1 cut(s) 198
BtsCI GGATG 1 cut(s) 437
Cac8I GCNNGC 1 cut(s) 770
Csp6I GTAC 2 cut(s) 94, 535
CviAII CATG 3 cut(s) 449, 640, 769
CviJI RGCY 7 cut(s) 5, 68, 198, 552, 800, 835, 842
CviKI_1 RGCY 7 cut(s) 5, 68, 198, 552, 800, 835, 842
CviQI GTAC 2 cut(s) 94, 535
DdeI CTNAG 5 cut(s) 11, 64, 203, 615, 710
DpnI GATC 2 cut(s) 807, 890
DpnII GATC 2 cut(s) 805, 888
Eam1104I CTCTTC 1 cut(s) 784
EarI CTCTTC 1 cut(s) 784
EcoNI CCTNNNNNAGG 1 cut(s) 567
EcoRII CCWGG 1 cut(s) 427
EcoT22I ATGCAT 1 cut(s) 55
FaeI CATG 3 cut(s) 452, 643, 772
FatI CATG 3 cut(s) 448, 639, 768
FblI GTMKAC 1 cut(s) 101
Fnu4HI GCNGC 1 cut(s) 843
FokI GGATG 1 cut(s) 444
Fsp4HI GCNGC 1 cut(s) 843
FspBI CTAG 2 cut(s) 6, 107
GluI GCNGC 1 cut(s) 843
HaeIII GGCC 1 cut(s) 198
HapII CCGG 1 cut(s) 658
Hin1II CATG 3 cut(s) 452, 643, 772
HinfI GANTC 4 cut(s) 75, 241, 338, 715
HpaII CCGG 1 cut(s) 658
Hpy166II GTNNAC 5 cut(s) 21, 102, 394, 686, 903
Hpy188I TCNGA 1 cut(s) 625
Hpy188III TCNNGA 2 cut(s) 299, 401
Hpy8I GTNNAC 5 cut(s) 21, 102, 394, 686, 903
Hpy99I CGWCG 1 cut(s) 750
HpyCH4III ACNGT 2 cut(s) 283, 509
HpyCH4IV ACGT 2 cut(s) 577, 745
HpyCH4V TGCA 4 cut(s) 53, 560, 768, 845
HpyF10VI GCNNNNNNNGC 2 cut(s) 50, 662
HpyF3I CTNAG 5 cut(s) 11, 64, 203, 615, 710
HpySE526I ACGT 2 cut(s) 577, 745
Hsp92II CATG 3 cut(s) 452, 643, 772
Kzo9I GATC 2 cut(s) 805, 888
LmnI GCTCC 1 cut(s) 777
LpnPI CCDG 6 cut(s) 258, 333, 414, 441, 627, 671
Lsp1109I GCAGC 1 cut(s) 829
LweI GCATC 2 cut(s) 112, 442
MaeI CTAG 2 cut(s) 6, 107
MaeII ACGT 2 cut(s) 577, 745
MaeIII GTNAC 1 cut(s) 512
MalI GATC 2 cut(s) 807, 890
MboI GATC 2 cut(s) 805, 888
MboII GAAGA 3 cut(s) 250, 801, 872
MflI RGATCY 2 cut(s) 805, 888
MhlI GDGCHC 2 cut(s) 32, 658
MluCI AATT 3 cut(s) 180, 497, 705
MlyI GAGTC 3 cut(s) 84, 332, 724
MmeI TCCRAC 1 cut(s) 837
MnlI CCTC 7 cut(s) 73, 223, 328, 430, 563, 619, 666
Mph1103I ATGCAT 1 cut(s) 55
MseI TTAA 4 cut(s) 366, 494, 650, 876
MslI CAYNNNNRTG 2 cut(s) 588, 651
MspCI CTTAAG 1 cut(s) 649
MspI CCGG 1 cut(s) 658
MspR9I CCNGG 2 cut(s) 429, 658
Mva1269I GAATGC 2 cut(s) 667, 821
MvaI CCWGG 1 cut(s) 429
MwoI GCNNNNNNNGC 2 cut(s) 50, 662
NciI CCSGG 1 cut(s) 658
NdeII GATC 2 cut(s) 805, 888
NlaIII CATG 3 cut(s) 452, 643, 772
NsiI ATGCAT 1 cut(s) 55
NspI RCATGY 1 cut(s) 772
OliI CACNNNNGTG 1 cut(s) 651
PaeI GCATGC 1 cut(s) 772
PctI GAATGC 2 cut(s) 667, 821
PfeI GAWTC 1 cut(s) 241
PkrI GCNGC 1 cut(s) 844
PleI GAGTC 3 cut(s) 83, 332, 723
PpsI GAGTC 3 cut(s) 83, 332, 723
Psp1406I AACGTT 1 cut(s) 577
Psp6I CCWGG 1 cut(s) 427
PspGI CCWGG 1 cut(s) 427
PstI CTGCAG 1 cut(s) 847
PsuI RGATCY 2 cut(s) 805, 888
RsaI GTAC 2 cut(s) 95, 536
RsaNI GTAC 2 cut(s) 94, 535
RseI CAYNNNNRTG 2 cut(s) 588, 651
SaqAI TTAA 4 cut(s) 366, 494, 650, 876
SatI GCNGC 1 cut(s) 843
Sau3AI GATC 2 cut(s) 805, 888
ScaI AGTACT 1 cut(s) 95
SchI GAGTC 3 cut(s) 84, 332, 724
ScrFI CCNGG 2 cut(s) 429, 658
SduI GDGCHC 2 cut(s) 32, 658
SetI ASST 8 cut(s) 272, 322, 328, 565, 580, 616, 748, 844
SfaNI GCATC 2 cut(s) 112, 442
SfcI CTRYAG 3 cut(s) 225, 801, 843
SmiMI CAYNNNNRTG 2 cut(s) 588, 651
SmlI CTYRAG 3 cut(s) 332, 399, 649
SmoI CTYRAG 3 cut(s) 332, 399, 649
SpeI ACTAGT 1 cut(s) 106
SphI GCATGC 1 cut(s) 772
Sse9I AATT 3 cut(s) 180, 497, 705
SspMI CTAG 2 cut(s) 6, 107
StyD4I CCNGG 2 cut(s) 427, 656
TaaI ACNGT 2 cut(s) 283, 509
TaiI ACGT 2 cut(s) 580, 748
TaqI TCGA 2 cut(s) 135, 825
TasI AATT 3 cut(s) 180, 497, 705
TatI WGTACW 1 cut(s) 93
TfiI GAWTC 1 cut(s) 241
Tru1I TTAA 4 cut(s) 366, 494, 650, 876
Tru9I TTAA 4 cut(s) 366, 494, 650, 876
TseI GCWGC 1 cut(s) 842
TspDTI ATGAA 3 cut(s) 155, 251, 656
Vha464I CTTAAG 1 cut(s) 649
XagI CCTNNNNNAGG 1 cut(s) 567
XapI RAATTY 2 cut(s) 180, 497
XceI RCATGY 1 cut(s) 772
XmiI GTMKAC 1 cut(s) 101
XspI CTAG 2 cut(s) 6, 107
ZrmI AGTACT 1 cut(s) 95
Zsp2I ATGCAT 1 cut(s) 55
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.