Rorug05G0177800

DNA binding domain with preference for A/T rich regions

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000005
OG0006724
Physical Location & Seq
Forward (+)
16600525 .. 16602095
1571 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug05G0177800.1

Sequence Viewer

Length: 852 bp
ATGGCCTTGAACTGGGAAGTACCTCAGTTTTTTGACTCAGACATGACTTGTATCCAGCAGAATCTAGAAGCAGAGCTAGTAGGAGATTTCCTTCAATGTGTTAATTCAGACTATTCCAATCCCCATAACTTTCTCGATCCATGGTATGACCCCTGTAATCTTCTTAACCTCGAAAATCCTGACTTTGATCATCTGCTTCCACCTTTTTCTCTCAAACCTGACATGTTTCCAGTACAAGATTTCGAACCTTACCCCCAACCGAAACGCCAAAAGTGCTCGAAAGAGTACTATTGCCGGGATCTTACACCCACTTTCTCTAATGGGTTTGCTCCAAATCCATGTCCTAGGCCCGAGTTTTTTTCCGGGGCCTTTACTACTCCGGTGCTCAACTTTCAGCATCCGGAGGTTGTTGATGGCAATACCAGAAAAACTAGTGTTGAAAATGTGGGGAAGAAAGTGGAAGAAAGAAGTGTATCGCCGCAGAGTATCGCGGCAAGAGAAAGGAGGAGGAAAATCACAGAGAAGACTCAAGAGCTAGGGAAGCTTGTTCCTGGAGGAAGCAAGATGAACACAGCTGAGATGCTCACTGCCGCTTACAACTATGTCAAGTTCTTGCAGGCTCAGATGGGGATTCTCGAGTTCATGGGGTCCTTTCAGGAAATGAAGGCAGATCATACAGCTACCAAGGAACTACATGTCGTTGCATCTCCTACTATTCAAGAGAAGCTCTATATGGAGCATAAGTGCTTGGTCCCAAAGGAGTTCGTAGAGGTATTAGCAAACCATTTTGATGCTGAATCGAAGCCTTCACTCTCCCACAAGCTCAACCAGCTGCTCAAATCTAGCGGATGA
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
No domains found.

Protein Analysis

283

Amino Acids

32.29

Weight (kDa)

5.54

Isoelectric Point (pI)

42.82

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HLH PF00010 165 - 206 7.6e-06 Helix-loop-helix DNA-binding 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)
AccII CGCG 1 cut(s) 491
AccIII TCCGGA 1 cut(s) 400
AciI CCGC 4 cut(s) 479, 491, 591, 846
AclWI GGATC 2 cut(s) 131, 306
AfaI GTAC 3 cut(s) 21, 234, 287
AfiI CCNNNNNNNGG 1 cut(s) 12
AflIII ACRYGT 2 cut(s) 222, 694
AgsI TTSAA 4 cut(s) 10, 95, 440, 719
AhlI ACTAGT 1 cut(s) 431
AjnI CCWGG 1 cut(s) 550
AluBI AGCT 8 cut(s) 76, 535, 544, 575, 680, 727, 823, 832
AluI AGCT 8 cut(s) 76, 535, 544, 575, 680, 727, 823, 832
Alw21I GWGCWC 2 cut(s) 278, 387
AlwI GGATC 2 cut(s) 131, 306
Ama87I CYCGRG 2 cut(s) 350, 635
Aor13HI TCCGGA 1 cut(s) 400
AoxI GGCC 3 cut(s) 3, 347, 366
ApeKI GCWGC 1 cut(s) 832
AspA2I CCTAGG 1 cut(s) 344
AspS9I GGNCC 4 cut(s) 348, 366, 648, 751
AsuC2I CCSGG 2 cut(s) 296, 364
AsuII TTCGAA 1 cut(s) 243
AvaI CYCGRG 2 cut(s) 350, 635
AvaII GGWCC 2 cut(s) 648, 751
AvrII CCTAGG 1 cut(s) 344
BbsI GAAGAC 1 cut(s) 530
Bbv12I GWGCWC 2 cut(s) 278, 387
BbvI GCAGC 1 cut(s) 819
BccI CCATC 2 cut(s) 407, 619
BciT130I CCWGG 1 cut(s) 552
BciVI GTATCC 1 cut(s) 62
BclI TGATCA 1 cut(s) 187
BcnI CCSGG 2 cut(s) 296, 364
BcuI ACTAGT 1 cut(s) 431
BfaI CTAG 6 cut(s) 65, 77, 345, 432, 536, 843
BfuI GTATCC 1 cut(s) 62
BisI GCNGC 4 cut(s) 479, 492, 591, 833
BlnI CCTAGG 1 cut(s) 344
BlsI GCNGC 4 cut(s) 480, 493, 592, 834
BmcAI AGTACT 1 cut(s) 287
Bme1390I CCNGG 3 cut(s) 296, 364, 552
Bme18I GGWCC 2 cut(s) 648, 751
BmeT110I CYCGRG 2 cut(s) 350, 635
BmgT120I GGNCC 4 cut(s) 348, 366, 648, 751
BmiI GGNNCC 3 cut(s) 367, 649, 753
BmrFI CCNGG 3 cut(s) 296, 364, 552
BmrI ACTGGG 1 cut(s) 22
BmsI GCATC 4 cut(s) 406, 570, 713, 781
BmuI ACTGGG 1 cut(s) 22
BpiI GAAGAC 1 cut(s) 530
BpmI CTGGAG 1 cut(s) 573
Bpu14I TTCGAA 1 cut(s) 243
BpuEI CTTGAG 1 cut(s) 513
BpuMI CCSGG 2 cut(s) 296, 364
BsaJI CCNNGG 4 cut(s) 140, 344, 363, 684
BsaWI WCCGGW 2 cut(s) 379, 400
BsaXI ACNNNNNCTCC 2 cut(s) 728, 758
Bsc4I CCNNNNNNNGG 1 cut(s) 12
Bse1I ACTGG 2 cut(s) 17, 230
BseAI TCCGGA 1 cut(s) 400
BseBI CCWGG 1 cut(s) 552
BseDI CCNNGG 4 cut(s) 140, 344, 363, 684
BseGI GGATG 1 cut(s) 397
BseLI CCNNNNNNNGG 1 cut(s) 12
BseMII CTCAG 4 cut(s) 38, 51, 567, 635
BseNI ACTGG 2 cut(s) 17, 230
BseRI GAGGAG 1 cut(s) 520
BseXI GCAGC 1 cut(s) 819
Bsh1236I CGCG 1 cut(s) 491
BshFI GGCC 3 cut(s) 5, 349, 368
BsiHKAI GWGCWC 2 cut(s) 278, 387
BsiHKCI CYCGRG 2 cut(s) 350, 635
BsiSI CCGG 4 cut(s) 295, 363, 380, 401
BslFI GGGAC 1 cut(s) 737
BslI CCNNNNNNNGG 1 cut(s) 12
BsmFI GGGAC 1 cut(s) 737
BsnI GGCC 3 cut(s) 5, 349, 368
BsoBI CYCGRG 2 cut(s) 350, 635
Bsp119I TTCGAA 1 cut(s) 243
Bsp1286I GDGCHC 2 cut(s) 278, 387
Bsp13I TCCGGA 1 cut(s) 400
Bsp143I GATC 4 cut(s) 136, 187, 298, 670
Bsp19I CCATGG 1 cut(s) 140
BspACI CCGC 4 cut(s) 479, 491, 591, 846
BspANI GGCC 3 cut(s) 5, 349, 368
BspCNI CTCAG 4 cut(s) 37, 50, 568, 634
BspEI TCCGGA 1 cut(s) 400
BspFNI CGCG 1 cut(s) 491
BspLI GGNNCC 3 cut(s) 367, 649, 753
BspPI GGATC 2 cut(s) 131, 306
BspT104I TTCGAA 1 cut(s) 243
BsrI ACTGG 2 cut(s) 17, 230
BssECI CCNNGG 4 cut(s) 140, 344, 363, 684
BssMI GATC 4 cut(s) 136, 187, 298, 670
BssT1I CCWWGG 3 cut(s) 140, 344, 684
Bst2UI CCWGG 1 cut(s) 552
BstBI TTCGAA 1 cut(s) 243
BstC8I GCNNGC 1 cut(s) 618
BstDEI CTNAG 4 cut(s) 24, 37, 576, 621
BstDSI CCRYGG 1 cut(s) 140
BstF5I GGATG 1 cut(s) 397
BstFNI CGCG 1 cut(s) 491
BstKTI GATC 4 cut(s) 139, 190, 301, 673
BstMBI GATC 4 cut(s) 136, 187, 298, 670
BstMWI GCNNNNNNNGC 3 cut(s) 273, 541, 829
BstNI CCWGG 1 cut(s) 552
BstNSI RCATGY 2 cut(s) 226, 698
BstSCI CCNGG 3 cut(s) 294, 362, 550
BstUI CGCG 1 cut(s) 491
BstV1I GCAGC 1 cut(s) 819
BstV2I GAAGAC 1 cut(s) 530
BstX2I RGATCY 1 cut(s) 298
BstYI RGATCY 1 cut(s) 298
BsuI GTATCC 1 cut(s) 62
BsuRI GGCC 3 cut(s) 5, 349, 368
BtgI CCRYGG 1 cut(s) 140
BtsCI GGATG 1 cut(s) 397
BtsI GCAGTG 1 cut(s) 585
BtsIMutI CAGTG 1 cut(s) 585
Cac8I GCNNGC 1 cut(s) 618
Cfr13I GGNCC 4 cut(s) 348, 366, 648, 751
Csp6I GTAC 3 cut(s) 20, 233, 286
CviAII CATG 6 cut(s) 43, 141, 223, 339, 643, 695
CviQI GTAC 3 cut(s) 20, 233, 286
DdeI CTNAG 4 cut(s) 24, 37, 576, 621
DpnI GATC 4 cut(s) 138, 189, 300, 672
DpnII GATC 4 cut(s) 136, 187, 298, 670
Eco130I CCWWGG 3 cut(s) 140, 344, 684
Eco47I GGWCC 2 cut(s) 648, 751
Eco88I CYCGRG 2 cut(s) 350, 635
EcoO109I RGGNCCY 2 cut(s) 366, 648
EcoRII CCWGG 1 cut(s) 550
EcoT14I CCWWGG 3 cut(s) 140, 344, 684
ErhI CCWWGG 3 cut(s) 140, 344, 684
FaeI CATG 6 cut(s) 46, 144, 226, 342, 646, 698
FaqI GGGAC 1 cut(s) 737
FatI CATG 6 cut(s) 42, 140, 222, 338, 642, 694
FbaI TGATCA 1 cut(s) 187
Fnu4HI GCNGC 4 cut(s) 479, 492, 591, 833
FokI GGATG 1 cut(s) 384
Fsp4HI GCNGC 4 cut(s) 479, 492, 591, 833
FspBI CTAG 6 cut(s) 65, 77, 345, 432, 536, 843
GluI GCNGC 4 cut(s) 479, 492, 591, 833
GsuI CTGGAG 1 cut(s) 573
HaeIII GGCC 3 cut(s) 5, 349, 368
HapII CCGG 4 cut(s) 295, 363, 380, 401
Hin1II CATG 6 cut(s) 46, 144, 226, 342, 646, 698
HindIII AAGCTT 1 cut(s) 542
HinfI GANTC 5 cut(s) 35, 61, 526, 631, 797
HpaII CCGG 4 cut(s) 295, 363, 380, 401
Hpy188I TCNGA 3 cut(s) 40, 109, 624
Hpy188III TCNNGA 8 cut(s) 65, 134, 179, 401, 530, 635, 656, 719
HpyAV CCTTC 3 cut(s) 101, 658, 816
HpyCH4V TGCA 2 cut(s) 616, 704
HpyF10VI GCNNNNNNNGC 3 cut(s) 273, 541, 829
HpyF3I CTNAG 4 cut(s) 24, 37, 576, 621
Hsp92II CATG 6 cut(s) 46, 144, 226, 342, 646, 698
Kpn2I TCCGGA 1 cut(s) 400
Ksp22I TGATCA 1 cut(s) 187
Kzo9I GATC 4 cut(s) 136, 187, 298, 670
LmnI GCTCC 2 cut(s) 334, 736
Lsp1109I GCAGC 1 cut(s) 819
LweI GCATC 4 cut(s) 406, 570, 713, 781
MaeI CTAG 6 cut(s) 65, 77, 345, 432, 536, 843
MalI GATC 4 cut(s) 138, 189, 300, 672
MboI GATC 4 cut(s) 136, 187, 298, 670
MboII GAAGA 4 cut(s) 152, 463, 473, 535
MflI RGATCY 1 cut(s) 298
MhlI GDGCHC 2 cut(s) 278, 387
MluCI AATT 1 cut(s) 103
MlyI GAGTC 2 cut(s) 29, 520
MnlI CCTC 7 cut(s) 33, 179, 397, 498, 501, 548, 763
MroI TCCGGA 1 cut(s) 400
MseI TTAA 2 cut(s) 102, 165
MslI CAYNNNNRTG 1 cut(s) 789
MspA1I CMGCKG 2 cut(s) 575, 832
MspI CCGG 4 cut(s) 295, 363, 380, 401
MspR9I CCNGG 3 cut(s) 296, 364, 552
MvaI CCWGG 1 cut(s) 552
MvnI CGCG 1 cut(s) 491
MwoI GCNNNNNNNGC 3 cut(s) 273, 541, 829
NciI CCSGG 2 cut(s) 296, 364
NcoI CCATGG 1 cut(s) 140
NdeII GATC 4 cut(s) 136, 187, 298, 670
NlaIII CATG 6 cut(s) 46, 144, 226, 342, 646, 698
NlaIV GGNNCC 3 cut(s) 367, 649, 753
NspI RCATGY 2 cut(s) 226, 698
NspV TTCGAA 1 cut(s) 243
PaeR7I CTCGAG 1 cut(s) 635
PciI ACATGT 2 cut(s) 222, 694
PfeI GAWTC 3 cut(s) 61, 631, 797
PfoI TCCNGGA 1 cut(s) 550
PkrI GCNGC 4 cut(s) 480, 493, 592, 834
PleI GAGTC 2 cut(s) 29, 520
PpsI GAGTC 2 cut(s) 29, 520
PpuMI RGGWCCY 1 cut(s) 648
PscI ACATGT 2 cut(s) 222, 694
Psp5II RGGWCCY 1 cut(s) 648
Psp6I CCWGG 1 cut(s) 550
PspGI CCWGG 1 cut(s) 550
PspN4I GGNNCC 3 cut(s) 367, 649, 753
PspPI GGNCC 4 cut(s) 348, 366, 648, 751
PspPPI RGGWCCY 1 cut(s) 648
PsuI RGATCY 1 cut(s) 298
PvuII CAGCTG 2 cut(s) 575, 832
RsaI GTAC 3 cut(s) 21, 234, 287
RsaNI GTAC 3 cut(s) 20, 233, 286
RseI CAYNNNNRTG 1 cut(s) 789
SaqAI TTAA 2 cut(s) 102, 165
SatI GCNGC 4 cut(s) 479, 492, 591, 833
Sau3AI GATC 4 cut(s) 136, 187, 298, 670
Sau96I GGNCC 4 cut(s) 348, 366, 648, 751
ScaI AGTACT 1 cut(s) 287
SchI GAGTC 2 cut(s) 29, 520
ScrFI CCNGG 3 cut(s) 296, 364, 552
SduI GDGCHC 2 cut(s) 278, 387
SfaNI GCATC 4 cut(s) 406, 570, 713, 781
Sfr274I CTCGAG 1 cut(s) 635
SfuI TTCGAA 1 cut(s) 243
SinI GGWCC 2 cut(s) 648, 751
SlaI CTCGAG 1 cut(s) 635
SmiMI CAYNNNNRTG 1 cut(s) 789
SmlI CTYRAG 2 cut(s) 528, 635
SmoI CTYRAG 2 cut(s) 528, 635
SpeI ACTAGT 1 cut(s) 431
Sse9I AATT 1 cut(s) 103
SsiI CCGC 4 cut(s) 479, 491, 591, 846
SspMI CTAG 6 cut(s) 65, 77, 345, 432, 536, 843
StyD4I CCNGG 3 cut(s) 294, 362, 550
StyI CCWWGG 3 cut(s) 140, 344, 684
TaqI TCGA 6 cut(s) 135, 171, 243, 278, 636, 800
TasI AATT 1 cut(s) 103
TatI WGTACW 2 cut(s) 232, 285
TauI GCSGC 3 cut(s) 481, 494, 593
TfiI GAWTC 3 cut(s) 61, 631, 797
Tru1I TTAA 2 cut(s) 102, 165
Tru9I TTAA 2 cut(s) 102, 165
TscAI CASTG 1 cut(s) 592
TseI GCWGC 1 cut(s) 832
TspDTI ATGAA 3 cut(s) 581, 631, 677
TspRI CASTG 1 cut(s) 592
VpaK11BI GGWCC 2 cut(s) 648, 751
XbaI TCTAGA 1 cut(s) 64
XceI RCATGY 2 cut(s) 226, 698
XhoI CTCGAG 1 cut(s) 635
XmaJI CCTAGG 1 cut(s) 344
XspI CTAG 6 cut(s) 65, 77, 345, 432, 536, 843
ZrmI AGTACT 1 cut(s) 287
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.