Rh6DG492400

Helix-hairpin-helix DNA-binding motif class 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6D
OG0013438
Physical Location & Seq
Reverse (-)
65201236 .. 65202633
1398 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6DG492400.1

Sequence Viewer

Length: 411 bp
ATGGAATTCGAGTGTGCTTCTCTCAGTCTCTGGAAGGAAGCCCTCTCTTCCTATTCATCTCGCATAGAATCTCTCAACAAACCCGATTTGATTTCCCTGGACGACTTTTACCGCAACCAGCTCCCTCCTCTCCTCCGCCACCGGAACCCTAACCCCCACCTCACCACCTCCGAGCTCTCCGATCTCATGCGCTGGAAGCTCACACGTGGCAAGTGGCGGTACCACTTTTTAATCTCTACATTAATTCCATTACTTGAATTGAGTGCAGAAGGGGAAACCTTCACACCATCAGATGTAGAAAGGGCTCTATGGAGTTGTGCTGTGGGGGCCAAATTGCTATCTTCACAGTCAGATCCAGACCCCAAAGTCACTGATAAAACTAAAAACCCCAAGAGAAAGAGAAAGCGCTGA
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

136

Amino Acids

15.74

Weight (kDa)

9.36

Isoelectric Point (pI)

48.76

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0013438)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G12210 AT3G12210
fragaria_vesca FvH4_2g32510
malus_domestica MD15G1064200.v1.1
prunus_persica Prupe.1G418200_v2.0.a1 Prupe.6G207800_v2.0.a1
pyrus_communis pycom15g06090
rosa_chinensis RchiOBHm_Chr6g0310141
rosa_laevigata RLG00000010505
rosa_multiflora Rmu_sc0000294.1_g000038 Rmu_sc0008163.1_g000003
rosa_roxburghii Rroxscaffold_7G00158820
rosa_rugosa Rorug06G0377700
rosa_samantha Rh6AG491800 Rh6BG501400 Rh6CG506500 Rh6DG492400
rosa_wichuraiana Rw6G042790

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 365
Acc65I GGTACC 1 cut(s) 219
AccB1I GGYRCC 1 cut(s) 219
AciI CCGC 3 cut(s) 112, 136, 217
AclWI GGATC 1 cut(s) 347
AcsI RAATTY 1 cut(s) 5
AcvI CACGTG 1 cut(s) 206
AfaI GTAC 1 cut(s) 221
AfeI AGCGCT 1 cut(s) 407
AflIII ACRYGT 1 cut(s) 203
AgsI TTSAA 1 cut(s) 257
AjnI CCWGG 1 cut(s) 96
AluBI AGCT 3 cut(s) 121, 175, 199
AluI AGCT 3 cut(s) 121, 175, 199
Alw21I GWGCWC 1 cut(s) 177
Alw26I GTCTC 1 cut(s) 32
AlwI GGATC 1 cut(s) 347
AlwNI CAGNNNCTG 1 cut(s) 30
Aor51HI AGCGCT 1 cut(s) 407
AoxI GGCC 1 cut(s) 327
ApoI RAATTY 1 cut(s) 5
AseI ATTAAT 1 cut(s) 242
Asp718I GGTACC 1 cut(s) 219
AspLEI GCGC 2 cut(s) 192, 408
AspS9I GGNCC 1 cut(s) 327
AsuHPI GGTGA 1 cut(s) 154
BanI GGYRCC 1 cut(s) 219
BanII GRGCYC 2 cut(s) 177, 307
BbrPI CACGTG 1 cut(s) 206
Bbv12I GWGCWC 1 cut(s) 177
BccI CCATC 1 cut(s) 295
BciT130I CCWGG 1 cut(s) 98
BcoDI GTCTC 1 cut(s) 32
BfoI RGCGCY 1 cut(s) 409
Bme1390I CCNGG 1 cut(s) 98
BmgT120I GGNCC 1 cut(s) 327
BmiI GGNNCC 3 cut(s) 146, 221, 328
BmrFI CCNGG 1 cut(s) 98
BsaAI YACGTR 1 cut(s) 206
BsaJI CCNNGG 1 cut(s) 96
BsaWI WCCGGW 1 cut(s) 141
BseBI CCWGG 1 cut(s) 98
BseDI CCNNGG 1 cut(s) 96
BseMII CTCAG 1 cut(s) 37
BseRI GAGGAG 2 cut(s) 117, 122
BsgI GTGCAG 1 cut(s) 285
BshFI GGCC 1 cut(s) 329
BshNI GGYRCC 1 cut(s) 219
BsiHKAI GWGCWC 1 cut(s) 177
BsiSI CCGG 1 cut(s) 142
BsmAI GTCTC 1 cut(s) 32
BsnI GGCC 1 cut(s) 329
Bsp1286I GDGCHC 2 cut(s) 177, 307
Bsp143I GATC 2 cut(s) 181, 352
BspACI CCGC 3 cut(s) 112, 136, 217
BspANI GGCC 1 cut(s) 329
BspCNI CTCAG 1 cut(s) 36
BspLI GGNNCC 3 cut(s) 146, 221, 328
BspPI GGATC 1 cut(s) 347
BspT107I GGYRCC 1 cut(s) 219
BssECI CCNNGG 1 cut(s) 96
BssMI GATC 2 cut(s) 181, 352
Bst2UI CCWGG 1 cut(s) 98
Bst4CI ACNGT 1 cut(s) 348
Bst6I CTCTTC 1 cut(s) 52
BstBAI YACGTR 1 cut(s) 206
BstDEI CTNAG 1 cut(s) 23
BstH2I RGCGCY 1 cut(s) 409
BstHHI GCGC 2 cut(s) 192, 408
BstKTI GATC 2 cut(s) 184, 355
BstMAI GTCTC 1 cut(s) 32
BstMBI GATC 2 cut(s) 181, 352
BstMWI GCNNNNNNNGC 2 cut(s) 196, 326
BstNI CCWGG 1 cut(s) 98
BstSCI CCNGG 1 cut(s) 96
BstX2I RGATCY 1 cut(s) 352
BstYI RGATCY 1 cut(s) 352
BsuRI GGCC 1 cut(s) 329
BtsIMutI CAGTG 1 cut(s) 369
CaiI CAGNNNCTG 1 cut(s) 30
CfoI GCGC 2 cut(s) 192, 408
Cfr13I GGNCC 1 cut(s) 327
Csp6I GTAC 1 cut(s) 220
CviAII CATG 1 cut(s) 187
CviJI RGCY 6 cut(s) 41, 121, 175, 199, 305, 329
CviKI_1 RGCY 6 cut(s) 41, 121, 175, 199, 305, 329
CviQI GTAC 1 cut(s) 220
DdeI CTNAG 1 cut(s) 23
DpnI GATC 2 cut(s) 183, 354
DpnII GATC 2 cut(s) 181, 352
DrdI GACNNNNNNGTC 1 cut(s) 365
DseDI GACNNNNNNGTC 1 cut(s) 365
Eam1104I CTCTTC 1 cut(s) 52
EarI CTCTTC 1 cut(s) 52
EciI GGCGGA 1 cut(s) 125
Ecl136II GAGCTC 1 cut(s) 175
Eco24I GRGCYC 2 cut(s) 177, 307
Eco47III AGCGCT 1 cut(s) 407
Eco53kI GAGCTC 1 cut(s) 175
Eco72I CACGTG 1 cut(s) 206
EcoICRI GAGCTC 1 cut(s) 175
EcoRI GAATTC 1 cut(s) 5
EcoRII CCWGG 1 cut(s) 96
EcoT38I GRGCYC 2 cut(s) 177, 307
FaeI CATG 1 cut(s) 190
FaiI YATR 3 cut(s) 65, 188, 310
FatI CATG 1 cut(s) 186
FriOI GRGCYC 2 cut(s) 177, 307
GlaI GCGC 2 cut(s) 191, 407
HaeII RGCGCY 1 cut(s) 409
HaeIII GGCC 1 cut(s) 329
HapII CCGG 1 cut(s) 142
HhaI GCGC 2 cut(s) 192, 408
Hin1II CATG 1 cut(s) 190
Hin6I GCGC 2 cut(s) 190, 406
HinP1I GCGC 2 cut(s) 190, 406
HinfI GANTC 1 cut(s) 68
HpaII CCGG 1 cut(s) 142
HphI GGTGA 1 cut(s) 154
Hpy188I TCNGA 4 cut(s) 172, 181, 292, 352
Hpy188III TCNNGA 2 cut(s) 31, 356
HpyAV CCTTC 3 cut(s) 28, 263, 289
HpyCH4III ACNGT 1 cut(s) 348
HpyCH4IV ACGT 1 cut(s) 205
HpyCH4V TGCA 1 cut(s) 266
HpyF10VI GCNNNNNNNGC 2 cut(s) 196, 326
HpyF3I CTNAG 1 cut(s) 23
HpySE526I ACGT 1 cut(s) 205
Hsp92II CATG 1 cut(s) 190
HspAI GCGC 2 cut(s) 190, 406
KpnI GGTACC 1 cut(s) 223
Kzo9I GATC 2 cut(s) 181, 352
LmnI GCTCC 1 cut(s) 126
LpnPI CCDG 7 cut(s) 16, 83, 110, 131, 155, 178, 369
MaeII ACGT 1 cut(s) 205
MaeIII GTNAC 1 cut(s) 367
MalI GATC 2 cut(s) 183, 354
MboI GATC 2 cut(s) 181, 352
MboII GAAGA 2 cut(s) 39, 333
MflI RGATCY 1 cut(s) 352
MhlI GDGCHC 2 cut(s) 177, 307
MluCI AATT 4 cut(s) 5, 243, 257, 332
MnlI CCTC 6 cut(s) 53, 135, 138, 143, 170, 178
MseI TTAA 2 cut(s) 230, 242
MspI CCGG 1 cut(s) 142
MspR9I CCNGG 1 cut(s) 98
MvaI CCWGG 1 cut(s) 98
MwoI GCNNNNNNNGC 2 cut(s) 196, 326
NdeII GATC 2 cut(s) 181, 352
NlaIII CATG 1 cut(s) 190
NlaIV GGNNCC 3 cut(s) 146, 221, 328
NmuCI GTSAC 1 cut(s) 367
PfeI GAWTC 1 cut(s) 68
PmaCI CACGTG 1 cut(s) 206
PmlI CACGTG 1 cut(s) 206
Ppu21I YACGTR 1 cut(s) 206
PshBI ATTAAT 1 cut(s) 242
Psp124BI GAGCTC 1 cut(s) 177
Psp6I CCWGG 1 cut(s) 96
PspCI CACGTG 1 cut(s) 206
PspGI CCWGG 1 cut(s) 96
PspN4I GGNNCC 3 cut(s) 146, 221, 328
PspPI GGNCC 1 cut(s) 327
PstNI CAGNNNCTG 1 cut(s) 30
PsuI RGATCY 1 cut(s) 352
RsaI GTAC 1 cut(s) 221
RsaNI GTAC 1 cut(s) 220
SacI GAGCTC 1 cut(s) 177
SaqAI TTAA 2 cut(s) 230, 242
Sau3AI GATC 2 cut(s) 181, 352
Sau96I GGNCC 1 cut(s) 327
ScrFI CCNGG 1 cut(s) 98
SduI GDGCHC 2 cut(s) 177, 307
SetI ASST 7 cut(s) 123, 162, 170, 177, 201, 208, 281
Sse9I AATT 4 cut(s) 5, 243, 257, 332
SsiI CCGC 3 cut(s) 112, 136, 217
SstI GAGCTC 1 cut(s) 177
StyD4I CCNGG 1 cut(s) 96
TaaI ACNGT 1 cut(s) 348
TaiI ACGT 1 cut(s) 208
TaqI TCGA 1 cut(s) 9
TasI AATT 4 cut(s) 5, 243, 257, 332
TfiI GAWTC 1 cut(s) 68
Tru1I TTAA 2 cut(s) 230, 242
Tru9I TTAA 2 cut(s) 230, 242
TscAI CASTG 1 cut(s) 376
TseFI GTSAC 1 cut(s) 367
Tsp45I GTSAC 1 cut(s) 367
TspDTI ATGAA 1 cut(s) 45
TspRI CASTG 1 cut(s) 376
VspI ATTAAT 1 cut(s) 242
XapI RAATTY 1 cut(s) 5
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.