Rh4DG212000

helix loop helix domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0015253
Physical Location & Seq
Forward (+)
40704483 .. 40705389
907 bp
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UTR
Exon/CDS
Intron
Rh4DG212000.1

Sequence Viewer

Length: 543 bp
ATGTCTCACATAGCTGTGGAGAGAAACAGAAGGAAACAGATGAACGAGCACCTCAAAGTTCTACGCTCTTTAACACCATGTTTCTACATCAAAAGGGGAGACCAAGCATCAATCATCGGGGGTGTGATAGAGTTCATCAAGGAGCTGCATCAAGTTTTGCAGTCTTTGGAATCTAATAAACGGAGGAGGAAGAGCCTAAGCCCTAGCCCCAATCCAAGCCCGAGGCAGCCACTGCTACTACTGCCACCGCCGGCTCTGCCCCAACTTGATCAAAGCCCTAAATTCAATTTTGGGTTGATTGATCAAAATCATGACCGTGCGGTCAAGGAACTAGGAGCATGCTGCAACTCTCCGGTGGCAGATGTGGAAGCCAAAATCTCGGGGTCGAACGTGGTGTTGAAGATAATATCCAGGCGAATTCCAGGTCAAGTTGTGAAGATAATTAGTGTGCTGGAGAGGTCTTCATTTGAGGTTCTTCATCTCAACATCAGTAGCATGGAAGACACTGTCTTATACTCTTTCGTGATCAAGGTACTAATTTAA

Protein Analysis

180

Amino Acids

20.22

Weight (kDa)

9.79

Isoelectric Point (pI)

75.33

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HLH PF00010 2 - 50 2.3e-10 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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Orthologous Genes (Group: OG0015253)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G06120
fragaria_vesca FvH4_4g14530
malus_domestica MD13G1184300.v1.1 MD16G1184500.v1.1
prunus_persica Prupe.1G151800_v2.0.a1
pyrus_communis pycom13g15880 pycom16g15500
rosa_chinensis RchiOBHm_Chr4g0418301
rosa_laevigata RLG00000007879
rosa_roxburghii Rroxscaffold_5G00361470
rosa_rugosa Rorug04G0151900
rosa_samantha Rh4AG213400 Rh4BG217200 Rh4CG225100 Rh4DG212000
rosa_wichuraiana Rw4G018130

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 320
AciI CCGC 2 cut(s) 248, 320
AcsI RAATTY 2 cut(s) 281, 417
AfaI GTAC 1 cut(s) 534
AgsI TTSAA 2 cut(s) 286, 400
AjnI CCWGG 2 cut(s) 410, 421
AluBI AGCT 2 cut(s) 14, 145
AluI AGCT 2 cut(s) 14, 145
Alw21I GWGCWC 1 cut(s) 51
Alw26I GTCTC 2 cut(s) 9, 93
AlwNI CAGNNNCTG 1 cut(s) 232
Ama87I CYCGRG 2 cut(s) 220, 379
ApeKI GCWGC 3 cut(s) 145, 226, 342
ApoI RAATTY 2 cut(s) 281, 417
ArsI GACNNNNNNTTYG 2 cut(s) 409, 441
AvaI CYCGRG 2 cut(s) 220, 379
BbsI GAAGAC 2 cut(s) 453, 507
Bbv12I GWGCWC 1 cut(s) 51
BbvI GCAGC 3 cut(s) 132, 238, 329
BciT130I CCWGG 2 cut(s) 412, 423
BclI TGATCA 3 cut(s) 268, 301, 525
BcoDI GTCTC 2 cut(s) 9, 93
BfaI CTAG 2 cut(s) 204, 332
BisI GCNGC 3 cut(s) 146, 227, 343
BlsI GCNGC 3 cut(s) 147, 228, 344
Bme1390I CCNGG 2 cut(s) 412, 423
BmeT110I CYCGRG 2 cut(s) 220, 379
BmrFI CCNGG 2 cut(s) 412, 423
BmsI GCATC 2 cut(s) 116, 157
BpiI GAAGAC 2 cut(s) 453, 507
BpmI CTGGAG 1 cut(s) 473
Bpu10I CCTNAGC 1 cut(s) 197
BsaBI GATNNNNATC 1 cut(s) 306
BsaI GGTCTC 1 cut(s) 93
BsaJI CCNNGG 1 cut(s) 221
BsaWI WCCGGW 1 cut(s) 352
Bse118I RCCGGY 1 cut(s) 250
Bse8I GATNNNNATC 1 cut(s) 306
BseBI CCWGG 2 cut(s) 412, 423
BseDI CCNNGG 1 cut(s) 221
BseJI GATNNNNATC 1 cut(s) 306
BseRI GAGGAG 1 cut(s) 199
BseXI GCAGC 3 cut(s) 132, 238, 329
BsiHKAI GWGCWC 1 cut(s) 51
BsiHKCI CYCGRG 2 cut(s) 220, 379
BsiSI CCGG 2 cut(s) 251, 353
BsmAI GTCTC 2 cut(s) 9, 93
Bso31I GGTCTC 1 cut(s) 93
BsoBI CYCGRG 2 cut(s) 220, 379
Bsp1286I GDGCHC 1 cut(s) 51
Bsp143I GATC 3 cut(s) 268, 301, 525
BspACI CCGC 2 cut(s) 248, 320
BspHI TCATGA 1 cut(s) 310
BspQI GCTCTTC 1 cut(s) 185
BspTNI GGTCTC 1 cut(s) 93
BsrFI RCCGGY 1 cut(s) 250
BssAI RCCGGY 1 cut(s) 250
BssECI CCNNGG 1 cut(s) 221
BssMI GATC 3 cut(s) 268, 301, 525
Bst2UI CCWGG 2 cut(s) 412, 423
Bst4CI ACNGT 2 cut(s) 317, 508
Bst6I CTCTTC 1 cut(s) 185
BstAPI GCANNNNNTGC 1 cut(s) 232
BstC8I GCNNGC 2 cut(s) 252, 340
BstDEI CTNAG 1 cut(s) 197
BstKTI GATC 3 cut(s) 271, 304, 528
BstMAI GTCTC 2 cut(s) 9, 93
BstMBI GATC 3 cut(s) 268, 301, 525
BstMWI GCNNNNNNNGC 3 cut(s) 232, 241, 256
BstNI CCWGG 2 cut(s) 412, 423
BstNSI RCATGY 1 cut(s) 342
BstSCI CCNGG 2 cut(s) 410, 421
BstV1I GCAGC 3 cut(s) 132, 238, 329
BstV2I GAAGAC 2 cut(s) 453, 507
BtsI GCAGTG 1 cut(s) 230
BtsIMutI CAGTG 2 cut(s) 230, 504
Cac8I GCNNGC 2 cut(s) 252, 340
CaiI CAGNNNCTG 1 cut(s) 232
CciI TCATGA 1 cut(s) 310
Cfr10I RCCGGY 1 cut(s) 250
Csp6I GTAC 1 cut(s) 533
CviAII CATG 4 cut(s) 78, 311, 339, 496
CviQI GTAC 1 cut(s) 533
DdeI CTNAG 1 cut(s) 197
DpnI GATC 3 cut(s) 270, 303, 527
DpnII GATC 3 cut(s) 268, 301, 525
DrdI GACNNNNNNGTC 1 cut(s) 320
DseDI GACNNNNNNGTC 1 cut(s) 320
Eam1104I CTCTTC 1 cut(s) 185
EarI CTCTTC 1 cut(s) 185
Eco31I GGTCTC 1 cut(s) 93
Eco88I CYCGRG 2 cut(s) 220, 379
EcoRI GAATTC 1 cut(s) 417
EcoRII CCWGG 2 cut(s) 410, 421
FaeI CATG 4 cut(s) 81, 314, 342, 499
FaiI YATR 6 cut(s) 11, 79, 312, 340, 497, 514
FatI CATG 4 cut(s) 77, 310, 338, 495
FbaI TGATCA 3 cut(s) 268, 301, 525
Fnu4HI GCNGC 3 cut(s) 146, 227, 343
Fsp4HI GCNGC 3 cut(s) 146, 227, 343
FspBI CTAG 2 cut(s) 204, 332
GluI GCNGC 3 cut(s) 146, 227, 343
GsuI CTGGAG 1 cut(s) 473
HapII CCGG 2 cut(s) 251, 353
Hin1II CATG 4 cut(s) 81, 314, 342, 499
HinfI GANTC 1 cut(s) 170
HpaII CCGG 2 cut(s) 251, 353
Hpy188III TCNNGA 2 cut(s) 311, 523
HpyAV CCTTC 1 cut(s) 24
HpyCH4III ACNGT 2 cut(s) 317, 508
HpyCH4IV ACGT 1 cut(s) 390
HpyCH4V TGCA 3 cut(s) 148, 160, 345
HpyF10VI GCNNNNNNNGC 3 cut(s) 232, 241, 256
HpyF3I CTNAG 1 cut(s) 197
HpySE526I ACGT 1 cut(s) 390
Hsp92II CATG 4 cut(s) 81, 314, 342, 499
KroI GCCGGC 1 cut(s) 250
KroNI GCCGGC 1 cut(s) 252
Ksp22I TGATCA 3 cut(s) 268, 301, 525
Kzo9I GATC 3 cut(s) 268, 301, 525
LguI GCTCTTC 1 cut(s) 185
LmnI GCTCC 2 cut(s) 142, 335
LpnPI CCDG 7 cut(s) 264, 366, 397, 408, 424, 435, 437
Lsp1109I GCAGC 3 cut(s) 132, 238, 329
LweI GCATC 2 cut(s) 116, 157
MaeI CTAG 2 cut(s) 204, 332
MaeII ACGT 1 cut(s) 390
MalI GATC 3 cut(s) 270, 303, 527
MboI GATC 3 cut(s) 268, 301, 525
MboII GAAGA 6 cut(s) 202, 412, 448, 453, 467, 512
MhlI GDGCHC 1 cut(s) 51
MluCI AATT 5 cut(s) 281, 286, 417, 441, 537
MnlI CCTC 6 cut(s) 62, 177, 180, 216, 450, 463
MroNI GCCGGC 1 cut(s) 250
MseI TTAA 2 cut(s) 71, 541
MslI CAYNNNNRTG 2 cut(s) 14, 315
MspI CCGG 2 cut(s) 251, 353
MspR9I CCNGG 2 cut(s) 412, 423
MvaI CCWGG 2 cut(s) 412, 423
MwoI GCNNNNNNNGC 3 cut(s) 232, 241, 256
NaeI GCCGGC 1 cut(s) 252
NdeII GATC 3 cut(s) 268, 301, 525
NgoMIV GCCGGC 1 cut(s) 250
NlaIII CATG 4 cut(s) 81, 314, 342, 499
NspI RCATGY 1 cut(s) 342
PaeI GCATGC 1 cut(s) 342
PagI TCATGA 1 cut(s) 310
PciSI GCTCTTC 1 cut(s) 185
PdiI GCCGGC 1 cut(s) 252
PfeI GAWTC 1 cut(s) 170
PflFI GACNNNGTC 1 cut(s) 506
PkrI GCNGC 3 cut(s) 147, 228, 344
Psp6I CCWGG 2 cut(s) 410, 421
PspGI CCWGG 2 cut(s) 410, 421
PstNI CAGNNNCTG 1 cut(s) 232
PsyI GACNNNGTC 1 cut(s) 506
RsaI GTAC 1 cut(s) 534
RsaNI GTAC 1 cut(s) 533
RseI CAYNNNNRTG 2 cut(s) 14, 315
SapI GCTCTTC 1 cut(s) 185
SaqAI TTAA 2 cut(s) 71, 541
SatI GCNGC 3 cut(s) 146, 227, 343
Sau3AI GATC 3 cut(s) 268, 301, 525
ScrFI CCNGG 2 cut(s) 412, 423
SduI GDGCHC 1 cut(s) 51
SetI ASST 8 cut(s) 16, 54, 147, 393, 427, 461, 474, 534
SfaNI GCATC 2 cut(s) 116, 157
SmiMI CAYNNNNRTG 2 cut(s) 14, 315
SphI GCATGC 1 cut(s) 342
Sse9I AATT 5 cut(s) 281, 286, 417, 441, 537
SsiI CCGC 2 cut(s) 248, 320
SspMI CTAG 2 cut(s) 204, 332
StyD4I CCNGG 2 cut(s) 410, 421
TaaI ACNGT 2 cut(s) 317, 508
TaiI ACGT 1 cut(s) 393
TaqI TCGA 1 cut(s) 386
TasI AATT 5 cut(s) 281, 286, 417, 441, 537
TfiI GAWTC 1 cut(s) 170
Tru1I TTAA 2 cut(s) 71, 541
Tru9I TTAA 2 cut(s) 71, 541
TscAI CASTG 2 cut(s) 237, 511
TseI GCWGC 3 cut(s) 145, 226, 342
TspDTI ATGAA 4 cut(s) 56, 124, 453, 467
TspGWI ACGGA 1 cut(s) 196
TspRI CASTG 2 cut(s) 237, 511
Tth111I GACNNNGTC 1 cut(s) 506
XapI RAATTY 2 cut(s) 281, 417
XceI RCATGY 1 cut(s) 342
XspI CTAG 2 cut(s) 204, 332
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.