Rh2DG239400

helix loop helix domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2D
OG0015520
Physical Location & Seq
Forward (+)
24231565 .. 24233487
1923 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2DG239400.1

Sequence Viewer

Length: 1002 bp
ATGACGTTAGAAGCTGTGGTGTTCCAGCCAGACCCATTTAGCTGTGGAAATTGTCTGGAAGGAAGTAGATCTTGGGACCATGGCTTTGGTTTCGGAGGAGATGATGATCAACAAGAAAAAGGCTACGCTCAACATGATATGCTCAACAATGGTAATATTGTAGGGCAAGGCCTTATGGGGTACTGTTCACCGTCACAGGTGAGAATGCAAAGTGTCAACACCGGCAACTCTAATTCCACGCCTGAAACCTGCACTGGCAACTTCAACTTCAACTTCAACAATTCTTTCTCTAGCCCGATGGCCACCACAGGCCGGAGAAAGAGGCGGCGCACGAGAAACATCAAGAACAAGGAAGAGGTGGAGACTCAGAGGATCACCCACATTGCTGTTGAACGCAATCGGAGGAAGCTCATGAATGACTATCTGGCCGCATTGCGCTCTATGATGCCTGCTTCCTATGCCCAAAGGGGTGACCAAGCATCAATCATAGGAGGAGCCATAAATTTTGTGAAGGAGCTTGAGCAACTTCTGCAATCTTTAGAAGTCGGTAGAAGAACCAAACAATCACACTTGGATTTGGCCTCCATATTCTCCAACTTCTTTACCTTCCCTCAGTACTCGACCTGTTCGAGTACTAACACCCACGGCCATGGCCATAGCGAGTACATGAACAACAACTTGGTGCATCCCGACGAGATAATGGGGGAGAAGCGGTCGGGGGCAATTGCAGATGTGGAAGTAACAATGGTAGAAAGTCATGCGAACATTAAAGTGCTTTTGAAAAGACACCCAAGACAGCTCTTAAAGATGGTGGTTGGGTTGCACTCTCTGCGTCTTATGATCCTTCACCTTAATGTCACAACTATGGATAGCATGATCCTCTACTCTTTCAGCGTCAAGGTTGAAGATAATTCTCAGTTGACCTCAATGAATGATATTGCAGCTGATGTGTATGAAATGGTGGGAAGGATTCAAGAAGAGGCCCAGTTTTTACTTCAATAA

Protein Analysis

333

Amino Acids

37.46

Weight (kDa)

6.64

Isoelectric Point (pI)

52.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HLH PF00010 123 - 174 3.2e-11 Helix-loop-helix DNA-binding domain
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: OG0015520)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g20160 FvH4_1g20160
malus_domestica MD01G1037100.v1.1
prunus_persica Prupe.6G194400_v2.0.a1
pyrus_communis pycom01g06400
rosa_chinensis RchiOBHm_Chr2g0112221
rosa_laevigata RLG00000017960
rosa_multiflora Rmu_sc0001386.1_g000016 Rmu_sc0004467.1_g000007
rosa_roxburghii Rroxscaffold_2G00131650
rosa_rugosa Rorug02G0179300
rosa_samantha Rh2AG231500 Rh2BG244700 Rh2CG235900 Rh2DG239400
rosa_wichuraiana Rw2G017940

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 257
AciI CCGC 3 cut(s) 325, 429, 712
AclWI GGATC 3 cut(s) 380, 835, 871
AcoI YGGCCR 4 cut(s) 300, 426, 646, 652
AcsI RAATTY 1 cut(s) 502
AfaI GTAC 4 cut(s) 182, 617, 634, 665
AfiI CCNNNNNNNGG 1 cut(s) 312
AgsI TTSAA 8 cut(s) 265, 271, 277, 392, 781, 905, 974, 998
AjuI GAANNNNNNNTTGG 4 cut(s) 55, 87, 662, 694
AluBI AGCT 6 cut(s) 14, 42, 409, 517, 799, 944
AluI AGCT 6 cut(s) 14, 42, 409, 517, 799, 944
Alw26I GTCTC 1 cut(s) 356
AlwI GGATC 3 cut(s) 380, 835, 871
AoxI GGCC 8 cut(s) 169, 300, 310, 426, 579, 646, 652, 981
ApeKI GCWGC 1 cut(s) 941
ApoI RAATTY 1 cut(s) 502
ArsI GACNNNNNNTTYG 2 cut(s) 68, 100
AspLEI GCGC 2 cut(s) 330, 438
AspS9I GGNCC 2 cut(s) 76, 982
AsuHPI GGTGA 5 cut(s) 180, 211, 367, 482, 839
AvaII GGWCC 1 cut(s) 76
BalI TGGCCA 2 cut(s) 302, 654
BauI CACGAG 1 cut(s) 331
BbvI GCAGC 1 cut(s) 953
BccI CCATC 2 cut(s) 292, 802
BceAI ACGGC 1 cut(s) 661
BclI TGATCA 1 cut(s) 106
BcoDI GTCTC 1 cut(s) 356
BfaI CTAG 1 cut(s) 291
BfuAI ACCTGC 1 cut(s) 257
BglII AGATCT 1 cut(s) 68
BisI GCNGC 3 cut(s) 326, 429, 942
BlsI GCNGC 3 cut(s) 327, 430, 943
BmcAI AGTACT 2 cut(s) 617, 634
Bme18I GGWCC 1 cut(s) 76
BmgT120I GGNCC 2 cut(s) 76, 982
BmiI GGNNCC 2 cut(s) 77, 496
BmrI ACTGGG 1 cut(s) 979
BmsI GCATC 3 cut(s) 435, 488, 694
BmuI ACTGGG 1 cut(s) 979
BpuEI CTTGAG 1 cut(s) 539
BsaBI GATNNNNATC 1 cut(s) 105
BsaJI CCNNGG 3 cut(s) 79, 643, 649
BsaXI ACNNNNNCTCC 2 cut(s) 698, 728
Bsc4I CCNNNNNNNGG 1 cut(s) 312
Bse118I RCCGGY 1 cut(s) 221
Bse1I ACTGG 2 cut(s) 259, 985
Bse3DI GCAATG 2 cut(s) 381, 431
Bse8I GATNNNNATC 1 cut(s) 105
BseDI CCNNGG 3 cut(s) 79, 643, 649
BseGI GGATG 1 cut(s) 685
BseJI GATNNNNATC 1 cut(s) 105
BseLI CCNNNNNNNGG 1 cut(s) 312
BseMI GCAATG 2 cut(s) 381, 431
BseMII CTCAG 3 cut(s) 380, 626, 929
BseNI ACTGG 2 cut(s) 259, 985
BseRI GAGGAG 2 cut(s) 111, 507
BseXI GCAGC 1 cut(s) 953
BsgI GTGCAG 1 cut(s) 235
Bsh1285I CGRYCG 1 cut(s) 716
BshFI GGCC 8 cut(s) 171, 302, 312, 428, 581, 648, 654, 983
BsiEI CGRYCG 1 cut(s) 716
BsiSI CCGG 2 cut(s) 222, 313
BslFI GGGAC 1 cut(s) 89
BslI CCNNNNNNNGG 1 cut(s) 312
BsmAI GTCTC 1 cut(s) 356
BsmFI GGGAC 1 cut(s) 89
BsmI GAATGC 1 cut(s) 210
BsnI GGCC 8 cut(s) 171, 302, 312, 428, 581, 648, 654, 983
Bsp143I GATC 5 cut(s) 68, 106, 372, 840, 876
Bsp19I CCATGG 2 cut(s) 79, 649
BspACI CCGC 3 cut(s) 325, 429, 712
BspANI GGCC 8 cut(s) 171, 302, 312, 428, 581, 648, 654, 983
BspCNI CTCAG 3 cut(s) 379, 625, 928
BspHI TCATGA 1 cut(s) 411
BspLI GGNNCC 2 cut(s) 77, 496
BspMI ACCTGC 1 cut(s) 257
BspPI GGATC 3 cut(s) 380, 835, 871
BsrDI GCAATG 2 cut(s) 381, 431
BsrFI RCCGGY 1 cut(s) 221
BsrI ACTGG 2 cut(s) 259, 985
BssAI RCCGGY 1 cut(s) 221
BssECI CCNNGG 3 cut(s) 79, 643, 649
BssMI GATC 5 cut(s) 68, 106, 372, 840, 876
BssSI CACGAG 1 cut(s) 331
BssT1I CCWWGG 2 cut(s) 79, 649
Bst2BI CACGAG 1 cut(s) 331
Bst4CI ACNGT 2 cut(s) 185, 192
Bst6I CTCTTC 2 cut(s) 348, 972
BstAPI GCANNNNNTGC 2 cut(s) 529, 829
BstC8I GCNNGC 1 cut(s) 450
BstDEI CTNAG 3 cut(s) 366, 612, 915
BstDSI CCRYGG 3 cut(s) 79, 643, 649
BstEII GGTNACC 1 cut(s) 470
BstF5I GGATG 1 cut(s) 685
BstHHI GCGC 2 cut(s) 330, 438
BstKTI GATC 5 cut(s) 71, 109, 375, 843, 879
BstMAI GTCTC 1 cut(s) 356
BstMBI GATC 5 cut(s) 68, 106, 372, 840, 876
BstMCI CGRYCG 1 cut(s) 716
BstMWI GCNNNNNNNGC 3 cut(s) 458, 529, 829
BstPI GGTNACC 1 cut(s) 470
BstV1I GCAGC 1 cut(s) 953
BstX2I RGATCY 1 cut(s) 68
BstXI CCANNNNNNTGG 2 cut(s) 86, 650
BstYI RGATCY 1 cut(s) 68
BsuRI GGCC 8 cut(s) 171, 302, 312, 428, 581, 648, 654, 983
BtgI CCRYGG 3 cut(s) 79, 643, 649
BtsCI GGATG 1 cut(s) 685
BtsIMutI CAGTG 1 cut(s) 252
BveI ACCTGC 1 cut(s) 257
Cac8I GCNNGC 1 cut(s) 450
CciI TCATGA 1 cut(s) 411
CfoI GCGC 2 cut(s) 330, 438
Cfr10I RCCGGY 1 cut(s) 221
Cfr13I GGNCC 2 cut(s) 76, 982
CseI GACGC 2 cut(s) 821, 883
Csp6I GTAC 4 cut(s) 181, 616, 633, 664
CviAII CATG 7 cut(s) 80, 134, 412, 650, 667, 758, 874
CviQI GTAC 4 cut(s) 181, 616, 633, 664
DdeI CTNAG 3 cut(s) 366, 612, 915
DpnI GATC 5 cut(s) 70, 108, 374, 842, 878
DpnII GATC 5 cut(s) 68, 106, 372, 840, 876
EaeI YGGCCR 4 cut(s) 300, 426, 646, 652
Eam1104I CTCTTC 2 cut(s) 348, 972
EarI CTCTTC 2 cut(s) 348, 972
Eco130I CCWWGG 2 cut(s) 79, 649
Eco147I AGGCCT 1 cut(s) 171
Eco47I GGWCC 1 cut(s) 76
Eco91I GGTNACC 1 cut(s) 470
EcoO65I GGTNACC 1 cut(s) 470
EcoT14I CCWWGG 2 cut(s) 79, 649
ErhI CCWWGG 2 cut(s) 79, 649
FaeI CATG 7 cut(s) 83, 137, 415, 653, 670, 761, 877
FalI AAGNNNNNCTT 2 cut(s) 55, 87
FaqI GGGAC 1 cut(s) 89
FatI CATG 7 cut(s) 79, 133, 411, 649, 666, 757, 873
FbaI TGATCA 1 cut(s) 106
Fnu4HI GCNGC 3 cut(s) 326, 429, 942
FokI GGATG 1 cut(s) 672
Fsp4HI GCNGC 3 cut(s) 326, 429, 942
FspBI CTAG 1 cut(s) 291
GlaI GCGC 2 cut(s) 329, 437
GluI GCNGC 3 cut(s) 326, 429, 942
HaeIII GGCC 8 cut(s) 171, 302, 312, 428, 581, 648, 654, 983
HapII CCGG 2 cut(s) 222, 313
HgaI GACGC 2 cut(s) 821, 883
HhaI GCGC 2 cut(s) 330, 438
Hin1II CATG 7 cut(s) 83, 137, 415, 653, 670, 761, 877
Hin6I GCGC 2 cut(s) 328, 436
HinP1I GCGC 2 cut(s) 328, 436
HincII GTYRAC 2 cut(s) 217, 921
HindII GTYRAC 2 cut(s) 217, 921
HinfI GANTC 2 cut(s) 364, 970
HpaII CCGG 2 cut(s) 222, 313
HphI GGTGA 5 cut(s) 180, 211, 367, 482, 839
Hpy166II GTNNAC 3 cut(s) 188, 217, 921
Hpy188I TCNGA 3 cut(s) 95, 369, 402
Hpy188III TCNNGA 5 cut(s) 56, 343, 412, 689, 974
Hpy8I GTNNAC 3 cut(s) 188, 217, 921
Hpy99I CGWCG 1 cut(s) 695
HpyAV CCTTC 5 cut(s) 53, 505, 616, 854, 960
HpyCH4III ACNGT 2 cut(s) 185, 192
HpyCH4IV ACGT 1 cut(s) 5
HpyCH4V TGCA 7 cut(s) 208, 252, 532, 685, 728, 823, 941
HpyF10VI GCNNNNNNNGC 3 cut(s) 458, 529, 829
HpyF3I CTNAG 3 cut(s) 366, 612, 915
HpySE526I ACGT 1 cut(s) 5
Hsp92II CATG 7 cut(s) 83, 137, 415, 653, 670, 761, 877
HspAI GCGC 2 cut(s) 328, 436
Ksp22I TGATCA 1 cut(s) 106
Kzo9I GATC 5 cut(s) 68, 106, 372, 840, 876
LmnI GCTCC 2 cut(s) 494, 514
Lsp1109I GCAGC 1 cut(s) 953
LweI GCATC 3 cut(s) 435, 488, 694
MaeI CTAG 1 cut(s) 291
MaeII ACGT 1 cut(s) 5
MaeIII GTNAC 4 cut(s) 192, 470, 739, 856
MalI GATC 5 cut(s) 70, 108, 374, 842, 878
MboI GATC 5 cut(s) 68, 106, 372, 840, 876
MboII GAAGA 4 cut(s) 365, 564, 917, 989
MfeI CAATTG 1 cut(s) 723
MflI RGATCY 1 cut(s) 68
MlsI TGGCCA 2 cut(s) 302, 654
MluCI AATT 6 cut(s) 49, 232, 280, 502, 723, 910
MluNI TGGCCA 2 cut(s) 302, 654
MlyI GAGTC 1 cut(s) 358
MmeI TCCRAC 1 cut(s) 618
Mox20I TGGCCA 2 cut(s) 302, 654
MscI TGGCCA 2 cut(s) 302, 654
MseI TTAA 3 cut(s) 768, 803, 852
MslI CAYNNNNRTG 4 cut(s) 648, 770, 852, 863
Msp20I TGGCCA 2 cut(s) 302, 654
MspA1I CMGCKG 1 cut(s) 944
MspI CCGG 2 cut(s) 222, 313
MunI CAATTG 1 cut(s) 723
Mva1269I GAATGC 1 cut(s) 210
MwoI GCNNNNNNNGC 3 cut(s) 458, 529, 829
NcoI CCATGG 2 cut(s) 79, 649
NdeII GATC 5 cut(s) 68, 106, 372, 840, 876
NlaIII CATG 7 cut(s) 83, 137, 415, 653, 670, 761, 877
NlaIV GGNNCC 2 cut(s) 77, 496
NmuCI GTSAC 3 cut(s) 192, 470, 856
PagI TCATGA 1 cut(s) 411
PceI AGGCCT 1 cut(s) 171
PcsI WCGNNNNNNNCGW 1 cut(s) 626
PctI GAATGC 1 cut(s) 210
PfeI GAWTC 1 cut(s) 970
PkrI GCNGC 3 cut(s) 327, 430, 943
PleI GAGTC 1 cut(s) 358
PpsI GAGTC 1 cut(s) 358
PspEI GGTNACC 1 cut(s) 470
PspN4I GGNNCC 2 cut(s) 77, 496
PspPI GGNCC 2 cut(s) 76, 982
PsuI RGATCY 1 cut(s) 68
PvuII CAGCTG 1 cut(s) 944
RsaI GTAC 4 cut(s) 182, 617, 634, 665
RsaNI GTAC 4 cut(s) 181, 616, 633, 664
RseI CAYNNNNRTG 4 cut(s) 648, 770, 852, 863
SaqAI TTAA 3 cut(s) 768, 803, 852
SatI GCNGC 3 cut(s) 326, 429, 942
Sau3AI GATC 5 cut(s) 68, 106, 372, 840, 876
Sau96I GGNCC 2 cut(s) 76, 982
ScaI AGTACT 2 cut(s) 617, 634
SchI GAGTC 1 cut(s) 358
SfaNI GCATC 3 cut(s) 435, 488, 694
SinI GGWCC 1 cut(s) 76
SmiMI CAYNNNNRTG 4 cut(s) 648, 770, 852, 863
SmlI CTYRAG 1 cut(s) 518
SmoI CTYRAG 1 cut(s) 518
Sse9I AATT 6 cut(s) 49, 232, 280, 502, 723, 910
SseBI AGGCCT 1 cut(s) 171
SsiI CCGC 3 cut(s) 325, 429, 712
SspI AATATT 1 cut(s) 157
SspMI CTAG 1 cut(s) 291
StuI AGGCCT 1 cut(s) 171
StyI CCWWGG 2 cut(s) 79, 649
TaaI ACNGT 2 cut(s) 185, 192
TaiI ACGT 1 cut(s) 8
TaqI TCGA 2 cut(s) 620, 629
TasI AATT 6 cut(s) 49, 232, 280, 502, 723, 910
TatI WGTACW 3 cut(s) 615, 632, 663
TauI GCSGC 2 cut(s) 328, 431
TfiI GAWTC 1 cut(s) 970
Tru1I TTAA 3 cut(s) 768, 803, 852
Tru9I TTAA 3 cut(s) 768, 803, 852
TscAI CASTG 1 cut(s) 259
TseFI GTSAC 3 cut(s) 192, 470, 856
TseI GCWGC 1 cut(s) 941
Tsp45I GTSAC 3 cut(s) 192, 470, 856
TspDTI ATGAA 4 cut(s) 428, 683, 944, 969
TspRI CASTG 1 cut(s) 259
VpaK11BI GGWCC 1 cut(s) 76
XapI RAATTY 1 cut(s) 502
XspI CTAG 1 cut(s) 291
ZrmI AGTACT 2 cut(s) 617, 634
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.