MD15G1064200.v1.1

Helix-hairpin-helix DNA-binding motif class 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr15
OG0013438
Physical Location & Seq
Forward (+)
4458969 .. 4461033
2065 bp
Loading structure...
UTR
Exon/CDS
Intron
MD15G1064200.v1.1.491

Sequence Viewer

Length: 654 bp
ATGGAATTATTTGAGAGCTCTACTCTCGGTCTCTGGAAAGAATCACTCTCTTCTTACTCGTCTCGCATCGAATTGCTCAACAAACCCGATCTGGTTTCTCTCGACGAATTCTACCGCCACCAACTCCCTCCTCTCCTCCGCCAGCGAAACCCTAACCCCTTCATCACCACCTCCGAGCTCTCCGACCTCATGCGCTGGAAGCTCAGCCGTGGAAAATGGCGGCCGCGGCTGCTGGATTTCGTTTCATCCTTGGATGATTCCGTGGTGAAATCGGCATCCGAAAAGGCGTTTCGGTCTCTTCCGGATATCTCGAAGGCCATCTCTGAGCTCACGGTGCTCAAAGGCGTGGGTCCCGCCACCGCCTCCGCCGTTCTTGCAGCTTATGCGCCCGACGTGGCGCCTTTCATGTCCGACGAGGCTATGGTTGCAGCTCTTGGAAACTCCAAAGACTATACACTTAAGCAGTACCTGTTATTTGCAAATAAATTGCAGGAGAAGGCAAAGGAATTGAGCGCAGAAGGCGAGACCTTCACGCCATCAGATGTAGAGAGAGCTCTGTGGAGTTGCACTGTTGGGGCCAAGTTATCTTCACAGAAAGTACAAGACCCCAAAAGTGATACAAGTAAAAGCTCCAAGCGGAAGAGAAAGCGTTGA
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

218

Amino Acids

24.24

Weight (kDa)

9.32

Isoelectric Point (pI)

53.02

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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Publication-ready
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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)
AccB1I GGYRCC 1 cut(s) 397
AccII CGCG 1 cut(s) 226
AccIII TCCGGA 1 cut(s) 301
AciI CCGC 9 cut(s) 115, 139, 220, 224, 226, 354, 360, 366, 637
AcoI YGGCCR 1 cut(s) 221
AcsI RAATTY 1 cut(s) 107
AcyI GRCGYC 1 cut(s) 398
AfaI GTAC 2 cut(s) 467, 600
AflII CTTAAG 1 cut(s) 458
AjiI CACGTC 1 cut(s) 394
AluBI AGCT 8 cut(s) 18, 178, 202, 328, 380, 431, 554, 630
AluI AGCT 8 cut(s) 18, 178, 202, 328, 380, 431, 554, 630
Alw21I GWGCWC 5 cut(s) 20, 180, 330, 339, 556
Alw26I GTCTC 4 cut(s) 35, 66, 300, 518
AlwNI CAGNNNCTG 1 cut(s) 469
Aor13HI TCCGGA 1 cut(s) 301
AoxI GGCC 3 cut(s) 221, 315, 576
ApeKI GCWGC 3 cut(s) 229, 377, 428
ApoI RAATTY 1 cut(s) 107
AspLEI GCGC 4 cut(s) 195, 388, 400, 515
AspS9I GGNCC 2 cut(s) 350, 576
AsuHPI GGTGA 2 cut(s) 157, 277
AvaII GGWCC 1 cut(s) 350
BanI GGYRCC 1 cut(s) 397
BanII GRGCYC 4 cut(s) 20, 180, 330, 556
Bbv12I GWGCWC 5 cut(s) 20, 180, 330, 339, 556
BbvI GCAGC 3 cut(s) 216, 389, 440
BccI CCATC 2 cut(s) 326, 544
BceAI ACGGC 2 cut(s) 192, 353
BcoDI GTCTC 4 cut(s) 35, 66, 300, 518
BfoI RGCGCY 1 cut(s) 401
BfrI CTTAAG 1 cut(s) 458
BisI GCNGC 6 cut(s) 221, 224, 227, 230, 378, 429
BlpI GCTNAGC 1 cut(s) 203
BlsI GCNGC 6 cut(s) 222, 225, 228, 231, 379, 430
Bme18I GGWCC 1 cut(s) 350
BmgBI CACGTC 1 cut(s) 394
BmgT120I GGNCC 2 cut(s) 350, 576
BmiI GGNNCC 4 cut(s) 351, 352, 399, 577
BmsI GCATC 2 cut(s) 75, 284
BplI GAGNNNNNCTC 2 cut(s) 7, 39
Bpu1102I GCTNAGC 1 cut(s) 203
BsaHI GRCGYC 1 cut(s) 398
BsaI GGTCTC 3 cut(s) 35, 300, 518
BsaJI CCNNGG 4 cut(s) 208, 224, 249, 261
BsaWI WCCGGW 1 cut(s) 301
BseAI TCCGGA 1 cut(s) 301
BseDI CCNNGG 4 cut(s) 208, 224, 249, 261
BseGI GGATG 3 cut(s) 245, 259, 275
BseMII CTCAG 2 cut(s) 217, 315
BseRI GAGGAG 2 cut(s) 120, 125
BseX3I CGGCCG 1 cut(s) 221
BseXI GCAGC 3 cut(s) 216, 389, 440
Bsh1236I CGCG 1 cut(s) 226
Bsh1285I CGRYCG 1 cut(s) 224
BshFI GGCC 3 cut(s) 223, 317, 578
BshNI GGYRCC 1 cut(s) 397
BsiEI CGRYCG 1 cut(s) 224
BsiHKAI GWGCWC 5 cut(s) 20, 180, 330, 339, 556
BsiSI CCGG 1 cut(s) 302
BslFI GGGAC 1 cut(s) 336
BsmAI GTCTC 4 cut(s) 35, 66, 300, 518
BsmBI CGTCTC 1 cut(s) 66
BsmFI GGGAC 1 cut(s) 336
BsnI GGCC 3 cut(s) 223, 317, 578
Bso31I GGTCTC 3 cut(s) 35, 300, 518
Bsp1286I GDGCHC 5 cut(s) 20, 180, 330, 339, 556
Bsp13I TCCGGA 1 cut(s) 301
Bsp143I GATC 1 cut(s) 88
Bsp1720I GCTNAGC 1 cut(s) 203
BspACI CCGC 9 cut(s) 115, 139, 220, 224, 226, 354, 360, 366, 637
BspANI GGCC 3 cut(s) 223, 317, 578
BspCNI CTCAG 2 cut(s) 216, 316
BspEI TCCGGA 1 cut(s) 301
BspFNI CGCG 1 cut(s) 226
BspLI GGNNCC 4 cut(s) 351, 352, 399, 577
BspT107I GGYRCC 1 cut(s) 397
BspTI CTTAAG 1 cut(s) 458
BspTNI GGTCTC 3 cut(s) 35, 300, 518
BssECI CCNNGG 4 cut(s) 208, 224, 249, 261
BssMI GATC 1 cut(s) 88
BssNI GRCGYC 1 cut(s) 398
BssT1I CCWWGG 1 cut(s) 249
Bst4CI ACNGT 2 cut(s) 334, 571
Bst6I CTCTTC 3 cut(s) 55, 303, 635
BstACI GRCGYC 1 cut(s) 398
BstAFI CTTAAG 1 cut(s) 458
BstAPI GCANNNNNTGC 1 cut(s) 383
BstC8I GCNNGC 1 cut(s) 143
BstDEI CTNAG 2 cut(s) 203, 324
BstDSI CCRYGG 3 cut(s) 208, 224, 261
BstF5I GGATG 3 cut(s) 245, 259, 275
BstFNI CGCG 1 cut(s) 226
BstH2I RGCGCY 1 cut(s) 401
BstHHI GCGC 4 cut(s) 195, 388, 400, 515
BstKTI GATC 1 cut(s) 91
BstMAI GTCTC 4 cut(s) 35, 66, 300, 518
BstMBI GATC 1 cut(s) 88
BstMCI CGRYCG 1 cut(s) 224
BstMWI GCNNNNNNNGC 8 cut(s) 199, 226, 229, 334, 374, 383, 425, 519
BstUI CGCG 1 cut(s) 226
BstV1I GCAGC 3 cut(s) 216, 389, 440
BstZI CGGCCG 1 cut(s) 221
BsuRI GGCC 3 cut(s) 223, 317, 578
BtgI CCRYGG 3 cut(s) 208, 224, 261
BtrI CACGTC 1 cut(s) 394
BtsCI GGATG 3 cut(s) 245, 259, 275
BtsIMutI CAGTG 1 cut(s) 567
Cac8I GCNNGC 1 cut(s) 143
CaiI CAGNNNCTG 1 cut(s) 469
CciNI GCGGCCGC 1 cut(s) 221
CfoI GCGC 4 cut(s) 195, 388, 400, 515
Cfr13I GGNCC 2 cut(s) 350, 576
Cfr42I CCGCGG 1 cut(s) 227
Csp6I GTAC 2 cut(s) 466, 599
CviAII CATG 2 cut(s) 190, 406
CviQI GTAC 2 cut(s) 466, 599
DdeI CTNAG 2 cut(s) 203, 324
DinI GGCGCC 1 cut(s) 399
DpnI GATC 1 cut(s) 90
DpnII GATC 1 cut(s) 88
EaeI YGGCCR 1 cut(s) 221
EagI CGGCCG 1 cut(s) 221
Eam1104I CTCTTC 3 cut(s) 55, 303, 635
EarI CTCTTC 3 cut(s) 55, 303, 635
EciI GGCGGA 2 cut(s) 128, 355
Ecl136II GAGCTC 4 cut(s) 18, 178, 328, 554
EclXI CGGCCG 1 cut(s) 221
Eco130I CCWWGG 1 cut(s) 249
Eco24I GRGCYC 4 cut(s) 20, 180, 330, 556
Eco31I GGTCTC 3 cut(s) 35, 300, 518
Eco32I GATATC 1 cut(s) 307
Eco47I GGWCC 1 cut(s) 350
Eco52I CGGCCG 1 cut(s) 221
Eco53kI GAGCTC 4 cut(s) 18, 178, 328, 554
EcoICRI GAGCTC 4 cut(s) 18, 178, 328, 554
EcoO109I RGGNCCY 1 cut(s) 350
EcoRI GAATTC 1 cut(s) 107
EcoRV GATATC 1 cut(s) 307
EcoT14I CCWWGG 1 cut(s) 249
EcoT38I GRGCYC 4 cut(s) 20, 180, 330, 556
EgeI GGCGCC 1 cut(s) 399
EheI GGCGCC 1 cut(s) 399
ErhI CCWWGG 1 cut(s) 249
Esp3I CGTCTC 1 cut(s) 66
FaeI CATG 2 cut(s) 193, 409
FaiI YATR 5 cut(s) 191, 384, 407, 422, 453
FaqI GGGAC 1 cut(s) 336
FatI CATG 2 cut(s) 189, 405
FauI CCCGC 1 cut(s) 361
Fnu4HI GCNGC 6 cut(s) 221, 224, 227, 230, 378, 429
FokI GGATG 3 cut(s) 232, 262, 266
FriOI GRGCYC 4 cut(s) 20, 180, 330, 556
Fsp4HI GCNGC 6 cut(s) 221, 224, 227, 230, 378, 429
GlaI GCGC 4 cut(s) 194, 387, 399, 514
GluI GCNGC 6 cut(s) 221, 224, 227, 230, 378, 429
HaeII RGCGCY 1 cut(s) 401
HaeIII GGCC 3 cut(s) 223, 317, 578
HapII CCGG 1 cut(s) 302
HhaI GCGC 4 cut(s) 195, 388, 400, 515
Hin1I GRCGYC 1 cut(s) 398
Hin1II CATG 2 cut(s) 193, 409
Hin6I GCGC 4 cut(s) 193, 386, 398, 513
HinP1I GCGC 4 cut(s) 193, 386, 398, 513
HinfI GANTC 2 cut(s) 41, 257
HpaII CCGG 1 cut(s) 302
HphI GGTGA 2 cut(s) 157, 277
Hpy188I TCNGA 6 cut(s) 175, 184, 280, 325, 412, 541
Hpy188III TCNNGA 4 cut(s) 34, 101, 302, 310
Hpy99I CGWCG 3 cut(s) 107, 395, 416
HpyAV CCTTC 5 cut(s) 169, 307, 490, 512, 538
HpyCH4III ACNGT 2 cut(s) 334, 571
HpyCH4IV ACGT 1 cut(s) 393
HpyCH4V TGCA 5 cut(s) 377, 428, 479, 490, 567
HpyF10VI GCNNNNNNNGC 8 cut(s) 199, 226, 229, 334, 374, 383, 425, 519
HpyF3I CTNAG 2 cut(s) 203, 324
HpySE526I ACGT 1 cut(s) 393
Hsp92I GRCGYC 1 cut(s) 398
Hsp92II CATG 2 cut(s) 193, 409
HspAI GCGC 4 cut(s) 193, 386, 398, 513
KasI GGCGCC 1 cut(s) 397
KflI GGGWCCC 1 cut(s) 350
Kpn2I TCCGGA 1 cut(s) 301
KspI CCGCGG 1 cut(s) 227
Kzo9I GATC 1 cut(s) 88
LmnI GCTCC 1 cut(s) 635
LpnPI CCDG 8 cut(s) 19, 77, 155, 181, 218, 315, 476, 482
Lsp1109I GCAGC 3 cut(s) 216, 389, 440
LweI GCATC 2 cut(s) 75, 284
MaeII ACGT 1 cut(s) 393
MalI GATC 1 cut(s) 90
MboI GATC 1 cut(s) 88
MboII GAAGA 4 cut(s) 42, 290, 579, 652
MhlI GDGCHC 5 cut(s) 20, 180, 330, 339, 556
MluCI AATT 5 cut(s) 5, 71, 107, 485, 506
Mly113I GGCGCC 1 cut(s) 398
MmeI TCCRAC 2 cut(s) 207, 435
MnlI CCTC 7 cut(s) 138, 141, 146, 181, 197, 373, 409
MroI TCCGGA 1 cut(s) 301
MseI TTAA 1 cut(s) 459
MspA1I CMGCKG 1 cut(s) 226
MspCI CTTAAG 1 cut(s) 458
MspI CCGG 1 cut(s) 302
MvnI CGCG 1 cut(s) 226
MwoI GCNNNNNNNGC 8 cut(s) 199, 226, 229, 334, 374, 383, 425, 519
NarI GGCGCC 1 cut(s) 398
NdeII GATC 1 cut(s) 88
NlaIII CATG 2 cut(s) 193, 409
NlaIV GGNNCC 4 cut(s) 351, 352, 399, 577
NotI GCGGCCGC 1 cut(s) 221
PfeI GAWTC 2 cut(s) 41, 257
PkrI GCNGC 6 cut(s) 222, 225, 228, 231, 379, 430
PluTI GGCGCC 1 cut(s) 401
PpuMI RGGWCCY 1 cut(s) 350
Psp124BI GAGCTC 4 cut(s) 20, 180, 330, 556
Psp5II RGGWCCY 1 cut(s) 350
PspN4I GGNNCC 4 cut(s) 351, 352, 399, 577
PspPI GGNCC 2 cut(s) 350, 576
PspPPI RGGWCCY 1 cut(s) 350
PstNI CAGNNNCTG 1 cut(s) 469
RsaI GTAC 2 cut(s) 467, 600
RsaNI GTAC 2 cut(s) 466, 599
SacI GAGCTC 4 cut(s) 20, 180, 330, 556
SacII CCGCGG 1 cut(s) 227
SaqAI TTAA 1 cut(s) 459
SatI GCNGC 6 cut(s) 221, 224, 227, 230, 378, 429
Sau3AI GATC 1 cut(s) 88
Sau96I GGNCC 2 cut(s) 350, 576
SduI GDGCHC 5 cut(s) 20, 180, 330, 339, 556
SfaNI GCATC 2 cut(s) 75, 284
SfoI GGCGCC 1 cut(s) 399
Sfr303I CCGCGG 1 cut(s) 227
SgrBI CCGCGG 1 cut(s) 227
SinI GGWCC 1 cut(s) 350
SmlI CTYRAG 1 cut(s) 458
SmoI CTYRAG 1 cut(s) 458
Sse9I AATT 5 cut(s) 5, 71, 107, 485, 506
SsiI CCGC 9 cut(s) 115, 139, 220, 224, 226, 354, 360, 366, 637
SspDI GGCGCC 1 cut(s) 397
SstI GAGCTC 4 cut(s) 20, 180, 330, 556
StyI CCWWGG 1 cut(s) 249
TaaI ACNGT 2 cut(s) 334, 571
TaiI ACGT 1 cut(s) 396
TaqI TCGA 3 cut(s) 69, 102, 311
TaqII GACCGA 2 cut(s) 17, 282
TasI AATT 5 cut(s) 5, 71, 107, 485, 506
TatI WGTACW 1 cut(s) 598
TauI GCSGC 3 cut(s) 223, 226, 229
TfiI GAWTC 2 cut(s) 41, 257
Tru1I TTAA 1 cut(s) 459
Tru9I TTAA 1 cut(s) 459
TscAI CASTG 1 cut(s) 574
TseI GCWGC 3 cut(s) 229, 377, 428
TspDTI ATGAA 3 cut(s) 151, 234, 394
TspGWI ACGGA 1 cut(s) 250
TspRI CASTG 1 cut(s) 574
Vha464I CTTAAG 1 cut(s) 458
VpaK11BI GGWCC 1 cut(s) 350
XapI RAATTY 1 cut(s) 107
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.