MD11G1133500.v1.1

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr11
OG0002778
Physical Location & Seq
Reverse (-)
12242911 .. 12244369
1459 bp
Loading structure...
UTR
Exon/CDS
Intron
MD11G1133500.v1.1.491

Sequence Viewer

Length: 1224 bp
ATGAGCACAAGCATTAAGTCGAATCCCAAGGCTAATGCTAGGGTTTCCTCCCTCGTCACTCCCTTATATAATCTCTTGTCGGACCATTTCTTTCCCATCAATTCTTCAGCTCACAACACAAACTACAATCAACAGAAGGAGAAGAGAAGCATACATATTTGGCAGCCAGAAATGGCGCCTACGATTAAAATGTCACATATTTTGGTGGCTGTTTTCGTCGTCCTTGTTTCGATGGAAGCCGCCTTGGTTATGGGGCAAGGCAATGGAAACGGGAACGCAAATGGCAAAAAAGCCGATGAGGCTAATTACGACGTGTTGACACCACTGGGATCCGGGCAGGAGCGAGGGTTCTGCAAAGCAAAGGGGGCTTGCTATTACAAGACCCTTACGTGCCCGTCGGAATGCCCTCAGAGAAAGCCGAAGAAGAACAAGAAGAACAAGGGTTGTTTCATTAACTGCGGTAGCAAGTGTGAAGCTACTTGCAAGTATAGGAAATCCAAGTGTGACGGATATGGCTCTCTGTGCTACGATCCTAGGTTTGTTGGCGGTGACGGTGTGATGTTCTACTTCCATGGAGCCAAGGGGGGAAACTTTGCCATTGTTTCAGACACCAACCTCCAAATCAACGCACACTTCATCGGGACTCGACCAACAGGAAGGACCCGGGATTTCACATGGGTTCAGGCTTTCGCAGTGATGTTCGACTCTCACACCCTTGTCATCGCAGCAAAGAGGGTCTCAAAGTGGGATGACAAAGTTGATGCTCTCATGGTAAAGTGGGACGACAAAGTTGTTACCGTCCCCACTGATGGAGATGCTGAATGGAGGACTAACGGCGAAGATAGAGAGGTAGTAGTGGAAAGAACCGACGACACCAACTACGTTAGGGTTACAGTGGCCGGCCTCGTCGAAATGGACATAAGGGTTAGGCCTATCGGAGAAAAGGAAAACAAGGTTCATAACTACCAAATACCAGCTGATGACACATTTGCTCACTTGGAGACACAGTTCAGGTTTACCAATTTATCCGATCTTGTGGAGGGAGTTTTGGGCAAGACTTACCGGCCAGGTTACGTTAGTCCGGTCAAGGTCGGAGTCCCGATGCCAATGGCAGGCGGGGAGGACAAGTACGAGACTTCATCCCTCTTTTCGCCTCTCTGCAAGGTTTGCAGGTTCCAAAAACAGCCTGAGCTTGCAGCTGCTGGAGGAATTGCTCAGTACTGA
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
Root_cap

Protein Analysis

408

Amino Acids

45.09

Weight (kDa)

8.84

Isoelectric Point (pI)

26.43

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 336 - 392 1.6e-28 Root cap
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 1161
AccB1I GGYRCC 1 cut(s) 175
AciI CCGC 4 cut(s) 240, 459, 546, 1116
AclWI GGATC 3 cut(s) 324, 337, 524
AcoI YGGCCR 2 cut(s) 897, 1064
AcuI CTGAAG 1 cut(s) 90
AcyI GRCGYC 1 cut(s) 176
AfaI GTAC 2 cut(s) 1130, 1220
AfiI CCNNNNNNNGG 2 cut(s) 809, 1112
AflIII ACRYGT 1 cut(s) 312
AjiI CACGTC 1 cut(s) 313
AjnI CCWGG 1 cut(s) 1066
AloI GAACNNNNNNTCC 4 cut(s) 332, 364, 992, 1024
AluBI AGCT 5 cut(s) 110, 476, 977, 1192, 1199
AluI AGCT 5 cut(s) 110, 476, 977, 1192, 1199
Alw21I GWGCWC 1 cut(s) 8
Alw26I GTCTC 3 cut(s) 742, 995, 1127
AlwI GGATC 3 cut(s) 324, 337, 524
AlwNI CAGNNNCTG 1 cut(s) 1202
Ama87I CYCGRG 1 cut(s) 663
AoxI GGCC 4 cut(s) 897, 901, 929, 1064
ApeKI GCWGC 4 cut(s) 163, 725, 1196, 1199
AspA2I CCTAGG 1 cut(s) 533
AspLEI GCGC 1 cut(s) 178
AspS9I GGNCC 2 cut(s) 82, 660
AsuC2I CCSGG 3 cut(s) 334, 664, 665
AsuHPI GGTGA 1 cut(s) 560
AvaI CYCGRG 1 cut(s) 663
AvaII GGWCC 2 cut(s) 82, 660
AvrII CCTAGG 1 cut(s) 533
BaeGI GKGCMC 1 cut(s) 395
BamHI GGATCC 1 cut(s) 329
BanI GGYRCC 1 cut(s) 175
Bbv12I GWGCWC 1 cut(s) 8
BbvI GCAGC 4 cut(s) 175, 737, 1186, 1208
BccI CCATC 3 cut(s) 104, 226, 803
BceAI ACGGC 1 cut(s) 850
BcgI CGANNNNNNTGC 2 cut(s) 333, 367
BciT130I CCWGG 1 cut(s) 1068
BcnI CCSGG 3 cut(s) 334, 664, 665
BcoDI GTCTC 3 cut(s) 742, 995, 1127
BfaI CTAG 2 cut(s) 39, 534
BfoI RGCGCY 1 cut(s) 179
BfuAI ACCTGC 1 cut(s) 1161
BglI GCCNNNNNGGC 1 cut(s) 299
BisI GCNGC 5 cut(s) 164, 240, 726, 1197, 1200
BlnI CCTAGG 1 cut(s) 533
BlsI GCNGC 5 cut(s) 165, 241, 727, 1198, 1201
BmcAI AGTACT 1 cut(s) 1220
Bme1390I CCNGG 4 cut(s) 334, 664, 665, 1068
Bme18I GGWCC 2 cut(s) 82, 660
BmeT110I CYCGRG 1 cut(s) 663
BmgBI CACGTC 1 cut(s) 313
BmgT120I GGNCC 2 cut(s) 82, 660
BmiI GGNNCC 5 cut(s) 177, 331, 577, 662, 1175
BmrFI CCNGG 4 cut(s) 334, 664, 665, 1068
BmrI ACTGGG 1 cut(s) 335
BmsI GCATC 3 cut(s) 751, 805, 1092
BmuI ACTGGG 1 cut(s) 335
BpmI CTGGAG 1 cut(s) 1224
Bpu10I CCTNAGC 1 cut(s) 1188
BpuMI CCSGG 3 cut(s) 334, 664, 665
BsaAI YACGTR 1 cut(s) 390
BsaHI GRCGYC 1 cut(s) 176
BsaI GGTCTC 1 cut(s) 742
BsaJI CCNNGG 6 cut(s) 27, 243, 533, 571, 579, 663
BsaWI WCCGGW 1 cut(s) 1081
BsaXI ACNNNNNCTCC 6 cut(s) 332, 362, 992, 1022, 1112, 1142
Bsc4I CCNNNNNNNGG 2 cut(s) 809, 1112
Bse118I RCCGGY 2 cut(s) 899, 1062
Bse1I ACTGG 1 cut(s) 330
Bse3DI GCAATG 1 cut(s) 268
BseBI CCWGG 1 cut(s) 1068
BseDI CCNNGG 6 cut(s) 27, 243, 533, 571, 579, 663
BseGI GGATG 2 cut(s) 754, 1139
BseLI CCNNNNNNNGG 2 cut(s) 809, 1112
BseMI GCAATG 1 cut(s) 268
BseMII CTCAG 2 cut(s) 422, 1179
BseNI ACTGG 1 cut(s) 330
BseSI GKGCMC 1 cut(s) 395
BseXI GCAGC 4 cut(s) 175, 737, 1186, 1208
BshFI GGCC 4 cut(s) 899, 903, 931, 1066
BshNI GGYRCC 1 cut(s) 175
BsiHKAI GWGCWC 1 cut(s) 8
BsiHKCI CYCGRG 1 cut(s) 663
BsiSI CCGG 5 cut(s) 333, 664, 900, 1063, 1082
BslFI GGGAC 4 cut(s) 655, 785, 794, 1082
BslI CCNNNNNNNGG 2 cut(s) 809, 1112
BsmAI GTCTC 3 cut(s) 742, 995, 1127
BsmFI GGGAC 4 cut(s) 655, 785, 794, 1082
BsmI GAATGC 1 cut(s) 407
BsnI GGCC 4 cut(s) 899, 903, 931, 1066
Bso31I GGTCTC 1 cut(s) 742
BsoBI CYCGRG 1 cut(s) 663
Bsp1286I GDGCHC 2 cut(s) 8, 395
Bsp143I GATC 3 cut(s) 329, 529, 1030
Bsp19I CCATGG 1 cut(s) 571
BspACI CCGC 4 cut(s) 240, 459, 546, 1116
BspANI GGCC 4 cut(s) 899, 903, 931, 1066
BspCNI CTCAG 2 cut(s) 421, 1180
BspLI GGNNCC 5 cut(s) 177, 331, 577, 662, 1175
BspMI ACCTGC 1 cut(s) 1161
BspPI GGATC 3 cut(s) 324, 337, 524
BspT107I GGYRCC 1 cut(s) 175
BspTNI GGTCTC 1 cut(s) 742
BsrDI GCAATG 1 cut(s) 268
BsrFI RCCGGY 2 cut(s) 899, 1062
BsrI ACTGG 1 cut(s) 330
BssAI RCCGGY 2 cut(s) 899, 1062
BssECI CCNNGG 6 cut(s) 27, 243, 533, 571, 579, 663
BssMI GATC 3 cut(s) 329, 529, 1030
BssNI GRCGYC 1 cut(s) 176
BssT1I CCWWGG 5 cut(s) 27, 243, 533, 571, 579
Bst2UI CCWGG 1 cut(s) 1068
Bst4CI ACNGT 4 cut(s) 554, 799, 895, 1008
Bst6I CTCTTC 1 cut(s) 137
BstACI GRCGYC 1 cut(s) 176
BstAPI GCANNNNNTGC 1 cut(s) 1167
BstBAI YACGTR 1 cut(s) 390
BstC8I GCNNGC 4 cut(s) 370, 901, 1114, 1194
BstDEI CTNAG 3 cut(s) 408, 1188, 1215
BstDSI CCRYGG 1 cut(s) 571
BstF5I GGATG 2 cut(s) 754, 1139
BstH2I RGCGCY 1 cut(s) 179
BstHHI GCGC 1 cut(s) 178
BstKTI GATC 3 cut(s) 332, 532, 1033
BstMAI GTCTC 3 cut(s) 742, 995, 1127
BstMBI GATC 3 cut(s) 329, 529, 1030
BstMWI GCNNNNNNNGC 4 cut(s) 299, 365, 522, 1167
BstNI CCWGG 1 cut(s) 1068
BstSCI CCNGG 4 cut(s) 332, 662, 663, 1066
BstSLI GKGCMC 1 cut(s) 395
BstV1I GCAGC 4 cut(s) 175, 737, 1186, 1208
BstX2I RGATCY 1 cut(s) 329
BstYI RGATCY 1 cut(s) 329
BsuRI GGCC 4 cut(s) 899, 903, 931, 1066
BtgI CCRYGG 1 cut(s) 571
BtgZI GCGATG 1 cut(s) 706
BtrI CACGTC 1 cut(s) 313
BtsCI GGATG 2 cut(s) 754, 1139
BtsI GCAGTG 1 cut(s) 699
BtsIMutI CAGTG 4 cut(s) 323, 699, 804, 900
BveI ACCTGC 1 cut(s) 1161
Cac8I GCNNGC 4 cut(s) 370, 901, 1114, 1194
CaiI CAGNNNCTG 1 cut(s) 1202
CfoI GCGC 1 cut(s) 178
Cfr10I RCCGGY 2 cut(s) 899, 1062
Cfr13I GGNCC 2 cut(s) 82, 660
Cfr9I CCCGGG 1 cut(s) 663
Csp6I GTAC 2 cut(s) 1129, 1219
CviAII CATG 3 cut(s) 572, 675, 769
CviQI GTAC 2 cut(s) 1129, 1219
DdeI CTNAG 3 cut(s) 408, 1188, 1215
DinI GGCGCC 1 cut(s) 177
DpnI GATC 3 cut(s) 331, 531, 1032
DpnII GATC 3 cut(s) 329, 529, 1030
EaeI YGGCCR 2 cut(s) 897, 1064
Eam1104I CTCTTC 1 cut(s) 137
EarI CTCTTC 1 cut(s) 137
Eco130I CCWWGG 5 cut(s) 27, 243, 533, 571, 579
Eco147I AGGCCT 1 cut(s) 931
Eco31I GGTCTC 1 cut(s) 742
Eco47I GGWCC 2 cut(s) 82, 660
Eco57I CTGAAG 1 cut(s) 90
Eco88I CYCGRG 1 cut(s) 663
EcoO109I RGGNCCY 1 cut(s) 660
EcoRII CCWGG 1 cut(s) 1066
EcoT14I CCWWGG 5 cut(s) 27, 243, 533, 571, 579
EgeI GGCGCC 1 cut(s) 177
EheI GGCGCC 1 cut(s) 177
ErhI CCWWGG 5 cut(s) 27, 243, 533, 571, 579
FaeI CATG 3 cut(s) 575, 678, 772
FaqI GGGAC 4 cut(s) 655, 785, 794, 1082
FatI CATG 3 cut(s) 571, 674, 768
FauI CCCGC 1 cut(s) 1109
Fnu4HI GCNGC 5 cut(s) 164, 240, 726, 1197, 1200
FokI GGATG 2 cut(s) 761, 1126
FseI GGCCGGCC 1 cut(s) 903
Fsp4HI GCNGC 5 cut(s) 164, 240, 726, 1197, 1200
FspBI CTAG 2 cut(s) 39, 534
GlaI GCGC 1 cut(s) 177
GluI GCNGC 5 cut(s) 164, 240, 726, 1197, 1200
GsuI CTGGAG 1 cut(s) 1224
HaeII RGCGCY 1 cut(s) 179
HaeIII GGCC 4 cut(s) 899, 903, 931, 1066
HapII CCGG 5 cut(s) 333, 664, 900, 1063, 1082
HhaI GCGC 1 cut(s) 178
Hin1I GRCGYC 1 cut(s) 176
Hin1II CATG 3 cut(s) 575, 678, 772
Hin6I GCGC 1 cut(s) 176
HinP1I GCGC 1 cut(s) 176
HincII GTYRAC 1 cut(s) 318
HindII GTYRAC 1 cut(s) 318
HinfI GANTC 4 cut(s) 22, 643, 704, 1095
HpaII CCGG 5 cut(s) 333, 664, 900, 1063, 1082
HphI GGTGA 1 cut(s) 560
Hpy166II GTNNAC 2 cut(s) 318, 1017
Hpy188I TCNGA 7 cut(s) 82, 400, 411, 607, 938, 1030, 1094
Hpy188III TCNNGA 2 cut(s) 640, 1099
Hpy8I GTNNAC 2 cut(s) 318, 1017
Hpy99I CGWCG 5 cut(s) 221, 314, 400, 872, 911
HpyAV CCTTC 2 cut(s) 130, 651
HpyCH4III ACNGT 4 cut(s) 554, 799, 895, 1008
HpyCH4IV ACGT 4 cut(s) 312, 389, 882, 1074
HpyCH4V TGCA 5 cut(s) 354, 483, 1161, 1170, 1196
HpyF10VI GCNNNNNNNGC 4 cut(s) 299, 365, 522, 1167
HpyF3I CTNAG 3 cut(s) 408, 1188, 1215
HpySE526I ACGT 4 cut(s) 312, 389, 882, 1074
Hsp92I GRCGYC 1 cut(s) 176
Hsp92II CATG 3 cut(s) 575, 678, 772
HspAI GCGC 1 cut(s) 176
KasI GGCGCC 1 cut(s) 175
KroI GCCGGC 1 cut(s) 899
KroNI GCCGGC 1 cut(s) 901
Kzo9I GATC 3 cut(s) 329, 529, 1030
LmnI GCTCC 2 cut(s) 340, 575
Lsp1109I GCAGC 4 cut(s) 175, 737, 1186, 1208
LweI GCATC 3 cut(s) 751, 805, 1092
MaeI CTAG 2 cut(s) 39, 534
MaeII ACGT 4 cut(s) 312, 389, 882, 1074
MaeIII GTNAC 7 cut(s) 55, 192, 503, 548, 793, 889, 1070
MalI GATC 3 cut(s) 331, 531, 1032
MboI GATC 3 cut(s) 329, 529, 1030
MboII GAAGA 6 cut(s) 96, 154, 433, 436, 445, 851
MflI RGATCY 1 cut(s) 329
MhlI GDGCHC 2 cut(s) 8, 395
MluCI AATT 4 cut(s) 100, 304, 1021, 1209
Mly113I GGCGCC 1 cut(s) 176
MlyI GAGTC 3 cut(s) 637, 698, 1104
MmeI TCCRAC 3 cut(s) 60, 378, 1072
MroNI GCCGGC 1 cut(s) 899
MseI TTAA 3 cut(s) 15, 186, 453
MspA1I CMGCKG 2 cut(s) 977, 1199
MspI CCGG 5 cut(s) 333, 664, 900, 1063, 1082
MspR9I CCNGG 4 cut(s) 334, 664, 665, 1068
Mva1269I GAATGC 1 cut(s) 407
MvaI CCWGG 1 cut(s) 1068
MwoI GCNNNNNNNGC 4 cut(s) 299, 365, 522, 1167
NaeI GCCGGC 1 cut(s) 901
NarI GGCGCC 1 cut(s) 176
NciI CCSGG 3 cut(s) 334, 664, 665
NcoI CCATGG 1 cut(s) 571
NdeII GATC 3 cut(s) 329, 529, 1030
NgoMIV GCCGGC 1 cut(s) 899
NlaIII CATG 3 cut(s) 575, 678, 772
NlaIV GGNNCC 5 cut(s) 177, 331, 577, 662, 1175
NmuCI GTSAC 4 cut(s) 55, 192, 503, 548
PceI AGGCCT 1 cut(s) 931
PctI GAATGC 1 cut(s) 407
PdiI GCCGGC 1 cut(s) 901
PfeI GAWTC 1 cut(s) 22
PkrI GCNGC 5 cut(s) 165, 241, 727, 1198, 1201
PleI GAGTC 3 cut(s) 637, 698, 1103
PluTI GGCGCC 1 cut(s) 179
PpsI GAGTC 3 cut(s) 637, 698, 1103
Ppu21I YACGTR 1 cut(s) 390
PpuMI RGGWCCY 1 cut(s) 660
Psp5II RGGWCCY 1 cut(s) 660
Psp6I CCWGG 1 cut(s) 1066
PspGI CCWGG 1 cut(s) 1066
PspN4I GGNNCC 5 cut(s) 177, 331, 577, 662, 1175
PspPI GGNCC 2 cut(s) 82, 660
PspPPI RGGWCCY 1 cut(s) 660
PstNI CAGNNNCTG 1 cut(s) 1202
PsuI RGATCY 1 cut(s) 329
PvuII CAGCTG 2 cut(s) 977, 1199
RigI GGCCGGCC 1 cut(s) 903
RsaI GTAC 2 cut(s) 1130, 1220
RsaNI GTAC 2 cut(s) 1129, 1219
SaqAI TTAA 3 cut(s) 15, 186, 453
SatI GCNGC 5 cut(s) 164, 240, 726, 1197, 1200
Sau3AI GATC 3 cut(s) 329, 529, 1030
Sau96I GGNCC 2 cut(s) 82, 660
ScaI AGTACT 1 cut(s) 1220
SchI GAGTC 3 cut(s) 637, 698, 1104
ScrFI CCNGG 4 cut(s) 334, 664, 665, 1068
SduI GDGCHC 2 cut(s) 8, 395
SfaNI GCATC 3 cut(s) 751, 805, 1092
SfoI GGCGCC 1 cut(s) 177
SinI GGWCC 2 cut(s) 82, 660
SmaI CCCGGG 1 cut(s) 665
Sse9I AATT 4 cut(s) 100, 304, 1021, 1209
SseBI AGGCCT 1 cut(s) 931
SsiI CCGC 4 cut(s) 240, 459, 546, 1116
SspDI GGCGCC 1 cut(s) 175
SspMI CTAG 2 cut(s) 39, 534
StuI AGGCCT 1 cut(s) 931
StyD4I CCNGG 4 cut(s) 332, 662, 663, 1066
StyI CCWWGG 5 cut(s) 27, 243, 533, 571, 579
TaaI ACNGT 4 cut(s) 554, 799, 895, 1008
TaiI ACGT 4 cut(s) 315, 392, 885, 1077
TaqI TCGA 5 cut(s) 20, 230, 646, 702, 909
TasI AATT 4 cut(s) 100, 304, 1021, 1209
TatI WGTACW 1 cut(s) 1218
TauI GCSGC 1 cut(s) 242
TfiI GAWTC 1 cut(s) 22
Tru1I TTAA 3 cut(s) 15, 186, 453
Tru9I TTAA 3 cut(s) 15, 186, 453
TscAI CASTG 4 cut(s) 330, 699, 811, 900
TseFI GTSAC 4 cut(s) 55, 192, 503, 548
TseI GCWGC 4 cut(s) 163, 725, 1196, 1199
Tsp45I GTSAC 4 cut(s) 55, 192, 503, 548
TspDTI ATGAA 4 cut(s) 439, 625, 947, 1128
TspGWI ACGGA 1 cut(s) 522
TspMI CCCGGG 1 cut(s) 663
TspRI CASTG 4 cut(s) 330, 699, 811, 900
VpaK11BI GGWCC 2 cut(s) 82, 660
XmaI CCCGGG 1 cut(s) 663
XmaJI CCTAGG 1 cut(s) 533
XspI CTAG 2 cut(s) 39, 534
ZrmI AGTACT 1 cut(s) 1220
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.