MD03G1114100.v1.1

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0002778
Physical Location & Seq
Forward (+)
9979718 .. 9981133
1416 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1114100.v1.1.491

Sequence Viewer

Length: 1293 bp
ATGGCTAGGATTACAATGTCGCATATTTTGGTGGCTCTTTTCGTCATCCTTGTTTCAATGGAAGCCGCCTTCGTTATGGGGCAAGGCAAGGGGAACGGGAACGGGAACGGGAGCGGAAATGGGAACGGGAACGGGAGCGGAAATGGGAACGGCAACGGCAATGGTAATGGCAATGGAAATGGCAACGGCGACGGAAATGGCAACGGCAGCGGAAATGGCAATGGGAACGGAAACGGCAATGGGAACGGGAGCGGAAATGGGAACGGCAACGGCAATGGTAATGGCAATAGCAATGGAAATGGCAATGGCAATGGCAACGGGAATGGGAATGGAAACGGCAATGGTAATGAAGCCGATGAGGCTGCTGTTTCCAATTATGACGTGTTGACACCAGTGGGATCCGGGCAGGAGCGAGGGTTCTGTAAAGCAAAGGGGGCTTGCTATTACAAGACTCTTACGTGCCCATCTGAATGCCCTCAGAGAAAGCCGAAGAAGAACAAGAAGAACAAGGGTTGTTTCATTAACTGCGGTAGCAAGTGTGAAGCTACTTGCAAGTTTAGGAAAGCCAAGTGTGATGGTTATGGCTCTCTGTGCTACGATCCCAGGTTTGTTGGCGGTGACGGTGTGATGTTCTACTTCCATGGAGCCAAGGGCGGAAACTTTGCCATTGTTTCAGACACCAACCTCCAAATCAACGCACACTTCATCGGGACTCGACCAACAGGAAGGACCCGCGATTTCACATGGATTCAGGCTTTCGCAGTGATGTTTGACTCTCACACCCTTGTCATCGCAGCAAAGAGGGTATCAAAGTGGGATGACAAAGTTGATGCTCTCATGGTAAAGTGGGATGACAAAGTTGTGACCATCCCCACTGATGGAGACGCCGAATGGAGGACTAACGGTGAAGATAGAGAGGTAATCGTCGAAAGAACTGATGAAACCAACTACGTTAGGGTTACAGTGGCCGGTCTCGTGGAAATGGACATTAGGGTTAGACCTATTGGAGAAGAGGAAAACAAGGTCCATAACTACCAAGTACCAGCTGATGACACATTTGCTCACTTGGAGACACAGTTCAGATTTACCAATTTATCCGATCTTGTGGAGGGAGTTTTGGGCAAGACTTACCGCCCAGGTTACGTTAGCCCGGTCAAAATCGGAGTCCCGATGCCGATGGTTGGTGGGGAGGACAAGTACAAAACTTCATCCCTCTTTTGTCCTCTCTGCAAGGTTTGCAGGTTCCAGAAACAGCCTGAGCTTGCAGCTGCTGGAGGAATTGCTCAGTACTGA
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

431

Amino Acids

45.46

Weight (kDa)

8.14

Isoelectric Point (pI)

2.51

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 359 - 415 3.2e-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) 1230
AccBSI CCGCTC 3 cut(s) 114, 138, 252
AccII CGCG 1 cut(s) 735
AclWI GGATC 3 cut(s) 393, 406, 593
AcoI YGGCCR 1 cut(s) 966
AcyI GRCGYC 1 cut(s) 885
AfaI GTAC 3 cut(s) 1041, 1199, 1289
AfiI CCNNNNNNNGG 3 cut(s) 878, 894, 1181
AflIII ACRYGT 1 cut(s) 381
AgsI TTSAA 1 cut(s) 57
AjiI CACGTC 1 cut(s) 382
AjnI CCWGG 2 cut(s) 602, 1135
AloI GAACNNNNNNTCC 4 cut(s) 401, 433, 1061, 1093
AluBI AGCT 4 cut(s) 545, 1046, 1261, 1268
AluI AGCT 4 cut(s) 545, 1046, 1261, 1268
Alw26I GTCTC 3 cut(s) 876, 977, 1064
AlwI GGATC 3 cut(s) 393, 406, 593
AlwNI CAGNNNCTG 1 cut(s) 1271
AoxI GGCC 1 cut(s) 966
ApeKI GCWGC 5 cut(s) 207, 362, 794, 1265, 1268
ArsI GACNNNNNNTTYG 2 cut(s) 1149, 1181
AspS9I GGNCC 2 cut(s) 729, 1024
AsuC2I CCSGG 2 cut(s) 403, 1151
AsuHPI GGTGA 2 cut(s) 629, 917
AvaII GGWCC 2 cut(s) 729, 1024
BaeGI GKGCMC 1 cut(s) 464
BamHI GGATCC 1 cut(s) 398
BauI CACGAG 1 cut(s) 974
BbvI GCAGC 5 cut(s) 219, 349, 806, 1255, 1277
BccI CCATC 5 cut(s) 472, 569, 872, 875, 1171
BceAI ACGGC 8 cut(s) 166, 172, 202, 220, 250, 280, 286, 352
BcgI CGANNNNNNTGC 2 cut(s) 344, 378
BciT130I CCWGG 2 cut(s) 604, 1137
BcnI CCSGG 2 cut(s) 403, 1151
BcoDI GTCTC 3 cut(s) 876, 977, 1064
BfaI CTAG 1 cut(s) 6
BfuAI ACCTGC 1 cut(s) 1230
BglI GCCNNNNNGGC 1 cut(s) 359
BisI GCNGC 6 cut(s) 66, 208, 363, 795, 1266, 1269
BlsI GCNGC 6 cut(s) 67, 209, 364, 796, 1267, 1270
BmcAI AGTACT 1 cut(s) 1289
Bme1390I CCNGG 4 cut(s) 403, 604, 1137, 1151
Bme18I GGWCC 2 cut(s) 729, 1024
BmgBI CACGTC 1 cut(s) 382
BmgT120I GGNCC 2 cut(s) 729, 1024
BmiI GGNNCC 4 cut(s) 400, 646, 731, 1244
BmrFI CCNGG 4 cut(s) 403, 604, 1137, 1151
BmsI GCATC 2 cut(s) 820, 1161
BpmI CTGGAG 1 cut(s) 1293
Bpu10I CCTNAGC 1 cut(s) 1257
BpuMI CCSGG 2 cut(s) 403, 1151
BsaAI YACGTR 1 cut(s) 459
BsaHI GRCGYC 1 cut(s) 885
BsaI GGTCTC 1 cut(s) 977
BsaJI CCNNGG 4 cut(s) 602, 640, 648, 1135
BsaXI ACNNNNNCTCC 6 cut(s) 401, 431, 1061, 1091, 1181, 1211
Bsc4I CCNNNNNNNGG 3 cut(s) 878, 894, 1181
Bse118I RCCGGY 1 cut(s) 968
Bse1I ACTGG 1 cut(s) 392
Bse3DI GCAATG 9 cut(s) 166, 178, 226, 244, 280, 298, 310, 316, 346
BseBI CCWGG 2 cut(s) 604, 1137
BseDI CCNNGG 4 cut(s) 602, 640, 648, 1135
BseGI GGATG 5 cut(s) 45, 823, 856, 867, 1208
BseLI CCNNNNNNNGG 3 cut(s) 878, 894, 1181
BseMI GCAATG 9 cut(s) 166, 178, 226, 244, 280, 298, 310, 316, 346
BseMII CTCAG 2 cut(s) 491, 1248
BseNI ACTGG 1 cut(s) 392
BseSI GKGCMC 1 cut(s) 464
BseXI GCAGC 5 cut(s) 219, 349, 806, 1255, 1277
Bsh1236I CGCG 1 cut(s) 735
BshFI GGCC 1 cut(s) 968
BsiSI CCGG 3 cut(s) 402, 969, 1151
BslFI GGGAC 2 cut(s) 724, 1151
BslI CCNNNNNNNGG 3 cut(s) 878, 894, 1181
BsmAI GTCTC 3 cut(s) 876, 977, 1064
BsmBI CGTCTC 1 cut(s) 876
BsmFI GGGAC 2 cut(s) 724, 1151
BsmI GAATGC 1 cut(s) 476
BsnI GGCC 1 cut(s) 968
Bso31I GGTCTC 1 cut(s) 977
Bsp1286I GDGCHC 1 cut(s) 464
Bsp143I GATC 3 cut(s) 398, 598, 1099
Bsp19I CCATGG 1 cut(s) 640
BspANI GGCC 1 cut(s) 968
BspCNI CTCAG 2 cut(s) 490, 1249
BspFNI CGCG 1 cut(s) 735
BspLI GGNNCC 4 cut(s) 400, 646, 731, 1244
BspMI ACCTGC 1 cut(s) 1230
BspPI GGATC 3 cut(s) 393, 406, 593
BspTNI GGTCTC 1 cut(s) 977
BsrBI CCGCTC 3 cut(s) 114, 138, 252
BsrDI GCAATG 9 cut(s) 166, 178, 226, 244, 280, 298, 310, 316, 346
BsrFI RCCGGY 1 cut(s) 968
BsrI ACTGG 1 cut(s) 392
BssAI RCCGGY 1 cut(s) 968
BssECI CCNNGG 4 cut(s) 602, 640, 648, 1135
BssMI GATC 3 cut(s) 398, 598, 1099
BssNI GRCGYC 1 cut(s) 885
BssSI CACGAG 1 cut(s) 974
BssT1I CCWWGG 2 cut(s) 640, 648
Bst2BI CACGAG 1 cut(s) 974
Bst2UI CCWGG 2 cut(s) 604, 1137
Bst4CI ACNGT 4 cut(s) 623, 905, 964, 1077
Bst6I CTCTTC 1 cut(s) 1005
BstACI GRCGYC 1 cut(s) 885
BstAPI GCANNNNNTGC 1 cut(s) 1236
BstBAI YACGTR 1 cut(s) 459
BstC8I GCNNGC 2 cut(s) 439, 1263
BstDEI CTNAG 3 cut(s) 477, 1257, 1284
BstDSI CCRYGG 1 cut(s) 640
BstF5I GGATG 5 cut(s) 45, 823, 856, 867, 1208
BstFNI CGCG 1 cut(s) 735
BstKTI GATC 3 cut(s) 401, 601, 1102
BstMAI GTCTC 3 cut(s) 876, 977, 1064
BstMBI GATC 3 cut(s) 398, 598, 1099
BstMWI GCNNNNNNNGC 6 cut(s) 207, 216, 359, 434, 591, 1236
BstNI CCWGG 2 cut(s) 604, 1137
BstSCI CCNGG 4 cut(s) 401, 602, 1135, 1149
BstSLI GKGCMC 1 cut(s) 464
BstUI CGCG 1 cut(s) 735
BstV1I GCAGC 5 cut(s) 219, 349, 806, 1255, 1277
BstX2I RGATCY 1 cut(s) 398
BstYI RGATCY 1 cut(s) 398
BsuRI GGCC 1 cut(s) 968
BtgI CCRYGG 1 cut(s) 640
BtgZI GCGATG 1 cut(s) 775
BtrI CACGTC 1 cut(s) 382
BtsCI GGATG 5 cut(s) 45, 823, 856, 867, 1208
BtsI GCAGTG 1 cut(s) 768
BtsIMutI CAGTG 4 cut(s) 399, 768, 873, 969
BveI ACCTGC 1 cut(s) 1230
Cac8I GCNNGC 2 cut(s) 439, 1263
CaiI CAGNNNCTG 1 cut(s) 1271
Cfr10I RCCGGY 1 cut(s) 968
Cfr13I GGNCC 2 cut(s) 729, 1024
CseI GACGC 1 cut(s) 893
Csp6I GTAC 3 cut(s) 1040, 1198, 1288
CviAII CATG 3 cut(s) 641, 744, 838
CviQI GTAC 3 cut(s) 1040, 1198, 1288
DdeI CTNAG 3 cut(s) 477, 1257, 1284
DpnI GATC 3 cut(s) 400, 600, 1101
DpnII GATC 3 cut(s) 398, 598, 1099
EaeI YGGCCR 1 cut(s) 966
Eam1104I CTCTTC 1 cut(s) 1005
EarI CTCTTC 1 cut(s) 1005
EciI GGCGGA 1 cut(s) 669
Eco130I CCWWGG 2 cut(s) 640, 648
Eco31I GGTCTC 1 cut(s) 977
Eco47I GGWCC 2 cut(s) 729, 1024
EcoO109I RGGNCCY 1 cut(s) 729
EcoRII CCWGG 2 cut(s) 602, 1135
EcoT14I CCWWGG 2 cut(s) 640, 648
ErhI CCWWGG 2 cut(s) 640, 648
Esp3I CGTCTC 1 cut(s) 876
FaeI CATG 3 cut(s) 644, 747, 841
FaiI YATR 8 cut(s) 24, 77, 378, 582, 642, 745, 839, 1029
FaqI GGGAC 2 cut(s) 724, 1151
FatI CATG 3 cut(s) 640, 743, 837
FauI CCCGC 1 cut(s) 740
Fnu4HI GCNGC 6 cut(s) 66, 208, 363, 795, 1266, 1269
FokI GGATG 5 cut(s) 32, 830, 854, 863, 1195
Fsp4HI GCNGC 6 cut(s) 66, 208, 363, 795, 1266, 1269
FspBI CTAG 1 cut(s) 6
GluI GCNGC 6 cut(s) 66, 208, 363, 795, 1266, 1269
GsuI CTGGAG 1 cut(s) 1293
HaeIII GGCC 1 cut(s) 968
HapII CCGG 3 cut(s) 402, 969, 1151
HgaI GACGC 1 cut(s) 893
Hin1I GRCGYC 1 cut(s) 885
Hin1II CATG 3 cut(s) 644, 747, 841
HincII GTYRAC 1 cut(s) 387
HindII GTYRAC 1 cut(s) 387
HinfI GANTC 5 cut(s) 451, 712, 748, 773, 1164
HpaII CCGG 3 cut(s) 402, 969, 1151
HphI GGTGA 2 cut(s) 629, 917
Hpy166II GTNNAC 1 cut(s) 387
Hpy188I TCNGA 6 cut(s) 469, 480, 676, 1082, 1099, 1163
Hpy188III TCNNGA 3 cut(s) 709, 1168, 1246
Hpy8I GTNNAC 1 cut(s) 387
Hpy99I CGWCG 2 cut(s) 194, 929
HpyAV CCTTC 2 cut(s) 79, 720
HpyCH4III ACNGT 4 cut(s) 623, 905, 964, 1077
HpyCH4IV ACGT 4 cut(s) 381, 458, 951, 1143
HpyCH4V TGCA 4 cut(s) 552, 1230, 1239, 1265
HpyF10VI GCNNNNNNNGC 6 cut(s) 207, 216, 359, 434, 591, 1236
HpyF3I CTNAG 3 cut(s) 477, 1257, 1284
HpySE526I ACGT 4 cut(s) 381, 458, 951, 1143
Hsp92I GRCGYC 1 cut(s) 885
Hsp92II CATG 3 cut(s) 644, 747, 841
Kzo9I GATC 3 cut(s) 398, 598, 1099
LmnI GCTCC 5 cut(s) 111, 135, 249, 409, 644
Lsp1109I GCAGC 5 cut(s) 219, 349, 806, 1255, 1277
LweI GCATC 2 cut(s) 820, 1161
MaeI CTAG 1 cut(s) 6
MaeII ACGT 4 cut(s) 381, 458, 951, 1143
MaeIII GTNAC 4 cut(s) 617, 862, 958, 1139
MalI GATC 3 cut(s) 400, 600, 1101
MbiI CCGCTC 3 cut(s) 114, 138, 252
MboI GATC 3 cut(s) 398, 598, 1099
MboII GAAGA 5 cut(s) 502, 505, 514, 920, 1022
MflI RGATCY 1 cut(s) 398
MhlI GDGCHC 1 cut(s) 464
MluCI AATT 3 cut(s) 373, 1090, 1278
MlyI GAGTC 4 cut(s) 445, 706, 767, 1173
MseI TTAA 1 cut(s) 522
MslI CAYNNNNRTG 1 cut(s) 469
MspA1I CMGCKG 3 cut(s) 210, 1046, 1268
MspI CCGG 3 cut(s) 402, 969, 1151
MspR9I CCNGG 4 cut(s) 403, 604, 1137, 1151
Mva1269I GAATGC 1 cut(s) 476
MvaI CCWGG 2 cut(s) 604, 1137
MvnI CGCG 1 cut(s) 735
MwoI GCNNNNNNNGC 6 cut(s) 207, 216, 359, 434, 591, 1236
NciI CCSGG 2 cut(s) 403, 1151
NcoI CCATGG 1 cut(s) 640
NdeII GATC 3 cut(s) 398, 598, 1099
NlaIII CATG 3 cut(s) 644, 747, 841
NlaIV GGNNCC 4 cut(s) 400, 646, 731, 1244
NmuCI GTSAC 2 cut(s) 617, 862
PctI GAATGC 1 cut(s) 476
PfeI GAWTC 1 cut(s) 748
PkrI GCNGC 6 cut(s) 67, 209, 364, 796, 1267, 1270
PleI GAGTC 4 cut(s) 445, 706, 767, 1172
PpsI GAGTC 4 cut(s) 445, 706, 767, 1172
Ppu21I YACGTR 1 cut(s) 459
PpuMI RGGWCCY 1 cut(s) 729
Psp5II RGGWCCY 1 cut(s) 729
Psp6I CCWGG 2 cut(s) 602, 1135
PspGI CCWGG 2 cut(s) 602, 1135
PspN4I GGNNCC 4 cut(s) 400, 646, 731, 1244
PspPI GGNCC 2 cut(s) 729, 1024
PspPPI RGGWCCY 1 cut(s) 729
PstNI CAGNNNCTG 1 cut(s) 1271
PsuI RGATCY 1 cut(s) 398
PvuII CAGCTG 2 cut(s) 1046, 1268
RsaI GTAC 3 cut(s) 1041, 1199, 1289
RsaNI GTAC 3 cut(s) 1040, 1198, 1288
RseI CAYNNNNRTG 1 cut(s) 469
SaqAI TTAA 1 cut(s) 522
SatI GCNGC 6 cut(s) 66, 208, 363, 795, 1266, 1269
Sau3AI GATC 3 cut(s) 398, 598, 1099
Sau96I GGNCC 2 cut(s) 729, 1024
ScaI AGTACT 1 cut(s) 1289
SchI GAGTC 4 cut(s) 445, 706, 767, 1173
ScrFI CCNGG 4 cut(s) 403, 604, 1137, 1151
SduI GDGCHC 1 cut(s) 464
SfaNI GCATC 2 cut(s) 820, 1161
SinI GGWCC 2 cut(s) 729, 1024
SmiMI CAYNNNNRTG 1 cut(s) 469
Sse9I AATT 3 cut(s) 373, 1090, 1278
SspMI CTAG 1 cut(s) 6
StyD4I CCNGG 4 cut(s) 401, 602, 1135, 1149
StyI CCWWGG 2 cut(s) 640, 648
TaaI ACNGT 4 cut(s) 623, 905, 964, 1077
TaiI ACGT 4 cut(s) 384, 461, 954, 1146
TaqI TCGA 2 cut(s) 715, 927
TasI AATT 3 cut(s) 373, 1090, 1278
TatI WGTACW 2 cut(s) 1197, 1287
TauI GCSGC 1 cut(s) 68
TfiI GAWTC 1 cut(s) 748
Tru1I TTAA 1 cut(s) 522
Tru9I TTAA 1 cut(s) 522
TscAI CASTG 4 cut(s) 399, 768, 880, 969
TseFI GTSAC 2 cut(s) 617, 862
TseI GCWGC 5 cut(s) 207, 362, 794, 1265, 1268
Tsp45I GTSAC 2 cut(s) 617, 862
TspDTI ATGAA 5 cut(s) 363, 508, 694, 954, 1197
TspGWI ACGGA 2 cut(s) 207, 243
TspRI CASTG 4 cut(s) 399, 768, 880, 969
VpaK11BI GGWCC 2 cut(s) 729, 1024
XspI CTAG 1 cut(s) 6
ZrmI AGTACT 1 cut(s) 1289
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.