MD03G1221200.v1.1

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0006038
Physical Location & Seq
Forward (+)
30495329 .. 30496742
1414 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1221200.v1.1.491

Sequence Viewer

Length: 1272 bp
ATGGTTTTCTTAGGTAGCAAAAGGGTTTTGATCCTTCTGGTAGTCCTTGTATCTGCTGCTGTTCTGGTGCAGAGTATGCAACCTCCAAACCGTAACCAACCTTTGAAACCTTCAGACGCAAATCAACCTCTGAATCCTCCAAATAGTAAGCAACCTCTGAATGCTCCAAATGGTAAGCAACCTCTGAATCCTTTAGACGGTAATCAACCTCTGAATCCTCCACATGGTAATCAACCTTTGAATCCTCCAAATGCTAAGCAACCTCCAAATCCTCCAAACGCTAAGCAACCTCCAAATCCTCCAAATCCTCCAAATGCTAACCATCCCCCAGATGTTAAAGTTTGCTCTGGCAAGAAAAGTCCGTGCTTTGGGAAGCAAGTACATTGCCCAAAGGAATGTCCATCCACTTCACCGACAGACAAAATGGCTAAAATGTGCTATCTCAACTGTGACTCTCCTATATGCAAAGCTGAGTGCAAAAGTCCCAAGCCCAACTGCAAAGGCCCTGGATCAGCATGCCTGGACCCTCGCTTCATTGGTGGAGACGGCGTTGTCTTTTACTTCCATGGCAAGAAAAATGAGTACTTCAACTTAGTTTCTGATCCCAACCTCCAAATCAACTCCCGCTTCATTGGTGTGCGCCCTGAAGGCCGAACCAGGGACAACACTTGGATTCAGGCCCTTGGACTCCTCTTTGACTCTAACAGCTTCTCCCTAGAGGCCAGCAAAGCATCAGTATGGGATGATGAAATCGACCACTTGAAATTCACTTACAATGGAGAGGAGCTAGTCATCCCAGAATACCATCTCTCCGCGTGGGAATCTCCGGAATATGACATTATAGTGAAGAGAACATCGAGCAAGAACAGTGTTCTGGTCACTCTCCCGGAAGTTGCTGAAATTTCAGTAAATGTGGTTCCTGTGACAAAGGAAGATGATAGGATCCACAATTATCAGATACCGTCAGATGACTGTTTTGCTCACCTGGAAGTACAGTTCAGATTCTATGACTTATCCTCAAACGTTGAAGGAGTGCTCGGAAGGACTTACCAGCCAGATTTCAAGAACCCGGCAAAGCCAGGAGTAGCTATGCCAGTGGTGGGAGGTGAAGACAAGTACAGAACAACATCACTCTTCTCTGCAGATTGCACTGCTTGTGTTTTCACTCAACCCGGTAAGCTGGATCAGACAGATTCAAGGCTGATGGATTACGGAATGCTTGACTGCACTGGTAATTCCTTCGGTGGGAATGGAATAGTTTGCAGGAAATAA
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

424

Amino Acids

46.44

Weight (kDa)

7.03

Isoelectric Point (pI)

46.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 332 - 388 4.6e-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)
AasI GACNNNNNNGTC 1 cut(s) 551
AccII CGCG 1 cut(s) 815
AccIII TCCGGA 1 cut(s) 826
AciI CCGC 2 cut(s) 625, 813
AclI AACGTT 1 cut(s) 1023
AclWI GGATC 6 cut(s) 25, 517, 596, 937, 950, 1191
AcsI RAATTY 2 cut(s) 764, 900
AcuI CTGAAG 2 cut(s) 96, 666
AfaI GTAC 4 cut(s) 381, 584, 993, 1118
AfiI CCNNNNNNNGG 6 cut(s) 197, 224, 368, 658, 1100, 1245
AgsI TTSAA 7 cut(s) 106, 241, 589, 763, 1028, 1063, 1197
AjnI CCWGG 5 cut(s) 505, 519, 656, 984, 1078
AloI GAACNNNNNNTCC 2 cut(s) 980, 1012
AluBI AGCT 5 cut(s) 470, 708, 787, 1088, 1180
AluI AGCT 5 cut(s) 470, 708, 787, 1088, 1180
Alw21I GWGCWC 1 cut(s) 1038
Alw26I GTCTC 1 cut(s) 537
AlwI GGATC 6 cut(s) 25, 517, 596, 937, 950, 1191
Aor13HI TCCGGA 1 cut(s) 826
AoxI GGCC 4 cut(s) 502, 649, 678, 720
ApeKI GCWGC 1 cut(s) 56
ApoI RAATTY 2 cut(s) 764, 900
AspLEI GCGC 1 cut(s) 642
AspS9I GGNCC 3 cut(s) 503, 523, 679
AsuC2I CCSGG 3 cut(s) 887, 1070, 1173
AsuHPI GGTGA 3 cut(s) 402, 974, 1118
AvaII GGWCC 1 cut(s) 523
BamHI GGATCC 1 cut(s) 942
BbsI GAAGAC 1 cut(s) 1116
Bbv12I GWGCWC 1 cut(s) 1038
BbvI GCAGC 1 cut(s) 43
BccI CCATC 4 cut(s) 330, 409, 813, 1198
BceAI ACGGC 1 cut(s) 562
BciT130I CCWGG 5 cut(s) 507, 521, 658, 986, 1080
BcnI CCSGG 3 cut(s) 887, 1070, 1173
BcoDI GTCTC 1 cut(s) 537
BfaI CTAG 2 cut(s) 716, 788
BfmI CTRYAG 1 cut(s) 1140
BglI GCCNNNNNGGC 1 cut(s) 648
BisI GCNGC 1 cut(s) 57
BlpI GCTNAGC 2 cut(s) 255, 282
BlsI GCNGC 1 cut(s) 58
BmcAI AGTACT 1 cut(s) 584
Bme1390I CCNGG 8 cut(s) 507, 521, 658, 887, 986, 1070, 1080, 1173
Bme18I GGWCC 1 cut(s) 523
BmgT120I GGNCC 3 cut(s) 503, 523, 679
BmiI GGNNCC 3 cut(s) 525, 918, 944
BmrFI CCNGG 8 cut(s) 507, 521, 658, 887, 986, 1070, 1080, 1173
BmsI GCATC 1 cut(s) 740
BpiI GAAGAC 1 cut(s) 1116
Bpu1102I GCTNAGC 2 cut(s) 255, 282
BpuMI CCSGG 3 cut(s) 887, 1070, 1173
BsaJI CCNNGG 4 cut(s) 505, 565, 657, 682
BsaWI WCCGGW 1 cut(s) 826
BsaXI ACNNNNNCTCC 6 cut(s) 534, 564, 695, 725, 794, 824
Bsc4I CCNNNNNNNGG 6 cut(s) 197, 224, 368, 658, 1100, 1245
Bse1I ACTGG 2 cut(s) 1094, 1234
Bse3DI GCAATG 1 cut(s) 382
BseAI TCCGGA 1 cut(s) 826
BseBI CCWGG 5 cut(s) 507, 521, 658, 986, 1080
BseDI CCNNGG 4 cut(s) 505, 565, 657, 682
BseGI GGATG 4 cut(s) 322, 401, 748, 792
BseLI CCNNNNNNNGG 6 cut(s) 197, 224, 368, 658, 1100, 1245
BseMI GCAATG 1 cut(s) 382
BseMII CTCAG 1 cut(s) 462
BseNI ACTGG 2 cut(s) 1094, 1234
BseRI GAGGAG 2 cut(s) 680, 797
BseXI GCAGC 1 cut(s) 43
BsgI GTGCAG 2 cut(s) 89, 1210
Bsh1236I CGCG 1 cut(s) 815
BshFI GGCC 4 cut(s) 504, 651, 680, 722
BsiHKAI GWGCWC 1 cut(s) 1038
BsiSI CCGG 4 cut(s) 827, 887, 1070, 1173
BslFI GGGAC 2 cut(s) 468, 674
BslI CCNNNNNNNGG 6 cut(s) 197, 224, 368, 658, 1100, 1245
BsmAI GTCTC 1 cut(s) 537
BsmBI CGTCTC 1 cut(s) 537
BsmFI GGGAC 2 cut(s) 468, 674
BsmI GAATGC 2 cut(s) 166, 1221
BsnI GGCC 4 cut(s) 504, 651, 680, 722
Bsp1286I GDGCHC 1 cut(s) 1038
Bsp13I TCCGGA 1 cut(s) 826
Bsp143I GATC 5 cut(s) 30, 509, 601, 942, 1183
Bsp1720I GCTNAGC 2 cut(s) 255, 282
Bsp19I CCATGG 1 cut(s) 565
BspACI CCGC 2 cut(s) 625, 813
BspANI GGCC 4 cut(s) 504, 651, 680, 722
BspCNI CTCAG 1 cut(s) 463
BspEI TCCGGA 1 cut(s) 826
BspFNI CGCG 1 cut(s) 815
BspLI GGNNCC 3 cut(s) 525, 918, 944
BspMAI CTGCAG 1 cut(s) 1144
BspPI GGATC 6 cut(s) 25, 517, 596, 937, 950, 1191
BsrDI GCAATG 1 cut(s) 382
BsrI ACTGG 2 cut(s) 1094, 1234
BssECI CCNNGG 4 cut(s) 505, 565, 657, 682
BssMI GATC 5 cut(s) 30, 509, 601, 942, 1183
BssT1I CCWWGG 2 cut(s) 565, 682
Bst2UI CCWGG 5 cut(s) 507, 521, 658, 986, 1080
Bst4CI ACNGT 7 cut(s) 92, 200, 449, 869, 963, 974, 996
Bst6I CTCTTC 2 cut(s) 842, 1139
BstAPI GCANNNNNTGC 1 cut(s) 76
BstC8I GCNNGC 2 cut(s) 517, 724
BstDEI CTNAG 5 cut(s) 10, 255, 282, 471, 592
BstDSI CCRYGG 1 cut(s) 565
BstF5I GGATG 4 cut(s) 322, 401, 748, 792
BstFNI CGCG 1 cut(s) 815
BstHHI GCGC 1 cut(s) 642
BstKTI GATC 5 cut(s) 33, 512, 604, 945, 1186
BstMAI GTCTC 1 cut(s) 537
BstMBI GATC 5 cut(s) 30, 509, 601, 942, 1183
BstMWI GCNNNNNNNGC 3 cut(s) 76, 648, 728
BstNI CCWGG 5 cut(s) 507, 521, 658, 986, 1080
BstNSI RCATGY 1 cut(s) 519
BstSCI CCNGG 8 cut(s) 505, 519, 656, 885, 984, 1068, 1078, 1171
BstSFI CTRYAG 1 cut(s) 1140
BstUI CGCG 1 cut(s) 815
BstV1I GCAGC 1 cut(s) 43
BstV2I GAAGAC 1 cut(s) 1116
BstX2I RGATCY 1 cut(s) 942
BstYI RGATCY 1 cut(s) 942
BsuRI GGCC 4 cut(s) 504, 651, 680, 722
BtgI CCRYGG 1 cut(s) 565
BtsCI GGATG 4 cut(s) 322, 401, 748, 792
BtsI GCAGTG 1 cut(s) 1149
BtsIMutI CAGTG 4 cut(s) 874, 1101, 1149, 1227
Cac8I GCNNGC 2 cut(s) 517, 724
CfoI GCGC 1 cut(s) 642
Cfr13I GGNCC 3 cut(s) 503, 523, 679
CseI GACGC 1 cut(s) 125
Csp6I GTAC 4 cut(s) 380, 583, 992, 1117
CviAII CATG 3 cut(s) 224, 516, 566
CviQI GTAC 4 cut(s) 380, 583, 992, 1117
DdeI CTNAG 5 cut(s) 10, 255, 282, 471, 592
DpnI GATC 5 cut(s) 32, 511, 603, 944, 1185
DpnII GATC 5 cut(s) 30, 509, 601, 942, 1183
DrdI GACNNNNNNGTC 1 cut(s) 551
DseDI GACNNNNNNGTC 1 cut(s) 551
Eam1104I CTCTTC 2 cut(s) 842, 1139
EarI CTCTTC 2 cut(s) 842, 1139
Eco130I CCWWGG 2 cut(s) 565, 682
Eco47I GGWCC 1 cut(s) 523
Eco57I CTGAAG 2 cut(s) 96, 666
EcoO109I RGGNCCY 2 cut(s) 503, 679
EcoRII CCWGG 5 cut(s) 505, 519, 656, 984, 1078
EcoT14I CCWWGG 2 cut(s) 565, 682
ErhI CCWWGG 2 cut(s) 565, 682
Esp3I CGTCTC 1 cut(s) 537
FaeI CATG 3 cut(s) 227, 519, 569
FaqI GGGAC 2 cut(s) 468, 674
FatI CATG 3 cut(s) 223, 515, 565
FauI CCCGC 1 cut(s) 632
Fnu4HI GCNGC 1 cut(s) 57
FokI GGATG 4 cut(s) 309, 388, 755, 779
Fsp4HI GCNGC 1 cut(s) 57
FspBI CTAG 2 cut(s) 716, 788
GlaI GCGC 1 cut(s) 641
GluI GCNGC 1 cut(s) 57
HaeIII GGCC 4 cut(s) 504, 651, 680, 722
HapII CCGG 4 cut(s) 827, 887, 1070, 1173
HgaI GACGC 1 cut(s) 125
HhaI GCGC 1 cut(s) 642
Hin1II CATG 3 cut(s) 227, 519, 569
Hin6I GCGC 1 cut(s) 640
HinP1I GCGC 1 cut(s) 640
HpaII CCGG 4 cut(s) 827, 887, 1070, 1173
HphI GGTGA 3 cut(s) 402, 974, 1118
Hpy188III TCNNGA 2 cut(s) 827, 1063
HpyAV CCTTC 6 cut(s) 44, 120, 641, 1022, 1035, 1249
HpyCH4III ACNGT 7 cut(s) 92, 200, 449, 869, 963, 974, 996
HpyCH4IV ACGT 1 cut(s) 1023
HpyCH4V TGCA 9 cut(s) 70, 79, 465, 477, 498, 1142, 1149, 1227, 1263
HpyF10VI GCNNNNNNNGC 3 cut(s) 76, 648, 728
HpyF3I CTNAG 5 cut(s) 10, 255, 282, 471, 592
HpySE526I ACGT 1 cut(s) 1023
Hsp92II CATG 3 cut(s) 227, 519, 569
HspAI GCGC 1 cut(s) 640
Kpn2I TCCGGA 1 cut(s) 826
Kzo9I GATC 5 cut(s) 30, 509, 601, 942, 1183
LmnI GCTCC 2 cut(s) 169, 784
Lsp1109I GCAGC 1 cut(s) 43
LweI GCATC 1 cut(s) 740
MaeI CTAG 2 cut(s) 716, 788
MaeII ACGT 1 cut(s) 1023
MaeIII GTNAC 4 cut(s) 92, 449, 877, 922
MalI GATC 5 cut(s) 32, 511, 603, 944, 1185
MboI GATC 5 cut(s) 30, 509, 601, 942, 1183
MboII GAAGA 4 cut(s) 859, 944, 1121, 1126
MflI RGATCY 1 cut(s) 942
MhlI GDGCHC 1 cut(s) 1038
MluCI AATT 4 cut(s) 764, 900, 949, 1234
MlyI GAGTC 3 cut(s) 446, 681, 692
MroI TCCGGA 1 cut(s) 826
MseI TTAA 1 cut(s) 336
MslI CAYNNNNRTG 3 cut(s) 635, 736, 842
MspI CCGG 4 cut(s) 827, 887, 1070, 1173
MspR9I CCNGG 8 cut(s) 507, 521, 658, 887, 986, 1070, 1080, 1173
Mva1269I GAATGC 2 cut(s) 166, 1221
MvaI CCWGG 5 cut(s) 507, 521, 658, 986, 1080
MvnI CGCG 1 cut(s) 815
MwoI GCNNNNNNNGC 3 cut(s) 76, 648, 728
NciI CCSGG 3 cut(s) 887, 1070, 1173
NcoI CCATGG 1 cut(s) 565
NdeII GATC 5 cut(s) 30, 509, 601, 942, 1183
NlaIII CATG 3 cut(s) 227, 519, 569
NlaIV GGNNCC 3 cut(s) 525, 918, 944
NmuCI GTSAC 3 cut(s) 449, 877, 922
NspI RCATGY 1 cut(s) 519
PaeI GCATGC 1 cut(s) 519
PctI GAATGC 2 cut(s) 166, 1221
PfeI GAWTC 8 cut(s) 133, 187, 214, 241, 673, 821, 1002, 1193
PfoI TCCNGGA 1 cut(s) 885
PkrI GCNGC 1 cut(s) 58
PleI GAGTC 3 cut(s) 446, 681, 692
PpsI GAGTC 3 cut(s) 446, 681, 692
Psp1406I AACGTT 1 cut(s) 1023
Psp6I CCWGG 5 cut(s) 505, 519, 656, 984, 1078
PspGI CCWGG 5 cut(s) 505, 519, 656, 984, 1078
PspN4I GGNNCC 3 cut(s) 525, 918, 944
PspPI GGNCC 3 cut(s) 503, 523, 679
PsrI GAACNNNNNNTAC 2 cut(s) 900, 932
PstI CTGCAG 1 cut(s) 1144
PsuI RGATCY 1 cut(s) 942
RsaI GTAC 4 cut(s) 381, 584, 993, 1118
RsaNI GTAC 4 cut(s) 380, 583, 992, 1117
RseI CAYNNNNRTG 3 cut(s) 635, 736, 842
SaqAI TTAA 1 cut(s) 336
SatI GCNGC 1 cut(s) 57
Sau3AI GATC 5 cut(s) 30, 509, 601, 942, 1183
Sau96I GGNCC 3 cut(s) 503, 523, 679
ScaI AGTACT 1 cut(s) 584
SchI GAGTC 3 cut(s) 446, 681, 692
ScrFI CCNGG 8 cut(s) 507, 521, 658, 887, 986, 1070, 1080, 1173
SduI GDGCHC 1 cut(s) 1038
SfaNI GCATC 1 cut(s) 740
SfcI CTRYAG 1 cut(s) 1140
SinI GGWCC 1 cut(s) 523
SmiMI CAYNNNNRTG 3 cut(s) 635, 736, 842
SphI GCATGC 1 cut(s) 519
Sse9I AATT 4 cut(s) 764, 900, 949, 1234
SsiI CCGC 2 cut(s) 625, 813
SspMI CTAG 2 cut(s) 716, 788
StyD4I CCNGG 8 cut(s) 505, 519, 656, 885, 984, 1068, 1078, 1171
StyI CCWWGG 2 cut(s) 565, 682
TaaI ACNGT 7 cut(s) 92, 200, 449, 869, 963, 974, 996
TaiI ACGT 1 cut(s) 1026
TaqI TCGA 2 cut(s) 753, 857
TasI AATT 4 cut(s) 764, 900, 949, 1234
TatI WGTACW 4 cut(s) 379, 582, 991, 1116
TfiI GAWTC 8 cut(s) 133, 187, 214, 241, 673, 821, 1002, 1193
Tru1I TTAA 1 cut(s) 336
Tru9I TTAA 1 cut(s) 336
TscAI CASTG 4 cut(s) 874, 1101, 1156, 1234
TseFI GTSAC 3 cut(s) 449, 877, 922
TseI GCWGC 1 cut(s) 56
Tsp45I GTSAC 3 cut(s) 449, 877, 922
TspDTI ATGAA 3 cut(s) 523, 619, 762
TspGWI ACGGA 2 cut(s) 351, 1227
TspRI CASTG 4 cut(s) 874, 1101, 1156, 1234
VpaK11BI GGWCC 1 cut(s) 523
XapI RAATTY 2 cut(s) 764, 900
XceI RCATGY 1 cut(s) 519
XspI CTAG 2 cut(s) 716, 788
ZrmI AGTACT 1 cut(s) 584
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.