MD03G1220800.v1.1

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0006038
Physical Location & Seq
Forward (+)
30474238 .. 30475548
1311 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1220800.v1.1.491

Sequence Viewer

Length: 1023 bp
ATGGAGTCCTTAGGCAGCAAACGTGTTTTGATCGTTCTGGTAATCCTAGTATCCGCTGCTGTTCTGGTACAATGTAAGACAGATCTTAAGGTTTGCTACAGCAAGAAAAGCCCGTGCTTTCTCAAGCAGGTATACTGCCCGAAGGAATGTCCATCCTCTTCACCGACAGACAAAACCGCTAAAATATGTTATCTGAACTGTGACTCACCTATATGCAAAGCTGAGTGCAAAGGTCGCAAGCCTAATTGTGAAGGCCCCGGATCAGCATGCATGGACCCTCGCTTCATCGGTGGAGATGGCATTGTCTTTTACTTCCACGGCAAGAAAAATGAGTATTTCAGCTTAGTTTCTGACCCCAACCTCCAAATCAACGCCCGGTTCATCGGTCTTCGCCCTGAAGGCAGAACCAGGGACTACACTTGGATTCAGGCCCTTGGACTCCTCTTTGACTCTAACAGCTTCTCCCTAGAGGCCAGCCAAGCATCGGCATGGGATAATCAAATCGACCACTTGAAATTTATTTACAATGGAGAGGAGCTAATCATCCCAGAGTCTCAGCTCTCCGTGTGGCAATCTCCGGAAAATGCCATTAGAGTAGAGAGAACATCGAGCAAGAACAGTGTTTTGGTCACTCTCCCGGAAGTTGCTGAAATTTCAGTAAATGTGGTGCCTGTGACAAAGGAAGATGATAGGATCCACAATTATCGGATACCATCAGATGACTGTTTTGCACATCTGGAAGTACAGTTCAGATTCTATGGCTTATCCTCAAACGTTGAGGGAGTGCTTGGAAGGACTTACCAGCCAGATTTCAAGAACCCGGCAAAGCCAGGAGTAGCTATGCCAGTTGTGGGAGGGGAAAACAAGTACAGAACAACATCACTTGTCTCCGCAGATTGCGCTGCTTGTGTTTTCACTAAATCCGGGAAGATGGATCAAACAGATTTAAGGGTGATGGATCACGGAAATCTTGACTGCACTGGTAATTCCTTCGGTGGGAATGGAATAGTTTGCAGGAAGTAA
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

341

Amino Acids

37.57

Weight (kDa)

7.41

Isoelectric Point (pI)

38.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 249 - 305 4.7e-27 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) 118
AccB1I GGYRCC 1 cut(s) 667
AccI GTMKAC 1 cut(s) 132
AccIII TCCGGA 1 cut(s) 577
AciI CCGC 3 cut(s) 54, 177, 891
AclI AACGTT 1 cut(s) 774
AclWI GGATC 5 cut(s) 268, 688, 701, 942, 966
AcsI RAATTY 2 cut(s) 515, 651
AcuI CTGAAG 1 cut(s) 417
AfaI GTAC 3 cut(s) 69, 744, 869
AfiI CCNNNNNNNGG 3 cut(s) 484, 851, 996
AflII CTTAAG 1 cut(s) 86
AflIII ACRYGT 1 cut(s) 22
AgsI TTSAA 2 cut(s) 514, 814
AjnI CCWGG 2 cut(s) 407, 829
AjuI GAANNNNNNNTTGG 2 cut(s) 608, 640
AloI GAACNNNNNNTCC 2 cut(s) 731, 763
AluBI AGCT 6 cut(s) 221, 342, 459, 538, 559, 839
AluI AGCT 6 cut(s) 221, 342, 459, 538, 559, 839
Alw26I GTCTC 2 cut(s) 558, 892
AlwI GGATC 5 cut(s) 268, 688, 701, 942, 966
Aor13HI TCCGGA 1 cut(s) 577
AoxI GGCC 3 cut(s) 253, 429, 471
ApeKI GCWGC 3 cut(s) 15, 56, 902
ApoI RAATTY 2 cut(s) 515, 651
AspLEI GCGC 1 cut(s) 902
AspS9I GGNCC 3 cut(s) 254, 274, 430
AsuC2I CCSGG 5 cut(s) 258, 376, 638, 821, 925
AsuHPI GGTGA 3 cut(s) 153, 198, 964
AvaII GGWCC 1 cut(s) 274
AxyI CCTNAGG 1 cut(s) 10
BamHI GGATCC 1 cut(s) 693
BanI GGYRCC 1 cut(s) 667
BbsI GAAGAC 1 cut(s) 380
BbvI GCAGC 3 cut(s) 27, 43, 889
BccI CCATC 5 cut(s) 160, 290, 721, 925, 949
BceAI ACGGC 1 cut(s) 334
BciT130I CCWGG 2 cut(s) 409, 831
BciVI GTATCC 2 cut(s) 61, 702
BcnI CCSGG 5 cut(s) 258, 376, 638, 821, 925
BcoDI GTCTC 2 cut(s) 558, 892
BfaI CTAG 2 cut(s) 47, 467
BfmI CTRYAG 1 cut(s) 97
BfrI CTTAAG 1 cut(s) 86
BfuAI ACCTGC 1 cut(s) 118
BfuI GTATCC 2 cut(s) 61, 702
BglI GCCNNNNNGGC 1 cut(s) 399
BglII AGATCT 1 cut(s) 82
BisI GCNGC 3 cut(s) 16, 57, 903
BlsI GCNGC 3 cut(s) 17, 58, 904
Bme1390I CCNGG 7 cut(s) 258, 376, 409, 638, 821, 831, 925
Bme18I GGWCC 1 cut(s) 274
BmgT120I GGNCC 3 cut(s) 254, 274, 430
BmiI GGNNCC 4 cut(s) 256, 276, 669, 695
BmrFI CCNGG 7 cut(s) 258, 376, 409, 638, 821, 831, 925
BmsI GCATC 1 cut(s) 491
BpiI GAAGAC 1 cut(s) 380
BpuEI CTTGAG 1 cut(s) 107
BpuMI CCSGG 5 cut(s) 258, 376, 638, 821, 925
BsaJI CCNNGG 4 cut(s) 256, 316, 408, 433
BsaWI WCCGGW 1 cut(s) 577
BsaXI ACNNNNNCTCC 2 cut(s) 446, 476
Bsc4I CCNNNNNNNGG 3 cut(s) 484, 851, 996
Bse1I ACTGG 2 cut(s) 845, 985
Bse21I CCTNAGG 1 cut(s) 10
BseAI TCCGGA 1 cut(s) 577
BseBI CCWGG 2 cut(s) 409, 831
BseDI CCNNGG 4 cut(s) 256, 316, 408, 433
BseGI GGATG 2 cut(s) 152, 543
BseLI CCNNNNNNNGG 3 cut(s) 484, 851, 996
BseMII CTCAG 2 cut(s) 213, 569
BseNI ACTGG 2 cut(s) 845, 985
BseRI GAGGAG 2 cut(s) 431, 548
BseXI GCAGC 3 cut(s) 27, 43, 889
BsgI GTGCAG 1 cut(s) 961
BshFI GGCC 3 cut(s) 255, 431, 473
BshNI GGYRCC 1 cut(s) 667
BsiSI CCGG 6 cut(s) 258, 376, 578, 638, 821, 924
BslFI GGGAC 1 cut(s) 425
BslI CCNNNNNNNGG 3 cut(s) 484, 851, 996
BsmAI GTCTC 2 cut(s) 558, 892
BsmFI GGGAC 1 cut(s) 425
BsnI GGCC 3 cut(s) 255, 431, 473
Bsp13I TCCGGA 1 cut(s) 577
Bsp143I GATC 6 cut(s) 30, 82, 260, 693, 934, 958
BspACI CCGC 3 cut(s) 54, 177, 891
BspANI GGCC 3 cut(s) 255, 431, 473
BspCNI CTCAG 2 cut(s) 214, 568
BspEI TCCGGA 1 cut(s) 577
BspLI GGNNCC 4 cut(s) 256, 276, 669, 695
BspMI ACCTGC 1 cut(s) 118
BspPI GGATC 5 cut(s) 268, 688, 701, 942, 966
BspT107I GGYRCC 1 cut(s) 667
BspTI CTTAAG 1 cut(s) 86
BsrI ACTGG 2 cut(s) 845, 985
BssECI CCNNGG 4 cut(s) 256, 316, 408, 433
BssMI GATC 6 cut(s) 30, 82, 260, 693, 934, 958
BssNAI GTATAC 1 cut(s) 133
BssT1I CCWWGG 1 cut(s) 433
Bst1107I GTATAC 1 cut(s) 133
Bst2UI CCWGG 2 cut(s) 409, 831
Bst4CI ACNGT 4 cut(s) 200, 620, 725, 747
Bst6I CTCTTC 1 cut(s) 163
BstAFI CTTAAG 1 cut(s) 86
BstC8I GCNNGC 3 cut(s) 239, 268, 475
BstDEI CTNAG 4 cut(s) 10, 222, 343, 555
BstDSI CCRYGG 1 cut(s) 316
BstF5I GGATG 2 cut(s) 152, 543
BstHHI GCGC 1 cut(s) 902
BstKTI GATC 6 cut(s) 33, 85, 263, 696, 937, 961
BstMAI GTCTC 2 cut(s) 558, 892
BstMBI GATC 6 cut(s) 30, 82, 260, 693, 934, 958
BstMWI GCNNNNNNNGC 5 cut(s) 108, 234, 399, 479, 899
BstNI CCWGG 2 cut(s) 409, 831
BstNSI RCATGY 1 cut(s) 270
BstSCI CCNGG 7 cut(s) 256, 374, 407, 636, 819, 829, 923
BstSFI CTRYAG 1 cut(s) 97
BstV1I GCAGC 3 cut(s) 27, 43, 889
BstV2I GAAGAC 1 cut(s) 380
BstX2I RGATCY 2 cut(s) 82, 693
BstYI RGATCY 2 cut(s) 82, 693
BstZ17I GTATAC 1 cut(s) 133
Bsu36I CCTNAGG 1 cut(s) 10
BsuI GTATCC 2 cut(s) 61, 702
BsuRI GGCC 3 cut(s) 255, 431, 473
BtgI CCRYGG 1 cut(s) 316
BtsCI GGATG 2 cut(s) 152, 543
BtsIMutI CAGTG 2 cut(s) 625, 978
BveI ACCTGC 1 cut(s) 118
Cac8I GCNNGC 3 cut(s) 239, 268, 475
CfoI GCGC 1 cut(s) 902
Cfr13I GGNCC 3 cut(s) 254, 274, 430
Csp6I GTAC 3 cut(s) 68, 743, 868
CviAII CATG 3 cut(s) 267, 271, 489
CviQI GTAC 3 cut(s) 68, 743, 868
DdeI CTNAG 4 cut(s) 10, 222, 343, 555
DpnI GATC 6 cut(s) 32, 84, 262, 695, 936, 960
DpnII GATC 6 cut(s) 30, 82, 260, 693, 934, 958
Eam1104I CTCTTC 1 cut(s) 163
EarI CTCTTC 1 cut(s) 163
Eco130I CCWWGG 1 cut(s) 433
Eco47I GGWCC 1 cut(s) 274
Eco57I CTGAAG 1 cut(s) 417
Eco81I CCTNAGG 1 cut(s) 10
EcoO109I RGGNCCY 2 cut(s) 254, 430
EcoRII CCWGG 2 cut(s) 407, 829
EcoT14I CCWWGG 1 cut(s) 433
EcoT22I ATGCAT 1 cut(s) 272
ErhI CCWWGG 1 cut(s) 433
FaeI CATG 3 cut(s) 270, 274, 492
FaiI YATR 9 cut(s) 133, 187, 212, 214, 268, 272, 490, 759, 842
FaqI GGGAC 1 cut(s) 425
FatI CATG 3 cut(s) 266, 270, 488
FblI GTMKAC 1 cut(s) 132
Fnu4HI GCNGC 3 cut(s) 16, 57, 903
FokI GGATG 2 cut(s) 139, 530
Fsp4HI GCNGC 3 cut(s) 16, 57, 903
FspBI CTAG 2 cut(s) 47, 467
GlaI GCGC 1 cut(s) 901
GluI GCNGC 3 cut(s) 16, 57, 903
HaeIII GGCC 3 cut(s) 255, 431, 473
HapII CCGG 6 cut(s) 258, 376, 578, 638, 821, 924
HhaI GCGC 1 cut(s) 902
Hin1II CATG 3 cut(s) 270, 274, 492
Hin6I GCGC 1 cut(s) 900
HinP1I GCGC 1 cut(s) 900
HinfI GANTC 7 cut(s) 5, 203, 424, 438, 449, 551, 753
HpaII CCGG 6 cut(s) 258, 376, 578, 638, 821, 924
HphI GGTGA 3 cut(s) 153, 198, 964
Hpy166II GTNNAC 1 cut(s) 133
Hpy188I TCNGA 5 cut(s) 195, 352, 708, 718, 752
Hpy188III TCNNGA 4 cut(s) 578, 737, 814, 971
Hpy8I GTNNAC 1 cut(s) 133
HpyAV CCTTC 5 cut(s) 136, 245, 392, 786, 1000
HpyCH4III ACNGT 4 cut(s) 200, 620, 725, 747
HpyCH4IV ACGT 2 cut(s) 22, 774
HpyCH4V TGCA 6 cut(s) 216, 228, 270, 731, 978, 1014
HpyF10VI GCNNNNNNNGC 5 cut(s) 108, 234, 399, 479, 899
HpyF3I CTNAG 4 cut(s) 10, 222, 343, 555
HpySE526I ACGT 2 cut(s) 22, 774
Hsp92II CATG 3 cut(s) 270, 274, 492
HspAI GCGC 1 cut(s) 900
Kpn2I TCCGGA 1 cut(s) 577
Kzo9I GATC 6 cut(s) 30, 82, 260, 693, 934, 958
LmnI GCTCC 1 cut(s) 535
Lsp1109I GCAGC 3 cut(s) 27, 43, 889
LweI GCATC 1 cut(s) 491
MaeI CTAG 2 cut(s) 47, 467
MaeII ACGT 2 cut(s) 22, 774
MaeIII GTNAC 3 cut(s) 200, 628, 673
MalI GATC 6 cut(s) 32, 84, 262, 695, 936, 960
MboI GATC 6 cut(s) 30, 82, 260, 693, 934, 958
MboII GAAGA 4 cut(s) 150, 380, 695, 940
MflI RGATCY 2 cut(s) 82, 693
MluCI AATT 5 cut(s) 244, 515, 651, 700, 985
MlyI GAGTC 5 cut(s) 14, 197, 432, 443, 560
MnlI CCTC 9 cut(s) 166, 288, 371, 452, 463, 526, 772, 778, 848
Mph1103I ATGCAT 1 cut(s) 272
MroI TCCGGA 1 cut(s) 577
MseI TTAA 2 cut(s) 87, 947
MslI CAYNNNNRTG 2 cut(s) 211, 487
MspA1I CMGCKG 1 cut(s) 56
MspCI CTTAAG 1 cut(s) 86
MspI CCGG 6 cut(s) 258, 376, 578, 638, 821, 924
MspR9I CCNGG 7 cut(s) 258, 376, 409, 638, 821, 831, 925
MvaI CCWGG 2 cut(s) 409, 831
MwoI GCNNNNNNNGC 5 cut(s) 108, 234, 399, 479, 899
NciI CCSGG 5 cut(s) 258, 376, 638, 821, 925
NdeII GATC 6 cut(s) 30, 82, 260, 693, 934, 958
NlaIII CATG 3 cut(s) 270, 274, 492
NlaIV GGNNCC 4 cut(s) 256, 276, 669, 695
NmuCI GTSAC 3 cut(s) 200, 628, 673
NsiI ATGCAT 1 cut(s) 272
NspI RCATGY 1 cut(s) 270
PaeI GCATGC 1 cut(s) 270
PfeI GAWTC 2 cut(s) 424, 753
PfoI TCCNGGA 2 cut(s) 636, 923
PkrI GCNGC 3 cut(s) 17, 58, 904
PleI GAGTC 5 cut(s) 13, 197, 432, 443, 559
PpsI GAGTC 5 cut(s) 13, 197, 432, 443, 559
Psp1406I AACGTT 1 cut(s) 774
Psp6I CCWGG 2 cut(s) 407, 829
PspGI CCWGG 2 cut(s) 407, 829
PspN4I GGNNCC 4 cut(s) 256, 276, 669, 695
PspPI GGNCC 3 cut(s) 254, 274, 430
PsuI RGATCY 2 cut(s) 82, 693
RsaI GTAC 3 cut(s) 69, 744, 869
RsaNI GTAC 3 cut(s) 68, 743, 868
RseI CAYNNNNRTG 2 cut(s) 211, 487
SaqAI TTAA 2 cut(s) 87, 947
SatI GCNGC 3 cut(s) 16, 57, 903
Sau3AI GATC 6 cut(s) 30, 82, 260, 693, 934, 958
Sau96I GGNCC 3 cut(s) 254, 274, 430
SchI GAGTC 5 cut(s) 14, 197, 432, 443, 560
ScrFI CCNGG 7 cut(s) 258, 376, 409, 638, 821, 831, 925
SfaNI GCATC 1 cut(s) 491
SfcI CTRYAG 1 cut(s) 97
SinI GGWCC 1 cut(s) 274
SmiMI CAYNNNNRTG 2 cut(s) 211, 487
SmlI CTYRAG 2 cut(s) 86, 122
SmoI CTYRAG 2 cut(s) 86, 122
SphI GCATGC 1 cut(s) 270
Sse9I AATT 5 cut(s) 244, 515, 651, 700, 985
SsiI CCGC 3 cut(s) 54, 177, 891
SspMI CTAG 2 cut(s) 47, 467
StyD4I CCNGG 7 cut(s) 256, 374, 407, 636, 819, 829, 923
StyI CCWWGG 1 cut(s) 433
TaaI ACNGT 4 cut(s) 200, 620, 725, 747
TaiI ACGT 2 cut(s) 25, 777
TaqI TCGA 2 cut(s) 504, 608
TaqII GACCGA 1 cut(s) 374
TasI AATT 5 cut(s) 244, 515, 651, 700, 985
TatI WGTACW 2 cut(s) 742, 867
TfiI GAWTC 2 cut(s) 424, 753
Tru1I TTAA 2 cut(s) 87, 947
Tru9I TTAA 2 cut(s) 87, 947
TscAI CASTG 2 cut(s) 625, 985
TseFI GTSAC 3 cut(s) 200, 628, 673
TseI GCWGC 3 cut(s) 15, 56, 902
Tsp45I GTSAC 3 cut(s) 200, 628, 673
TspDTI ATGAA 2 cut(s) 274, 370
TspGWI ACGGA 2 cut(s) 553, 978
TspRI CASTG 2 cut(s) 625, 985
Vha464I CTTAAG 1 cut(s) 86
VpaK11BI GGWCC 1 cut(s) 274
XapI RAATTY 2 cut(s) 515, 651
XceI RCATGY 1 cut(s) 270
XmiI GTMKAC 1 cut(s) 132
XspI CTAG 2 cut(s) 47, 467
Zsp2I ATGCAT 1 cut(s) 272
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.