MD05G1087500.v1.1

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr05
OG0002618
Physical Location & Seq
Reverse (-)
18720086 .. 18722122
2037 bp
Loading structure...
UTR
Exon/CDS
Intron
MD05G1087500.v1.1.491

Sequence Viewer

Length: 1737 bp
ATGGCTCACTACAAAATGCAAGTTCTTGTTCCGATTCTCCTGCTGATGATTACGGCAGTGGTAGAGGCGAAAACCCCTCCAGGAATTGCCAAGAATCCAAGCAATGCAAGGTGTTTGATAAAAAAGTATAAGCATTGTTACAATTTGGTGCATGTATGCCCCAAGTTTTGCCCAAATCAATGCACAGTGGAGTGTGTCTCTTGTAAGCCCATCTGTTCTGGGGGCTCAAGCCCTCCACCAGCCTCTCCCACCCCTCCCACACCTTCACCTACACCTCCAACTAAAACTCCCACACCACCAACATATTATTCGCCTCCTCCTCCGACAACTAGCCCAACTCCACCGTTATCTCCTCCAACTACCCCAACTATAACTCCCACACCACCAACATATTATTCGCCTCCTCCACTAAAAACTAACCCAACTCCACCAGTTTCTCCTCCTACTCCATCAACCCCAACACCCCCAACTACAACTCCTACACCACCAACTAAAACTCCCACACCACCAACATATTCGCCTCCTCCACCAAAAACTAACCCAACTCGACCACTATCTCCTCCTACTCCAACAACCCCAACACCCCCAACTACAACTCCTACACCACCAACTACAACTCCCACACCTCCATCCACCGCTCCAACACCTCAAGCAACACCTCCTTCACCTTCACCACGACAAGCGACACCAAATTACCCTCCTCCTACCCCTTCCCCATCTTCGCCGTCACCTCCTTCACCACCATCATCTAATCCTCCTTCCTCTCCTTCACCCCCAACGCCGTCTCCATCTACATCCTCTTCTCCTCCTCCATCAACTCCTACTTCACCAAAGAAGGCCAAGTGCAAGAACAAGAACTACCCTCAATGTTACAACATTCAACATGTATGCCCTACGGCTTGCTCTGGTGGATGTGAGGTTGACTGTGTCACTTGCAAGCCAGTCTGCAAATGTGATCAGCCAGGAGCAGTATGCCAAGACCCCCGTTTTATAGGTGGAGATGGCATCACCTTTTACTTCCACGGCAAGAAAGACCATGATTTCTGCCTCTTGTCCGACTCCAACCTCCACATCAACGCTCACTTCATTGGCAGGCGCAACCACAACATGAAGAGGGACTTCACTTGGGTCCATTCCATTGCCATTCTTTTTGGCAAACACCAACTCTTCATCGGTGCCCAAAAGACCGCTATATGGGACGATGCCACTGACCGCCTTGCCCTCTCCTTTGATGGCGTGCCCATCACCCTTCCCGAATCCGAAGGTGCCAGGTGGCAATCCACAAGTGTTCCGACTGTGTCCCTTGGAAGGGTGAGTGGGACCAACAATGTAATGGTTGAAGTTGAAGGAAGCTTCAGGATCACAGCCAAGGTTGTGCCTATAACTGAACAAGACTCAAGGGTTCACAACTATGGAATTACCAAAGATGATACATTTGCACATCTTGATCTTGGGTTTAAGTTCTTCTCTTTGAGCGACCAAGTGAGTGGTGTGTTGGGACAAACATATAGGCCTGACTACATCAGCCGGGTCAATATCGGCGCGAGCATGCCTCTGATGGGAGGGGACAAGGAGTTTGAAACTTCAAGCCTTCTAACCACTGATTGTGCCGCTGCAAGGTTTAGTGGTGGCAATGTTGGCTCTGAAAGCGAAGCTAATTCTTTGGAGGATTTGGAGTTGCCAAGCGTGAGCTGTGCAAGCGGGATGGATGGTCGAGGAGTTGTGTGCAAGAGATAG
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

579

Amino Acids

61.31

Weight (kDa)

8.67

Isoelectric Point (pI)

66.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 485 - 541 3.1e-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)
AccB1I GGYRCC 2 cut(s) 1175, 1265
AccBSI CCGCTC 1 cut(s) 638
AccII CGCG 1 cut(s) 1544
AciI CCGC 5 cut(s) 636, 1188, 1213, 1611, 1701
AclWI GGATC 1 cut(s) 1367
AcuI CTGAAG 1 cut(s) 1339
AfiI CCNNNNNNNGG 5 cut(s) 1194, 1308, 1309, 1559, 1617
AflIII ACRYGT 1 cut(s) 883
AgsI TTSAA 5 cut(s) 881, 1340, 1346, 1580, 1587
AjnI CCWGG 3 cut(s) 79, 961, 1268
AjuI GAANNNNNNNTTGG 4 cut(s) 292, 324, 379, 411
AluBI AGCT 3 cut(s) 1353, 1655, 1692
AluI AGCT 3 cut(s) 1353, 1655, 1692
Alw26I GTCTC 2 cut(s) 202, 789
AlwI GGATC 1 cut(s) 1367
AoxI GGCC 2 cut(s) 837, 1511
ApeKI GCWGC 1 cut(s) 1613
ArsI GACNNNNNNTTYG 2 cut(s) 1559, 1591
AspLEI GCGC 2 cut(s) 1098, 1544
AspS9I GGNCC 2 cut(s) 1129, 1320
AsuC2I CCSGG 1 cut(s) 1529
AvaII GGWCC 2 cut(s) 1129, 1320
BaeGI GKGCMC 2 cut(s) 1180, 1242
BanI GGYRCC 2 cut(s) 1175, 1265
BanII GRGCYC 1 cut(s) 227
BbvI GCAGC 1 cut(s) 1600
BceAI ACGGC 5 cut(s) 69, 709, 766, 912, 1039
BcgI CGANNNNNNTGC 2 cut(s) 22, 56
BciT130I CCWGG 3 cut(s) 81, 963, 1270
BclI TGATCA 1 cut(s) 955
BcnI CCSGG 1 cut(s) 1529
BcoDI GTCTC 2 cut(s) 202, 789
BfaI CTAG 1 cut(s) 330
BisI GCNGC 2 cut(s) 1611, 1614
BlsI GCNGC 2 cut(s) 1612, 1615
Bme1390I CCNGG 4 cut(s) 81, 963, 1270, 1529
Bme18I GGWCC 2 cut(s) 1129, 1320
BmgT120I GGNCC 2 cut(s) 1129, 1320
BmiI GGNNCC 4 cut(s) 1130, 1177, 1267, 1321
BmrFI CCNGG 4 cut(s) 81, 963, 1270, 1529
BmsI GCATC 2 cut(s) 1014, 1192
BplI GAGNNNNNCTC 4 cut(s) 182, 214, 1537, 1569
BpmI CTGGAG 1 cut(s) 63
BpuEI CTTGAG 3 cut(s) 211, 633, 1381
BpuMI CCSGG 1 cut(s) 1529
BsaJI CCNNGG 3 cut(s) 1021, 1303, 1368
Bsc4I CCNNNNNNNGG 5 cut(s) 1194, 1308, 1309, 1559, 1617
Bse1I ACTGG 2 cut(s) 431, 941
Bse3DI GCAATG 3 cut(s) 109, 1137, 1639
BseBI CCWGG 3 cut(s) 81, 963, 1270
BseDI CCNNGG 3 cut(s) 1021, 1303, 1368
BseGI GGATG 5 cut(s) 629, 794, 917, 1710, 1714
BseLI CCNNNNNNNGG 5 cut(s) 1194, 1308, 1309, 1559, 1617
BseMI GCAATG 3 cut(s) 109, 1137, 1639
BseNI ACTGG 2 cut(s) 431, 941
BseSI GKGCMC 2 cut(s) 1180, 1242
BseXI GCAGC 1 cut(s) 1600
Bsh1236I CGCG 1 cut(s) 1544
BshFI GGCC 2 cut(s) 839, 1513
BshNI GGYRCC 2 cut(s) 1175, 1265
BsiSI CCGG 1 cut(s) 1528
BslFI GGGAC 6 cut(s) 1130, 1211, 1285, 1333, 1512, 1580
BslI CCNNNNNNNGG 5 cut(s) 1194, 1308, 1309, 1559, 1617
BsmAI GTCTC 2 cut(s) 202, 789
BsmBI CGTCTC 1 cut(s) 789
BsmFI GGGAC 6 cut(s) 1130, 1211, 1285, 1333, 1512, 1580
BsnI GGCC 2 cut(s) 839, 1513
Bsp1286I GDGCHC 3 cut(s) 227, 1180, 1242
Bsp143I GATC 3 cut(s) 955, 1359, 1447
BspACI CCGC 5 cut(s) 636, 1188, 1213, 1611, 1701
BspANI GGCC 2 cut(s) 839, 1513
BspFNI CGCG 1 cut(s) 1544
BspLI GGNNCC 4 cut(s) 1130, 1177, 1267, 1321
BspPI GGATC 1 cut(s) 1367
BspT107I GGYRCC 2 cut(s) 1175, 1265
BsrBI CCGCTC 1 cut(s) 638
BsrDI GCAATG 3 cut(s) 109, 1137, 1639
BsrI ACTGG 2 cut(s) 431, 941
BssECI CCNNGG 3 cut(s) 1021, 1303, 1368
BssMI GATC 3 cut(s) 955, 1359, 1447
BssT1I CCWWGG 2 cut(s) 1303, 1368
Bst2UI CCWGG 3 cut(s) 81, 963, 1270
Bst4CI ACNGT 4 cut(s) 187, 345, 926, 1297
Bst6I CTCTTC 3 cut(s) 805, 1106, 1172
BstC8I GCNNGC 7 cut(s) 901, 938, 1094, 1238, 1546, 1550, 1699
BstDSI CCRYGG 1 cut(s) 1021
BstF5I GGATG 5 cut(s) 629, 794, 917, 1710, 1714
BstFNI CGCG 1 cut(s) 1544
BstHHI GCGC 2 cut(s) 1098, 1544
BstKTI GATC 3 cut(s) 958, 1362, 1450
BstMAI GTCTC 2 cut(s) 202, 789
BstMBI GATC 3 cut(s) 955, 1359, 1447
BstMWI GCNNNNNNNGC 3 cut(s) 1638, 1647, 1698
BstNI CCWGG 3 cut(s) 81, 963, 1270
BstNSI RCATGY 3 cut(s) 155, 887, 1552
BstSCI CCNGG 4 cut(s) 79, 961, 1268, 1527
BstSLI GKGCMC 2 cut(s) 1180, 1242
BstUI CGCG 1 cut(s) 1544
BstV1I GCAGC 1 cut(s) 1600
BstXI CCANNNNNNTGG 1 cut(s) 1487
BsuRI GGCC 2 cut(s) 839, 1513
BtgI CCRYGG 1 cut(s) 1021
BtsCI GGATG 5 cut(s) 629, 794, 917, 1710, 1714
BtsI GCAGTG 1 cut(s) 63
BtsIMutI CAGTG 4 cut(s) 63, 192, 1206, 1599
Cac8I GCNNGC 7 cut(s) 901, 938, 1094, 1238, 1546, 1550, 1699
CfoI GCGC 2 cut(s) 1098, 1544
Cfr13I GGNCC 2 cut(s) 1129, 1320
CviAII CATG 5 cut(s) 152, 884, 1037, 1108, 1549
DpnI GATC 3 cut(s) 957, 1361, 1449
DpnII GATC 3 cut(s) 955, 1359, 1447
Eam1104I CTCTTC 3 cut(s) 805, 1106, 1172
EarI CTCTTC 3 cut(s) 805, 1106, 1172
Eco130I CCWWGG 2 cut(s) 1303, 1368
Eco147I AGGCCT 1 cut(s) 1513
Eco24I GRGCYC 1 cut(s) 227
Eco47I GGWCC 2 cut(s) 1129, 1320
Eco57I CTGAAG 1 cut(s) 1339
EcoRII CCWGG 3 cut(s) 79, 961, 1268
EcoT14I CCWWGG 2 cut(s) 1303, 1368
EcoT38I GRGCYC 1 cut(s) 227
ErhI CCWWGG 2 cut(s) 1303, 1368
Esp3I CGTCTC 1 cut(s) 789
FaeI CATG 5 cut(s) 155, 887, 1040, 1111, 1552
FalI AAGNNNNNCTT 2 cut(s) 1103, 1135
FaqI GGGAC 6 cut(s) 1130, 1211, 1285, 1333, 1512, 1580
FatI CATG 5 cut(s) 151, 883, 1036, 1107, 1548
FauI CCCGC 1 cut(s) 1694
FbaI TGATCA 1 cut(s) 955
Fnu4HI GCNGC 2 cut(s) 1611, 1614
FokI GGATG 5 cut(s) 616, 781, 924, 1717, 1721
FriOI GRGCYC 1 cut(s) 227
Fsp4HI GCNGC 2 cut(s) 1611, 1614
FspBI CTAG 1 cut(s) 330
GlaI GCGC 2 cut(s) 1097, 1543
GluI GCNGC 2 cut(s) 1611, 1614
GsuI CTGGAG 1 cut(s) 63
HaeIII GGCC 2 cut(s) 839, 1513
HapII CCGG 1 cut(s) 1528
HhaI GCGC 2 cut(s) 1098, 1544
Hin1II CATG 5 cut(s) 155, 887, 1040, 1111, 1552
Hin6I GCGC 2 cut(s) 1096, 1542
HinP1I GCGC 2 cut(s) 1096, 1542
HincII GTYRAC 1 cut(s) 922
HindII GTYRAC 1 cut(s) 922
HindIII AAGCTT 1 cut(s) 1351
HinfI GANTC 5 cut(s) 34, 94, 1058, 1256, 1394
HpaII CCGG 1 cut(s) 1528
Hpy166II GTNNAC 2 cut(s) 922, 1405
Hpy188I TCNGA 7 cut(s) 33, 324, 1057, 1261, 1293, 1557, 1645
Hpy188III TCNNGA 3 cut(s) 1253, 1357, 1445
Hpy8I GTNNAC 2 cut(s) 922, 1405
HpyCH4III ACNGT 4 cut(s) 187, 345, 926, 1297
HpyF10VI GCNNNNNNNGC 3 cut(s) 1638, 1647, 1698
Hsp92II CATG 5 cut(s) 155, 887, 1040, 1111, 1552
HspAI GCGC 2 cut(s) 1096, 1542
Ksp22I TGATCA 1 cut(s) 955
Kzo9I GATC 3 cut(s) 955, 1359, 1447
LmnI GCTCC 2 cut(s) 643, 965
Lsp1109I GCAGC 1 cut(s) 1600
LweI GCATC 2 cut(s) 1014, 1192
MaeI CTAG 1 cut(s) 330
MaeIII GTNAC 4 cut(s) 137, 726, 869, 928
MalI GATC 3 cut(s) 957, 1361, 1449
MbiI CCGCTC 1 cut(s) 638
MboI GATC 3 cut(s) 955, 1359, 1447
MboII GAAGA 5 cut(s) 711, 792, 1123, 1159, 1456
MhlI GDGCHC 3 cut(s) 227, 1180, 1242
MluCI AATT 5 cut(s) 84, 142, 691, 1416, 1657
MlyI GAGTC 2 cut(s) 1052, 1388
MmeI TCCRAC 8 cut(s) 302, 347, 380, 593, 665, 1080, 1086, 1316
MseI TTAA 1 cut(s) 1458
MslI CAYNNNNRTG 1 cut(s) 1410
MspA1I CMGCKG 1 cut(s) 1613
MspI CCGG 1 cut(s) 1528
MspR9I CCNGG 4 cut(s) 81, 963, 1270, 1529
MvaI CCWGG 3 cut(s) 81, 963, 1270
MvnI CGCG 1 cut(s) 1544
MwoI GCNNNNNNNGC 3 cut(s) 1638, 1647, 1698
NciI CCSGG 1 cut(s) 1529
NdeII GATC 3 cut(s) 955, 1359, 1447
NlaIII CATG 5 cut(s) 155, 887, 1040, 1111, 1552
NlaIV GGNNCC 4 cut(s) 1130, 1177, 1267, 1321
NmuCI GTSAC 2 cut(s) 726, 928
NspI RCATGY 3 cut(s) 155, 887, 1552
PaeI GCATGC 1 cut(s) 1552
PceI AGGCCT 1 cut(s) 1513
PciI ACATGT 1 cut(s) 883
PfeI GAWTC 3 cut(s) 34, 94, 1256
PflFI GACNNNGTC 2 cut(s) 926, 1297
PfoI TCCNGGA 1 cut(s) 79
PkrI GCNGC 2 cut(s) 1612, 1615
PleI GAGTC 2 cut(s) 1052, 1388
PpsI GAGTC 2 cut(s) 1052, 1388
PscI ACATGT 1 cut(s) 883
Psp6I CCWGG 3 cut(s) 79, 961, 1268
PspGI CCWGG 3 cut(s) 79, 961, 1268
PspN4I GGNNCC 4 cut(s) 1130, 1177, 1267, 1321
PspPI GGNCC 2 cut(s) 1129, 1320
PsrI GAACNNNNNNTAC 2 cut(s) 842, 874
PsyI GACNNNGTC 2 cut(s) 926, 1297
RseI CAYNNNNRTG 1 cut(s) 1410
SaqAI TTAA 1 cut(s) 1458
SatI GCNGC 2 cut(s) 1611, 1614
Sau3AI GATC 3 cut(s) 955, 1359, 1447
Sau96I GGNCC 2 cut(s) 1129, 1320
SchI GAGTC 2 cut(s) 1052, 1388
ScrFI CCNGG 4 cut(s) 81, 963, 1270, 1529
SduI GDGCHC 3 cut(s) 227, 1180, 1242
SfaNI GCATC 2 cut(s) 1014, 1192
SinI GGWCC 2 cut(s) 1129, 1320
SmiMI CAYNNNNRTG 1 cut(s) 1410
SmlI CTYRAG 3 cut(s) 226, 648, 1396
SmoI CTYRAG 3 cut(s) 226, 648, 1396
SphI GCATGC 1 cut(s) 1552
Sse9I AATT 5 cut(s) 84, 142, 691, 1416, 1657
SseBI AGGCCT 1 cut(s) 1513
SsiI CCGC 5 cut(s) 636, 1188, 1213, 1611, 1701
SspMI CTAG 1 cut(s) 330
StuI AGGCCT 1 cut(s) 1513
StyD4I CCNGG 4 cut(s) 79, 961, 1268, 1527
StyI CCWWGG 2 cut(s) 1303, 1368
TaaI ACNGT 4 cut(s) 187, 345, 926, 1297
TaqI TCGA 2 cut(s) 547, 1714
TasI AATT 5 cut(s) 84, 142, 691, 1416, 1657
TauI GCSGC 1 cut(s) 1613
TfiI GAWTC 3 cut(s) 34, 94, 1256
Tru1I TTAA 1 cut(s) 1458
Tru9I TTAA 1 cut(s) 1458
TscAI CASTG 4 cut(s) 63, 192, 1213, 1606
TseFI GTSAC 2 cut(s) 726, 928
TseI GCWGC 1 cut(s) 1613
Tsp45I GTSAC 2 cut(s) 726, 928
TspDTI ATGAA 3 cut(s) 1075, 1124, 1159
TspRI CASTG 4 cut(s) 63, 192, 1213, 1606
Tth111I GACNNNGTC 2 cut(s) 926, 1297
VpaK11BI GGWCC 2 cut(s) 1129, 1320
XceI RCATGY 3 cut(s) 155, 887, 1552
XcmI CCANNNNNNNNNTGG 1 cut(s) 1330
XspI CTAG 1 cut(s) 330
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.