MD11G1238500.v1.1

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr11
OG0006038
Physical Location & Seq
Forward (+)
34611459 .. 34612794
1336 bp
Loading structure...
UTR
Exon/CDS
Intron
MD11G1238500.v1.1.491

Sequence Viewer

Length: 894 bp
ATGGAGTTCTTAGGCAGCAAAAGTGTTTTGATCGTTCTGATCTTAAGGTTTGCTACAGCAAGAAAAGCCCGTGCTTTCTCAAGCAGGTATACTGCCCTGCGGAATACCCATCCTTCACCGATAGACAAAAAGGCTAAAATTTGCTATCTCAACTGTGACTCACCTATATGCAAAGCTGAGTGCAAAGGTCGCAAACCTAATTGTGAAGGCCCCGGATCAGCATGCATGGACCCTCGCTTCATCGGTGGAGATGGCATTGTCTTTTACTTCCACGGGAAGAAAAATGAGTATTTCAGCTTAGCCCTTGGACTCCTCTTTGGCTCTAATAGCTTCTCCGTAGAGGCCAGCCAAGCATCGTCATGGGATGATGAAACAGACCACTTAAAATTTACTTACAATGGAGAGGAGCTAGTCATCCCAGAATCCCAACTCTCCGCATGGCAATCTCCGGAAAATGCCATTAGAGTAGAGAGAACATCTAGCAAGAACAGTGTTTTGGTCACTCTCCAGGAAGTTGCTGAAATTTCAGTAAATGTGGTGCCTGTGACAAAGGAAGATGATAGGATCCGCAATTATCAGATACCATCAGATGACTGTTTTGCACATCTGGAAGTACAGTTCAGATTCTACGGCTTATCCTCAAATGTTGAGCGAGTGCTTGGAAGGACTTACCAGCCAGATTTCAGGAACCCGGCAAAGCCAGGAGTAGCGATGCCAGTTGTGGGAGGGGAACACAAGTACAGAACAACTTCACTGGTCTCCGTAGATTGCACTGCTTGTGTTTTCACTAAATCCAGGAAGATGGATCAAACAGATTCAAGGGTGATGAATTACGGAAATCTTGACTGCACCGGTAATTCCTTCAGTGGGAATGGAATCGTTTGCAGGAAGTAA
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

298

Amino Acids

33.04

Weight (kDa)

8.43

Isoelectric Point (pI)

39.14

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 206 - 262 2.2e-24 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) 75
AccB1I GGYRCC 1 cut(s) 538
AccI GTMKAC 1 cut(s) 89
AccIII TCCGGA 1 cut(s) 448
AciI CCGC 3 cut(s) 100, 435, 568
AclWI GGATC 4 cut(s) 223, 559, 572, 813
AcsI RAATTY 3 cut(s) 138, 386, 522
AcuI CTGAAG 1 cut(s) 847
AfaI GTAC 2 cut(s) 615, 740
AfiI CCNNNNNNNGG 2 cut(s) 722, 867
AflII CTTAAG 1 cut(s) 43
AgeI ACCGGT 1 cut(s) 851
AgsI TTSAA 1 cut(s) 819
AjnI CCWGG 3 cut(s) 507, 700, 794
AjuI GAANNNNNNNTTGG 2 cut(s) 479, 511
AloI GAACNNNNNNTCC 2 cut(s) 602, 634
AluBI AGCT 4 cut(s) 176, 297, 330, 409
AluI AGCT 4 cut(s) 176, 297, 330, 409
Alw26I GTCTC 1 cut(s) 763
AlwI GGATC 4 cut(s) 223, 559, 572, 813
Aor13HI TCCGGA 1 cut(s) 448
AoxI GGCC 2 cut(s) 208, 342
ApeKI GCWGC 1 cut(s) 15
ApoI RAATTY 3 cut(s) 138, 386, 522
AsiGI ACCGGT 1 cut(s) 851
Asp700I GAANNNNTTC 1 cut(s) 748
AspS9I GGNCC 2 cut(s) 209, 229
AsuC2I CCSGG 2 cut(s) 213, 692
AsuHPI GGTGA 3 cut(s) 108, 153, 835
AvaII GGWCC 1 cut(s) 229
BamHI GGATCC 1 cut(s) 564
BanI GGYRCC 1 cut(s) 538
BbvI GCAGC 1 cut(s) 27
BccI CCATC 4 cut(s) 117, 245, 592, 796
BceAI ACGGC 1 cut(s) 646
BciT130I CCWGG 3 cut(s) 509, 702, 796
BcnI CCSGG 2 cut(s) 213, 692
BcoDI GTCTC 1 cut(s) 763
BfaI CTAG 2 cut(s) 410, 480
BfmI CTRYAG 1 cut(s) 54
BfrI CTTAAG 1 cut(s) 43
BfuAI ACCTGC 1 cut(s) 75
BisI GCNGC 1 cut(s) 16
BlpI GCTNAGC 1 cut(s) 298
BlsI GCNGC 1 cut(s) 17
Bme1390I CCNGG 5 cut(s) 213, 509, 692, 702, 796
Bme18I GGWCC 1 cut(s) 229
BmgT120I GGNCC 2 cut(s) 209, 229
BmiI GGNNCC 5 cut(s) 211, 231, 540, 566, 689
BmrFI CCNGG 5 cut(s) 213, 509, 692, 702, 796
BmsI GCATC 2 cut(s) 362, 702
BpmI CTGGAG 1 cut(s) 491
Bpu1102I GCTNAGC 1 cut(s) 298
BpuEI CTTGAG 1 cut(s) 64
BpuMI CCSGG 2 cut(s) 213, 692
BsaI GGTCTC 1 cut(s) 763
BsaJI CCNNGG 3 cut(s) 211, 271, 304
BsaWI WCCGGW 2 cut(s) 448, 851
Bsc4I CCNNNNNNNGG 2 cut(s) 722, 867
Bse118I RCCGGY 1 cut(s) 851
Bse1I ACTGG 2 cut(s) 716, 759
BseAI TCCGGA 1 cut(s) 448
BseBI CCWGG 3 cut(s) 509, 702, 796
BseDI CCNNGG 3 cut(s) 211, 271, 304
BseGI GGATG 3 cut(s) 109, 370, 414
BseLI CCNNNNNNNGG 2 cut(s) 722, 867
BseMII CTCAG 1 cut(s) 168
BseNI ACTGG 2 cut(s) 716, 759
BseRI GAGGAG 2 cut(s) 302, 419
BseXI GCAGC 1 cut(s) 27
BsgI GTGCAG 1 cut(s) 832
BshFI GGCC 2 cut(s) 210, 344
BshNI GGYRCC 1 cut(s) 538
BshTI ACCGGT 1 cut(s) 851
BsiSI CCGG 4 cut(s) 213, 449, 692, 852
BslI CCNNNNNNNGG 2 cut(s) 722, 867
BsmAI GTCTC 1 cut(s) 763
BsnI GGCC 2 cut(s) 210, 344
Bso31I GGTCTC 1 cut(s) 763
Bsp13I TCCGGA 1 cut(s) 448
Bsp143I GATC 5 cut(s) 30, 39, 215, 564, 805
Bsp1720I GCTNAGC 1 cut(s) 298
BspACI CCGC 3 cut(s) 100, 435, 568
BspANI GGCC 2 cut(s) 210, 344
BspCNI CTCAG 1 cut(s) 169
BspEI TCCGGA 1 cut(s) 448
BspLI GGNNCC 5 cut(s) 211, 231, 540, 566, 689
BspMI ACCTGC 1 cut(s) 75
BspPI GGATC 4 cut(s) 223, 559, 572, 813
BspT107I GGYRCC 1 cut(s) 538
BspTI CTTAAG 1 cut(s) 43
BspTNI GGTCTC 1 cut(s) 763
BsrFI RCCGGY 1 cut(s) 851
BsrI ACTGG 2 cut(s) 716, 759
BssAI RCCGGY 1 cut(s) 851
BssECI CCNNGG 3 cut(s) 211, 271, 304
BssMI GATC 5 cut(s) 30, 39, 215, 564, 805
BssNAI GTATAC 1 cut(s) 90
BssT1I CCWWGG 1 cut(s) 304
Bst1107I GTATAC 1 cut(s) 90
Bst2UI CCWGG 3 cut(s) 509, 702, 796
Bst4CI ACNGT 4 cut(s) 155, 491, 596, 618
BstAFI CTTAAG 1 cut(s) 43
BstC8I GCNNGC 2 cut(s) 223, 346
BstDEI CTNAG 3 cut(s) 10, 177, 298
BstDSI CCRYGG 1 cut(s) 271
BstF5I GGATG 3 cut(s) 109, 370, 414
BstKTI GATC 5 cut(s) 33, 42, 218, 567, 808
BstMAI GTCTC 1 cut(s) 763
BstMBI GATC 5 cut(s) 30, 39, 215, 564, 805
BstMWI GCNNNNNNNGC 4 cut(s) 65, 189, 327, 350
BstNI CCWGG 3 cut(s) 509, 702, 796
BstNSI RCATGY 1 cut(s) 225
BstSCI CCNGG 5 cut(s) 211, 507, 690, 700, 794
BstSFI CTRYAG 1 cut(s) 54
BstV1I GCAGC 1 cut(s) 27
BstX2I RGATCY 1 cut(s) 564
BstXI CCANNNNNNTGG 1 cut(s) 802
BstYI RGATCY 1 cut(s) 564
BstZ17I GTATAC 1 cut(s) 90
BsuRI GGCC 2 cut(s) 210, 344
BtgI CCRYGG 1 cut(s) 271
BtgZI GCGATG 1 cut(s) 725
BtsCI GGATG 3 cut(s) 109, 370, 414
BtsI GCAGTG 1 cut(s) 771
BtsIMutI CAGTG 4 cut(s) 496, 752, 771, 871
BveI ACCTGC 1 cut(s) 75
Cac8I GCNNGC 2 cut(s) 223, 346
Cfr10I RCCGGY 1 cut(s) 851
Cfr13I GGNCC 2 cut(s) 209, 229
Csp6I GTAC 2 cut(s) 614, 739
CspAI ACCGGT 1 cut(s) 851
CviAII CATG 4 cut(s) 222, 226, 360, 438
CviQI GTAC 2 cut(s) 614, 739
DdeI CTNAG 3 cut(s) 10, 177, 298
DpnI GATC 5 cut(s) 32, 41, 217, 566, 807
DpnII GATC 5 cut(s) 30, 39, 215, 564, 805
Eco130I CCWWGG 1 cut(s) 304
Eco31I GGTCTC 1 cut(s) 763
Eco47I GGWCC 1 cut(s) 229
Eco57I CTGAAG 1 cut(s) 847
EcoO109I RGGNCCY 1 cut(s) 209
EcoRII CCWGG 3 cut(s) 507, 700, 794
EcoT14I CCWWGG 1 cut(s) 304
EcoT22I ATGCAT 1 cut(s) 227
ErhI CCWWGG 1 cut(s) 304
FaeI CATG 4 cut(s) 225, 229, 363, 441
FaiI YATR 7 cut(s) 90, 167, 169, 223, 227, 361, 439
FatI CATG 4 cut(s) 221, 225, 359, 437
FblI GTMKAC 1 cut(s) 89
Fnu4HI GCNGC 1 cut(s) 16
FokI GGATG 3 cut(s) 96, 377, 401
Fsp4HI GCNGC 1 cut(s) 16
FspBI CTAG 2 cut(s) 410, 480
GluI GCNGC 1 cut(s) 16
GsuI CTGGAG 1 cut(s) 491
HaeIII GGCC 2 cut(s) 210, 344
HapII CCGG 4 cut(s) 213, 449, 692, 852
Hin1II CATG 4 cut(s) 225, 229, 363, 441
HinfI GANTC 6 cut(s) 158, 309, 422, 624, 815, 876
HpaII CCGG 4 cut(s) 213, 449, 692, 852
HphI GGTGA 3 cut(s) 108, 153, 835
Hpy166II GTNNAC 1 cut(s) 90
Hpy188I TCNGA 4 cut(s) 39, 579, 589, 623
Hpy188III TCNNGA 4 cut(s) 449, 608, 685, 842
Hpy8I GTNNAC 1 cut(s) 90
HpyAV CCTTC 4 cut(s) 123, 200, 657, 871
HpyCH4III ACNGT 4 cut(s) 155, 491, 596, 618
HpyCH4V TGCA 7 cut(s) 171, 183, 225, 602, 771, 849, 885
HpyF10VI GCNNNNNNNGC 4 cut(s) 65, 189, 327, 350
HpyF3I CTNAG 3 cut(s) 10, 177, 298
Hsp92II CATG 4 cut(s) 225, 229, 363, 441
Kpn2I TCCGGA 1 cut(s) 448
Kzo9I GATC 5 cut(s) 30, 39, 215, 564, 805
LmnI GCTCC 1 cut(s) 406
Lsp1109I GCAGC 1 cut(s) 27
LweI GCATC 2 cut(s) 362, 702
MaeI CTAG 2 cut(s) 410, 480
MaeIII GTNAC 3 cut(s) 155, 499, 544
MalI GATC 5 cut(s) 32, 41, 217, 566, 807
MboI GATC 5 cut(s) 30, 39, 215, 564, 805
MboII GAAGA 3 cut(s) 289, 566, 811
MflI RGATCY 1 cut(s) 564
MluCI AATT 7 cut(s) 138, 199, 386, 522, 571, 829, 856
MlyI GAGTC 2 cut(s) 152, 303
MnlI CCTC 6 cut(s) 243, 323, 334, 397, 649, 719
Mph1103I ATGCAT 1 cut(s) 227
MroI TCCGGA 1 cut(s) 448
MroXI GAANNNNTTC 1 cut(s) 748
MseI TTAA 2 cut(s) 44, 383
MslI CAYNNNNRTG 2 cut(s) 166, 358
MspCI CTTAAG 1 cut(s) 43
MspI CCGG 4 cut(s) 213, 449, 692, 852
MspR9I CCNGG 5 cut(s) 213, 509, 692, 702, 796
MvaI CCWGG 3 cut(s) 509, 702, 796
MwoI GCNNNNNNNGC 4 cut(s) 65, 189, 327, 350
NciI CCSGG 2 cut(s) 213, 692
NdeII GATC 5 cut(s) 30, 39, 215, 564, 805
NlaIII CATG 4 cut(s) 225, 229, 363, 441
NlaIV GGNNCC 5 cut(s) 211, 231, 540, 566, 689
NmuCI GTSAC 3 cut(s) 155, 499, 544
NsiI ATGCAT 1 cut(s) 227
NspI RCATGY 1 cut(s) 225
PaeI GCATGC 1 cut(s) 225
PdmI GAANNNNTTC 1 cut(s) 748
PfeI GAWTC 4 cut(s) 422, 624, 815, 876
PfoI TCCNGGA 2 cut(s) 507, 794
PinAI ACCGGT 1 cut(s) 851
PkrI GCNGC 1 cut(s) 17
PleI GAGTC 2 cut(s) 152, 303
PpsI GAGTC 2 cut(s) 152, 303
Psp6I CCWGG 3 cut(s) 507, 700, 794
PspGI CCWGG 3 cut(s) 507, 700, 794
PspN4I GGNNCC 5 cut(s) 211, 231, 540, 566, 689
PspPI GGNCC 2 cut(s) 209, 229
PsuI RGATCY 1 cut(s) 564
RsaI GTAC 2 cut(s) 615, 740
RsaNI GTAC 2 cut(s) 614, 739
RseI CAYNNNNRTG 2 cut(s) 166, 358
SaqAI TTAA 2 cut(s) 44, 383
SatI GCNGC 1 cut(s) 16
Sau3AI GATC 5 cut(s) 30, 39, 215, 564, 805
Sau96I GGNCC 2 cut(s) 209, 229
SchI GAGTC 2 cut(s) 152, 303
ScrFI CCNGG 5 cut(s) 213, 509, 692, 702, 796
SetI ASST 9 cut(s) 50, 89, 166, 178, 190, 199, 299, 332, 411
SfaNI GCATC 2 cut(s) 362, 702
SfcI CTRYAG 1 cut(s) 54
SinI GGWCC 1 cut(s) 229
SmiMI CAYNNNNRTG 2 cut(s) 166, 358
SmlI CTYRAG 2 cut(s) 43, 79
SmoI CTYRAG 2 cut(s) 43, 79
SphI GCATGC 1 cut(s) 225
Sse9I AATT 7 cut(s) 138, 199, 386, 522, 571, 829, 856
SsiI CCGC 3 cut(s) 100, 435, 568
SspMI CTAG 2 cut(s) 410, 480
StyD4I CCNGG 5 cut(s) 211, 507, 690, 700, 794
StyI CCWWGG 1 cut(s) 304
TaaI ACNGT 4 cut(s) 155, 491, 596, 618
TasI AATT 7 cut(s) 138, 199, 386, 522, 571, 829, 856
TatI WGTACW 2 cut(s) 613, 738
TfiI GAWTC 4 cut(s) 422, 624, 815, 876
Tru1I TTAA 2 cut(s) 44, 383
Tru9I TTAA 2 cut(s) 44, 383
TscAI CASTG 4 cut(s) 496, 759, 778, 871
TseFI GTSAC 3 cut(s) 155, 499, 544
TseI GCWGC 1 cut(s) 15
Tsp45I GTSAC 3 cut(s) 155, 499, 544
TspDTI ATGAA 3 cut(s) 229, 384, 842
TspGWI ACGGA 3 cut(s) 325, 751, 849
TspRI CASTG 4 cut(s) 496, 759, 778, 871
Vha464I CTTAAG 1 cut(s) 43
VpaK11BI GGWCC 1 cut(s) 229
XapI RAATTY 3 cut(s) 138, 386, 522
XceI RCATGY 1 cut(s) 225
XmiI GTMKAC 1 cut(s) 89
XmnI GAANNNNTTC 1 cut(s) 748
XspI CTAG 2 cut(s) 410, 480
Zsp2I ATGCAT 1 cut(s) 227
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.