MD06G1060400.v1.1

HIT zinc finger

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr06
OG0010570
Physical Location & Seq
Reverse (-)
9343335 .. 9349071
5737 bp
Loading structure...
UTR
Exon/CDS
Intron
MD06G1060400.v1.1.491

Sequence Viewer

Length: 1335 bp
ATGTCGACGAGGTCAAATTTCTACAAGAACCCTTCGATTTCTTACAAGAAGGACCTCAGTCTCTCCTCCGTTCTTCAAAACCTCCAAGCTTACAACGTCGTCACCGGCAATGCTCCGCCGCTTCAACAACATATGCCAGCCGGTGATGGTGAAACTATATGTTGCAAACGCCGTCGTGATCAGAAACCAAAACCAAAACCGCCTCCCCCTCGCCGTCAGAACCGCGAAATCGAGGAGAACGACGCACCTATGTCGCACCAGGATTACATAGACAGGAGAAGAAAAGAAGTTTGTACATCGCAGAATTACGAGGAATTAACTTGTGATGTTCTGGGAAAGCCAGGAACTTCGAAGTCGTGTTTAAGTTTGGTGCAATATGATAGTGATGAAAGTACGTCTTCAGAATGTGAAGGGAAGCAGGATCTTCCAAATCCTGGTCACTTAAATGAATCTGATCAAGTAAAAAGCAGAACTGAACAGCGTTTCCCTAATCCAGGAGAACCTGTTTGTGTCATGTGTGGTAAATACGGAGAATATATTTGCAATGAGACTGATGATGATATCTGCAGCATGGAGTGCAAAGCTGATCTGTTGCAAGCTCTTAAAGTTGTGAAGGACCCCTTGAGCAATCAAAGACCAGATGTCTCATCTGGACCCAAATGTACCTTACCGATGCATGATTTTGGGGACACTTGGGATTATGAACGCCATTGCTGGTCCAAGAAGAGTTCCATTCTTTCTACTTATGATTGTTGGAAATGTAGAAGGCCTGGACACCTTGCTGAAGATTGTTTGGTGATAACAAGTAACGAGGTGACTTTGGGCCATAGCAAAGCCAATTCAATACCCCCAGACCTTCTTGCATTATACAGAAGATGCCACCAGATAGGCAAAAACATATCGGCTTCAAAGTGCAATGAATGCTACAACTCAATAAGTTTGGCCACTTGCCTTCATTGTAGCATTGCCCTCTGTGACAATGCAGGTCATTTGATTGAGCATATACAGACACATCCATCCCATCGACAATATTATTCTCATAAACTCTCTCGTCTGGTGAAATGCTGTAAATCAACATGCCAGGTGACTGATATCAGGGATCTTTTGACATGCCAGTACTGTTTCGATAAAGCTTTTGATAAGTTCTATGACATGTATACTGCAACTTGGAAAGGCACTGGGCTTTCAATCATATCAGGATCTATTTGCTGCGAAGATCACTTTGATTGGCATAGTATGAACTGTATGAATGCTAATGTGGAAGAGAGTGGATATATTATCAGTAGGAATTCCCAGAAAGGCAAACGTATTCAGCTTAGCGACTTCATTTTCTGA
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
zf-CCHC zf-HIT

Protein Analysis

445

Amino Acids

50.36

Weight (kDa)

6.74

Isoelectric Point (pI)

58.22

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-HIT PF04438 167 - 194 2.5e-06 HIT zinc finger
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) 974
AccB7I CCANNNNNTGG 1 cut(s) 434
AccI GTMKAC 2 cut(s) 5, 1157
AccII CGCG 1 cut(s) 225
AciI CCGC 4 cut(s) 116, 119, 200, 223
AclWI GGATC 3 cut(s) 429, 1107, 1207
AcoI YGGCCR 1 cut(s) 942
AcsI RAATTY 2 cut(s) 16, 1288
AcuI CTGAAG 2 cut(s) 384, 804
AfaI GTAC 4 cut(s) 295, 394, 664, 1118
AfiI CCNNNNNNNGG 2 cut(s) 434, 494
AflIII ACRYGT 1 cut(s) 1152
AgsI TTSAA 5 cut(s) 77, 125, 843, 909, 1188
AhdI GACNNNNNGTC 1 cut(s) 641
AjnI CCWGG 6 cut(s) 258, 340, 433, 493, 769, 1080
AloI GAACNNNNNNTCC 2 cut(s) 468, 500
AluBI AGCT 5 cut(s) 89, 584, 599, 1133, 1315
AluI AGCT 5 cut(s) 89, 584, 599, 1133, 1315
Alw26I GTCTC 3 cut(s) 65, 542, 649
AlwI GGATC 3 cut(s) 429, 1107, 1207
AoxI GGCC 3 cut(s) 767, 823, 942
ApeKI GCWGC 2 cut(s) 567, 1209
ApoI RAATTY 2 cut(s) 16, 1288
AspS9I GGNCC 5 cut(s) 52, 616, 653, 717, 823
AsuHPI GGTGA 7 cut(s) 94, 155, 161, 808, 826, 1069, 1096
AsuII TTCGAA 1 cut(s) 350
AvaII GGWCC 4 cut(s) 52, 616, 653, 717
BalI TGGCCA 1 cut(s) 944
BbsI GAAGAC 1 cut(s) 390
BbvI GCAGC 2 cut(s) 579, 1196
BccI CCATC 3 cut(s) 140, 1024, 1029
BceAI ACGGC 2 cut(s) 156, 198
BcgI CGANNNNNNTGC 2 cut(s) 234, 268
BciT130I CCWGG 6 cut(s) 260, 342, 435, 495, 771, 1082
BclI TGATCA 2 cut(s) 178, 454
BcoDI GTCTC 3 cut(s) 65, 542, 649
BfmI CTRYAG 1 cut(s) 565
BfuAI ACCTGC 1 cut(s) 974
BisI GCNGC 3 cut(s) 119, 568, 1210
BlpI GCTNAGC 1 cut(s) 1316
BlsI GCNGC 3 cut(s) 120, 569, 1211
BmcAI AGTACT 1 cut(s) 1118
Bme1390I CCNGG 6 cut(s) 260, 342, 435, 495, 771, 1082
Bme18I GGWCC 4 cut(s) 52, 616, 653, 717
BmeRI GACNNNNNGTC 1 cut(s) 641
BmgT120I GGNCC 5 cut(s) 52, 616, 653, 717, 823
BmiI GGNNCC 2 cut(s) 618, 655
BmrFI CCNGG 6 cut(s) 260, 342, 435, 495, 771, 1082
BmrI ACTGGG 1 cut(s) 1188
BmsI GCATC 2 cut(s) 663, 866
BmuI ACTGGG 1 cut(s) 1188
BoxI GACNNNNGTC 1 cut(s) 57
BpiI GAAGAC 1 cut(s) 390
Bpu1102I GCTNAGC 1 cut(s) 1316
Bpu14I TTCGAA 1 cut(s) 350
BpuEI CTTGAG 1 cut(s) 643
BsaXI ACNNNNNCTCC 2 cut(s) 489, 519
Bsc4I CCNNNNNNNGG 2 cut(s) 434, 494
Bse118I RCCGGY 2 cut(s) 104, 140
Bse1I ACTGG 2 cut(s) 1114, 1183
Bse3DI GCAATG 5 cut(s) 115, 550, 709, 922, 963
BseBI CCWGG 6 cut(s) 260, 342, 435, 495, 771, 1082
BseGI GGATG 2 cut(s) 1012, 1016
BseLI CCNNNNNNNGG 2 cut(s) 434, 494
BseMI GCAATG 5 cut(s) 115, 550, 709, 922, 963
BseMII CTCAG 1 cut(s) 70
BseNI ACTGG 2 cut(s) 1114, 1183
BseRI GAGGAG 2 cut(s) 55, 248
BseXI GCAGC 2 cut(s) 579, 1196
Bsh1236I CGCG 1 cut(s) 225
BshFI GGCC 3 cut(s) 769, 825, 944
BsiSI CCGG 2 cut(s) 105, 141
BslFI GGGAC 1 cut(s) 701
BslI CCNNNNNNNGG 2 cut(s) 434, 494
BsmAI GTCTC 3 cut(s) 65, 542, 649
BsmFI GGGAC 1 cut(s) 701
BsmI GAATGC 2 cut(s) 926, 1255
BsnI GGCC 3 cut(s) 769, 825, 944
Bsp119I TTCGAA 1 cut(s) 350
Bsp1407I TGTACA 1 cut(s) 293
Bsp143I GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
Bsp1720I GCTNAGC 1 cut(s) 1316
BspACI CCGC 4 cut(s) 116, 119, 200, 223
BspANI GGCC 3 cut(s) 769, 825, 944
BspCNI CTCAG 1 cut(s) 69
BspFNI CGCG 1 cut(s) 225
BspLI GGNNCC 2 cut(s) 618, 655
BspMAI CTGCAG 1 cut(s) 569
BspMI ACCTGC 1 cut(s) 974
BspPI GGATC 3 cut(s) 429, 1107, 1207
BspT104I TTCGAA 1 cut(s) 350
BsrDI GCAATG 5 cut(s) 115, 550, 709, 922, 963
BsrFI RCCGGY 2 cut(s) 104, 140
BsrGI TGTACA 1 cut(s) 293
BsrI ACTGG 2 cut(s) 1114, 1183
BssAI RCCGGY 2 cut(s) 104, 140
BssMI GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
BssNAI GTATAC 1 cut(s) 1158
Bst1107I GTATAC 1 cut(s) 1158
Bst2UI CCWGG 6 cut(s) 260, 342, 435, 495, 771, 1082
Bst4CI ACNGT 2 cut(s) 1121, 1244
Bst6I CTCTTC 2 cut(s) 719, 1257
BstAPI GCANNNNNTGC 2 cut(s) 576, 921
BstAUI TGTACA 1 cut(s) 293
BstBI TTCGAA 1 cut(s) 350
BstC8I GCNNGC 2 cut(s) 138, 597
BstDEI CTNAG 2 cut(s) 56, 1316
BstENI CCTNNNNNAGG 1 cut(s) 492
BstF5I GGATG 2 cut(s) 1012, 1016
BstFNI CGCG 1 cut(s) 225
BstKTI GATC 7 cut(s) 181, 424, 457, 589, 1102, 1202, 1219
BstMAI GTCTC 3 cut(s) 65, 542, 649
BstMBI GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
BstMWI GCNNNNNNNGC 2 cut(s) 576, 921
BstNI CCWGG 6 cut(s) 260, 342, 435, 495, 771, 1082
BstNSI RCATGY 3 cut(s) 1080, 1113, 1156
BstPAI GACNNNNGTC 1 cut(s) 57
BstSCI CCNGG 6 cut(s) 258, 340, 433, 493, 769, 1080
BstSFI CTRYAG 1 cut(s) 565
BstUI CGCG 1 cut(s) 225
BstV1I GCAGC 2 cut(s) 579, 1196
BstV2I GAAGAC 1 cut(s) 390
BstX2I RGATCY 3 cut(s) 421, 1099, 1199
BstYI RGATCY 3 cut(s) 421, 1099, 1199
BstZ17I GTATAC 1 cut(s) 1158
BsuRI GGCC 3 cut(s) 769, 825, 944
BtgZI GCGATG 1 cut(s) 282
BtsCI GGATG 2 cut(s) 1012, 1016
BtsIMutI CAGTG 1 cut(s) 1176
BveI ACCTGC 1 cut(s) 974
Cac8I GCNNGC 2 cut(s) 138, 597
Cfr10I RCCGGY 2 cut(s) 104, 140
Cfr13I GGNCC 5 cut(s) 52, 616, 653, 717, 823
CseI GACGC 1 cut(s) 251
Csp6I GTAC 4 cut(s) 294, 393, 663, 1117
CviAII CATG 6 cut(s) 514, 571, 677, 1077, 1110, 1153
CviQI GTAC 4 cut(s) 294, 393, 663, 1117
DdeI CTNAG 2 cut(s) 56, 1316
DpnI GATC 7 cut(s) 180, 423, 456, 588, 1101, 1201, 1218
DpnII GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
DriI GACNNNNNGTC 1 cut(s) 641
EaeI YGGCCR 1 cut(s) 942
Eam1104I CTCTTC 2 cut(s) 719, 1257
Eam1105I GACNNNNNGTC 1 cut(s) 641
EarI CTCTTC 2 cut(s) 719, 1257
EciI GGCGGA 1 cut(s) 105
Eco147I AGGCCT 1 cut(s) 769
Eco32I GATATC 2 cut(s) 562, 1093
Eco47I GGWCC 4 cut(s) 52, 616, 653, 717
Eco57I CTGAAG 2 cut(s) 384, 804
EcoNI CCTNNNNNAGG 1 cut(s) 492
EcoO109I RGGNCCY 2 cut(s) 52, 616
EcoRI GAATTC 1 cut(s) 1288
EcoRII CCWGG 6 cut(s) 258, 340, 433, 493, 769, 1080
EcoRV GATATC 2 cut(s) 562, 1093
EcoT22I ATGCAT 1 cut(s) 678
FaeI CATG 6 cut(s) 517, 574, 680, 1080, 1113, 1156
FalI AAGNNNNNCTT 4 cut(s) 382, 414, 605, 637
FaqI GGGAC 1 cut(s) 701
FatI CATG 6 cut(s) 513, 570, 676, 1076, 1109, 1152
FauNDI CATATG 1 cut(s) 132
FbaI TGATCA 2 cut(s) 178, 454
FblI GTMKAC 2 cut(s) 5, 1157
Fnu4HI GCNGC 3 cut(s) 119, 568, 1210
FokI GGATG 2 cut(s) 999, 1003
Fsp4HI GCNGC 3 cut(s) 119, 568, 1210
GluI GCNGC 3 cut(s) 119, 568, 1210
HaeIII GGCC 3 cut(s) 769, 825, 944
HapII CCGG 2 cut(s) 105, 141
HgaI GACGC 1 cut(s) 251
Hin1II CATG 6 cut(s) 517, 574, 680, 1080, 1113, 1156
HincII GTYRAC 1 cut(s) 6
HindII GTYRAC 1 cut(s) 6
HindIII AAGCTT 2 cut(s) 87, 1131
HinfI GANTC 1 cut(s) 449
HpaII CCGG 2 cut(s) 105, 141
HphI GGTGA 7 cut(s) 94, 155, 161, 808, 826, 1069, 1096
Hpy166II GTNNAC 2 cut(s) 6, 1158
Hpy188I TCNGA 5 cut(s) 183, 219, 403, 454, 1334
Hpy188III TCNNGA 3 cut(s) 176, 651, 1197
Hpy8I GTNNAC 2 cut(s) 6, 1158
Hpy99I CGWCG 4 cut(s) 10, 101, 177, 245
HpyAV CCTTC 7 cut(s) 42, 43, 404, 607, 759, 866, 962
HpyCH4III ACNGT 2 cut(s) 1121, 1244
HpyCH4IV ACGT 3 cut(s) 96, 395, 1306
HpyF10VI GCNNNNNNNGC 2 cut(s) 576, 921
HpyF3I CTNAG 2 cut(s) 56, 1316
HpySE526I ACGT 3 cut(s) 96, 395, 1306
Hsp92II CATG 6 cut(s) 517, 574, 680, 1080, 1113, 1156
Ksp22I TGATCA 2 cut(s) 178, 454
Kzo9I GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
LmnI GCTCC 1 cut(s) 118
Lsp1109I GCAGC 2 cut(s) 579, 1196
LweI GCATC 2 cut(s) 663, 866
MaeII ACGT 3 cut(s) 96, 395, 1306
MaeIII GTNAC 6 cut(s) 100, 437, 806, 814, 974, 1084
MalI GATC 7 cut(s) 180, 423, 456, 588, 1101, 1201, 1218
MboI GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
MboII GAAGA 9 cut(s) 65, 291, 390, 416, 736, 797, 885, 1226, 1274
MflI RGATCY 3 cut(s) 421, 1099, 1199
MlsI TGGCCA 1 cut(s) 944
MluCI AATT 5 cut(s) 16, 304, 314, 838, 1288
MluNI TGGCCA 1 cut(s) 944
MmeI TCCRAC 1 cut(s) 734
Mox20I TGGCCA 1 cut(s) 944
Mph1103I ATGCAT 1 cut(s) 678
MscI TGGCCA 1 cut(s) 944
MseI TTAA 4 cut(s) 317, 362, 443, 603
MslI CAYNNNNRTG 1 cut(s) 444
Msp20I TGGCCA 1 cut(s) 944
MspI CCGG 2 cut(s) 105, 141
MspR9I CCNGG 6 cut(s) 260, 342, 435, 495, 771, 1082
Mva1269I GAATGC 2 cut(s) 926, 1255
MvaI CCWGG 6 cut(s) 260, 342, 435, 495, 771, 1082
MvnI CGCG 1 cut(s) 225
MwoI GCNNNNNNNGC 2 cut(s) 576, 921
NdeI CATATG 1 cut(s) 132
NdeII GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
NlaIII CATG 6 cut(s) 517, 574, 680, 1080, 1113, 1156
NlaIV GGNNCC 2 cut(s) 618, 655
NmuCI GTSAC 5 cut(s) 100, 437, 814, 974, 1084
NsiI ATGCAT 1 cut(s) 678
NspI RCATGY 3 cut(s) 1080, 1113, 1156
NspV TTCGAA 1 cut(s) 350
PceI AGGCCT 1 cut(s) 769
PciI ACATGT 1 cut(s) 1152
PcsI WCGNNNNNNNCGW 1 cut(s) 237
PctI GAATGC 2 cut(s) 926, 1255
PfeI GAWTC 1 cut(s) 449
PflFI GACNNNGTC 1 cut(s) 10
PflMI CCANNNNNTGG 1 cut(s) 434
PfoI TCCNGGA 1 cut(s) 493
PkrI GCNGC 3 cut(s) 120, 569, 1211
PpuMI RGGWCCY 2 cut(s) 52, 616
PscI ACATGT 1 cut(s) 1152
PshAI GACNNNNGTC 1 cut(s) 57
Psp5II RGGWCCY 2 cut(s) 52, 616
Psp6I CCWGG 6 cut(s) 258, 340, 433, 493, 769, 1080
PspGI CCWGG 6 cut(s) 258, 340, 433, 493, 769, 1080
PspN4I GGNNCC 2 cut(s) 618, 655
PspPI GGNCC 5 cut(s) 52, 616, 653, 717, 823
PspPPI RGGWCCY 2 cut(s) 52, 616
PstI CTGCAG 1 cut(s) 569
PsuI RGATCY 3 cut(s) 421, 1099, 1199
PsyI GACNNNGTC 1 cut(s) 10
RsaI GTAC 4 cut(s) 295, 394, 664, 1118
RsaNI GTAC 4 cut(s) 294, 393, 663, 1117
RseI CAYNNNNRTG 1 cut(s) 444
SalI GTCGAC 1 cut(s) 4
SaqAI TTAA 4 cut(s) 317, 362, 443, 603
SatI GCNGC 3 cut(s) 119, 568, 1210
Sau3AI GATC 7 cut(s) 178, 421, 454, 586, 1099, 1199, 1216
Sau96I GGNCC 5 cut(s) 52, 616, 653, 717, 823
ScaI AGTACT 1 cut(s) 1118
ScrFI CCNGG 6 cut(s) 260, 342, 435, 495, 771, 1082
SfaNI GCATC 2 cut(s) 663, 866
SfcI CTRYAG 1 cut(s) 565
SfuI TTCGAA 1 cut(s) 350
SinI GGWCC 4 cut(s) 52, 616, 653, 717
SmiMI CAYNNNNRTG 1 cut(s) 444
SmlI CTYRAG 1 cut(s) 622
SmoI CTYRAG 1 cut(s) 622
Sse9I AATT 5 cut(s) 16, 304, 314, 838, 1288
SseBI AGGCCT 1 cut(s) 769
SsiI CCGC 4 cut(s) 116, 119, 200, 223
SspI AATATT 1 cut(s) 1031
StuI AGGCCT 1 cut(s) 769
StyD4I CCNGG 6 cut(s) 258, 340, 433, 493, 769, 1080
TaaI ACNGT 2 cut(s) 1121, 1244
TaiI ACGT 3 cut(s) 99, 398, 1309
TaqI TCGA 6 cut(s) 5, 35, 231, 350, 1024, 1125
TasI AATT 5 cut(s) 16, 304, 314, 838, 1288
TatI WGTACW 2 cut(s) 293, 1116
TauI GCSGC 1 cut(s) 121
TfiI GAWTC 1 cut(s) 449
Tru1I TTAA 4 cut(s) 317, 362, 443, 603
Tru9I TTAA 4 cut(s) 317, 362, 443, 603
TscAI CASTG 1 cut(s) 1183
TseFI GTSAC 5 cut(s) 100, 437, 814, 974, 1084
TseI GCWGC 2 cut(s) 567, 1209
Tsp45I GTSAC 5 cut(s) 100, 437, 814, 974, 1084
TspDTI ATGAA 8 cut(s) 402, 462, 717, 933, 944, 1253, 1262, 1315
TspGWI ACGGA 2 cut(s) 58, 543
TspRI CASTG 1 cut(s) 1183
Tth111I GACNNNGTC 1 cut(s) 10
Van91I CCANNNNNTGG 1 cut(s) 434
VpaK11BI GGWCC 4 cut(s) 52, 616, 653, 717
XagI CCTNNNNNAGG 1 cut(s) 492
XapI RAATTY 2 cut(s) 16, 1288
XceI RCATGY 3 cut(s) 1080, 1113, 1156
XmiI GTMKAC 2 cut(s) 5, 1157
ZrmI AGTACT 1 cut(s) 1118
Zsp2I ATGCAT 1 cut(s) 678
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.