MD04G1048800.v1.1

DNA polymerase I

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr04
OG0004379
Physical Location & Seq
Reverse (-)
5711223 .. 5722409
11187 bp
Loading structure...
UTR
Exon/CDS
Intron
MD04G1048800.v1.1.491

Sequence Viewer

Length: 1362 bp
ATGGCCTGGTGTCACTCGCACTCTTGGCTGCTTCACAATACTCAATCCCTTTCCCTCTGGAAATGGAGAAGCTTCACTCTCAGATTCGTAGGAACAAGAAGAAGAAGAAGCAGCATTCAATCTCCAAATTCACTCCGATTTTCTCCCCTAATTTCCCATAAGGGCTACTGCAATACATTCAATCGTAGTTTTAATTCGGCTTCAACGGGAGTTGTTAGTGAGAGTGGTGATGCCGCGGCGGCGGCCTTTTACTCTAAAAGTGAGGGAGTAGTAAGCCGGGACATGCTGCTGGCTTCGACTTTGTTCAAGCGTGAAGAGAAAACAGTGAACAGAAACCCTTCAGATGGTAGAGTAATGCTCATCGACGGCACATCCATCATTTATAGAGCATACTATAAGCTTTTAGTAGCAAAGCTGCATCATGGCCATTTGTCACATGCCGATGGAAATGGAGATTGGGTGTTGACCATCTTCTCAGCACTTTCTCTTATAATTGATGTCCTGATGTTTATCCCTTCCCATGTAGCGGTGGTGTTTGACCATGATGGAGTTTCATTTGGTCAAACTTGTAATTCATCCAAAGAAAGTTTTAAAGGAAAAGGCCTGAATTTTCGTCACACTCTGTACCCCGCATACAAGAGCAATCGCCCCCCTACACCTGATACCATTGTCCAGGGACTCCAATACTTGAAAGCATCCATCAAGGCTATGTCCATTAAGGTGATTGAGGTGCCTGGTGTGGAAGCTGATGATGTGATTGGAACGTTGGCTGTTAGAAGTGTTGATAGTGGGTACAAGGTACGGGTTGTCTCCCCAGACAAAGACTTTTTTCAGATTCTATCTCCTTCATTGCGCCTTCTACGAATTGCTCCACGTGGCTTTGATATGATTTCATTTGGAATGGAGGATTTTACTGAAAAATATGGAAGCCTTCAACCTTCTCAGTTTGTTGATGTGATCTCGCTTGTCGGTGACAAATCTGATAATATTCCAGGAGTCCATGGAATTGGAAATGTTCATGCTGTGCAACTCATCACTAAATTTGGCACATTGGAGAATTTATTGCAGTGTGTTGATCAAGTTGAAGAGGAACGAATAAGAAAGACCTTGATAGAAAATGCTGACCAGGCTCTCTTGAGCAAGAACTTGGTAATCGCGCTACTACGCTCTGATCTTCCACTGTACATGGTACCTTTTGCCACAAAAGATCTGCCATTTCACAAGCCTGAGGACAATGGGGAGAAATTCACGAGCCTCCTAACTGCTATAAGTGCATATGCGGAAGGATTTTCAGCTGATCCAATCATCAGGAGAGCATTTTACTTATGGAACAAACTTGAAAACCAAAATCAAGTTACGTAG
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
5_3_exonuc 5_3_exonuc_N

Protein Analysis

454

Amino Acids

50.57

Weight (kDa)

8.95

Isoelectric Point (pI)

44.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
5_3_exonuc_N PF02739 118 - 185 2.8e-06 5'-3' exonuclease, N-terminal resolvase-like domain
5_3_exonuc_N PF02739 201 - 309 1e-28 5'-3' exonuclease, N-terminal resolvase-like domain
5_3_exonuc PF01367 312 - 409 7.2e-25 5'-3' exonuclease, C-terminal SAM fold
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 491
Acc65I GGTACC 1 cut(s) 1189
AccB1I GGYRCC 2 cut(s) 730, 1189
AccII CGCG 2 cut(s) 236, 1157
AciI CCGC 7 cut(s) 234, 236, 239, 242, 527, 630, 1280
AclI AACGTT 1 cut(s) 764
AclWI GGATC 1 cut(s) 1292
AcoI YGGCCR 1 cut(s) 424
AcsI RAATTY 5 cut(s) 127, 607, 1040, 1057, 1244
AcuI CTGAAG 1 cut(s) 324
AcvI CACGTG 1 cut(s) 875
AfaI GTAC 5 cut(s) 626, 794, 801, 1184, 1191
AfiI CCNNNNNNNGG 2 cut(s) 344, 526
AgsI TTSAA 8 cut(s) 119, 181, 204, 307, 691, 935, 1085, 1340
AjnI CCWGG 5 cut(s) 5, 672, 733, 991, 1125
AjuI GAANNNNNNNTTGG 2 cut(s) 439, 471
AluBI AGCT 5 cut(s) 72, 400, 415, 746, 1295
AluI AGCT 5 cut(s) 72, 400, 415, 746, 1295
Alw26I GTCTC 1 cut(s) 814
AlwI GGATC 1 cut(s) 1292
AoxI GGCC 4 cut(s) 3, 243, 424, 601
ApeKI GCWGC 4 cut(s) 28, 111, 286, 415
ApoI RAATTY 5 cut(s) 127, 607, 1040, 1057, 1244
Asp700I GAANNNNTTC 1 cut(s) 337
Asp718I GGTACC 1 cut(s) 1189
AspLEI GCGC 2 cut(s) 855, 1159
AsuC2I CCSGG 1 cut(s) 278
AsuHPI GGTGA 3 cut(s) 239, 733, 983
AxyI CCTNAGG 1 cut(s) 1227
BaeI ACNNNNGTAYC 2 cut(s) 654, 687
BalI TGGCCA 1 cut(s) 426
BanI GGYRCC 2 cut(s) 730, 1189
BauI CACGAG 1 cut(s) 1249
BbrPI CACGTG 1 cut(s) 875
BbvI GCAGC 4 cut(s) 15, 123, 273, 402
BccI CCATC 6 cut(s) 338, 383, 437, 476, 539, 707
BceAI ACGGC 1 cut(s) 382
BciT130I CCWGG 5 cut(s) 7, 674, 735, 993, 1127
BclI TGATCA 1 cut(s) 1075
BcnI CCSGG 1 cut(s) 278
BcoDI GTCTC 1 cut(s) 814
BglI GCCNNNNNGGC 1 cut(s) 239
BglII AGATCT 1 cut(s) 1207
BisI GCNGC 8 cut(s) 29, 112, 234, 237, 240, 243, 287, 416
BlsI GCNGC 8 cut(s) 30, 113, 235, 238, 241, 244, 288, 417
Bme1390I CCNGG 6 cut(s) 7, 278, 674, 735, 993, 1127
BmiI GGNNCC 2 cut(s) 732, 1191
BmrFI CCNGG 6 cut(s) 7, 278, 674, 735, 993, 1127
BmsI GCATC 3 cut(s) 220, 427, 704
BplI GAGNNNNNCTC 2 cut(s) 342, 374
BpuEI CTTGAG 1 cut(s) 1156
BpuMI CCSGG 1 cut(s) 278
BsaAI YACGTR 2 cut(s) 875, 1359
BsaBI GATNNNNATC 1 cut(s) 509
BsaJI CCNNGG 3 cut(s) 234, 673, 1000
BsaXI ACNNNNNCTCC 2 cut(s) 444, 474
Bsc4I CCNNNNNNNGG 2 cut(s) 344, 526
Bse21I CCTNAGG 1 cut(s) 1227
Bse3DI GCAATG 1 cut(s) 848
Bse8I GATNNNNATC 1 cut(s) 509
BseBI CCWGG 5 cut(s) 7, 674, 735, 993, 1127
BseDI CCNNGG 3 cut(s) 234, 673, 1000
BseGI GGATG 3 cut(s) 371, 575, 695
BseJI GATNNNNATC 1 cut(s) 509
BseLI CCNNNNNNNGG 2 cut(s) 344, 526
BseMI GCAATG 1 cut(s) 848
BseMII CTCAG 4 cut(s) 94, 489, 956, 1218
BseXI GCAGC 4 cut(s) 15, 123, 273, 402
Bsh1236I CGCG 2 cut(s) 236, 1157
BshFI GGCC 4 cut(s) 5, 245, 426, 603
BshNI GGYRCC 2 cut(s) 730, 1189
BsiSI CCGG 1 cut(s) 277
BslFI GGGAC 2 cut(s) 293, 690
BslI CCNNNNNNNGG 2 cut(s) 344, 526
BsmAI GTCTC 1 cut(s) 814
BsmFI GGGAC 2 cut(s) 293, 690
BsmI GAATGC 1 cut(s) 114
BsnI GGCC 4 cut(s) 5, 245, 426, 603
Bsp1407I TGTACA 1 cut(s) 1182
Bsp143I GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
Bsp19I CCATGG 1 cut(s) 1000
BspACI CCGC 7 cut(s) 234, 236, 239, 242, 527, 630, 1280
BspANI GGCC 4 cut(s) 5, 245, 426, 603
BspCNI CTCAG 4 cut(s) 93, 488, 955, 1219
BspFNI CGCG 2 cut(s) 236, 1157
BspLI GGNNCC 2 cut(s) 732, 1191
BspPI GGATC 1 cut(s) 1292
BspT107I GGYRCC 2 cut(s) 730, 1189
BsrDI GCAATG 1 cut(s) 848
BsrGI TGTACA 1 cut(s) 1182
BssECI CCNNGG 3 cut(s) 234, 673, 1000
BssMI GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
BssSI CACGAG 1 cut(s) 1249
BssT1I CCWWGG 1 cut(s) 1000
Bst2BI CACGAG 1 cut(s) 1249
Bst2UI CCWGG 5 cut(s) 7, 674, 735, 993, 1127
Bst4CI ACNGT 2 cut(s) 325, 1182
Bst6I CTCTTC 2 cut(s) 309, 1080
BstAUI TGTACA 1 cut(s) 1182
BstBAI YACGTR 2 cut(s) 875, 1359
BstC8I GCNNGC 1 cut(s) 291
BstDEI CTNAG 4 cut(s) 80, 475, 942, 1227
BstDSI CCRYGG 2 cut(s) 234, 1000
BstF5I GGATG 3 cut(s) 371, 575, 695
BstFNI CGCG 2 cut(s) 236, 1157
BstHHI GCGC 2 cut(s) 855, 1159
BstKTI GATC 5 cut(s) 960, 1078, 1174, 1210, 1300
BstMAI GTCTC 1 cut(s) 814
BstMBI GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
BstMWI GCNNNNNNNGC 5 cut(s) 25, 239, 242, 1127, 1271
BstNI CCWGG 5 cut(s) 7, 674, 735, 993, 1127
BstNSI RCATGY 2 cut(s) 286, 440
BstSCI CCNGG 6 cut(s) 5, 276, 672, 733, 991, 1125
BstSNI TACGTA 1 cut(s) 1359
BstUI CGCG 2 cut(s) 236, 1157
BstV1I GCAGC 4 cut(s) 15, 123, 273, 402
BstX2I RGATCY 1 cut(s) 1207
BstXI CCANNNNNNTGG 1 cut(s) 1007
BstYI RGATCY 1 cut(s) 1207
Bsu36I CCTNAGG 1 cut(s) 1227
BsuRI GGCC 4 cut(s) 5, 245, 426, 603
BtgI CCRYGG 2 cut(s) 234, 1000
BtsCI GGATG 3 cut(s) 371, 575, 695
BtsI GCAGTG 1 cut(s) 1073
BtsIMutI CAGTG 3 cut(s) 330, 1073, 1178
Cac8I GCNNGC 1 cut(s) 291
CfoI GCGC 2 cut(s) 855, 1159
Cfr42I CCGCGG 1 cut(s) 237
Csp6I GTAC 5 cut(s) 625, 793, 800, 1183, 1190
CviAII CATG 8 cut(s) 283, 422, 437, 521, 542, 1001, 1019, 1186
CviQI GTAC 5 cut(s) 625, 793, 800, 1183, 1190
DdeI CTNAG 4 cut(s) 80, 475, 942, 1227
DpnI GATC 5 cut(s) 959, 1077, 1173, 1209, 1299
DpnII GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
DraI TTTAAA 1 cut(s) 592
EaeI YGGCCR 1 cut(s) 424
Eam1104I CTCTTC 2 cut(s) 309, 1080
EarI CTCTTC 2 cut(s) 309, 1080
Eco105I TACGTA 1 cut(s) 1359
Eco130I CCWWGG 1 cut(s) 1000
Eco147I AGGCCT 1 cut(s) 603
Eco57I CTGAAG 1 cut(s) 324
Eco72I CACGTG 1 cut(s) 875
Eco81I CCTNAGG 1 cut(s) 1227
EcoRII CCWGG 5 cut(s) 5, 672, 733, 991, 1125
EcoT14I CCWWGG 1 cut(s) 1000
ErhI CCWWGG 1 cut(s) 1000
FaeI CATG 8 cut(s) 286, 425, 440, 524, 545, 1004, 1022, 1189
FaqI GGGAC 2 cut(s) 293, 690
FatI CATG 8 cut(s) 282, 421, 436, 520, 541, 1000, 1018, 1185
FauI CCCGC 1 cut(s) 637
FauNDI CATATG 1 cut(s) 1276
FbaI TGATCA 1 cut(s) 1075
Fnu4HI GCNGC 8 cut(s) 29, 112, 234, 237, 240, 243, 287, 416
FokI GGATG 3 cut(s) 358, 562, 682
Fsp4HI GCNGC 8 cut(s) 29, 112, 234, 237, 240, 243, 287, 416
GlaI GCGC 2 cut(s) 854, 1158
GluI GCNGC 8 cut(s) 29, 112, 234, 237, 240, 243, 287, 416
HaeIII GGCC 4 cut(s) 5, 245, 426, 603
HapII CCGG 1 cut(s) 277
HhaI GCGC 2 cut(s) 855, 1159
Hin1II CATG 8 cut(s) 286, 425, 440, 524, 545, 1004, 1022, 1189
Hin6I GCGC 2 cut(s) 853, 1157
HinP1I GCGC 2 cut(s) 853, 1157
HincII GTYRAC 1 cut(s) 465
HindII GTYRAC 1 cut(s) 465
HindIII AAGCTT 2 cut(s) 70, 398
HinfI GANTC 4 cut(s) 84, 678, 835, 996
HpaII CCGG 1 cut(s) 277
HphI GGTGA 3 cut(s) 239, 733, 983
Hpy166II GTNNAC 2 cut(s) 328, 465
Hpy188I TCNGA 6 cut(s) 83, 137, 343, 834, 982, 1171
Hpy188III TCNNGA 5 cut(s) 58, 502, 1135, 1249, 1309
Hpy8I GTNNAC 2 cut(s) 328, 465
Hpy99I CGWCG 1 cut(s) 368
HpyAV CCTTC 7 cut(s) 348, 525, 855, 866, 941, 948, 1277
HpyCH4III ACNGT 2 cut(s) 325, 1182
HpyCH4IV ACGT 3 cut(s) 764, 874, 1358
HpyCH4V TGCA 5 cut(s) 171, 418, 1027, 1066, 1274
HpyF10VI GCNNNNNNNGC 5 cut(s) 25, 239, 242, 1127, 1271
HpyF3I CTNAG 4 cut(s) 80, 475, 942, 1227
HpySE526I ACGT 3 cut(s) 764, 874, 1358
Hsp92II CATG 8 cut(s) 286, 425, 440, 524, 545, 1004, 1022, 1189
HspAI GCGC 2 cut(s) 853, 1157
KpnI GGTACC 1 cut(s) 1193
Ksp22I TGATCA 1 cut(s) 1075
KspI CCGCGG 1 cut(s) 237
Kzo9I GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
LmnI GCTCC 1 cut(s) 874
Lsp1109I GCAGC 4 cut(s) 15, 123, 273, 402
LweI GCATC 3 cut(s) 220, 427, 704
MaeII ACGT 3 cut(s) 764, 874, 1358
MaeIII GTNAC 5 cut(s) 11, 432, 614, 971, 1354
MalI GATC 5 cut(s) 959, 1077, 1173, 1209, 1299
MboI GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
MboII GAAGA 7 cut(s) 111, 114, 117, 326, 463, 1097, 1166
MflI RGATCY 1 cut(s) 1207
MlsI TGGCCA 1 cut(s) 426
MluNI TGGCCA 1 cut(s) 426
MlyI GAGTC 2 cut(s) 672, 1005
MnlI CCTC 7 cut(s) 65, 256, 721, 898, 1081, 1222, 1265
Mox20I TGGCCA 1 cut(s) 426
MroXI GAANNNNTTC 1 cut(s) 337
MscI TGGCCA 1 cut(s) 426
MseI TTAA 3 cut(s) 192, 591, 717
MslI CAYNNNNRTG 2 cut(s) 441, 719
Msp20I TGGCCA 1 cut(s) 426
MspA1I CMGCKG 2 cut(s) 236, 1295
MspI CCGG 1 cut(s) 277
MspR9I CCNGG 6 cut(s) 7, 278, 674, 735, 993, 1127
Mva1269I GAATGC 1 cut(s) 114
MvaI CCWGG 5 cut(s) 7, 674, 735, 993, 1127
MvnI CGCG 2 cut(s) 236, 1157
MwoI GCNNNNNNNGC 5 cut(s) 25, 239, 242, 1127, 1271
NciI CCSGG 1 cut(s) 278
NcoI CCATGG 1 cut(s) 1000
NdeI CATATG 1 cut(s) 1276
NdeII GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
NlaIII CATG 8 cut(s) 286, 425, 440, 524, 545, 1004, 1022, 1189
NlaIV GGNNCC 2 cut(s) 732, 1191
NmuCI GTSAC 4 cut(s) 11, 432, 614, 971
NspI RCATGY 2 cut(s) 286, 440
PceI AGGCCT 1 cut(s) 603
PctI GAATGC 1 cut(s) 114
PdmI GAANNNNTTC 1 cut(s) 337
PfeI GAWTC 2 cut(s) 84, 835
PfoI TCCNGGA 1 cut(s) 991
PkrI GCNGC 8 cut(s) 30, 113, 235, 238, 241, 244, 288, 417
PleI GAGTC 2 cut(s) 672, 1004
PmaCI CACGTG 1 cut(s) 875
PmlI CACGTG 1 cut(s) 875
PpsI GAGTC 2 cut(s) 672, 1004
Ppu21I YACGTR 2 cut(s) 875, 1359
PsiI TTATAA 1 cut(s) 491
Psp1406I AACGTT 1 cut(s) 764
Psp6I CCWGG 5 cut(s) 5, 672, 733, 991, 1125
PspCI CACGTG 1 cut(s) 875
PspGI CCWGG 5 cut(s) 5, 672, 733, 991, 1125
PspN4I GGNNCC 2 cut(s) 732, 1191
PsuI RGATCY 1 cut(s) 1207
PvuII CAGCTG 1 cut(s) 1295
RsaI GTAC 5 cut(s) 626, 794, 801, 1184, 1191
RsaNI GTAC 5 cut(s) 625, 793, 800, 1183, 1190
RseI CAYNNNNRTG 2 cut(s) 441, 719
SacII CCGCGG 1 cut(s) 237
SaqAI TTAA 3 cut(s) 192, 591, 717
SatI GCNGC 8 cut(s) 29, 112, 234, 237, 240, 243, 287, 416
Sau3AI GATC 5 cut(s) 957, 1075, 1171, 1207, 1297
SchI GAGTC 2 cut(s) 672, 1005
ScrFI CCNGG 6 cut(s) 7, 278, 674, 735, 993, 1127
SfaNI GCATC 3 cut(s) 220, 427, 704
Sfr303I CCGCGG 1 cut(s) 237
SgrBI CCGCGG 1 cut(s) 237
SmiMI CAYNNNNRTG 2 cut(s) 441, 719
SmlI CTYRAG 1 cut(s) 1135
SmoI CTYRAG 1 cut(s) 1135
SnaBI TACGTA 1 cut(s) 1359
SseBI AGGCCT 1 cut(s) 603
SsiI CCGC 7 cut(s) 234, 236, 239, 242, 527, 630, 1280
SspI AATATT 1 cut(s) 988
StuI AGGCCT 1 cut(s) 603
StyD4I CCNGG 6 cut(s) 5, 276, 672, 733, 991, 1125
StyI CCWWGG 1 cut(s) 1000
TaaI ACNGT 2 cut(s) 325, 1182
TaiI ACGT 3 cut(s) 767, 877, 1361
TaqI TCGA 2 cut(s) 296, 363
TatI WGTACW 1 cut(s) 1182
TauI GCSGC 4 cut(s) 236, 239, 242, 245
TfiI GAWTC 2 cut(s) 84, 835
Tru1I TTAA 3 cut(s) 192, 591, 717
Tru9I TTAA 3 cut(s) 192, 591, 717
TscAI CASTG 3 cut(s) 330, 1073, 1185
TseFI GTSAC 4 cut(s) 11, 432, 614, 971
TseI GCWGC 4 cut(s) 28, 111, 286, 415
Tsp45I GTSAC 4 cut(s) 11, 432, 614, 971
TspDTI ATGAA 5 cut(s) 543, 564, 837, 882, 1007
TspRI CASTG 3 cut(s) 330, 1073, 1185
XapI RAATTY 5 cut(s) 127, 607, 1040, 1057, 1244
XceI RCATGY 2 cut(s) 286, 440
XmnI GAANNNNTTC 1 cut(s) 337
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.