Rh4DG069100

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0010648
Physical Location & Seq
Reverse (-)
10246410 .. 10250207
3798 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4DG069100.1

Sequence Viewer

Length: 1359 bp
ATGGCGGTTTCCGAGAGTAAGAAATGGATTCTGGCTTGCGTGTCGGTGCTTCTCTTGTTCTGCTTCGTCGCTGTAATGTCCGGTAGAGTTAGCCTCGACGGCACCTCTCTCATCAGGAATGGAGGGACTGAGGAGTTGTTGAAGAGCTCGAGCAATTCATCAATGGCGGCCAGGGTGAATGAGAATGATGATGGAGGCTTGAATAAGCATGCAGTTGAGAACCCTGAGGAAATTGCTTCAATGGTTGACATGAGTATCCGCAACAGCACTGAAAGGAGAAAGCTGGGCTACTTCTCATGTGGAACTGGAAATCCCATTGATGATTGCTGGCGTTGTGATCCCAACTGGCAAAAGAACCGCAAGCGTCTTGCAGACTGTGGCATTGGTTTCGGCAGAAATGCCATTGGTGGTCGTGATGGACGCTTCTATGTTGTCACTGACCCTAAAGATGATGATCCCGTTAACCCCAGACCCGGTACTCTGCGCCATGCTGTCATCCAGGATGAGCCTCTCTGGATTGTGTTCAAACGTGACATGGTGATCCAATTGAAGCAGGAGCTTCTCATGAATAGCTTCAAGACCATTGATGGCCGTGGAGTCAATGTCCACATTGCTAATGGAGCATGCATTACAATCCAGTTTGTTACAAACGTTATAGTTCATGGTCTGCATATCCATGACTGCAAGCCCACAGGAAATGCTATGGTAAGGAGCTCCCCATCTCACTTTGGGTGGAGGACAATGGCTGATGGTGATGCTGTCTCCATCTTCGGGTCAAGCCATATCTGGGTTGATCACAATTCCCTCTCCAATTGTGCTGATGGTCTTGTTGATGCTGTCATGGGGTCAACTGCTATTACCATCTCAAACAACCACTTTACCCACCACAATGAAGTTATGCTGTTGGGCCACAGTGATTCTTATACCAGGGACAAGCAAATGCAGGTGACTATTGCCTACAACCACTTTGGAGAGGGACTTATCCAACGAATGCCAAGGTGTAGACACGGATATTTCCATGTGGTGAACAATGACTACACTCACTGGGAGATGTATGCCATTGGTGGAAGTGCAGAACCCACTATCAACAGCCAAGGCAACAGATATGCAGCTCCAACCAACCCCTTTGCAAAGGAGGTTACCAAGAGAGTGGAGACAGCACAAACTCAGTGGAGGGGCTGGAACTGGAGGTCAGAAGGTGATCTTCTACTCAATGGTGCCTTCTTCACTCCATCTGGAGCTGGAGCTTCAGCTGTCTATGCCAGGGCCTCAAGCTTGGGAGCCAAGTCATCTGCCATGGTGGGAACCATAACTGCTGGTGCTGGTGTACTGGGTTGCCGCAGAGGACATACCTGCTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00040 ko02024 map00040 map02024
Pfam Domains
Protein Families
Pec_lyase_C

Protein Analysis

452

Amino Acids

49.54

Weight (kDa)

7.98

Isoelectric Point (pI)

36.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 186 - 385 2.3e-20 Pectate lyase
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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Orthologous Genes (Group: OG0010648)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G24230 AT4G13710 AT4G13710
fragaria_vesca FvH4_4g05760 FvH4_4g05760 FvH4_4g05760 FvH4_4g05760 FvH4_4g05760
malus_domestica MD13G1231000.v1.1 MD16G1236000.v1.1
prunus_persica Prupe.1G060900_v2.0.a1
pyrus_communis pycom13g20360 pycom16g19790
rosa_chinensis RchiOBHm_Chr4g0396921
rosa_laevigata RLG00000009489
rosa_roxburghii Rroxscaffold_5G00341840
rosa_rugosa Rorug03G0346100
rosa_samantha Rh4AG075300 Rh4DG069100
rosa_wichuraiana Rw4G006040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 934
Acc36I ACCTGC 1 cut(s) 934
AccB1I GGYRCC 2 cut(s) 101, 1217
AccI GTMKAC 1 cut(s) 1003
AciI CCGC 5 cut(s) 5, 167, 259, 358, 1339
AclI AACGTT 1 cut(s) 651
AclWI GGATC 3 cut(s) 332, 449, 535
AcoI YGGCCR 2 cut(s) 168, 589
AcuI CTGAAG 1 cut(s) 1233
AfaI GTAC 2 cut(s) 478, 1329
AfiI CCNNNNNNNGG 3 cut(s) 473, 771, 787
AgsI TTSAA 6 cut(s) 142, 202, 240, 526, 550, 577
AjnI CCWGG 4 cut(s) 170, 498, 926, 1262
AloI GAACNNNNNNTCC 2 cut(s) 295, 327
Alw21I GWGCWC 2 cut(s) 149, 716
Alw26I GTCTC 2 cut(s) 766, 1148
AlwI GGATC 3 cut(s) 332, 449, 535
Ama87I CYCGRG 1 cut(s) 148
AoxI GGCC 4 cut(s) 168, 589, 907, 1266
ApeKI GCWGC 1 cut(s) 1109
Asp700I GAANNNNTTC 1 cut(s) 572
AspLEI GCGC 1 cut(s) 486
AspS9I GGNCC 2 cut(s) 907, 1266
AsuC2I CCSGG 1 cut(s) 474
AsuHPI GGTGA 6 cut(s) 187, 550, 764, 958, 1036, 1211
AvaI CYCGRG 1 cut(s) 148
AxyI CCTNAGG 1 cut(s) 225
BaeI ACNNNNGTAYC 2 cut(s) 238, 271
BanI GGYRCC 2 cut(s) 101, 1217
BanII GRGCYC 2 cut(s) 149, 716
Bbv12I GWGCWC 2 cut(s) 149, 716
BbvI GCAGC 1 cut(s) 1121
BccI CCATC 9 cut(s) 185, 410, 581, 727, 743, 773, 815, 869, 1240
BceAI ACGGC 2 cut(s) 115, 576
BcgI CGANNNNNNTGC 2 cut(s) 370, 404
BciT130I CCWGG 4 cut(s) 172, 500, 928, 1264
BciVI GTATCC 1 cut(s) 266
BclI TGATCA 1 cut(s) 793
BcnI CCSGG 1 cut(s) 474
BcoDI GTCTC 2 cut(s) 766, 1148
BfaI CTAG 1 cut(s) 1357
BfuAI ACCTGC 1 cut(s) 934
BfuI GTATCC 1 cut(s) 266
BglI GCCNNNNNGGC 1 cut(s) 99
BisI GCNGC 3 cut(s) 168, 1110, 1339
BlsI GCNGC 3 cut(s) 169, 1111, 1340
Bme1390I CCNGG 5 cut(s) 172, 474, 500, 928, 1264
BmeT110I CYCGRG 1 cut(s) 148
BmgT120I GGNCC 2 cut(s) 907, 1266
BmiI GGNNCC 4 cut(s) 103, 1219, 1282, 1306
BmrFI CCNGG 5 cut(s) 172, 474, 500, 928, 1264
BmrI ACTGGG 2 cut(s) 1054, 1340
BmsI GCATC 2 cut(s) 745, 823
BmuI ACTGGG 2 cut(s) 1054, 1340
BplI GAGNNNNNCTC 2 cut(s) 78, 110
BpmI CTGGAG 3 cut(s) 1207, 1257, 1263
BpuEI CTTGAG 1 cut(s) 1255
BpuMI CCSGG 1 cut(s) 474
BsaBI GATNNNNATC 1 cut(s) 453
BsaJI CCNNGG 7 cut(s) 171, 592, 927, 995, 1093, 1263, 1296
BsaWI WCCGGW 1 cut(s) 80
BsaXI ACNNNNNCTCC 2 cut(s) 588, 618
Bsc4I CCNNNNNNNGG 3 cut(s) 473, 771, 787
Bse1I ACTGG 6 cut(s) 310, 350, 637, 1049, 1190, 1335
Bse21I CCTNAGG 1 cut(s) 225
Bse3DI GCAATG 1 cut(s) 609
Bse8I GATNNNNATC 1 cut(s) 453
BseBI CCWGG 4 cut(s) 172, 500, 928, 1264
BseDI CCNNGG 7 cut(s) 171, 592, 927, 995, 1093, 1263, 1296
BseGI GGATG 2 cut(s) 495, 508
BseJI GATNNNNATC 1 cut(s) 453
BseLI CCNNNNNNNGG 3 cut(s) 473, 771, 787
BseMI GCAATG 1 cut(s) 609
BseMII CTCAG 3 cut(s) 120, 216, 1181
BseNI ACTGG 6 cut(s) 310, 350, 637, 1049, 1190, 1335
BseRI GAGGAG 1 cut(s) 146
BseXI GCAGC 1 cut(s) 1121
BseYI CCCAGC 1 cut(s) 283
BsgI GTGCAG 1 cut(s) 1092
BshFI GGCC 4 cut(s) 170, 591, 909, 1268
BshNI GGYRCC 2 cut(s) 101, 1217
BsiHKAI GWGCWC 2 cut(s) 149, 716
BsiHKCI CYCGRG 1 cut(s) 148
BsiSI CCGG 2 cut(s) 81, 474
BslFI GGGAC 3 cut(s) 139, 944, 990
BslI CCNNNNNNNGG 3 cut(s) 473, 771, 787
BsmAI GTCTC 2 cut(s) 766, 1148
BsmFI GGGAC 3 cut(s) 139, 944, 990
BsmI GAATGC 1 cut(s) 996
BsnI GGCC 4 cut(s) 170, 591, 909, 1268
BsoBI CYCGRG 1 cut(s) 148
Bsp1286I GDGCHC 2 cut(s) 149, 716
Bsp143I GATC 5 cut(s) 337, 454, 540, 793, 1201
Bsp19I CCATGG 1 cut(s) 1296
BspACI CCGC 5 cut(s) 5, 167, 259, 358, 1339
BspANI GGCC 4 cut(s) 170, 591, 909, 1268
BspCNI CTCAG 3 cut(s) 121, 217, 1180
BspHI TCATGA 1 cut(s) 564
BspLI GGNNCC 4 cut(s) 103, 1219, 1282, 1306
BspMI ACCTGC 1 cut(s) 934
BspPI GGATC 3 cut(s) 332, 449, 535
BspQI GCTCTTC 1 cut(s) 137
BspT107I GGYRCC 2 cut(s) 101, 1217
BsrDI GCAATG 1 cut(s) 609
BsrI ACTGG 6 cut(s) 310, 350, 637, 1049, 1190, 1335
BssECI CCNNGG 7 cut(s) 171, 592, 927, 995, 1093, 1263, 1296
BssMI GATC 5 cut(s) 337, 454, 540, 793, 1201
BssT1I CCWWGG 3 cut(s) 995, 1093, 1296
Bst2UI CCWGG 4 cut(s) 172, 500, 928, 1264
Bst4CI ACNGT 2 cut(s) 377, 914
Bst6I CTCTTC 1 cut(s) 137
BstC8I GCNNGC 6 cut(s) 37, 210, 329, 362, 625, 686
BstDEI CTNAG 3 cut(s) 129, 225, 1167
BstDSI CCRYGG 2 cut(s) 592, 1296
BstEII GGTNACC 1 cut(s) 1138
BstF5I GGATG 2 cut(s) 495, 508
BstHHI GCGC 1 cut(s) 486
BstKTI GATC 5 cut(s) 340, 457, 543, 796, 1204
BstMAI GTCTC 2 cut(s) 766, 1148
BstMBI GATC 5 cut(s) 337, 454, 540, 793, 1201
BstMWI GCNNNNNNNGC 3 cut(s) 99, 620, 1259
BstNI CCWGG 4 cut(s) 172, 500, 928, 1264
BstNSI RCATGY 2 cut(s) 212, 627
BstPI GGTNACC 1 cut(s) 1138
BstSCI CCNGG 5 cut(s) 170, 472, 498, 926, 1262
BstV1I GCAGC 1 cut(s) 1121
BstXI CCANNNNNNTGG 1 cut(s) 1150
Bsu36I CCTNAGG 1 cut(s) 225
BsuI GTATCC 1 cut(s) 266
BsuRI GGCC 4 cut(s) 170, 591, 909, 1268
BtgI CCRYGG 2 cut(s) 592, 1296
BtsCI GGATG 2 cut(s) 495, 508
BtsIMutI CAGTG 5 cut(s) 267, 435, 919, 1042, 1175
BveI ACCTGC 1 cut(s) 934
Cac8I GCNNGC 6 cut(s) 37, 210, 329, 362, 625, 686
CciI TCATGA 1 cut(s) 564
CfoI GCGC 1 cut(s) 486
Cfr13I GGNCC 2 cut(s) 907, 1266
CseI GACGC 2 cut(s) 353, 429
Csp6I GTAC 2 cut(s) 477, 1328
CspCI CAANNNNNGTGG 2 cut(s) 1151, 1186
CviQI GTAC 2 cut(s) 477, 1328
DdeI CTNAG 3 cut(s) 129, 225, 1167
DpnI GATC 5 cut(s) 339, 456, 542, 795, 1203
DpnII GATC 5 cut(s) 337, 454, 540, 793, 1201
EaeI YGGCCR 2 cut(s) 168, 589
Eam1104I CTCTTC 1 cut(s) 137
EarI CTCTTC 1 cut(s) 137
Ecl136II GAGCTC 2 cut(s) 147, 714
Eco130I CCWWGG 3 cut(s) 995, 1093, 1296
Eco24I GRGCYC 2 cut(s) 149, 716
Eco53kI GAGCTC 2 cut(s) 147, 714
Eco57I CTGAAG 1 cut(s) 1233
Eco81I CCTNAGG 1 cut(s) 225
Eco88I CYCGRG 1 cut(s) 148
Eco91I GGTNACC 1 cut(s) 1138
EcoICRI GAGCTC 2 cut(s) 147, 714
EcoO109I RGGNCCY 1 cut(s) 1266
EcoO65I GGTNACC 1 cut(s) 1138
EcoRII CCWGG 4 cut(s) 170, 498, 926, 1262
EcoT14I CCWWGG 3 cut(s) 995, 1093, 1296
EcoT22I ATGCAT 1 cut(s) 629
EcoT38I GRGCYC 2 cut(s) 149, 716
ErhI CCWWGG 3 cut(s) 995, 1093, 1296
FalI AAGNNNNNCTT 2 cut(s) 1188, 1220
FaqI GGGAC 3 cut(s) 139, 944, 990
FbaI TGATCA 1 cut(s) 793
FblI GTMKAC 1 cut(s) 1003
Fnu4HI GCNGC 3 cut(s) 168, 1110, 1339
FokI GGATG 2 cut(s) 482, 515
FriOI GRGCYC 2 cut(s) 149, 716
Fsp4HI GCNGC 3 cut(s) 168, 1110, 1339
FspBI CTAG 1 cut(s) 1357
GlaI GCGC 1 cut(s) 485
GluI GCNGC 3 cut(s) 168, 1110, 1339
GsaI CCCAGC 1 cut(s) 287
GsuI CTGGAG 3 cut(s) 1207, 1257, 1263
HaeIII GGCC 4 cut(s) 170, 591, 909, 1268
HapII CCGG 2 cut(s) 81, 474
HgaI GACGC 2 cut(s) 353, 429
HhaI GCGC 1 cut(s) 486
Hin6I GCGC 1 cut(s) 484
HinP1I GCGC 1 cut(s) 484
HincII GTYRAC 3 cut(s) 247, 463, 849
HindII GTYRAC 3 cut(s) 247, 463, 849
HindIII AAGCTT 1 cut(s) 1273
HinfI GANTC 3 cut(s) 28, 597, 917
HpaI GTTAAC 1 cut(s) 463
HpaII CCGG 2 cut(s) 81, 474
HphI GGTGA 6 cut(s) 187, 550, 764, 958, 1036, 1211
Hpy166II GTNNAC 7 cut(s) 247, 463, 607, 849, 1004, 1027, 1328
Hpy188I TCNGA 2 cut(s) 13, 1195
Hpy188III TCNNGA 6 cut(s) 115, 413, 514, 565, 577, 1236
Hpy8I GTNNAC 7 cut(s) 247, 463, 607, 849, 1004, 1027, 1328
Hpy99I CGWCG 2 cut(s) 71, 101
HpyAV CCTTC 2 cut(s) 1190, 1231
HpyCH4III ACNGT 2 cut(s) 377, 914
HpyCH4IV ACGT 2 cut(s) 529, 651
HpyCH4V TGCA 9 cut(s) 212, 371, 627, 670, 684, 943, 1073, 1109, 1130
HpyF10VI GCNNNNNNNGC 3 cut(s) 99, 620, 1259
HpyF3I CTNAG 3 cut(s) 129, 225, 1167
HpySE526I ACGT 2 cut(s) 529, 651
HspAI GCGC 1 cut(s) 484
Ksp22I TGATCA 1 cut(s) 793
KspAI GTTAAC 1 cut(s) 463
Kzo9I GATC 5 cut(s) 337, 454, 540, 793, 1201
LguI GCTCTTC 1 cut(s) 137
LmnI GCTCC 8 cut(s) 556, 620, 711, 719, 1117, 1238, 1244, 1280
Lsp1109I GCAGC 1 cut(s) 1121
LweI GCATC 2 cut(s) 745, 823
MaeI CTAG 1 cut(s) 1357
MaeII ACGT 2 cut(s) 529, 651
MaeIII GTNAC 5 cut(s) 433, 530, 643, 946, 1138
MalI GATC 5 cut(s) 339, 456, 542, 795, 1203
MboI GATC 5 cut(s) 337, 454, 540, 793, 1201
MboII GAAGA 4 cut(s) 154, 760, 1196, 1216
MfeI CAATTG 2 cut(s) 545, 811
MhlI GDGCHC 2 cut(s) 149, 716
MluCI AATT 5 cut(s) 154, 231, 545, 799, 811
MlyI GAGTC 1 cut(s) 606
MmeI TCCRAC 2 cut(s) 1009, 1139
Mph1103I ATGCAT 1 cut(s) 629
MroXI GAANNNNTTC 1 cut(s) 572
MseI TTAA 1 cut(s) 462
MslI CAYNNNNRTG 2 cut(s) 675, 888
MspA1I CMGCKG 1 cut(s) 1253
MspI CCGG 2 cut(s) 81, 474
MspR9I CCNGG 5 cut(s) 172, 474, 500, 928, 1264
MunI CAATTG 2 cut(s) 545, 811
Mva1269I GAATGC 1 cut(s) 996
MvaI CCWGG 4 cut(s) 172, 500, 928, 1264
MwoI GCNNNNNNNGC 3 cut(s) 99, 620, 1259
NciI CCSGG 1 cut(s) 474
NcoI CCATGG 1 cut(s) 1296
NdeII GATC 5 cut(s) 337, 454, 540, 793, 1201
NlaIV GGNNCC 4 cut(s) 103, 1219, 1282, 1306
NmuCI GTSAC 3 cut(s) 433, 530, 946
NsiI ATGCAT 1 cut(s) 629
NspI RCATGY 2 cut(s) 212, 627
PaeI GCATGC 2 cut(s) 212, 627
PaeR7I CTCGAG 1 cut(s) 148
PagI TCATGA 1 cut(s) 564
PaqCI CACCTGC 1 cut(s) 934
PciSI GCTCTTC 1 cut(s) 137
PctI GAATGC 1 cut(s) 996
PdmI GAANNNNTTC 1 cut(s) 572
PfeI GAWTC 2 cut(s) 28, 917
PfoI TCCNGGA 1 cut(s) 498
PkrI GCNGC 3 cut(s) 169, 1111, 1340
PleI GAGTC 1 cut(s) 605
PpsI GAGTC 1 cut(s) 605
Psp124BI GAGCTC 2 cut(s) 149, 716
Psp1406I AACGTT 1 cut(s) 651
Psp6I CCWGG 4 cut(s) 170, 498, 926, 1262
PspEI GGTNACC 1 cut(s) 1138
PspFI CCCAGC 1 cut(s) 283
PspGI CCWGG 4 cut(s) 170, 498, 926, 1262
PspN4I GGNNCC 4 cut(s) 103, 1219, 1282, 1306
PspPI GGNCC 2 cut(s) 907, 1266
PspXI VCTCGAGB 1 cut(s) 148
PsrI GAACNNNNNNTAC 2 cut(s) 1019, 1051
PvuII CAGCTG 1 cut(s) 1253
RsaI GTAC 2 cut(s) 478, 1329
RsaNI GTAC 2 cut(s) 477, 1328
RseI CAYNNNNRTG 2 cut(s) 675, 888
SacI GAGCTC 2 cut(s) 149, 716
SapI GCTCTTC 1 cut(s) 137
SaqAI TTAA 1 cut(s) 462
SatI GCNGC 3 cut(s) 168, 1110, 1339
Sau3AI GATC 5 cut(s) 337, 454, 540, 793, 1201
Sau96I GGNCC 2 cut(s) 907, 1266
SchI GAGTC 1 cut(s) 606
ScrFI CCNGG 5 cut(s) 172, 474, 500, 928, 1264
SduI GDGCHC 2 cut(s) 149, 716
SfaNI GCATC 2 cut(s) 745, 823
Sfr274I CTCGAG 1 cut(s) 148
SlaI CTCGAG 1 cut(s) 148
SmiMI CAYNNNNRTG 2 cut(s) 675, 888
SmlI CTYRAG 2 cut(s) 148, 1270
SmoI CTYRAG 2 cut(s) 148, 1270
SphI GCATGC 2 cut(s) 212, 627
Sse9I AATT 5 cut(s) 154, 231, 545, 799, 811
SsiI CCGC 5 cut(s) 5, 167, 259, 358, 1339
SspMI CTAG 1 cut(s) 1357
SstI GAGCTC 2 cut(s) 149, 716
StyD4I CCNGG 5 cut(s) 170, 472, 498, 926, 1262
StyI CCWWGG 3 cut(s) 995, 1093, 1296
TaaI ACNGT 2 cut(s) 377, 914
TaiI ACGT 2 cut(s) 532, 654
TaqI TCGA 2 cut(s) 96, 149
TasI AATT 5 cut(s) 154, 231, 545, 799, 811
TatI WGTACW 1 cut(s) 1327
TauI GCSGC 2 cut(s) 170, 1341
TfiI GAWTC 2 cut(s) 28, 917
Tru1I TTAA 1 cut(s) 462
Tru9I TTAA 1 cut(s) 462
TscAI CASTG 5 cut(s) 274, 442, 919, 1049, 1175
TseFI GTSAC 3 cut(s) 433, 530, 946
TseI GCWGC 1 cut(s) 1109
Tsp45I GTSAC 3 cut(s) 433, 530, 946
TspDTI ATGAA 4 cut(s) 147, 581, 650, 906
TspGWI ACGGA 1 cut(s) 1023
TspRI CASTG 5 cut(s) 274, 442, 919, 1049, 1175
XceI RCATGY 2 cut(s) 212, 627
XcmI CCANNNNNNNNNTGG 1 cut(s) 614
XhoI CTCGAG 1 cut(s) 148
XmiI GTMKAC 1 cut(s) 1003
XmnI GAANNNNTTC 1 cut(s) 572
XspI CTAG 1 cut(s) 1357
Zsp2I ATGCAT 1 cut(s) 629
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.