Rroxscaffold_5G00356480

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0008415
Physical Location & Seq
Forward (+)
35793494 .. 35794359
866 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00356480.1

Sequence Viewer

Length: 771 bp
ATGTGCTCGGTAGGATTTGCTAGGAAAATGAGCAACAATATTGGAAAAGACGTCATAAACTATGAAGTGATCAACTCTAGTGACAATGCATTAGATCCAAAACCAAGAACCTTGAGATATGGAGCTACCATGTTGAAAGGAAAAAAATGGTTCACATTCCGGAGGGATATGAAAATTAAGCTCGAGAAACCACTACTCATTAGTAGCTTTACCGCCATTGAAGGAAGAGGTACTAACATCCATATTGCTGGTAACGCTTGCTTGAGGGTGTTTAGGGCAACCAATTTGATTATCCACGGCCTTCGAATCCGCCATTGCAAGTCACAACCATCGAGTTTAGTTATGGGTCCAGATGGATTAATATTACTAGGTGGGGTTGATGGAGATGCAATAAGGTTGGTTACCGCATCAAAGGTTTGGATAGACCATAATACATTGTATGAGTGTGAGGATGGTCTTCTCAATGTCACTCGTGGATCAACCAATGTCACCATCTCCAACAATTGGTTTAGAGACCAGGACAAGGTAATGCTCCTTGGTCACGATGATGGATACTTTCGGGATAAGAACATGAAGGTGACTATTGTCTACAATTATTTTGGACCAAATTGCAACCAAAGAATGCCAAGGATTCGCCATGGTTATGCACATGTAGTGAACAACTTATACAAAGAATGGTCACAATATGCCATTGGGGGAAGTATGAATCCTAGAGTTAAGAGCGAAGCCAACCTCTTTATTGCGCCAAAACAAAACAAAACAAAGAGGTAA
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

256

Amino Acids

29.01

Weight (kDa)

9.84

Isoelectric Point (pI)

31.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 67 - 249 9.1e-26 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 54
AccB7I CCANNNNNTGG 1 cut(s) 504
AccI GTMKAC 1 cut(s) 588
AccIII TCCGGA 1 cut(s) 159
AciI CCGC 3 cut(s) 213, 310, 405
AclWI GGATC 2 cut(s) 89, 484
AcyI GRCGYC 1 cut(s) 51
AfaI GTAC 1 cut(s) 232
AfiI CCNNNNNNNGG 2 cut(s) 504, 523
AflIII ACRYGT 1 cut(s) 649
AgsI TTSAA 2 cut(s) 136, 221
AjnI CCWGG 1 cut(s) 516
AluBI AGCT 3 cut(s) 125, 181, 207
AluI AGCT 3 cut(s) 125, 181, 207
Alw21I GWGCWC 1 cut(s) 8
Alw26I GTCTC 1 cut(s) 507
AlwI GGATC 2 cut(s) 89, 484
Ama87I CYCGRG 1 cut(s) 182
Aor13HI TCCGGA 1 cut(s) 159
AoxI GGCC 1 cut(s) 298
AseI ATTAAT 1 cut(s) 359
AspLEI GCGC 1 cut(s) 745
AspS9I GGNCC 2 cut(s) 347, 602
AsuHPI GGTGA 2 cut(s) 481, 589
AsuII TTCGAA 1 cut(s) 304
AvaI CYCGRG 1 cut(s) 182
AvaII GGWCC 2 cut(s) 347, 602
BauI CACGAG 1 cut(s) 471
BbsI GAAGAC 1 cut(s) 449
Bbv12I GWGCWC 1 cut(s) 8
BccI CCATC 6 cut(s) 337, 347, 374, 446, 500, 542
BceAI ACGGC 1 cut(s) 313
BciT130I CCWGG 1 cut(s) 518
BciVI GTATCC 1 cut(s) 545
BclI TGATCA 1 cut(s) 69
BcoDI GTCTC 1 cut(s) 507
BfaI CTAG 4 cut(s) 21, 78, 368, 711
BfuI GTATCC 1 cut(s) 545
Bme1390I CCNGG 1 cut(s) 518
Bme18I GGWCC 2 cut(s) 347, 602
BmeT110I CYCGRG 1 cut(s) 182
BmgT120I GGNCC 2 cut(s) 347, 602
BmiI GGNNCC 1 cut(s) 348
BmrFI CCNGG 1 cut(s) 518
BmsI GCATC 2 cut(s) 376, 416
BoxI GACNNNNGTC 1 cut(s) 584
BpiI GAAGAC 1 cut(s) 449
Bpu14I TTCGAA 1 cut(s) 304
BpuEI CTTGAG 2 cut(s) 133, 283
BsaHI GRCGYC 1 cut(s) 51
BsaI GGTCTC 1 cut(s) 507
BsaJI CCNNGG 4 cut(s) 295, 535, 626, 637
BsaWI WCCGGW 1 cut(s) 159
Bsc4I CCNNNNNNNGG 2 cut(s) 504, 523
Bse3DI GCAATG 1 cut(s) 313
BseAI TCCGGA 1 cut(s) 159
BseBI CCWGG 1 cut(s) 518
BseDI CCNNGG 4 cut(s) 295, 535, 626, 637
BseGI GGATG 2 cut(s) 237, 457
BseLI CCNNNNNNNGG 2 cut(s) 504, 523
BseMI GCAATG 1 cut(s) 313
BshFI GGCC 1 cut(s) 300
BsiHKAI GWGCWC 1 cut(s) 8
BsiHKCI CYCGRG 1 cut(s) 182
BsiSI CCGG 1 cut(s) 160
BslI CCNNNNNNNGG 2 cut(s) 504, 523
BsmAI GTCTC 1 cut(s) 507
BsmI GAATGC 1 cut(s) 627
BsnI GGCC 1 cut(s) 300
Bso31I GGTCTC 1 cut(s) 507
BsoBI CYCGRG 1 cut(s) 182
Bsp119I TTCGAA 1 cut(s) 304
Bsp1286I GDGCHC 1 cut(s) 8
Bsp13I TCCGGA 1 cut(s) 159
Bsp143I GATC 3 cut(s) 69, 94, 476
Bsp19I CCATGG 1 cut(s) 637
BspACI CCGC 3 cut(s) 213, 310, 405
BspANI GGCC 1 cut(s) 300
BspEI TCCGGA 1 cut(s) 159
BspLI GGNNCC 1 cut(s) 348
BspPI GGATC 2 cut(s) 89, 484
BspT104I TTCGAA 1 cut(s) 304
BspTNI GGTCTC 1 cut(s) 507
BsrDI GCAATG 1 cut(s) 313
BssECI CCNNGG 4 cut(s) 295, 535, 626, 637
BssMI GATC 3 cut(s) 69, 94, 476
BssNI GRCGYC 1 cut(s) 51
BssSI CACGAG 1 cut(s) 471
BssT1I CCWWGG 3 cut(s) 535, 626, 637
Bst2BI CACGAG 1 cut(s) 471
Bst2UI CCWGG 1 cut(s) 518
Bst6I CTCTTC 1 cut(s) 220
BstACI GRCGYC 1 cut(s) 51
BstBI TTCGAA 1 cut(s) 304
BstC8I GCNNGC 1 cut(s) 259
BstDSI CCRYGG 2 cut(s) 295, 637
BstEII GGTNACC 1 cut(s) 400
BstF5I GGATG 2 cut(s) 237, 457
BstHHI GCGC 1 cut(s) 745
BstKTI GATC 3 cut(s) 72, 97, 479
BstMAI GTCTC 1 cut(s) 507
BstMBI GATC 3 cut(s) 69, 94, 476
BstMWI GCNNNNNNNGC 1 cut(s) 254
BstNI CCWGG 1 cut(s) 518
BstNSI RCATGY 1 cut(s) 653
BstPAI GACNNNNGTC 1 cut(s) 584
BstPI GGTNACC 1 cut(s) 400
BstSCI CCNGG 1 cut(s) 516
BstV2I GAAGAC 1 cut(s) 449
BstX2I RGATCY 1 cut(s) 94
BstXI CCANNNNNNTGG 1 cut(s) 248
BstYI RGATCY 1 cut(s) 94
BsuI GTATCC 1 cut(s) 545
BsuRI GGCC 1 cut(s) 300
BtgI CCRYGG 2 cut(s) 295, 637
BtsCI GGATG 2 cut(s) 237, 457
Cac8I GCNNGC 1 cut(s) 259
CfoI GCGC 1 cut(s) 745
Cfr13I GGNCC 2 cut(s) 347, 602
Csp6I GTAC 1 cut(s) 231
CviAII CATG 4 cut(s) 130, 571, 638, 650
CviJI RGCY 5 cut(s) 125, 181, 207, 300, 728
CviKI_1 RGCY 5 cut(s) 125, 181, 207, 300, 728
CviQI GTAC 1 cut(s) 231
DpnI GATC 3 cut(s) 71, 96, 478
DpnII GATC 3 cut(s) 69, 94, 476
Eam1104I CTCTTC 1 cut(s) 220
EarI CTCTTC 1 cut(s) 220
EciI GGCGGA 1 cut(s) 299
Eco130I CCWWGG 3 cut(s) 535, 626, 637
Eco31I GGTCTC 1 cut(s) 507
Eco47I GGWCC 2 cut(s) 347, 602
Eco88I CYCGRG 1 cut(s) 182
Eco91I GGTNACC 1 cut(s) 400
EcoO65I GGTNACC 1 cut(s) 400
EcoRII CCWGG 1 cut(s) 516
EcoT14I CCWWGG 3 cut(s) 535, 626, 637
EcoT22I ATGCAT 1 cut(s) 91
ErhI CCWWGG 3 cut(s) 535, 626, 637
FaeI CATG 4 cut(s) 133, 574, 641, 653
FatI CATG 4 cut(s) 129, 570, 637, 649
FbaI TGATCA 1 cut(s) 69
FblI GTMKAC 1 cut(s) 588
FokI GGATG 2 cut(s) 224, 464
FspBI CTAG 4 cut(s) 21, 78, 368, 711
GlaI GCGC 1 cut(s) 744
HaeIII GGCC 1 cut(s) 300
HapII CCGG 1 cut(s) 160
HhaI GCGC 1 cut(s) 745
Hin1I GRCGYC 1 cut(s) 51
Hin1II CATG 4 cut(s) 133, 574, 641, 653
Hin6I GCGC 1 cut(s) 743
HinP1I GCGC 1 cut(s) 743
HinfI GANTC 3 cut(s) 306, 631, 706
HpaII CCGG 1 cut(s) 160
HphI GGTGA 2 cut(s) 481, 589
Hpy166II GTNNAC 3 cut(s) 153, 589, 658
Hpy188III TCNNGA 5 cut(s) 160, 184, 350, 542, 560
Hpy8I GTNNAC 3 cut(s) 153, 589, 658
HpyAV CCTTC 3 cut(s) 215, 311, 568
HpyCH4IV ACGT 1 cut(s) 51
HpyCH4V TGCA 5 cut(s) 89, 318, 389, 612, 647
HpyF10VI GCNNNNNNNGC 1 cut(s) 254
HpySE526I ACGT 1 cut(s) 51
Hsp92I GRCGYC 1 cut(s) 51
Hsp92II CATG 4 cut(s) 133, 574, 641, 653
HspAI GCGC 1 cut(s) 743
Kpn2I TCCGGA 1 cut(s) 159
Ksp22I TGATCA 1 cut(s) 69
Kzo9I GATC 3 cut(s) 69, 94, 476
LmnI GCTCC 2 cut(s) 122, 537
LpnPI CCDG 5 cut(s) 173, 234, 363, 503, 530
LweI GCATC 2 cut(s) 376, 416
MaeI CTAG 4 cut(s) 21, 78, 368, 711
MaeII ACGT 1 cut(s) 51
MaeIII GTNAC 9 cut(s) 80, 251, 321, 400, 466, 487, 539, 577, 678
MalI GATC 3 cut(s) 71, 96, 478
MboI GATC 3 cut(s) 69, 94, 476
MboII GAAGA 2 cut(s) 237, 449
MfeI CAATTG 1 cut(s) 502
MflI RGATCY 1 cut(s) 94
MhlI GDGCHC 1 cut(s) 8
MluCI AATT 5 cut(s) 174, 283, 502, 592, 607
MmeI TCCRAC 1 cut(s) 522
MnlI CCTC 6 cut(s) 156, 221, 258, 442, 743, 759
Mph1103I ATGCAT 1 cut(s) 91
MroI TCCGGA 1 cut(s) 159
MseI TTAA 3 cut(s) 177, 359, 717
MslI CAYNNNNRTG 3 cut(s) 546, 575, 642
MspI CCGG 1 cut(s) 160
MspR9I CCNGG 1 cut(s) 518
MunI CAATTG 1 cut(s) 502
Mva1269I GAATGC 1 cut(s) 627
MvaI CCWGG 1 cut(s) 518
MwoI GCNNNNNNNGC 1 cut(s) 254
NcoI CCATGG 1 cut(s) 637
NdeII GATC 3 cut(s) 69, 94, 476
NlaIII CATG 4 cut(s) 133, 574, 641, 653
NlaIV GGNNCC 1 cut(s) 348
NmuCI GTSAC 7 cut(s) 80, 321, 466, 487, 539, 577, 678
NsiI ATGCAT 1 cut(s) 91
NspI RCATGY 1 cut(s) 653
NspV TTCGAA 1 cut(s) 304
PaeR7I CTCGAG 1 cut(s) 182
PciI ACATGT 1 cut(s) 649
PctI GAATGC 1 cut(s) 627
PfeI GAWTC 3 cut(s) 306, 631, 706
PflMI CCANNNNNTGG 1 cut(s) 504
PscI ACATGT 1 cut(s) 649
PshAI GACNNNNGTC 1 cut(s) 584
PshBI ATTAAT 1 cut(s) 359
Psp6I CCWGG 1 cut(s) 516
PspEI GGTNACC 1 cut(s) 400
PspGI CCWGG 1 cut(s) 516
PspN4I GGNNCC 1 cut(s) 348
PspPI GGNCC 2 cut(s) 347, 602
PsrI GAACNNNNNNTAC 2 cut(s) 650, 682
PsuI RGATCY 1 cut(s) 94
RsaI GTAC 1 cut(s) 232
RsaNI GTAC 1 cut(s) 231
RseI CAYNNNNRTG 3 cut(s) 546, 575, 642
SaqAI TTAA 3 cut(s) 177, 359, 717
Sau3AI GATC 3 cut(s) 69, 94, 476
Sau96I GGNCC 2 cut(s) 347, 602
ScrFI CCNGG 1 cut(s) 518
SduI GDGCHC 1 cut(s) 8
SfaNI GCATC 2 cut(s) 376, 416
Sfr274I CTCGAG 1 cut(s) 182
SfuI TTCGAA 1 cut(s) 304
SinI GGWCC 2 cut(s) 347, 602
SlaI CTCGAG 1 cut(s) 182
SmiMI CAYNNNNRTG 3 cut(s) 546, 575, 642
SmlI CTYRAG 3 cut(s) 112, 182, 262
SmoI CTYRAG 3 cut(s) 112, 182, 262
Sse9I AATT 5 cut(s) 174, 283, 502, 592, 607
SsiI CCGC 3 cut(s) 213, 310, 405
SspI AATATT 2 cut(s) 40, 363
SspMI CTAG 4 cut(s) 21, 78, 368, 711
StyD4I CCNGG 1 cut(s) 516
StyI CCWWGG 3 cut(s) 535, 626, 637
TaiI ACGT 1 cut(s) 54
TaqI TCGA 3 cut(s) 183, 304, 332
TasI AATT 5 cut(s) 174, 283, 502, 592, 607
TfiI GAWTC 3 cut(s) 306, 631, 706
Tru1I TTAA 3 cut(s) 177, 359, 717
Tru9I TTAA 3 cut(s) 177, 359, 717
TseFI GTSAC 7 cut(s) 80, 321, 466, 487, 539, 577, 678
Tsp45I GTSAC 7 cut(s) 80, 321, 466, 487, 539, 577, 678
TspDTI ATGAA 4 cut(s) 78, 185, 587, 719
Van91I CCANNNNNTGG 1 cut(s) 504
VpaK11BI GGWCC 2 cut(s) 347, 602
VspI ATTAAT 1 cut(s) 359
XceI RCATGY 1 cut(s) 653
XhoI CTCGAG 1 cut(s) 182
XmiI GTMKAC 1 cut(s) 588
XspI CTAG 4 cut(s) 21, 78, 368, 711
ZraI GACGTC 1 cut(s) 52
Zsp2I ATGCAT 1 cut(s) 91
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.