Rh4AG075300

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4A
OG0010648
Physical Location & Seq
Reverse (-)
15360131 .. 15365167
5037 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4AG075300.1

Sequence Viewer

Length: 1119 bp
ATGGTTGACATGAGTATCCGCAACAGCACTGAAAGGAGAAAGCTGGGCTACTTCTCATGTGGAACTGGAAATCCTATTGATGATTGCTGGCGTTGTGATCCCAACTGGCAAAAGAACCGCAAGCGTCTTGCAGACTGTGGCATTGGTTTCGGCAGAAATGCCATTGGTGGTCGTGATGGACGCTTCTATGTTGTCACTGACCCTAAAGATGATGATCCCGTTAACCCCAGACCCGGTACCCTGCGCCATGCTGTCATCCAGGATGAGCCTCTCTGGATTGTGTTCAAACGTGACATGGTGATCCAATTGAAGCAGGAGCTTCTCATGAATAGCTTCAAGACCATTGATGGCCGTGGAGTCAATGTCCACATTGCTAATGGAGCATGCATTACAATCCAGTTTGTTACAAACATTATAGTTCATGGTCTGCATATCCATGACTGCAAGCCTACAGGAAATGCTATGGTGAGGAGCTCCCCATCTCACTTTGGGTGGAGGACAATGGCTGATGGTGATGCTGTCTCCATCTTCGGGTCAAGCCATATCTGGGTTGATCACAATTCCCTCTCCAATTGTGCTGATGGTCTTGTTGATGCTGTCATGGGGTCAACTGCTATTACCATCTCAAACAACCACTTTACCCACCACAATGAAGTTATGCTGTTGGGCCACAGTGATTCTTATACCAGGGACAAGCAAATGCAGGTGACTATTGCCTACAACCACTTTGGAGAGGGACTTATCCAACGAATGCCAAGGTGTAGACACGGATATTTCCATGTGGTGAACAATGACTACACTCACTGGGAGATGTATGCCATTGGTGGAAGTGCAGAACCCACTATCAACAGCCAAGGCAACAGATATGCAGCTCCAGCCAACCCCTTTGCAAAGGAGGTTACCAAGAGAGTCGAGACAGCACAAACTCAGTGGAGGGGCTGGAACTGGAGGTCAGAAGGTGATCTTCTACTCAATGGTGCCTTCTTCACTCCATCTGGAGCTGGAGCTTCAGCTGTCTATGCCAGGGCCTCAAGCTTGGGAGCCAAGTCATCTGCCATGGTGGGAACCATAACTGCTGGTGCTGGTGTACTGGGGTGCCGCAGAGGACATACCTGCTAG
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

372

Amino Acids

41.05

Weight (kDa)

8.66

Isoelectric Point (pI)

34.49

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 105 - 305 2e-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) 694
Acc36I ACCTGC 1 cut(s) 694
Acc65I GGTACC 1 cut(s) 236
AccB1I GGYRCC 3 cut(s) 236, 977, 1095
AccI GTMKAC 1 cut(s) 763
AciI CCGC 3 cut(s) 19, 118, 1099
AclWI GGATC 3 cut(s) 92, 209, 295
AcoI YGGCCR 1 cut(s) 349
AcuI CTGAAG 1 cut(s) 993
AfaI GTAC 2 cut(s) 238, 1089
AfiI CCNNNNNNNGG 3 cut(s) 233, 531, 547
AgsI TTSAA 3 cut(s) 286, 310, 337
AjnI CCWGG 3 cut(s) 258, 686, 1022
AloI GAACNNNNNNTCC 2 cut(s) 55, 87
AluBI AGCT 9 cut(s) 43, 319, 333, 474, 872, 1001, 1007, 1013, 1035
AluI AGCT 9 cut(s) 43, 319, 333, 474, 872, 1001, 1007, 1013, 1035
Alw21I GWGCWC 1 cut(s) 476
Alw26I GTCTC 2 cut(s) 526, 908
AlwI GGATC 3 cut(s) 92, 209, 295
AoxI GGCC 3 cut(s) 349, 667, 1026
ApeKI GCWGC 1 cut(s) 869
Asp700I GAANNNNTTC 1 cut(s) 332
Asp718I GGTACC 1 cut(s) 236
AspLEI GCGC 1 cut(s) 246
AspS9I GGNCC 2 cut(s) 667, 1026
AsuC2I CCSGG 1 cut(s) 234
AsuHPI GGTGA 6 cut(s) 310, 478, 524, 718, 796, 971
BaeI ACNNNNGTAYC 1 cut(s) 31
BanI GGYRCC 3 cut(s) 236, 977, 1095
BanII GRGCYC 1 cut(s) 476
Bbv12I GWGCWC 1 cut(s) 476
BbvI GCAGC 1 cut(s) 881
BccI CCATC 8 cut(s) 170, 341, 487, 503, 533, 575, 629, 1000
BceAI ACGGC 1 cut(s) 336
BcgI CGANNNNNNTGC 2 cut(s) 130, 164
BciT130I CCWGG 3 cut(s) 260, 688, 1024
BciVI GTATCC 1 cut(s) 26
BclI TGATCA 1 cut(s) 553
BcnI CCSGG 1 cut(s) 234
BcoDI GTCTC 2 cut(s) 526, 908
BfaI CTAG 1 cut(s) 1117
BfmI CTRYAG 1 cut(s) 450
BfuAI ACCTGC 1 cut(s) 694
BfuI GTATCC 1 cut(s) 26
BisI GCNGC 2 cut(s) 870, 1099
BlsI GCNGC 2 cut(s) 871, 1100
Bme1390I CCNGG 4 cut(s) 234, 260, 688, 1024
BmgT120I GGNCC 2 cut(s) 667, 1026
BmiI GGNNCC 5 cut(s) 238, 979, 1042, 1066, 1097
BmrFI CCNGG 4 cut(s) 234, 260, 688, 1024
BmrI ACTGGG 2 cut(s) 814, 1100
BmsI GCATC 2 cut(s) 505, 583
BmuI ACTGGG 2 cut(s) 814, 1100
BpmI CTGGAG 4 cut(s) 858, 967, 1017, 1023
BpuEI CTTGAG 1 cut(s) 1015
BpuMI CCSGG 1 cut(s) 234
BsaBI GATNNNNATC 1 cut(s) 213
BsaJI CCNNGG 6 cut(s) 352, 687, 755, 853, 1023, 1056
BsaXI ACNNNNNCTCC 2 cut(s) 348, 378
Bsc4I CCNNNNNNNGG 3 cut(s) 233, 531, 547
Bse1I ACTGG 6 cut(s) 70, 110, 397, 809, 950, 1095
Bse3DI GCAATG 1 cut(s) 369
Bse8I GATNNNNATC 1 cut(s) 213
BseBI CCWGG 3 cut(s) 260, 688, 1024
BseDI CCNNGG 6 cut(s) 352, 687, 755, 853, 1023, 1056
BseGI GGATG 2 cut(s) 255, 268
BseJI GATNNNNATC 1 cut(s) 213
BseLI CCNNNNNNNGG 3 cut(s) 233, 531, 547
BseMI GCAATG 1 cut(s) 369
BseMII CTCAG 1 cut(s) 941
BseNI ACTGG 6 cut(s) 70, 110, 397, 809, 950, 1095
BseRI GAGGAG 1 cut(s) 484
BseXI GCAGC 1 cut(s) 881
BseYI CCCAGC 1 cut(s) 43
BsgI GTGCAG 1 cut(s) 852
BshFI GGCC 3 cut(s) 351, 669, 1028
BshNI GGYRCC 3 cut(s) 236, 977, 1095
BsiHKAI GWGCWC 1 cut(s) 476
BsiSI CCGG 1 cut(s) 234
BslFI GGGAC 2 cut(s) 704, 750
BslI CCNNNNNNNGG 3 cut(s) 233, 531, 547
BsmAI GTCTC 2 cut(s) 526, 908
BsmFI GGGAC 2 cut(s) 704, 750
BsmI GAATGC 1 cut(s) 756
BsnI GGCC 3 cut(s) 351, 669, 1028
Bsp1286I GDGCHC 1 cut(s) 476
Bsp143I GATC 5 cut(s) 97, 214, 300, 553, 961
Bsp19I CCATGG 1 cut(s) 1056
BspACI CCGC 3 cut(s) 19, 118, 1099
BspANI GGCC 3 cut(s) 351, 669, 1028
BspCNI CTCAG 1 cut(s) 940
BspHI TCATGA 1 cut(s) 324
BspLI GGNNCC 5 cut(s) 238, 979, 1042, 1066, 1097
BspMI ACCTGC 1 cut(s) 694
BspPI GGATC 3 cut(s) 92, 209, 295
BspT107I GGYRCC 3 cut(s) 236, 977, 1095
BsrDI GCAATG 1 cut(s) 369
BsrI ACTGG 6 cut(s) 70, 110, 397, 809, 950, 1095
BssECI CCNNGG 6 cut(s) 352, 687, 755, 853, 1023, 1056
BssMI GATC 5 cut(s) 97, 214, 300, 553, 961
BssT1I CCWWGG 3 cut(s) 755, 853, 1056
Bst2UI CCWGG 3 cut(s) 260, 688, 1024
Bst4CI ACNGT 2 cut(s) 137, 674
BstC8I GCNNGC 4 cut(s) 89, 122, 385, 446
BstDEI CTNAG 1 cut(s) 927
BstDSI CCRYGG 2 cut(s) 352, 1056
BstEII GGTNACC 1 cut(s) 898
BstF5I GGATG 2 cut(s) 255, 268
BstHHI GCGC 1 cut(s) 246
BstKTI GATC 5 cut(s) 100, 217, 303, 556, 964
BstMAI GTCTC 2 cut(s) 526, 908
BstMBI GATC 5 cut(s) 97, 214, 300, 553, 961
BstMWI GCNNNNNNNGC 3 cut(s) 380, 875, 1019
BstNI CCWGG 3 cut(s) 260, 688, 1024
BstNSI RCATGY 1 cut(s) 387
BstPI GGTNACC 1 cut(s) 898
BstSCI CCNGG 4 cut(s) 232, 258, 686, 1022
BstSFI CTRYAG 1 cut(s) 450
BstV1I GCAGC 1 cut(s) 881
BsuI GTATCC 1 cut(s) 26
BsuRI GGCC 3 cut(s) 351, 669, 1028
BtgI CCRYGG 2 cut(s) 352, 1056
BtsCI GGATG 2 cut(s) 255, 268
BtsIMutI CAGTG 5 cut(s) 27, 195, 679, 802, 935
BveI ACCTGC 1 cut(s) 694
Cac8I GCNNGC 4 cut(s) 89, 122, 385, 446
CciI TCATGA 1 cut(s) 324
CfoI GCGC 1 cut(s) 246
Cfr13I GGNCC 2 cut(s) 667, 1026
CseI GACGC 2 cut(s) 113, 189
Csp6I GTAC 2 cut(s) 237, 1088
CspCI CAANNNNNGTGG 2 cut(s) 911, 946
CviQI GTAC 2 cut(s) 237, 1088
DdeI CTNAG 1 cut(s) 927
DpnI GATC 5 cut(s) 99, 216, 302, 555, 963
DpnII GATC 5 cut(s) 97, 214, 300, 553, 961
EaeI YGGCCR 1 cut(s) 349
Ecl136II GAGCTC 1 cut(s) 474
Eco130I CCWWGG 3 cut(s) 755, 853, 1056
Eco24I GRGCYC 1 cut(s) 476
Eco53kI GAGCTC 1 cut(s) 474
Eco57I CTGAAG 1 cut(s) 993
Eco91I GGTNACC 1 cut(s) 898
EcoICRI GAGCTC 1 cut(s) 474
EcoO109I RGGNCCY 1 cut(s) 1026
EcoO65I GGTNACC 1 cut(s) 898
EcoRII CCWGG 3 cut(s) 258, 686, 1022
EcoT14I CCWWGG 3 cut(s) 755, 853, 1056
EcoT22I ATGCAT 1 cut(s) 389
EcoT38I GRGCYC 1 cut(s) 476
ErhI CCWWGG 3 cut(s) 755, 853, 1056
FalI AAGNNNNNCTT 2 cut(s) 948, 980
FaqI GGGAC 2 cut(s) 704, 750
FbaI TGATCA 1 cut(s) 553
FblI GTMKAC 1 cut(s) 763
Fnu4HI GCNGC 2 cut(s) 870, 1099
FokI GGATG 2 cut(s) 242, 275
FriOI GRGCYC 1 cut(s) 476
Fsp4HI GCNGC 2 cut(s) 870, 1099
FspBI CTAG 1 cut(s) 1117
GlaI GCGC 1 cut(s) 245
GluI GCNGC 2 cut(s) 870, 1099
GsaI CCCAGC 1 cut(s) 47
GsuI CTGGAG 4 cut(s) 858, 967, 1017, 1023
HaeIII GGCC 3 cut(s) 351, 669, 1028
HapII CCGG 1 cut(s) 234
HgaI GACGC 2 cut(s) 113, 189
HhaI GCGC 1 cut(s) 246
Hin6I GCGC 1 cut(s) 244
HinP1I GCGC 1 cut(s) 244
HincII GTYRAC 3 cut(s) 7, 223, 609
HindII GTYRAC 3 cut(s) 7, 223, 609
HindIII AAGCTT 1 cut(s) 1033
HinfI GANTC 3 cut(s) 357, 677, 909
HpaI GTTAAC 1 cut(s) 223
HpaII CCGG 1 cut(s) 234
HphI GGTGA 6 cut(s) 310, 478, 524, 718, 796, 971
Hpy166II GTNNAC 7 cut(s) 7, 223, 367, 609, 764, 787, 1088
Hpy188I TCNGA 1 cut(s) 955
Hpy188III TCNNGA 6 cut(s) 173, 274, 325, 337, 913, 996
Hpy8I GTNNAC 7 cut(s) 7, 223, 367, 609, 764, 787, 1088
HpyAV CCTTC 2 cut(s) 950, 991
HpyCH4III ACNGT 2 cut(s) 137, 674
HpyCH4IV ACGT 1 cut(s) 289
HpyCH4V TGCA 8 cut(s) 131, 387, 430, 444, 703, 833, 869, 890
HpyF10VI GCNNNNNNNGC 3 cut(s) 380, 875, 1019
HpyF3I CTNAG 1 cut(s) 927
HpySE526I ACGT 1 cut(s) 289
HspAI GCGC 1 cut(s) 244
KpnI GGTACC 1 cut(s) 240
Ksp22I TGATCA 1 cut(s) 553
KspAI GTTAAC 1 cut(s) 223
Kzo9I GATC 5 cut(s) 97, 214, 300, 553, 961
LmnI GCTCC 8 cut(s) 316, 380, 471, 479, 877, 998, 1004, 1040
Lsp1109I GCAGC 1 cut(s) 881
LweI GCATC 2 cut(s) 505, 583
MaeI CTAG 1 cut(s) 1117
MaeII ACGT 1 cut(s) 289
MaeIII GTNAC 5 cut(s) 193, 290, 403, 706, 898
MalI GATC 5 cut(s) 99, 216, 302, 555, 963
MboI GATC 5 cut(s) 97, 214, 300, 553, 961
MboII GAAGA 3 cut(s) 520, 956, 976
MfeI CAATTG 2 cut(s) 305, 571
MhlI GDGCHC 1 cut(s) 476
MluCI AATT 3 cut(s) 305, 559, 571
MlyI GAGTC 2 cut(s) 366, 918
MmeI TCCRAC 1 cut(s) 769
Mph1103I ATGCAT 1 cut(s) 389
MroXI GAANNNNTTC 1 cut(s) 332
MseI TTAA 1 cut(s) 222
MslI CAYNNNNRTG 2 cut(s) 435, 648
MspA1I CMGCKG 1 cut(s) 1013
MspI CCGG 1 cut(s) 234
MspR9I CCNGG 4 cut(s) 234, 260, 688, 1024
MunI CAATTG 2 cut(s) 305, 571
Mva1269I GAATGC 1 cut(s) 756
MvaI CCWGG 3 cut(s) 260, 688, 1024
MwoI GCNNNNNNNGC 3 cut(s) 380, 875, 1019
NciI CCSGG 1 cut(s) 234
NcoI CCATGG 1 cut(s) 1056
NdeII GATC 5 cut(s) 97, 214, 300, 553, 961
NlaIV GGNNCC 5 cut(s) 238, 979, 1042, 1066, 1097
NmuCI GTSAC 3 cut(s) 193, 290, 706
NsiI ATGCAT 1 cut(s) 389
NspI RCATGY 1 cut(s) 387
PaeI GCATGC 1 cut(s) 387
PagI TCATGA 1 cut(s) 324
PaqCI CACCTGC 1 cut(s) 694
PctI GAATGC 1 cut(s) 756
PdmI GAANNNNTTC 1 cut(s) 332
PfeI GAWTC 1 cut(s) 677
PfoI TCCNGGA 1 cut(s) 258
PkrI GCNGC 2 cut(s) 871, 1100
PleI GAGTC 2 cut(s) 365, 917
PpsI GAGTC 2 cut(s) 365, 917
Psp124BI GAGCTC 1 cut(s) 476
Psp6I CCWGG 3 cut(s) 258, 686, 1022
PspEI GGTNACC 1 cut(s) 898
PspFI CCCAGC 1 cut(s) 43
PspGI CCWGG 3 cut(s) 258, 686, 1022
PspN4I GGNNCC 5 cut(s) 238, 979, 1042, 1066, 1097
PspPI GGNCC 2 cut(s) 667, 1026
PsrI GAACNNNNNNTAC 2 cut(s) 779, 811
PvuII CAGCTG 1 cut(s) 1013
RsaI GTAC 2 cut(s) 238, 1089
RsaNI GTAC 2 cut(s) 237, 1088
RseI CAYNNNNRTG 2 cut(s) 435, 648
SacI GAGCTC 1 cut(s) 476
SaqAI TTAA 1 cut(s) 222
SatI GCNGC 2 cut(s) 870, 1099
Sau3AI GATC 5 cut(s) 97, 214, 300, 553, 961
Sau96I GGNCC 2 cut(s) 667, 1026
SchI GAGTC 2 cut(s) 366, 918
ScrFI CCNGG 4 cut(s) 234, 260, 688, 1024
SduI GDGCHC 1 cut(s) 476
SfaNI GCATC 2 cut(s) 505, 583
SfcI CTRYAG 1 cut(s) 450
SmiMI CAYNNNNRTG 2 cut(s) 435, 648
SmlI CTYRAG 1 cut(s) 1030
SmoI CTYRAG 1 cut(s) 1030
SphI GCATGC 1 cut(s) 387
Sse9I AATT 3 cut(s) 305, 559, 571
SsiI CCGC 3 cut(s) 19, 118, 1099
SspMI CTAG 1 cut(s) 1117
SstI GAGCTC 1 cut(s) 476
StyD4I CCNGG 4 cut(s) 232, 258, 686, 1022
StyI CCWWGG 3 cut(s) 755, 853, 1056
TaaI ACNGT 2 cut(s) 137, 674
TaiI ACGT 1 cut(s) 292
TaqI TCGA 1 cut(s) 912
TasI AATT 3 cut(s) 305, 559, 571
TatI WGTACW 1 cut(s) 1087
TauI GCSGC 1 cut(s) 1101
TfiI GAWTC 1 cut(s) 677
Tru1I TTAA 1 cut(s) 222
Tru9I TTAA 1 cut(s) 222
TscAI CASTG 5 cut(s) 34, 202, 679, 809, 935
TseFI GTSAC 3 cut(s) 193, 290, 706
TseI GCWGC 1 cut(s) 869
Tsp45I GTSAC 3 cut(s) 193, 290, 706
TspDTI ATGAA 3 cut(s) 341, 410, 666
TspGWI ACGGA 1 cut(s) 783
TspRI CASTG 5 cut(s) 34, 202, 679, 809, 935
XceI RCATGY 1 cut(s) 387
XcmI CCANNNNNNNNNTGG 1 cut(s) 374
XmiI GTMKAC 1 cut(s) 763
XmnI GAANNNNTTC 1 cut(s) 332
XspI CTAG 1 cut(s) 1117
Zsp2I ATGCAT 1 cut(s) 389
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.