Rh5BG022800

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0009756
Physical Location & Seq
Forward (+)
1657538 .. 1659017
1480 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5BG022800.1

Sequence Viewer

Length: 1158 bp
ATGGCCAACATATCCCTTCTCTTACTGCTTCTCTGTATACTAGCCTACAATGCTCCAACGTTACAAGCAGCCTATGCCCCAAGCTACTCCTACGACCCCAAACCCACAACAAAGAATGTAGTCGACTCATGCTGGCGCAGCAATACCAATTGGGCAAGAAATCGCCAAGCCTTGGCTAACTGCGCAGTAGGCTTCGGCAAAGATGCCATTGGAGGAAAATATGGGCGTATTTACGTAGTCACCACCTCGTTTGATGACCCCATAAACCCTAAACCGGGCACCCTCCGGTATGGTGTGATCCAAACGCAGCCGTTGTGGATCGTTTTTGCCAAAGACATGGTTATCACCCTCAAGAATGAGCTCATTATGAATAGTTTCAAGACCATAGACGGTAGAGGGGCTGAAGTAGAGATTGCATATGGACCATGCATAACTGTGCAGGGTATCAGTCATGTTATTATCCATGGAATAAGTATTCATAATTGTAAGCCGGGGAAGTCCGGTATGGTTAGGAGCACTCCTACACATGTCGGGCAGCGCCTAGGGTGCGACGGTGATTCCATTAGTATCTTTGCTTCTTCGCATGTTTGGGTTGACCATTGCTTTTTGGCACATGGCGCTGATGGCCTCATTGATATCACCCATGCTTCCACGGCAGTCACCGTCACTAACAACTATTTCTCCCAGCACGACAAGGTGATGCTGCTTGGACACAATGATAAATTTACTGCAGATAAAATTATGAAGGTCACAATAGCCTTTAACCGTTTTGGGGCAGGCCTAATTGAAAGGATGCCAAGGGTCAGATTTGGCTATGCCCATGTTGCCAACAATAGATATGATGAGTGGAAGATGTACGCCATTGGTGGCAGTGCTAATCCAACCATTTTCAGTGAAGGCAACTACTTCATAGCTCCTGAAAATCATGATGCCAAACAGGTTACGAAAAGAGAGGCCTACGATGGTTGGAAGAGTTGGAAATGGAGATCTTCTAATGATGTGCTTCAAAATGGTGCTTATTTTATTCAATCTGGATGGGGAAGTTGTTATCCAATGTACACTCGAACACAGAAGTTCAAGGTCTCTCCAGGATCGATGGTTCCTGCTTTGACTTCAAATGCAGGTCCACTGCACTGCATTGTTGGTAAAGCATGTTGA
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

385

Amino Acids

42.48

Weight (kDa)

9.1

Isoelectric Point (pI)

29.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 122 - 317 4.2e-25 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: OG0009756)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G11920 AT1G30350 AT4G22080 AT4G22090
fragaria_vesca FvH4_3g01680
malus_domestica MD00G1202500.v1.1 MD05G1350000.v1.1 MD10G1324800.v1.1
prunus_persica Prupe.4G017400_v2.0.a1 Prupe.4G020600_v2.0.a1
pyrus_communis pycom10g27510
rosa_chinensis RchiOBHm_Chr5g0002531
rosa_laevigata RLG00000031037
rosa_multiflora Rmu_sc0010731.1_g000004
rosa_roxburghii Rroxscaffold_1G00073370
rosa_rugosa Rorug04G0396700
rosa_samantha Rh5AG020100 Rh5BG022800 Rh5CG022100 Rh5DG021200
rosa_wichuraiana Rw5G001850

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 184
Acc36I ACCTGC 1 cut(s) 1112
AccB1I GGYRCC 1 cut(s) 278
AccB7I CCANNNNNTGG 1 cut(s) 172
AccI GTMKAC 2 cut(s) 37, 123
AclI AACGTT 1 cut(s) 59
AclWI GGATC 3 cut(s) 292, 326, 1099
AcoI YGGCCR 1 cut(s) 3
AcsI RAATTY 1 cut(s) 722
AcuI CTGAAG 1 cut(s) 423
AfaI GTAC 2 cut(s) 857, 1058
AfiI CCNNNNNNNGG 4 cut(s) 172, 274, 275, 772
AflIII ACRYGT 1 cut(s) 526
AgsI TTSAA 6 cut(s) 379, 788, 1007, 1028, 1078, 1116
AjnI CCWGG 1 cut(s) 1087
AloI GAACNNNNNNTCC 2 cut(s) 1083, 1115
AluBI AGCT 3 cut(s) 84, 361, 914
AluI AGCT 3 cut(s) 84, 361, 914
Alw21I GWGCWC 2 cut(s) 363, 518
Alw26I GTCTC 1 cut(s) 1087
AlwI GGATC 3 cut(s) 292, 326, 1099
AoxI GGCC 4 cut(s) 3, 625, 778, 954
ApeKI GCWGC 5 cut(s) 68, 138, 307, 535, 703
ApoI RAATTY 1 cut(s) 722
Asp700I GAANNNNTTC 1 cut(s) 374
AspA2I CCTAGG 1 cut(s) 541
AspLEI GCGC 4 cut(s) 138, 185, 540, 620
AspS9I GGNCC 2 cut(s) 422, 1124
AsuC2I CCSGG 2 cut(s) 276, 492
AsuHPI GGTGA 6 cut(s) 232, 337, 566, 631, 652, 709
AvaII GGWCC 2 cut(s) 422, 1124
AvrII CCTAGG 1 cut(s) 541
BaeGI GKGCMC 1 cut(s) 281
BalI TGGCCA 1 cut(s) 5
BanI GGYRCC 1 cut(s) 278
BanII GRGCYC 1 cut(s) 363
BarI GAAGNNNNNNTAC 2 cut(s) 559, 591
Bbv12I GWGCWC 2 cut(s) 363, 518
BbvI GCAGC 5 cut(s) 80, 150, 319, 547, 690
BccI CCATC 4 cut(s) 617, 956, 1029, 1090
BceAI ACGGC 2 cut(s) 295, 669
BciT130I CCWGG 1 cut(s) 1089
BcnI CCSGG 2 cut(s) 276, 492
BcoDI GTCTC 1 cut(s) 1087
BfaI CTAG 2 cut(s) 41, 542
BfmI CTRYAG 1 cut(s) 729
BfoI RGCGCY 2 cut(s) 541, 621
BfuAI ACCTGC 1 cut(s) 1112
BglII AGATCT 1 cut(s) 986
BisI GCNGC 5 cut(s) 69, 139, 308, 536, 704
BlnI CCTAGG 1 cut(s) 541
BlsI GCNGC 5 cut(s) 70, 140, 309, 537, 705
Bme1390I CCNGG 3 cut(s) 276, 492, 1089
Bme18I GGWCC 2 cut(s) 422, 1124
BmgT120I GGNCC 2 cut(s) 422, 1124
BmiI GGNNCC 2 cut(s) 280, 1101
BmrFI CCNGG 3 cut(s) 276, 492, 1089
BmsI GCATC 4 cut(s) 193, 690, 783, 919
BpmI CTGGAG 1 cut(s) 1071
BpuEI CTTGAG 1 cut(s) 335
BpuMI CCSGG 2 cut(s) 276, 492
Bsa29I ATCGAT 1 cut(s) 1094
BsaAI YACGTR 1 cut(s) 235
BsaI GGTCTC 1 cut(s) 1087
BsaJI CCNNGG 6 cut(s) 171, 463, 491, 541, 651, 797
BsaWI WCCGGW 2 cut(s) 285, 500
BsaXI ACNNNNNCTCC 2 cut(s) 665, 695
Bsc4I CCNNNNNNNGG 4 cut(s) 172, 274, 275, 772
Bse3DI GCAATG 1 cut(s) 598
BseBI CCWGG 1 cut(s) 1089
BseCI ATCGAT 1 cut(s) 1094
BseDI CCNNGG 6 cut(s) 171, 463, 491, 541, 651, 797
BseGI GGATG 2 cut(s) 798, 1040
BseLI CCNNNNNNNGG 4 cut(s) 172, 274, 275, 772
BseMI GCAATG 1 cut(s) 598
BseSI GKGCMC 1 cut(s) 281
BseXI GCAGC 5 cut(s) 80, 150, 319, 547, 690
BseYI CCCAGC 1 cut(s) 684
BsgI GTGCAG 2 cut(s) 458, 1115
BshFI GGCC 4 cut(s) 5, 627, 780, 956
BshNI GGYRCC 1 cut(s) 278
BshVI ATCGAT 1 cut(s) 1094
BsiHKAI GWGCWC 2 cut(s) 363, 518
BsiSI CCGG 4 cut(s) 275, 286, 491, 501
BslI CCNNNNNNNGG 4 cut(s) 172, 274, 275, 772
BsmAI GTCTC 1 cut(s) 1087
BsnI GGCC 4 cut(s) 5, 627, 780, 956
Bso31I GGTCTC 1 cut(s) 1087
Bsp1286I GDGCHC 3 cut(s) 281, 363, 518
Bsp1407I TGTACA 1 cut(s) 1056
Bsp143I GATC 4 cut(s) 297, 318, 986, 1091
Bsp19I CCATGG 1 cut(s) 463
BspANI GGCC 4 cut(s) 5, 627, 780, 956
BspDI ATCGAT 1 cut(s) 1094
BspHI TCATGA 1 cut(s) 925
BspLI GGNNCC 2 cut(s) 280, 1101
BspMAI CTGCAG 1 cut(s) 733
BspMI ACCTGC 1 cut(s) 1112
BspPI GGATC 3 cut(s) 292, 326, 1099
BspT107I GGYRCC 1 cut(s) 278
BspTNI GGTCTC 1 cut(s) 1087
BsrDI GCAATG 1 cut(s) 598
BsrGI TGTACA 1 cut(s) 1056
BssECI CCNNGG 6 cut(s) 171, 463, 491, 541, 651, 797
BssMI GATC 4 cut(s) 297, 318, 986, 1091
BssNAI GTATAC 1 cut(s) 38
BssT1I CCWWGG 4 cut(s) 171, 463, 541, 797
Bst1107I GTATAC 1 cut(s) 38
Bst2UI CCWGG 1 cut(s) 1089
Bst4CI ACNGT 5 cut(s) 392, 436, 554, 664, 767
Bst6I CTCTTC 1 cut(s) 965
BstAPI GCANNNNNTGC 1 cut(s) 74
BstAUI TGTACA 1 cut(s) 1056
BstBAI YACGTR 1 cut(s) 235
BstC8I GCNNGC 2 cut(s) 134, 778
BstDSI CCRYGG 2 cut(s) 463, 651
BstF5I GGATG 2 cut(s) 798, 1040
BstH2I RGCGCY 2 cut(s) 541, 621
BstHHI GCGC 4 cut(s) 138, 185, 540, 620
BstKTI GATC 4 cut(s) 300, 321, 989, 1094
BstMAI GTCTC 1 cut(s) 1087
BstMBI GATC 4 cut(s) 297, 318, 986, 1091
BstNI CCWGG 1 cut(s) 1089
BstNSI RCATGY 3 cut(s) 530, 587, 1155
BstSCI CCNGG 3 cut(s) 274, 490, 1087
BstSFI CTRYAG 1 cut(s) 729
BstSLI GKGCMC 1 cut(s) 281
BstSNI TACGTA 1 cut(s) 235
BstV1I GCAGC 5 cut(s) 80, 150, 319, 547, 690
BstX2I RGATCY 1 cut(s) 986
BstXI CCANNNNNNTGG 1 cut(s) 337
BstYI RGATCY 1 cut(s) 986
BstZ17I GTATAC 1 cut(s) 38
Bsu15I ATCGAT 1 cut(s) 1094
BsuRI GGCC 4 cut(s) 5, 627, 780, 956
BsuTUI ATCGAT 1 cut(s) 1094
BtgI CCRYGG 2 cut(s) 463, 651
BtsCI GGATG 2 cut(s) 798, 1040
BtsI GCAGTG 3 cut(s) 877, 1127, 1132
BtsIMutI CAGTG 4 cut(s) 877, 898, 1127, 1132
BveI ACCTGC 1 cut(s) 1112
Cac8I GCNNGC 2 cut(s) 134, 778
CciI TCATGA 1 cut(s) 925
CfoI GCGC 4 cut(s) 138, 185, 540, 620
Cfr13I GGNCC 2 cut(s) 422, 1124
ClaI ATCGAT 1 cut(s) 1094
Csp6I GTAC 2 cut(s) 856, 1057
CspCI CAANNNNNGTGG 2 cut(s) 232, 267
CviQI GTAC 2 cut(s) 856, 1057
DpnI GATC 4 cut(s) 299, 320, 988, 1093
DpnII GATC 4 cut(s) 297, 318, 986, 1091
EaeI YGGCCR 1 cut(s) 3
Eam1104I CTCTTC 1 cut(s) 965
EarI CTCTTC 1 cut(s) 965
Ecl136II GAGCTC 1 cut(s) 361
Eco105I TACGTA 1 cut(s) 235
Eco130I CCWWGG 4 cut(s) 171, 463, 541, 797
Eco147I AGGCCT 2 cut(s) 780, 956
Eco24I GRGCYC 1 cut(s) 363
Eco31I GGTCTC 1 cut(s) 1087
Eco32I GATATC 1 cut(s) 637
Eco47I GGWCC 2 cut(s) 422, 1124
Eco53kI GAGCTC 1 cut(s) 361
Eco57I CTGAAG 1 cut(s) 423
EcoICRI GAGCTC 1 cut(s) 361
EcoRII CCWGG 1 cut(s) 1087
EcoRV GATATC 1 cut(s) 637
EcoT14I CCWWGG 4 cut(s) 171, 463, 541, 797
EcoT22I ATGCAT 1 cut(s) 431
EcoT38I GRGCYC 1 cut(s) 363
ErhI CCWWGG 4 cut(s) 171, 463, 541, 797
FauNDI CATATG 1 cut(s) 418
FblI GTMKAC 2 cut(s) 37, 123
Fnu4HI GCNGC 5 cut(s) 69, 139, 308, 536, 704
FokI GGATG 2 cut(s) 805, 1047
FriOI GRGCYC 1 cut(s) 363
Fsp4HI GCNGC 5 cut(s) 69, 139, 308, 536, 704
FspBI CTAG 2 cut(s) 41, 542
FspI TGCGCA 1 cut(s) 184
GlaI GCGC 4 cut(s) 137, 184, 539, 619
GluI GCNGC 5 cut(s) 69, 139, 308, 536, 704
GsaI CCCAGC 1 cut(s) 688
GsuI CTGGAG 1 cut(s) 1071
HaeII RGCGCY 2 cut(s) 541, 621
HaeIII GGCC 4 cut(s) 5, 627, 780, 956
HapII CCGG 4 cut(s) 275, 286, 491, 501
HhaI GCGC 4 cut(s) 138, 185, 540, 620
Hin6I GCGC 4 cut(s) 136, 183, 538, 618
HinP1I GCGC 4 cut(s) 136, 183, 538, 618
HincII GTYRAC 2 cut(s) 124, 595
HindII GTYRAC 2 cut(s) 124, 595
HinfI GANTC 2 cut(s) 125, 557
HpaII CCGG 4 cut(s) 275, 286, 491, 501
HphI GGTGA 6 cut(s) 232, 337, 566, 631, 652, 709
Hpy166II GTNNAC 5 cut(s) 38, 124, 595, 1059, 1127
Hpy188I TCNGA 1 cut(s) 806
Hpy188III TCNNGA 5 cut(s) 352, 379, 917, 926, 1032
Hpy8I GTNNAC 5 cut(s) 38, 124, 595, 1059, 1127
Hpy99I CGWCG 1 cut(s) 554
HpyAV CCTTC 3 cut(s) 26, 739, 890
HpyCH4III ACNGT 5 cut(s) 392, 436, 554, 664, 767
HpyCH4IV ACGT 2 cut(s) 59, 234
HpyCH4V TGCA 7 cut(s) 416, 429, 439, 731, 1121, 1132, 1137
HpySE526I ACGT 2 cut(s) 59, 234
HspAI GCGC 4 cut(s) 136, 183, 538, 618
Kzo9I GATC 4 cut(s) 297, 318, 986, 1091
LmnI GCTCC 3 cut(s) 58, 513, 919
Lsp1109I GCAGC 5 cut(s) 80, 150, 319, 547, 690
LweI GCATC 4 cut(s) 193, 690, 783, 919
MaeI CTAG 2 cut(s) 41, 542
MaeII ACGT 2 cut(s) 59, 234
MaeIII GTNAC 6 cut(s) 60, 238, 658, 664, 748, 940
MalI GATC 4 cut(s) 299, 320, 988, 1093
MboI GATC 4 cut(s) 297, 318, 986, 1091
MboII GAAGA 4 cut(s) 570, 862, 981, 982
MfeI CAATTG 1 cut(s) 148
MflI RGATCY 1 cut(s) 986
MhlI GDGCHC 3 cut(s) 281, 363, 518
MlsI TGGCCA 1 cut(s) 5
MluCI AATT 5 cut(s) 148, 481, 722, 738, 783
MluNI TGGCCA 1 cut(s) 5
MlyI GAGTC 1 cut(s) 119
MmeI TCCRAC 4 cut(s) 80, 905, 947, 956
MnlI CCTC 7 cut(s) 206, 256, 293, 359, 389, 638, 946
Mox20I TGGCCA 1 cut(s) 5
Mph1103I ATGCAT 1 cut(s) 431
MroXI GAANNNNTTC 1 cut(s) 374
MscI TGGCCA 1 cut(s) 5
MseI TTAA 1 cut(s) 762
MslI CAYNNNNRTG 1 cut(s) 434
Msp20I TGGCCA 1 cut(s) 5
MspI CCGG 4 cut(s) 275, 286, 491, 501
MspR9I CCNGG 3 cut(s) 276, 492, 1089
MunI CAATTG 1 cut(s) 148
MvaI CCWGG 1 cut(s) 1089
NciI CCSGG 2 cut(s) 276, 492
NcoI CCATGG 1 cut(s) 463
NdeI CATATG 1 cut(s) 418
NdeII GATC 4 cut(s) 297, 318, 986, 1091
NlaIV GGNNCC 2 cut(s) 280, 1101
NmuCI GTSAC 4 cut(s) 238, 658, 664, 748
NsbI TGCGCA 1 cut(s) 184
NsiI ATGCAT 1 cut(s) 431
NspI RCATGY 3 cut(s) 530, 587, 1155
PagI TCATGA 1 cut(s) 925
PceI AGGCCT 2 cut(s) 780, 956
PciI ACATGT 1 cut(s) 526
PdmI GAANNNNTTC 1 cut(s) 374
PfeI GAWTC 1 cut(s) 557
PflMI CCANNNNNTGG 1 cut(s) 172
PfoI TCCNGGA 1 cut(s) 1087
PkrI GCNGC 5 cut(s) 70, 140, 309, 537, 705
PleI GAGTC 1 cut(s) 119
PpsI GAGTC 1 cut(s) 119
Ppu21I YACGTR 1 cut(s) 235
PscI ACATGT 1 cut(s) 526
Psp124BI GAGCTC 1 cut(s) 363
Psp1406I AACGTT 1 cut(s) 59
Psp6I CCWGG 1 cut(s) 1087
PspFI CCCAGC 1 cut(s) 684
PspGI CCWGG 1 cut(s) 1087
PspN4I GGNNCC 2 cut(s) 280, 1101
PspPI GGNCC 2 cut(s) 422, 1124
PstI CTGCAG 1 cut(s) 733
PsuI RGATCY 1 cut(s) 986
RsaI GTAC 2 cut(s) 857, 1058
RsaNI GTAC 2 cut(s) 856, 1057
RseI CAYNNNNRTG 1 cut(s) 434
SacI GAGCTC 1 cut(s) 363
SalI GTCGAC 1 cut(s) 122
SaqAI TTAA 1 cut(s) 762
SatI GCNGC 5 cut(s) 69, 139, 308, 536, 704
Sau3AI GATC 4 cut(s) 297, 318, 986, 1091
Sau96I GGNCC 2 cut(s) 422, 1124
SchI GAGTC 1 cut(s) 119
ScrFI CCNGG 3 cut(s) 276, 492, 1089
SduI GDGCHC 3 cut(s) 281, 363, 518
SfaNI GCATC 4 cut(s) 193, 690, 783, 919
SfcI CTRYAG 1 cut(s) 729
SinI GGWCC 2 cut(s) 422, 1124
SmiMI CAYNNNNRTG 1 cut(s) 434
SmlI CTYRAG 1 cut(s) 350
SmoI CTYRAG 1 cut(s) 350
SnaBI TACGTA 1 cut(s) 235
Sse9I AATT 5 cut(s) 148, 481, 722, 738, 783
SseBI AGGCCT 2 cut(s) 780, 956
SspMI CTAG 2 cut(s) 41, 542
SstI GAGCTC 1 cut(s) 363
StuI AGGCCT 2 cut(s) 780, 956
StyD4I CCNGG 3 cut(s) 274, 490, 1087
StyI CCWWGG 4 cut(s) 171, 463, 541, 797
TaaI ACNGT 5 cut(s) 392, 436, 554, 664, 767
TaiI ACGT 2 cut(s) 62, 237
TaqI TCGA 3 cut(s) 123, 1063, 1094
TasI AATT 5 cut(s) 148, 481, 722, 738, 783
TatI WGTACW 1 cut(s) 1056
TfiI GAWTC 1 cut(s) 557
Tru1I TTAA 1 cut(s) 762
Tru9I TTAA 1 cut(s) 762
TscAI CASTG 4 cut(s) 877, 898, 1134, 1139
TseFI GTSAC 4 cut(s) 238, 658, 664, 748
TseI GCWGC 5 cut(s) 68, 138, 307, 535, 703
Tsp45I GTSAC 4 cut(s) 238, 658, 664, 748
TspDTI ATGAA 4 cut(s) 383, 467, 758, 898
TspRI CASTG 4 cut(s) 877, 898, 1134, 1139
Van91I CCANNNNNTGG 1 cut(s) 172
VpaK11BI GGWCC 2 cut(s) 422, 1124
XapI RAATTY 1 cut(s) 722
XceI RCATGY 3 cut(s) 530, 587, 1155
XmaJI CCTAGG 1 cut(s) 541
XmiI GTMKAC 2 cut(s) 37, 123
XmnI GAANNNNTTC 1 cut(s) 374
XspI CTAG 2 cut(s) 41, 542
Zsp2I ATGCAT 1 cut(s) 431
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.