Rh6CG253700

Exopolygalacturonase-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6C
OG0014404
Physical Location & Seq
Reverse (-)
42440005 .. 42441977
1973 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6CG253700.1

Sequence Viewer

Length: 1266 bp
ATGATGAGCCTCGACTACTTCTATGTTAGATTGCTCTTATTGCTGTCCTTATTTTGCTTCGAATGTGTGTTTGGCAGAGAAAGAGGAGCAGGTTCAGGCTTGCAGACCATCAATGTAGATCGCAAGGCCAAAAGCTCTCTTCTTTTTAATGTCAAGAGCTTTGGTGCCAAAGCAGATGGCCAAACCGATGACAGCAAGGCCTTCACAGCAGCATGGAAAGAGGCTTGCCAGTCCAAAGGTAGAGTCCACTTAATAATCCCAAGAGGAACATACATGATTGGCCCTCTTAAGTTTTCAGGCCCCTGCCAAAACGTATCGGCTCTAAATCTTCGAGTAAAGGGTTACTTGAAGGCTACAGCAGAGTTGTCCAAGTATGAATTCGGTGGCGGTTGGATTGAATTTGCTTGGATGAAGGGGCTAACCTTGACCGGAGGCGGAACCTTTGATGGTCAAGGTGCTAAAGCCTGGCCTCACAATAAGTGCTCTAAAGACTCCAATTGCAAACTTCTTCCAACTAGTTTGAAATTTGTTGCAATGAATAAGACAGTGATCCGGGGCATATCCTCGGTGAACAGCAAGTTCTTTCATATAGCTGTTGTGGAATGTCACAACTTCAAAGGTAGTAAACTCAAGATTCAAGCCCCAGAAACTAGTCCTAATACTGATGGAATCCACATTGAACGAAGCTCGAGTGTGTACTTCTCTTCGTCACACATTGCTACTGGCGATGACTGCATCTCAGTTGGACAAGGGAACTCCCACGTCACCATAACTAGCATTGCTTGTGGACCTGGTCATGGCATCAGTGTGGGAAGTTTGGGAAAATATCCGAATGAAGGAGATGTTAGTGGGCTTGTGGTCAGAGACTGCACCATTTCAGGTACCACAAATGGTATTAGGATCAAGACATGGGCTAACTCTCCAGGTAGAAGTGCAGCCACCAACATGACATTCACAAACATCATCATGAACAATGTGACCAACCCCATCATAATCGATCAGACATATTGTCCATTCACGTCTTGCGCTTCTAAGGTGCCATCCAAAGTGAAGCTGAGTGACATTTACTTCAAGAACATAAGAGGGACCTCGTCGTCTCAAGTAGCGGTTGCACTTGAATGTAGCAAAGGGATTCCATGCCAGAACATTTACCTTGAAGATGTTCATCTGGACTTGTCATCTGGGAAGAAGGAAGCCACTTCAACTTGCAGTAATGTTAAAGCCAAATTCATTGGCACCCAAATCCCACCACCATGTACTGATTAG

Protein Analysis

421

Amino Acids

45.29

Weight (kDa)

9.17

Isoelectric Point (pI)

35.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 49 - 93 8e-07 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 76 - 409 3.5e-93 Glycosyl hydrolases family 28
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: OG0014404)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G18180
fragaria_vesca FvH4_2g16950
malus_domestica MD05G1141300.v1.1 MD05G1142200.v1.1
prunus_persica Prupe.8G181300_v2.0.a1
pyrus_communis pycom05g13670
rosa_chinensis RchiOBHm_Chr6g0281151
rosa_laevigata RLG00000012990
rosa_multiflora Rmu_co8202118.1_g000001 Rmu_sc0035236.1_g000002
rosa_roxburghii Rroxscaffold_7G00187250
rosa_rugosa Rorug06G0139300
rosa_samantha Rh6AG251100 Rh6BG254300 Rh6CG253700 Rh6DG245700
rosa_wichuraiana Rw6G021800

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 1093
Acc36I ACCTGC 1 cut(s) 80
Acc65I GGTACC 1 cut(s) 881
AccB1I GGYRCC 4 cut(s) 164, 881, 1036, 1235
AciI CCGC 3 cut(s) 387, 435, 1106
AclWI GGATC 2 cut(s) 544, 908
AcoI YGGCCR 1 cut(s) 178
AcsI RAATTY 4 cut(s) 377, 398, 524, 1226
AfaI GTAC 3 cut(s) 698, 883, 1258
AfiI CCNNNNNNNGG 2 cut(s) 797, 836
AflII CTTAAG 1 cut(s) 287
AhdI GACNNNNNGTC 1 cut(s) 1008
AhlI ACTAGT 2 cut(s) 515, 650
AjiI CACGTC 2 cut(s) 763, 1020
AjnI CCWGG 3 cut(s) 464, 790, 922
AjuI GAANNNNNNNTTGG 6 cut(s) 54, 86, 362, 394, 935, 967
AluBI AGCT 5 cut(s) 135, 159, 593, 687, 1054
AluI AGCT 5 cut(s) 135, 159, 593, 687, 1054
Alw21I GWGCWC 1 cut(s) 485
Alw26I GTCTC 2 cut(s) 858, 1101
AlwI GGATC 2 cut(s) 544, 908
AlwNI CAGNNNCTG 1 cut(s) 867
Ama87I CYCGRG 1 cut(s) 688
AoxI GGCC 6 cut(s) 126, 178, 198, 280, 298, 467
ApeKI GCWGC 2 cut(s) 209, 935
ApoI RAATTY 4 cut(s) 377, 398, 524, 1226
ArsI GACNNNNNNTTYG 2 cut(s) 228, 260
Asp700I GAANNNNTTC 1 cut(s) 1161
Asp718I GGTACC 1 cut(s) 881
AspLEI GCGC 1 cut(s) 1028
AspS9I GGNCC 4 cut(s) 281, 299, 788, 1086
AsuC2I CCSGG 1 cut(s) 554
AsuHPI GGTGA 2 cut(s) 580, 757
AsuII TTCGAA 1 cut(s) 60
AvaI CYCGRG 1 cut(s) 688
AvaII GGWCC 2 cut(s) 788, 1086
BalI TGGCCA 1 cut(s) 180
BanI GGYRCC 4 cut(s) 164, 881, 1036, 1235
Bbv12I GWGCWC 1 cut(s) 485
BbvI GCAGC 2 cut(s) 221, 947
BccI CCATC 6 cut(s) 116, 170, 440, 659, 995, 1048
BciT130I CCWGG 3 cut(s) 466, 792, 924
BcnI CCSGG 1 cut(s) 554
BcoDI GTCTC 2 cut(s) 858, 1101
BcuI ACTAGT 2 cut(s) 515, 650
BfaI CTAG 3 cut(s) 516, 651, 774
BfmI CTRYAG 1 cut(s) 354
BfrI CTTAAG 1 cut(s) 287
BfuAI ACCTGC 1 cut(s) 80
BisI GCNGC 2 cut(s) 210, 936
BlsI GCNGC 2 cut(s) 211, 937
Bme1390I CCNGG 4 cut(s) 466, 554, 792, 924
Bme18I GGWCC 2 cut(s) 788, 1086
BmeRI GACNNNNNGTC 1 cut(s) 1008
BmeT110I CYCGRG 1 cut(s) 688
BmgBI CACGTC 2 cut(s) 763, 1020
BmgT120I GGNCC 4 cut(s) 281, 299, 788, 1086
BmiI GGNNCC 7 cut(s) 166, 301, 439, 883, 1038, 1087, 1237
BmrFI CCNGG 4 cut(s) 466, 554, 792, 924
BmsI GCATC 2 cut(s) 744, 810
BpmI CTGGAG 1 cut(s) 906
Bpu14I TTCGAA 1 cut(s) 60
BpuEI CTTGAG 2 cut(s) 614, 1083
BpuMI CCSGG 1 cut(s) 554
Bsa29I ATCGAT 1 cut(s) 996
BsaBI GATNNNNATC 1 cut(s) 1164
BsaJI CCNNGG 2 cut(s) 553, 564
BsaWI WCCGGW 1 cut(s) 428
Bsc4I CCNNNNNNNGG 2 cut(s) 797, 836
Bse1I ACTGG 2 cut(s) 229, 727
Bse3DI GCAATG 3 cut(s) 540, 714, 777
Bse8I GATNNNNATC 1 cut(s) 1164
BseBI CCWGG 3 cut(s) 466, 792, 924
BseCI ATCGAT 1 cut(s) 996
BseDI CCNNGG 2 cut(s) 553, 564
BseGI GGATG 2 cut(s) 414, 1040
BseJI GATNNNNATC 1 cut(s) 1164
BseLI CCNNNNNNNGG 2 cut(s) 797, 836
BseMI GCAATG 3 cut(s) 540, 714, 777
BseMII CTCAG 2 cut(s) 753, 1046
BseNI ACTGG 2 cut(s) 229, 727
BseRI GAGGAG 1 cut(s) 99
BseXI GCAGC 2 cut(s) 221, 947
BsgI GTGCAG 2 cut(s) 853, 954
BshFI GGCC 6 cut(s) 128, 180, 200, 282, 300, 469
BshNI GGYRCC 4 cut(s) 164, 881, 1036, 1235
BshVI ATCGAT 1 cut(s) 996
BsiHKAI GWGCWC 1 cut(s) 485
BsiHKCI CYCGRG 1 cut(s) 688
BsiSI CCGG 2 cut(s) 429, 553
BslFI GGGAC 1 cut(s) 1099
BslI CCNNNNNNNGG 2 cut(s) 797, 836
BsmAI GTCTC 2 cut(s) 858, 1101
BsmBI CGTCTC 1 cut(s) 1101
BsmFI GGGAC 1 cut(s) 1099
BsnI GGCC 6 cut(s) 128, 180, 200, 282, 300, 469
BsoBI CYCGRG 1 cut(s) 688
Bsp119I TTCGAA 1 cut(s) 60
Bsp1286I GDGCHC 1 cut(s) 485
Bsp143I GATC 4 cut(s) 118, 549, 900, 997
BspACI CCGC 3 cut(s) 387, 435, 1106
BspANI GGCC 6 cut(s) 128, 180, 200, 282, 300, 469
BspCNI CTCAG 2 cut(s) 752, 1047
BspDI ATCGAT 1 cut(s) 996
BspHI TCATGA 1 cut(s) 966
BspLI GGNNCC 7 cut(s) 166, 301, 439, 883, 1038, 1087, 1237
BspMI ACCTGC 1 cut(s) 80
BspPI GGATC 2 cut(s) 544, 908
BspT104I TTCGAA 1 cut(s) 60
BspT107I GGYRCC 4 cut(s) 164, 881, 1036, 1235
BspTI CTTAAG 1 cut(s) 287
BsrDI GCAATG 3 cut(s) 540, 714, 777
BsrI ACTGG 2 cut(s) 229, 727
BssECI CCNNGG 2 cut(s) 553, 564
BssMI GATC 4 cut(s) 118, 549, 900, 997
Bst2UI CCWGG 3 cut(s) 466, 792, 924
Bst4CI ACNGT 1 cut(s) 547
Bst6I CTCTTC 2 cut(s) 144, 709
BstAFI CTTAAG 1 cut(s) 287
BstBI TTCGAA 1 cut(s) 60
BstC8I GCNNGC 2 cut(s) 101, 226
BstDEI CTNAG 3 cut(s) 739, 1032, 1055
BstF5I GGATG 2 cut(s) 414, 1040
BstHHI GCGC 1 cut(s) 1028
BstKTI GATC 4 cut(s) 121, 552, 903, 1000
BstMAI GTCTC 2 cut(s) 858, 1101
BstMBI GATC 4 cut(s) 118, 549, 900, 997
BstMWI GCNNNNNNNGC 3 cut(s) 40, 206, 732
BstNI CCWGG 3 cut(s) 466, 792, 924
BstSCI CCNGG 4 cut(s) 464, 552, 790, 922
BstSFI CTRYAG 1 cut(s) 354
BstV1I GCAGC 2 cut(s) 221, 947
Bsu15I ATCGAT 1 cut(s) 996
BsuRI GGCC 6 cut(s) 128, 180, 200, 282, 300, 469
BsuTUI ATCGAT 1 cut(s) 996
BtgZI GCGATG 1 cut(s) 741
BtrI CACGTC 2 cut(s) 763, 1020
BtsCI GGATG 2 cut(s) 414, 1040
BtsIMutI CAGTG 2 cut(s) 552, 811
BveI ACCTGC 1 cut(s) 80
Cac8I GCNNGC 2 cut(s) 101, 226
CaiI CAGNNNCTG 1 cut(s) 867
CciI TCATGA 1 cut(s) 966
CfoI GCGC 1 cut(s) 1028
Cfr13I GGNCC 4 cut(s) 281, 299, 788, 1086
ClaI ATCGAT 1 cut(s) 996
CsiI ACCWGGT 1 cut(s) 790
Csp6I GTAC 3 cut(s) 697, 882, 1257
CviAII CATG 8 cut(s) 213, 274, 797, 909, 946, 967, 1137, 1254
CviQI GTAC 3 cut(s) 697, 882, 1257
DdeI CTNAG 3 cut(s) 739, 1032, 1055
DpnI GATC 4 cut(s) 120, 551, 902, 999
DpnII GATC 4 cut(s) 118, 549, 900, 997
DrdI GACNNNNNNGTC 1 cut(s) 1093
DriI GACNNNNNGTC 1 cut(s) 1008
DseDI GACNNNNNNGTC 1 cut(s) 1093
EaeI YGGCCR 1 cut(s) 178
Eam1104I CTCTTC 2 cut(s) 144, 709
Eam1105I GACNNNNNGTC 1 cut(s) 1008
EarI CTCTTC 2 cut(s) 144, 709
EciI GGCGGA 1 cut(s) 450
Eco147I AGGCCT 1 cut(s) 200
Eco47I GGWCC 2 cut(s) 788, 1086
Eco88I CYCGRG 1 cut(s) 688
EcoO109I RGGNCCY 2 cut(s) 299, 1086
EcoRI GAATTC 1 cut(s) 377
EcoRII CCWGG 3 cut(s) 464, 790, 922
Esp3I CGTCTC 1 cut(s) 1101
FaeI CATG 8 cut(s) 216, 277, 800, 912, 949, 970, 1140, 1257
FalI AAGNNNNNCTT 2 cut(s) 329, 361
FaqI GGGAC 1 cut(s) 1099
FatI CATG 8 cut(s) 212, 273, 796, 908, 945, 966, 1136, 1253
Fnu4HI GCNGC 2 cut(s) 210, 936
FokI GGATG 2 cut(s) 421, 1027
Fsp4HI GCNGC 2 cut(s) 210, 936
FspBI CTAG 3 cut(s) 516, 651, 774
GlaI GCGC 1 cut(s) 1027
GluI GCNGC 2 cut(s) 210, 936
GsuI CTGGAG 1 cut(s) 906
HaeIII GGCC 6 cut(s) 128, 180, 200, 282, 300, 469
HapII CCGG 2 cut(s) 429, 553
HhaI GCGC 1 cut(s) 1028
Hin1II CATG 8 cut(s) 216, 277, 800, 912, 949, 970, 1140, 1257
Hin6I GCGC 1 cut(s) 1026
HinP1I GCGC 1 cut(s) 1026
HinfI GANTC 5 cut(s) 243, 491, 634, 669, 1132
HpaII CCGG 2 cut(s) 429, 553
HphI GGTGA 2 cut(s) 580, 757
Hpy166II GTNNAC 5 cut(s) 247, 571, 626, 697, 788
Hpy188I TCNGA 3 cut(s) 831, 863, 1002
Hpy188III TCNNGA 6 cut(s) 154, 631, 904, 967, 1072, 1169
Hpy8I GTNNAC 5 cut(s) 247, 571, 626, 697, 788
Hpy99I CGWCG 1 cut(s) 1096
HpyAV CCTTC 5 cut(s) 211, 343, 406, 830, 1183
HpyCH4III ACNGT 1 cut(s) 547
HpyCH4IV ACGT 3 cut(s) 312, 762, 1019
HpyCH4V TGCA 8 cut(s) 103, 501, 533, 735, 870, 935, 1112, 1209
HpyF10VI GCNNNNNNNGC 3 cut(s) 40, 206, 732
HpyF3I CTNAG 3 cut(s) 739, 1032, 1055
HpySE526I ACGT 3 cut(s) 312, 762, 1019
Hsp92II CATG 8 cut(s) 216, 277, 800, 912, 949, 970, 1140, 1257
HspAI GCGC 1 cut(s) 1026
KpnI GGTACC 1 cut(s) 885
Kzo9I GATC 4 cut(s) 118, 549, 900, 997
LmnI GCTCC 1 cut(s) 86
Lsp1109I GCAGC 2 cut(s) 221, 947
LweI GCATC 2 cut(s) 744, 810
MabI ACCWGGT 1 cut(s) 790
MaeI CTAG 3 cut(s) 516, 651, 774
MaeII ACGT 3 cut(s) 312, 762, 1019
MaeIII GTNAC 6 cut(s) 341, 605, 708, 763, 976, 1058
MalI GATC 4 cut(s) 120, 551, 902, 999
MboI GATC 4 cut(s) 118, 549, 900, 997
MboII GAAGA 6 cut(s) 131, 320, 500, 696, 1169, 1198
MfeI CAATTG 1 cut(s) 496
MhlI GDGCHC 1 cut(s) 485
MlsI TGGCCA 1 cut(s) 180
MluCI AATT 5 cut(s) 377, 398, 496, 524, 1226
MluNI TGGCCA 1 cut(s) 180
MlyI GAGTC 2 cut(s) 252, 485
MmeI TCCRAC 3 cut(s) 371, 536, 724
Mox20I TGGCCA 1 cut(s) 180
MroXI GAANNNNTTC 1 cut(s) 1161
MscI TGGCCA 1 cut(s) 180
MseI TTAA 4 cut(s) 147, 251, 288, 1218
MslI CAYNNNNRTG 5 cut(s) 806, 944, 965, 1117, 1252
Msp20I TGGCCA 1 cut(s) 180
MspCI CTTAAG 1 cut(s) 287
MspI CCGG 2 cut(s) 429, 553
MspR9I CCNGG 4 cut(s) 466, 554, 792, 924
MunI CAATTG 1 cut(s) 496
MvaI CCWGG 3 cut(s) 466, 792, 924
MwoI GCNNNNNNNGC 3 cut(s) 40, 206, 732
NciI CCSGG 1 cut(s) 554
NdeII GATC 4 cut(s) 118, 549, 900, 997
NlaIII CATG 8 cut(s) 216, 277, 800, 912, 949, 970, 1140, 1257
NlaIV GGNNCC 7 cut(s) 166, 301, 439, 883, 1038, 1087, 1237
NmuCI GTSAC 5 cut(s) 605, 708, 763, 976, 1058
NspV TTCGAA 1 cut(s) 60
PaeR7I CTCGAG 1 cut(s) 688
PagI TCATGA 1 cut(s) 966
PceI AGGCCT 1 cut(s) 200
PdmI GAANNNNTTC 1 cut(s) 1161
PfeI GAWTC 3 cut(s) 634, 669, 1132
PflFI GACNNNGTC 2 cut(s) 792, 1090
PkrI GCNGC 2 cut(s) 211, 937
PleI GAGTC 2 cut(s) 251, 485
PpsI GAGTC 2 cut(s) 251, 485
PpuMI RGGWCCY 1 cut(s) 1086
Psp5II RGGWCCY 1 cut(s) 1086
Psp6I CCWGG 3 cut(s) 464, 790, 922
PspGI CCWGG 3 cut(s) 464, 790, 922
PspN4I GGNNCC 7 cut(s) 166, 301, 439, 883, 1038, 1087, 1237
PspPI GGNCC 4 cut(s) 281, 299, 788, 1086
PspPPI RGGWCCY 1 cut(s) 1086
PspXI VCTCGAGB 1 cut(s) 688
PstNI CAGNNNCTG 1 cut(s) 867
PsyI GACNNNGTC 2 cut(s) 792, 1090
RsaI GTAC 3 cut(s) 698, 883, 1258
RsaNI GTAC 3 cut(s) 697, 882, 1257
RseI CAYNNNNRTG 5 cut(s) 806, 944, 965, 1117, 1252
SaqAI TTAA 4 cut(s) 147, 251, 288, 1218
SatI GCNGC 2 cut(s) 210, 936
Sau3AI GATC 4 cut(s) 118, 549, 900, 997
Sau96I GGNCC 4 cut(s) 281, 299, 788, 1086
SchI GAGTC 2 cut(s) 252, 485
ScrFI CCNGG 4 cut(s) 466, 554, 792, 924
SduI GDGCHC 1 cut(s) 485
SexAI ACCWGGT 1 cut(s) 790
SfaNI GCATC 2 cut(s) 744, 810
SfcI CTRYAG 1 cut(s) 354
Sfr274I CTCGAG 1 cut(s) 688
SfuI TTCGAA 1 cut(s) 60
SinI GGWCC 2 cut(s) 788, 1086
SlaI CTCGAG 1 cut(s) 688
SmiMI CAYNNNNRTG 5 cut(s) 806, 944, 965, 1117, 1252
SmlI CTYRAG 4 cut(s) 287, 629, 688, 1098
SmoI CTYRAG 4 cut(s) 287, 629, 688, 1098
SpeI ACTAGT 2 cut(s) 515, 650
Sse9I AATT 5 cut(s) 377, 398, 496, 524, 1226
SseBI AGGCCT 1 cut(s) 200
SsiI CCGC 3 cut(s) 387, 435, 1106
SspMI CTAG 3 cut(s) 516, 651, 774
StuI AGGCCT 1 cut(s) 200
StyD4I CCNGG 4 cut(s) 464, 552, 790, 922
TaaI ACNGT 1 cut(s) 547
TaiI ACGT 3 cut(s) 315, 765, 1022
TaqI TCGA 5 cut(s) 12, 60, 331, 689, 996
TasI AATT 5 cut(s) 377, 398, 496, 524, 1226
TatI WGTACW 2 cut(s) 696, 1256
TfiI GAWTC 3 cut(s) 634, 669, 1132
Tru1I TTAA 4 cut(s) 147, 251, 288, 1218
Tru9I TTAA 4 cut(s) 147, 251, 288, 1218
TscAI CASTG 2 cut(s) 552, 811
TseFI GTSAC 5 cut(s) 605, 708, 763, 976, 1058
TseI GCWGC 2 cut(s) 209, 935
Tsp45I GTSAC 5 cut(s) 605, 708, 763, 976, 1058
TspDTI ATGAA 8 cut(s) 390, 425, 551, 575, 849, 983, 1154, 1219
TspRI CASTG 2 cut(s) 552, 811
Tth111I GACNNNGTC 2 cut(s) 792, 1090
Vha464I CTTAAG 1 cut(s) 287
VpaK11BI GGWCC 2 cut(s) 788, 1086
XapI RAATTY 4 cut(s) 377, 398, 524, 1226
XhoI CTCGAG 1 cut(s) 688
XmnI GAANNNNTTC 1 cut(s) 1161
XspI CTAG 3 cut(s) 516, 651, 774
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.