Rroxscaffold_2G00128740

Polygalacturonase-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0000702
Physical Location & Seq
Forward (+)
64478620 .. 64489131
10512 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00128740.1

Sequence Viewer

Length: 1218 bp
ATGGCAAACTACTGTAGAAGCCTTTTTGTTCTCTCACTTGTCCTTGTCTTCATGAATGTCAACTTAGCCTTAGGCGCAACTGCTTCAGTCACTTACACTGTGACAAGTCTGGGAGCGAATCCTGATGGCAAGACCGACTCAACCAAAGCATTCCTCTCTGCATGGGCCAAAGCTTGTGTCTCCGCCAAGCCTGCTGTCATTTATGTTCCGGTGGGGAGCTTCTTGCTTCGCAAATCGGTCTTCAACGGGCCATGCAAGAATAGCGCCATCACATTTCAAATTGCCGGCACACTCGTTGCCCCATCAGATTACTGGGTGATAGGAAATGCCGGTAACTGGCTTTTCTTTGAGCATGTGAATGGGGTTACCATCTCCGGTGGTATTCTTGACGGACAAGGCACTGGACTGTGGGACTGCAAGGACTCCGGCAAGGGGTTGCCCCAAAGGAGCGACTTGATCAACGGCTGCCACAACGTGAAAATGCTAGGTGTTAGGGTTTCTGCCTCTGGCAACAGCCCCAACACAGATGGCATTCACGTTCAAATGTCTACCAGTGTCACTATTCTCAACTCCAAAATTGCGACGGGAGATGATTGTGTTTCAATTGGCCCCGGCACCATTAATTTGTGGATTGAAAACGTTGCATGTGGTCCTGGGCATGGAATTAGCATTGGGAGTTTAGGCAAGGAGCAAGAGGAAGTGGGAGTGCAAAACATAACGGTTAAAACAGTTACATTCACCGGTACTCAGAATGGTGTGAGAATTAAGTCATGGGGTAGACCCAGTACTGGGTTTGCCAGGAACATTCTTTTTCAACATGCTGTAATGGTCAATGTCAAAAATCCTATTGTTATAGATCAAAATTACTGCCCCGACGAAAAGCGTTGCCCTGGTCAGGAGTCTGGAGTTCAAATTAGCAACATTATGTACCAAGACATTCACGGCACATCGGCAACAGAAGTTGCCTTACAATCACCATTTGGAGATAGTGATTCCTGTCATCAAGACGGGAATGAAGTTTCAACTTGTGATGAATATGATACTGTGTATGATGTGTTTCCACAGCTACGTGATCCGCCAGAAGAAAATCTGGATTCACTCTTTGGTCCACATCAGCCACAAGATTTACTGCCGTCCATACTGCAGTCACCACAAGATTACTGCCGGGACCCACAAGTCATGGTGGGACCCAACGGCGACATGCATCCCGTAGCCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005576 GO:0005618 GO:0005623 GO:0030312 GO:0044464 GO:0071944
KEGG Pathways
Metabolic & Signaling
ko00040 ko01100 map00040 map01100
Pfam Domains
Protein Families
Glyco_hydro_28

Protein Analysis

405

Amino Acids

43.26

Weight (kDa)

5.12

Isoelectric Point (pI)

46.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 34 - 259 4.2e-13 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 59 - 141 2.5e-08 Glycosyl hydrolases family 28
Glyco_hydro_28 PF00295 153 - 325 1.5e-55 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: OG0000702)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G43870 AT3G59850 AT3G59850
fragaria_vesca FvH4_1g00290 FvH4_1g00290 FvH4_1g21842 FvH4_1g21850 FvH4_1g21851
malus_domestica MD00G1070500.v1.1 MD00G1087900.v1.1
prunus_persica Prupe.4G261700_v2.0.a1 Prupe.4G261800_v2.0.a1 Prupe.4G261900_v2.0.a1 Prupe.4G262200_v2.0.a1 Prupe.4G262200_v2.0.a1 Prupe.7G269200_v2.0.a1
pyrus_communis pycom02g00030 pycom03g19680
rosa_chinensis RchiOBHm_Chr2g0084591 RchiOBHm_Chr2g0085391 RchiOBHm_Chr2g0115741 RchiOBHm_Chr2g0115771 RchiOBHm_Chr2g0115801 RchiOBHm_Chr2g0115811 RchiOBHm_Chr2g0115821 RchiOBHm_Chr5g0021021 RchiOBHm_Chr5g0021031
rosa_laevigata RLG00000015683 RLG00000018208 RLG00000018211 RLG00000018212
rosa_multiflora Rmu_co8137638.1_g000001 Rmu_sc0000742.1_g000006 Rmu_sc0004926.1_g000013 Rmu_sc0008355.1_g000010 Rmu_sc0011452.1_g000015 Rmu_ssc0000197.1_g000031 Rmu_ssc0000197.1_g000032 Rmu_ssc0000197.1_g000056
rosa_roxburghii Rroxscaffold_2G00127770 Rroxscaffold_2G00127780 Rroxscaffold_2G00127790 Rroxscaffold_2G00127830 Rroxscaffold_2G00127850 Rroxscaffold_2G00128630 Rroxscaffold_2G00128640 Rroxscaffold_2G00128680 Rroxscaffold_2G00128730 Rroxscaffold_2G00128740
rosa_rugosa Rorug01G0455200 Rorug01G0460100 Rorug02G0199800 Rorug02G0199900
rosa_samantha Rh2BG003000 Rh2BG267500 Rh2BG267700 Rh2BG267800 Rh2BG267900 Rh2CG003400 Rh2CG010000 Rh2CG262800 Rh2CG263200 Rh2CG263300 Rh2CG263400 Rh5CG165700 Rh5CG165800
rosa_wichuraiana Rw0G014320 Rw0G014330 Rw1G010220 Rw2G000800 Rw2G020110 Rw2G020130 Rw2G020150 Rw2G020160

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 1175
AccB1I GGYRCC 1 cut(s) 614
AccI GTMKAC 2 cut(s) 548, 778
AciI CCGC 2 cut(s) 183, 1076
AclI AACGTT 1 cut(s) 639
AclWI GGATC 1 cut(s) 1067
AcuI CTGAAG 1 cut(s) 69
AdeI CACNNNGTG 1 cut(s) 475
AfaI GTAC 3 cut(s) 745, 787, 929
AfiI CCNNNNNNNGG 6 cut(s) 336, 432, 659, 788, 789, 895
AgeI ACCGGT 1 cut(s) 740
AgsI TTSAA 8 cut(s) 244, 278, 542, 603, 635, 815, 911, 1023
AjnI CCWGG 3 cut(s) 652, 797, 889
AluBI AGCT 3 cut(s) 173, 219, 1066
AluI AGCT 3 cut(s) 173, 219, 1066
Alw26I GTCTC 1 cut(s) 184
AlwI GGATC 1 cut(s) 1067
AoxI GGCC 3 cut(s) 165, 248, 607
ApeKI GCWGC 1 cut(s) 465
ArsI GACNNNNNNTTYG 2 cut(s) 162, 194
AseI ATTAAT 1 cut(s) 621
AsiGI ACCGGT 1 cut(s) 740
AspLEI GCGC 2 cut(s) 77, 266
AspS9I GGNCC 7 cut(s) 165, 248, 608, 650, 1106, 1168, 1187
AsuC2I CCSGG 2 cut(s) 612, 1166
AsuHPI GGTGA 4 cut(s) 328, 730, 966, 1140
AvaII GGWCC 4 cut(s) 650, 1106, 1168, 1187
AxyI CCTNAGG 1 cut(s) 70
BanI GGYRCC 1 cut(s) 614
BarI GAAGNNNNNNTAC 2 cut(s) 951, 983
BbsI GAAGAC 2 cut(s) 40, 232
BbvI GCAGC 1 cut(s) 452
BccI CCATC 5 cut(s) 119, 275, 310, 377, 521
BceAI ACGGC 4 cut(s) 478, 958, 1117, 1210
BciT130I CCWGG 3 cut(s) 654, 799, 891
BclI TGATCA 1 cut(s) 456
BcnI CCSGG 2 cut(s) 612, 1166
BcoDI GTCTC 1 cut(s) 184
BfaI CTAG 1 cut(s) 485
BfmI CTRYAG 2 cut(s) 13, 1142
BfoI RGCGCY 1 cut(s) 267
BisI GCNGC 1 cut(s) 466
BlsI GCNGC 1 cut(s) 467
BmcAI AGTACT 1 cut(s) 787
Bme1390I CCNGG 5 cut(s) 612, 654, 799, 891, 1166
Bme18I GGWCC 4 cut(s) 650, 1106, 1168, 1187
BmgT120I GGNCC 7 cut(s) 165, 248, 608, 650, 1106, 1168, 1187
BmiI GGNNCC 6 cut(s) 610, 616, 1169, 1170, 1188, 1189
BmrFI CCNGG 5 cut(s) 612, 654, 799, 891, 1166
BmrI ACTGGG 3 cut(s) 322, 777, 798
BmsI GCATC 1 cut(s) 1213
BmuI ACTGGG 3 cut(s) 322, 777, 798
BpiI GAAGAC 2 cut(s) 40, 232
BpmI CTGGAG 1 cut(s) 924
BpuMI CCSGG 2 cut(s) 612, 1166
BsaAI YACGTR 1 cut(s) 1070
BsaJI CCNNGG 3 cut(s) 610, 653, 889
BsaWI WCCGGW 3 cut(s) 208, 374, 740
Bsc4I CCNNNNNNNGG 6 cut(s) 336, 432, 659, 788, 789, 895
Bse118I RCCGGY 3 cut(s) 284, 329, 740
Bse1I ACTGG 6 cut(s) 317, 341, 406, 552, 783, 793
Bse21I CCTNAGG 1 cut(s) 70
BseBI CCWGG 3 cut(s) 654, 799, 891
BseDI CCNNGG 3 cut(s) 610, 653, 889
BseGI GGATG 1 cut(s) 1204
BseLI CCNNNNNNNGG 6 cut(s) 336, 432, 659, 788, 789, 895
BseMII CTCAG 1 cut(s) 761
BseNI ACTGG 6 cut(s) 317, 341, 406, 552, 783, 793
BseXI GCAGC 1 cut(s) 452
BshFI GGCC 3 cut(s) 167, 250, 609
BshNI GGYRCC 1 cut(s) 614
BshTI ACCGGT 1 cut(s) 740
BsiSI CCGG 8 cut(s) 209, 285, 330, 375, 426, 612, 741, 1165
BslFI GGGAC 3 cut(s) 425, 1181, 1200
BslI CCNNNNNNNGG 6 cut(s) 336, 432, 659, 788, 789, 895
BsmAI GTCTC 1 cut(s) 184
BsmFI GGGAC 3 cut(s) 425, 1181, 1200
BsmI GAATGC 2 cut(s) 149, 531
BsnI GGCC 3 cut(s) 167, 250, 609
Bsp143I GATC 3 cut(s) 456, 856, 1072
BspACI CCGC 2 cut(s) 183, 1076
BspANI GGCC 3 cut(s) 167, 250, 609
BspCNI CTCAG 1 cut(s) 760
BspHI TCATGA 1 cut(s) 51
BspLI GGNNCC 6 cut(s) 610, 616, 1169, 1170, 1188, 1189
BspMAI CTGCAG 1 cut(s) 1146
BspPI GGATC 1 cut(s) 1067
BspT107I GGYRCC 1 cut(s) 614
BsrFI RCCGGY 3 cut(s) 284, 329, 740
BsrI ACTGG 6 cut(s) 317, 341, 406, 552, 783, 793
BssAI RCCGGY 3 cut(s) 284, 329, 740
BssECI CCNNGG 3 cut(s) 610, 653, 889
BssMI GATC 3 cut(s) 456, 856, 1072
Bst2UI CCWGG 3 cut(s) 654, 799, 891
Bst4CI ACNGT 6 cut(s) 14, 100, 408, 721, 730, 1045
BstBAI YACGTR 1 cut(s) 1070
BstC8I GCNNGC 2 cut(s) 192, 286
BstDEI CTNAG 3 cut(s) 64, 70, 747
BstEII GGTNACC 1 cut(s) 364
BstF5I GGATG 1 cut(s) 1204
BstH2I RGCGCY 1 cut(s) 267
BstHHI GCGC 2 cut(s) 77, 266
BstKTI GATC 3 cut(s) 459, 859, 1075
BstMAI GTCTC 1 cut(s) 184
BstMBI GATC 3 cut(s) 456, 856, 1072
BstMWI GCNNNNNNNGC 3 cut(s) 74, 191, 261
BstNI CCWGG 3 cut(s) 654, 799, 891
BstNSI RCATGY 4 cut(s) 356, 648, 821, 1204
BstPI GGTNACC 1 cut(s) 364
BstSCI CCNGG 5 cut(s) 610, 652, 797, 889, 1164
BstSFI CTRYAG 2 cut(s) 13, 1142
BstV1I GCAGC 1 cut(s) 452
BstV2I GAAGAC 2 cut(s) 40, 232
Bsu36I CCTNAGG 1 cut(s) 70
BsuRI GGCC 3 cut(s) 167, 250, 609
BtsCI GGATG 1 cut(s) 1204
BtsIMutI CAGTG 3 cut(s) 96, 399, 559
Cac8I GCNNGC 2 cut(s) 192, 286
CciI TCATGA 1 cut(s) 51
CfoI GCGC 2 cut(s) 77, 266
Cfr10I RCCGGY 3 cut(s) 284, 329, 740
Cfr13I GGNCC 7 cut(s) 165, 248, 608, 650, 1106, 1168, 1187
Csp6I GTAC 3 cut(s) 744, 786, 928
CspAI ACCGGT 1 cut(s) 740
CviQI GTAC 3 cut(s) 744, 786, 928
DdeI CTNAG 3 cut(s) 64, 70, 747
DpnI GATC 3 cut(s) 458, 858, 1074
DpnII GATC 3 cut(s) 456, 856, 1072
DraIII CACNNNGTG 1 cut(s) 475
DrdI GACNNNNNNGTC 1 cut(s) 1175
DseDI GACNNNNNNGTC 1 cut(s) 1175
EciI GGCGGA 2 cut(s) 172, 1065
Eco47I GGWCC 4 cut(s) 650, 1106, 1168, 1187
Eco57I CTGAAG 1 cut(s) 69
Eco81I CCTNAGG 1 cut(s) 70
Eco91I GGTNACC 1 cut(s) 364
EcoO109I RGGNCCY 2 cut(s) 1168, 1187
EcoO65I GGTNACC 1 cut(s) 364
EcoRII CCWGG 3 cut(s) 652, 797, 889
EcoT22I ATGCAT 1 cut(s) 1206
FaqI GGGAC 3 cut(s) 425, 1181, 1200
FbaI TGATCA 1 cut(s) 456
FblI GTMKAC 2 cut(s) 548, 778
Fnu4HI GCNGC 1 cut(s) 466
FokI GGATG 1 cut(s) 1191
Fsp4HI GCNGC 1 cut(s) 466
FspBI CTAG 1 cut(s) 485
GlaI GCGC 2 cut(s) 76, 265
GluI GCNGC 1 cut(s) 466
GsuI CTGGAG 1 cut(s) 924
HaeII RGCGCY 1 cut(s) 267
HaeIII GGCC 3 cut(s) 167, 250, 609
HapII CCGG 8 cut(s) 209, 285, 330, 375, 426, 612, 741, 1165
HhaI GCGC 2 cut(s) 77, 266
Hin6I GCGC 2 cut(s) 75, 264
HinP1I GCGC 2 cut(s) 75, 264
HincII GTYRAC 1 cut(s) 61
HindII GTYRAC 1 cut(s) 61
HindIII AAGCTT 1 cut(s) 171
HinfI GANTC 6 cut(s) 118, 137, 422, 899, 992, 1094
HpaII CCGG 8 cut(s) 209, 285, 330, 375, 426, 612, 741, 1165
HphI GGTGA 4 cut(s) 328, 730, 966, 1140
Hpy166II GTNNAC 4 cut(s) 61, 549, 779, 1109
Hpy188I TCNGA 2 cut(s) 307, 750
Hpy188III TCNNGA 7 cut(s) 52, 122, 386, 896, 903, 1004, 1091
Hpy8I GTNNAC 4 cut(s) 61, 549, 779, 1109
Hpy99I CGWCG 2 cut(s) 586, 878
HpyCH4III ACNGT 6 cut(s) 14, 100, 408, 721, 730, 1045
HpyCH4IV ACGT 4 cut(s) 474, 537, 639, 1069
HpyCH4V TGCA 7 cut(s) 161, 255, 417, 644, 709, 1144, 1204
HpyF10VI GCNNNNNNNGC 3 cut(s) 74, 191, 261
HpyF3I CTNAG 3 cut(s) 64, 70, 747
HpySE526I ACGT 4 cut(s) 474, 537, 639, 1069
HspAI GCGC 2 cut(s) 75, 264
KflI GGGWCCC 2 cut(s) 1168, 1187
KroI GCCGGC 1 cut(s) 284
KroNI GCCGGC 1 cut(s) 286
Ksp22I TGATCA 1 cut(s) 456
Kzo9I GATC 3 cut(s) 456, 856, 1072
LmnI GCTCC 4 cut(s) 113, 216, 447, 688
Lsp1109I GCAGC 1 cut(s) 452
LweI GCATC 1 cut(s) 1213
MaeI CTAG 1 cut(s) 485
MaeII ACGT 4 cut(s) 474, 537, 639, 1069
MaeIII GTNAC 7 cut(s) 88, 100, 332, 364, 556, 730, 1146
MalI GATC 3 cut(s) 458, 858, 1074
MboI GATC 3 cut(s) 456, 856, 1072
MboII GAAGA 3 cut(s) 40, 232, 1094
MfeI CAATTG 1 cut(s) 603
MluCI AATT 8 cut(s) 279, 576, 603, 622, 663, 762, 862, 912
MlyI GAGTC 3 cut(s) 131, 416, 908
MnlI CCTC 3 cut(s) 164, 514, 688
Mph1103I ATGCAT 1 cut(s) 1206
MroNI GCCGGC 1 cut(s) 284
MseI TTAA 3 cut(s) 621, 723, 765
MslI CAYNNNNRTG 1 cut(s) 357
MspI CCGG 8 cut(s) 209, 285, 330, 375, 426, 612, 741, 1165
MspR9I CCNGG 5 cut(s) 612, 654, 799, 891, 1166
MunI CAATTG 1 cut(s) 603
Mva1269I GAATGC 2 cut(s) 149, 531
MvaI CCWGG 3 cut(s) 654, 799, 891
MwoI GCNNNNNNNGC 3 cut(s) 74, 191, 261
NaeI GCCGGC 1 cut(s) 286
NciI CCSGG 2 cut(s) 612, 1166
NdeII GATC 3 cut(s) 456, 856, 1072
NgoMIV GCCGGC 1 cut(s) 284
NlaIV GGNNCC 6 cut(s) 610, 616, 1169, 1170, 1188, 1189
NmuCI GTSAC 4 cut(s) 88, 100, 556, 1146
NsiI ATGCAT 1 cut(s) 1206
NspI RCATGY 4 cut(s) 356, 648, 821, 1204
PagI TCATGA 1 cut(s) 51
PctI GAATGC 2 cut(s) 149, 531
PdiI GCCGGC 1 cut(s) 286
PfeI GAWTC 3 cut(s) 118, 992, 1094
PinAI ACCGGT 1 cut(s) 740
PkrI GCNGC 1 cut(s) 467
PleI GAGTC 3 cut(s) 131, 416, 907
PpsI GAGTC 3 cut(s) 131, 416, 907
Ppu21I YACGTR 1 cut(s) 1070
PpuMI RGGWCCY 2 cut(s) 1168, 1187
PshBI ATTAAT 1 cut(s) 621
Psp1406I AACGTT 1 cut(s) 639
Psp5II RGGWCCY 2 cut(s) 1168, 1187
Psp6I CCWGG 3 cut(s) 652, 797, 889
PspEI GGTNACC 1 cut(s) 364
PspGI CCWGG 3 cut(s) 652, 797, 889
PspN4I GGNNCC 6 cut(s) 610, 616, 1169, 1170, 1188, 1189
PspPI GGNCC 7 cut(s) 165, 248, 608, 650, 1106, 1168, 1187
PspPPI RGGWCCY 2 cut(s) 1168, 1187
PstI CTGCAG 1 cut(s) 1146
RsaI GTAC 3 cut(s) 745, 787, 929
RsaNI GTAC 3 cut(s) 744, 786, 928
RseI CAYNNNNRTG 1 cut(s) 357
SaqAI TTAA 3 cut(s) 621, 723, 765
SatI GCNGC 1 cut(s) 466
Sau3AI GATC 3 cut(s) 456, 856, 1072
Sau96I GGNCC 7 cut(s) 165, 248, 608, 650, 1106, 1168, 1187
ScaI AGTACT 1 cut(s) 787
SchI GAGTC 3 cut(s) 131, 416, 908
ScrFI CCNGG 5 cut(s) 612, 654, 799, 891, 1166
SetI ASST 8 cut(s) 175, 221, 477, 490, 540, 642, 1068, 1072
SfaNI GCATC 1 cut(s) 1213
SfcI CTRYAG 2 cut(s) 13, 1142
SinI GGWCC 4 cut(s) 650, 1106, 1168, 1187
SmiMI CAYNNNNRTG 1 cut(s) 357
Sse9I AATT 8 cut(s) 279, 576, 603, 622, 663, 762, 862, 912
SsiI CCGC 2 cut(s) 183, 1076
SspMI CTAG 1 cut(s) 485
StyD4I CCNGG 5 cut(s) 610, 652, 797, 889, 1164
TaaI ACNGT 6 cut(s) 14, 100, 408, 721, 730, 1045
TaiI ACGT 4 cut(s) 477, 540, 642, 1072
TaqII GACCGA 2 cut(s) 149, 226
TasI AATT 8 cut(s) 279, 576, 603, 622, 663, 762, 862, 912
TatI WGTACW 1 cut(s) 785
TfiI GAWTC 3 cut(s) 118, 992, 1094
Tru1I TTAA 3 cut(s) 621, 723, 765
Tru9I TTAA 3 cut(s) 621, 723, 765
TscAI CASTG 3 cut(s) 103, 406, 559
TseFI GTSAC 4 cut(s) 88, 100, 556, 1146
TseI GCWGC 1 cut(s) 465
Tsp45I GTSAC 4 cut(s) 88, 100, 556, 1146
TspDTI ATGAA 4 cut(s) 40, 68, 1029, 1047
TspGWI ACGGA 1 cut(s) 405
TspRI CASTG 3 cut(s) 103, 406, 559
VpaK11BI GGWCC 4 cut(s) 650, 1106, 1168, 1187
VspI ATTAAT 1 cut(s) 621
XceI RCATGY 4 cut(s) 356, 648, 821, 1204
XcmI CCANNNNNNNNNTGG 1 cut(s) 309
XmiI GTMKAC 2 cut(s) 548, 778
XspI CTAG 1 cut(s) 485
ZrmI AGTACT 1 cut(s) 787
Zsp2I ATGCAT 1 cut(s) 1206
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.