Rroxscaffold_2G00127850

Polygalacturonase-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0000702
Physical Location & Seq
Forward (+)
63420193 .. 63423482
3290 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00127850.1

Sequence Viewer

Length: 1191 bp
ATGGCAAACTACTGTAGAAGCCTTTTTGTTCTCTCACTTGTCCTTGTCTTCATGAATGTCAACTTAGCCTTAGGCGCAACTGCTTCAGTCACTTACACTGTGACAAGTCTGGGAGCGAATCCTGATGGCAAGACCGACTCAACCAAAGCATTCCTCTCTGCATGGGCCAAAGCTTGTGTCTCCGCCAAGCCTGCTGTCATTTATGTTCCGGTGGGGAGCTTCTTGCTTCGCAAATCGGTCTTCAACGGGCCATGCAAGAATAGCGCCATCACATTTCAAATTGCCGGCACACTCGTTGCCCCATCAGATTACTGGGTGATAGGAAATGCCGGTAACTGGCTTTTCTTTGAGCATGTGAATGGGGTTACCATCTCCGGTGGTATTCTTGACGGACAAGGCACTGGACTGTGGGACTGCAAGGACTCCGGCAAGGGTTGCCCCAAAGGAGCGACTACACTTGGTTTTTCCAATTCGAACAACATTGTGATGAATGGAGTGTCATCCCTAAACAGCCAAATGTTTCACATAGTGATCAACGGCTGCCACAACGTGAAAATGCTAGGTGTTAGGGTTTCTGCCTCTGGCAACAGCCCCAACACAGATGGCATTCACGTTCAAATGTCTACCAGTGTCACTATTCTCAACTCCAAAATTGCGACGGGAGATGATTGTGTTTCAATTGGCCCCGGCACCATTAATTTGTGGATTGAAAACGTTGCATGTGGTCCTGGGCATGGAATTAGCATTGGGAGTTTAGGCAAGGAGCAAGAGGAAGTGGGAGTGCAAAACATAACGGTTAAAACAGTTACATTCACCGGTACTCAGAATGGTGTGAGAATTAAGTCATGGGGTAGACCCAGTACTGGGTTTGCCAGGAACATTCTTTTTCAACATGCTGTAATGGTCAATGTCAAAAATCCTATTGTTATAGATCAAAATTACTGCCCCGACGAAAAGCGTTGCCCTGGTCAGGAGTCTGGAGTTCAAATTAGCAACATTATGTACCAAGACATTCACGGCACATCGGCAACAGAAGTTGCCGTGAAATTCGATTGCAGCTCCAAATATCCTTGTAACAAAATCACATTGGAGGATATTAAGCTCACTTACAAGAACCAAGCTGCTGAAGCTTCTTGTAGCCATGCAGGTGGAACAGCTGAGGGTACGGTTCAACCTACAAGTTGTCTGTAG
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

396

Amino Acids

41.76

Weight (kDa)

8.15

Isoelectric Point (pI)

32.01

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 34 - 284 1e-10 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 59 - 380 1.5e-85 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)
AarI CACCTGC 1 cut(s) 1136
Acc36I ACCTGC 1 cut(s) 1136
AccB1I GGYRCC 1 cut(s) 689
AccI GTMKAC 2 cut(s) 623, 853
AciI CCGC 1 cut(s) 183
AclI AACGTT 1 cut(s) 714
AcsI RAATTY 1 cut(s) 1046
AcuI CTGAAG 2 cut(s) 69, 1146
AdeI CACNNNGTG 2 cut(s) 529, 550
AfaI GTAC 4 cut(s) 820, 862, 1004, 1165
AfiI CCNNNNNNNGG 5 cut(s) 336, 734, 863, 864, 970
AgeI ACCGGT 1 cut(s) 815
AgsI TTSAA 8 cut(s) 244, 278, 617, 678, 710, 890, 986, 1172
AjnI CCWGG 3 cut(s) 727, 872, 964
AluBI AGCT 7 cut(s) 173, 219, 1059, 1102, 1121, 1130, 1157
AluI AGCT 7 cut(s) 173, 219, 1059, 1102, 1121, 1130, 1157
Alw26I GTCTC 1 cut(s) 184
AoxI GGCC 3 cut(s) 165, 248, 682
ApeKI GCWGC 3 cut(s) 540, 1056, 1121
ApoI RAATTY 1 cut(s) 1046
ArsI GACNNNNNNTTYG 2 cut(s) 162, 194
AseI ATTAAT 1 cut(s) 696
AsiGI ACCGGT 1 cut(s) 815
AspLEI GCGC 2 cut(s) 77, 266
AspS9I GGNCC 4 cut(s) 165, 248, 683, 725
AsuC2I CCSGG 1 cut(s) 687
AsuHPI GGTGA 2 cut(s) 328, 805
AsuII TTCGAA 1 cut(s) 473
AvaII GGWCC 1 cut(s) 725
AxyI CCTNAGG 1 cut(s) 70
BanI GGYRCC 1 cut(s) 689
BbsI GAAGAC 2 cut(s) 40, 232
BbvCI CCTCAGC 1 cut(s) 1158
BbvI GCAGC 3 cut(s) 527, 1068, 1108
BccI CCATC 5 cut(s) 119, 275, 310, 377, 596
BceAI ACGGC 3 cut(s) 553, 1025, 1033
BciT130I CCWGG 3 cut(s) 729, 874, 966
BclI TGATCA 1 cut(s) 531
BcnI CCSGG 1 cut(s) 687
BcoDI GTCTC 1 cut(s) 184
BfaI CTAG 1 cut(s) 560
BfmI CTRYAG 2 cut(s) 13, 1187
BfoI RGCGCY 1 cut(s) 267
BfuAI ACCTGC 1 cut(s) 1136
BisI GCNGC 3 cut(s) 541, 1057, 1122
BlsI GCNGC 3 cut(s) 542, 1058, 1123
BmcAI AGTACT 1 cut(s) 862
Bme1390I CCNGG 4 cut(s) 687, 729, 874, 966
Bme18I GGWCC 1 cut(s) 725
BmgT120I GGNCC 4 cut(s) 165, 248, 683, 725
BmiI GGNNCC 2 cut(s) 685, 691
BmrFI CCNGG 4 cut(s) 687, 729, 874, 966
BmrI ACTGGG 3 cut(s) 322, 852, 873
BmuI ACTGGG 3 cut(s) 322, 852, 873
BpiI GAAGAC 2 cut(s) 40, 232
BpmI CTGGAG 1 cut(s) 999
Bpu10I CCTNAGC 1 cut(s) 1158
Bpu14I TTCGAA 1 cut(s) 473
BpuMI CCSGG 1 cut(s) 687
BsaJI CCNNGG 3 cut(s) 685, 728, 964
BsaWI WCCGGW 3 cut(s) 208, 374, 815
Bsc4I CCNNNNNNNGG 5 cut(s) 336, 734, 863, 864, 970
Bse118I RCCGGY 3 cut(s) 284, 329, 815
Bse1I ACTGG 6 cut(s) 317, 341, 406, 627, 858, 868
Bse21I CCTNAGG 1 cut(s) 70
BseBI CCWGG 3 cut(s) 729, 874, 966
BseDI CCNNGG 3 cut(s) 685, 728, 964
BseGI GGATG 1 cut(s) 500
BseLI CCNNNNNNNGG 5 cut(s) 336, 734, 863, 864, 970
BseMII CTCAG 2 cut(s) 836, 1149
BseNI ACTGG 6 cut(s) 317, 341, 406, 627, 858, 868
BseXI GCAGC 3 cut(s) 527, 1068, 1108
BshFI GGCC 3 cut(s) 167, 250, 684
BshNI GGYRCC 1 cut(s) 689
BshTI ACCGGT 1 cut(s) 815
BsiSI CCGG 7 cut(s) 209, 285, 330, 375, 426, 687, 816
BslFI GGGAC 1 cut(s) 425
BslI CCNNNNNNNGG 5 cut(s) 336, 734, 863, 864, 970
BsmAI GTCTC 1 cut(s) 184
BsmFI GGGAC 1 cut(s) 425
BsmI GAATGC 2 cut(s) 149, 606
BsnI GGCC 3 cut(s) 167, 250, 684
Bsp119I TTCGAA 1 cut(s) 473
Bsp143I GATC 2 cut(s) 531, 931
BspACI CCGC 1 cut(s) 183
BspANI GGCC 3 cut(s) 167, 250, 684
BspCNI CTCAG 2 cut(s) 835, 1150
BspHI TCATGA 1 cut(s) 51
BspLI GGNNCC 2 cut(s) 685, 691
BspMI ACCTGC 1 cut(s) 1136
BspT104I TTCGAA 1 cut(s) 473
BspT107I GGYRCC 1 cut(s) 689
BsrFI RCCGGY 3 cut(s) 284, 329, 815
BsrI ACTGG 6 cut(s) 317, 341, 406, 627, 858, 868
BssAI RCCGGY 3 cut(s) 284, 329, 815
BssECI CCNNGG 3 cut(s) 685, 728, 964
BssMI GATC 2 cut(s) 531, 931
Bst2UI CCWGG 3 cut(s) 729, 874, 966
Bst4CI ACNGT 6 cut(s) 14, 100, 408, 796, 805, 1168
BstAPI GCANNNNNTGC 1 cut(s) 435
BstBI TTCGAA 1 cut(s) 473
BstC8I GCNNGC 2 cut(s) 192, 286
BstDEI CTNAG 4 cut(s) 64, 70, 822, 1158
BstEII GGTNACC 1 cut(s) 364
BstF5I GGATG 1 cut(s) 500
BstH2I RGCGCY 1 cut(s) 267
BstHHI GCGC 2 cut(s) 77, 266
BstKTI GATC 2 cut(s) 534, 934
BstMAI GTCTC 1 cut(s) 184
BstMBI GATC 2 cut(s) 531, 931
BstMWI GCNNNNNNNGC 5 cut(s) 74, 191, 261, 435, 1127
BstNI CCWGG 3 cut(s) 729, 874, 966
BstNSI RCATGY 3 cut(s) 356, 723, 896
BstPI GGTNACC 1 cut(s) 364
BstSCI CCNGG 4 cut(s) 685, 727, 872, 964
BstSFI CTRYAG 2 cut(s) 13, 1187
BstV1I GCAGC 3 cut(s) 527, 1068, 1108
BstV2I GAAGAC 2 cut(s) 40, 232
BstXI CCANNNNNNTGG 1 cut(s) 1148
Bsu36I CCTNAGG 1 cut(s) 70
BsuRI GGCC 3 cut(s) 167, 250, 684
BtsCI GGATG 1 cut(s) 500
BtsIMutI CAGTG 3 cut(s) 96, 399, 634
BveI ACCTGC 1 cut(s) 1136
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, 815
Cfr13I GGNCC 4 cut(s) 165, 248, 683, 725
Csp6I GTAC 4 cut(s) 819, 861, 1003, 1164
CspAI ACCGGT 1 cut(s) 815
CviAII CATG 9 cut(s) 52, 162, 252, 353, 720, 734, 846, 893, 1142
CviQI GTAC 4 cut(s) 819, 861, 1003, 1164
DdeI CTNAG 4 cut(s) 64, 70, 822, 1158
DpnI GATC 2 cut(s) 533, 933
DpnII GATC 2 cut(s) 531, 931
DraIII CACNNNGTG 2 cut(s) 529, 550
EciI GGCGGA 1 cut(s) 172
Eco47I GGWCC 1 cut(s) 725
Eco57I CTGAAG 2 cut(s) 69, 1146
Eco81I CCTNAGG 1 cut(s) 70
Eco91I GGTNACC 1 cut(s) 364
EcoO65I GGTNACC 1 cut(s) 364
EcoRII CCWGG 3 cut(s) 727, 872, 964
FaeI CATG 9 cut(s) 55, 165, 255, 356, 723, 737, 849, 896, 1145
FaqI GGGAC 1 cut(s) 425
FatI CATG 9 cut(s) 51, 161, 251, 352, 719, 733, 845, 892, 1141
FbaI TGATCA 1 cut(s) 531
FblI GTMKAC 2 cut(s) 623, 853
Fnu4HI GCNGC 3 cut(s) 541, 1057, 1122
FokI GGATG 1 cut(s) 487
Fsp4HI GCNGC 3 cut(s) 541, 1057, 1122
FspBI CTAG 1 cut(s) 560
GlaI GCGC 2 cut(s) 76, 265
GluI GCNGC 3 cut(s) 541, 1057, 1122
GsuI CTGGAG 1 cut(s) 999
HaeII RGCGCY 1 cut(s) 267
HaeIII GGCC 3 cut(s) 167, 250, 684
HapII CCGG 7 cut(s) 209, 285, 330, 375, 426, 687, 816
HhaI GCGC 2 cut(s) 77, 266
Hin1II CATG 9 cut(s) 55, 165, 255, 356, 723, 737, 849, 896, 1145
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 2 cut(s) 171, 1128
HinfI GANTC 4 cut(s) 118, 137, 422, 974
HpaII CCGG 7 cut(s) 209, 285, 330, 375, 426, 687, 816
HphI GGTGA 2 cut(s) 328, 805
Hpy166II GTNNAC 3 cut(s) 61, 624, 854
Hpy188I TCNGA 2 cut(s) 307, 825
Hpy188III TCNNGA 5 cut(s) 52, 122, 386, 971, 978
Hpy8I GTNNAC 3 cut(s) 61, 624, 854
Hpy99I CGWCG 2 cut(s) 661, 953
HpyCH4III ACNGT 6 cut(s) 14, 100, 408, 796, 805, 1168
HpyCH4IV ACGT 3 cut(s) 549, 612, 714
HpyCH4V TGCA 7 cut(s) 161, 255, 417, 719, 784, 1056, 1145
HpyF10VI GCNNNNNNNGC 5 cut(s) 74, 191, 261, 435, 1127
HpyF3I CTNAG 4 cut(s) 64, 70, 822, 1158
HpySE526I ACGT 3 cut(s) 549, 612, 714
Hsp92II CATG 9 cut(s) 55, 165, 255, 356, 723, 737, 849, 896, 1145
HspAI GCGC 2 cut(s) 75, 264
KroI GCCGGC 1 cut(s) 284
KroNI GCCGGC 1 cut(s) 286
Ksp22I TGATCA 1 cut(s) 531
Kzo9I GATC 2 cut(s) 531, 931
LmnI GCTCC 5 cut(s) 113, 216, 446, 763, 1064
Lsp1109I GCAGC 3 cut(s) 527, 1068, 1108
MaeI CTAG 1 cut(s) 560
MaeII ACGT 3 cut(s) 549, 612, 714
MaeIII GTNAC 7 cut(s) 88, 100, 332, 364, 631, 805, 1073
MalI GATC 2 cut(s) 533, 933
MboI GATC 2 cut(s) 531, 931
MboII GAAGA 2 cut(s) 40, 232
MfeI CAATTG 1 cut(s) 678
MlyI GAGTC 3 cut(s) 131, 416, 983
MnlI CCTC 5 cut(s) 164, 589, 763, 1084, 1153
MroNI GCCGGC 1 cut(s) 284
MseI TTAA 4 cut(s) 696, 798, 840, 1098
MslI CAYNNNNRTG 3 cut(s) 357, 485, 1146
MspA1I CMGCKG 1 cut(s) 1157
MspI CCGG 7 cut(s) 209, 285, 330, 375, 426, 687, 816
MspR9I CCNGG 4 cut(s) 687, 729, 874, 966
MunI CAATTG 1 cut(s) 678
Mva1269I GAATGC 2 cut(s) 149, 606
MvaI CCWGG 3 cut(s) 729, 874, 966
MwoI GCNNNNNNNGC 5 cut(s) 74, 191, 261, 435, 1127
NaeI GCCGGC 1 cut(s) 286
NciI CCSGG 1 cut(s) 687
NdeII GATC 2 cut(s) 531, 931
NgoMIV GCCGGC 1 cut(s) 284
NlaIII CATG 9 cut(s) 55, 165, 255, 356, 723, 737, 849, 896, 1145
NlaIV GGNNCC 2 cut(s) 685, 691
NmuCI GTSAC 3 cut(s) 88, 100, 631
NspI RCATGY 3 cut(s) 356, 723, 896
NspV TTCGAA 1 cut(s) 473
PagI TCATGA 1 cut(s) 51
PaqCI CACCTGC 1 cut(s) 1136
PctI GAATGC 2 cut(s) 149, 606
PdiI GCCGGC 1 cut(s) 286
PfeI GAWTC 1 cut(s) 118
PinAI ACCGGT 1 cut(s) 815
PkrI GCNGC 3 cut(s) 542, 1058, 1123
PleI GAGTC 3 cut(s) 131, 416, 982
PpsI GAGTC 3 cut(s) 131, 416, 982
PshBI ATTAAT 1 cut(s) 696
Psp1406I AACGTT 1 cut(s) 714
Psp6I CCWGG 3 cut(s) 727, 872, 964
PspEI GGTNACC 1 cut(s) 364
PspGI CCWGG 3 cut(s) 727, 872, 964
PspN4I GGNNCC 2 cut(s) 685, 691
PspPI GGNCC 4 cut(s) 165, 248, 683, 725
PvuII CAGCTG 1 cut(s) 1157
RsaI GTAC 4 cut(s) 820, 862, 1004, 1165
RsaNI GTAC 4 cut(s) 819, 861, 1003, 1164
RseI CAYNNNNRTG 3 cut(s) 357, 485, 1146
SaqAI TTAA 4 cut(s) 696, 798, 840, 1098
SatI GCNGC 3 cut(s) 541, 1057, 1122
Sau3AI GATC 2 cut(s) 531, 931
Sau96I GGNCC 4 cut(s) 165, 248, 683, 725
ScaI AGTACT 1 cut(s) 862
SchI GAGTC 3 cut(s) 131, 416, 983
ScrFI CCNGG 4 cut(s) 687, 729, 874, 966
SfcI CTRYAG 2 cut(s) 13, 1187
SfuI TTCGAA 1 cut(s) 473
SinI GGWCC 1 cut(s) 725
SmiMI CAYNNNNRTG 3 cut(s) 357, 485, 1146
SsiI CCGC 1 cut(s) 183
SspMI CTAG 1 cut(s) 560
StyD4I CCNGG 4 cut(s) 685, 727, 872, 964
TaaI ACNGT 6 cut(s) 14, 100, 408, 796, 805, 1168
TaiI ACGT 3 cut(s) 552, 615, 717
TaqI TCGA 2 cut(s) 473, 1050
TaqII GACCGA 2 cut(s) 149, 226
TatI WGTACW 1 cut(s) 860
TfiI GAWTC 1 cut(s) 118
Tru1I TTAA 4 cut(s) 696, 798, 840, 1098
Tru9I TTAA 4 cut(s) 696, 798, 840, 1098
TscAI CASTG 3 cut(s) 103, 406, 634
TseFI GTSAC 3 cut(s) 88, 100, 631
TseI GCWGC 3 cut(s) 540, 1056, 1121
Tsp45I GTSAC 3 cut(s) 88, 100, 631
TspDTI ATGAA 3 cut(s) 40, 68, 503
TspGWI ACGGA 1 cut(s) 405
TspRI CASTG 3 cut(s) 103, 406, 634
VpaK11BI GGWCC 1 cut(s) 725
VspI ATTAAT 1 cut(s) 696
XapI RAATTY 1 cut(s) 1046
XceI RCATGY 3 cut(s) 356, 723, 896
XcmI CCANNNNNNNNNTGG 1 cut(s) 309
XmiI GTMKAC 2 cut(s) 623, 853
XspI CTAG 1 cut(s) 560
ZrmI AGTACT 1 cut(s) 862
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.