Rroxscaffold_5G00344370

Polygalacturonase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0000579
Physical Location & Seq
Reverse (-)
14442644 .. 14444362
1719 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00344370.1

Sequence Viewer

Length: 738 bp
ATGGGTCTTCCTTCACTACTTAGCTCTGTTGTGCTTTTATGGATTGTTGCTTCATCTAGTTTCGTCATTGGGTATGGCCAAAATGGTAATCTTAGTGTACTTGATTTTGGTGCCTCCGGCGACGGCGTGGGAGATGATACCCAAGCTTTCTTGAATGCATGGAAGACACTTTGTGCGACTGGCCAAACCCTAACTATTCCTGCGGGGAAGACCTTTGTACTCAAACCTCTTCAACTTGTAGGTCCTTGCAAATCCAGCAGTGTTGTAATTCAGATTGATGGGAATATTGTTGGTCCATCCACTCTTAGCGAATGGGCAGACGTGTGCAAAATGGGACAGTGCTGGCTATGCTTCCAAAACGTGAAGGGCCTCGTCATCAAAGGCGGAGGACTTATAGATGGCAAGGGTTCAATTTGGTGGAACCAAAAAACCCAATCCATAAATGCTTTACACTTCCACAAATGCGACCAACTTCGATTATCTGGATTTACTTCCCGTAATAGTCCGAAAGCTCATATATTTATACATAGCAGCAATGATGTACGTATCTCAAACATTCATTTGAATGCACCGGAGAACAGCCCAAATACTGATGGCATCGGCATCTCTTTATCAAGCCAAGTAACTATACAAGACTCTTCCATTGGAACTGGTGATGATTGTATTGCAATTAAGGGAGGGTCCGCTTTTGTAAACGTAACTCATGTGACATGCGGACCAGGTCATGGTTTCAGGTAG

Protein Analysis

245

Amino Acids

25.8

Weight (kDa)

7.61

Isoelectric Point (pI)

30.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 32 - 232 4.7e-10 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 62 - 244 1.6e-42 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: OG0000579)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G32370 AT4G32375 AT4G32380 AT4G32380
fragaria_vesca FvH4_2g29242 FvH4_2g29270 FvH4_4g07180 FvH4_4g07190 FvH4_6g32320 FvH4_6g35100
malus_domestica MD03G1260700.v1.1 MD03G1260800.v1.1 MD09G1203400.v1.1 MD15G1065500.v1.1 MD15G1124200.v1.1 MD15G1124300.v1.1
prunus_persica Prupe.1G247300_v2.0.a1 Prupe.1G247300_v2.0.a1 Prupe.1G479600_v2.0.a1 Prupe.1G479700_v2.0.a1 Prupe.3G043600_v2.0.a1 Prupe.4G130600_v2.0.a1 Prupe.7G064200_v2.0.a1
pyrus_communis pycom03g20830 pycom15g06200
rosa_chinensis RchiOBHm_Chr2g0140421 RchiOBHm_Chr2g0146281 RchiOBHm_Chr3g0458021 RchiOBHm_Chr3g0481551 RchiOBHm_Chr4g0399361 RchiOBHm_Chr4g0399381 RchiOBHm_Chr4g0399391 RchiOBHm_Chr4g0399401 RchiOBHm_Chr4g0399411 RchiOBHm_Chr4g0399471
rosa_laevigata RLG00000009265 RLG00000009272 RLG00000011536 RLG00000011537 RLG00000019863 RLG00000020193 RLG00000023386
rosa_multiflora Rmu_sc0000384.1_g000011 Rmu_sc0002800.1_g000011 Rmu_sc0002800.1_g000012 Rmu_sc0017309.1_g000001 Rmu_sc0022824.1_g000003
rosa_roxburghii Rroxscaffold_153G00436780 Rroxscaffold_2G00100180 Rroxscaffold_5G00344320 Rroxscaffold_5G00344370 Rroxscaffold_6G00400330 Rroxscaffold_6G00421350 Rroxscaffold_7G00169940 Rroxscaffold_7G00169950
rosa_rugosa Rorug02G0362600 Rorug02G0394100 Rorug03G0024300 Rorug03G0192500 Rorug04G0016900 Rorug04G0017100 Rorug06G0278700
rosa_samantha Rh2CG399600 Rh2CG437200 Rh3AG084800 Rh3BG087600 Rh3CG088100 Rh3DG088500 Rh3DG270800 Rh4BG091900 Rh4BG092300 Rh5AG287300 Rh6DG389600
rosa_wichuraiana Rw0G012400 Rw2G033880 Rw2G036760 Rw3G007220 Rw3G021790 Rw4G007750 Rw4G007770 Rw4G007810

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 110
AccB7I CCANNNNNTGG 1 cut(s) 725
AciI CCGC 4 cut(s) 203, 384, 684, 714
AcoI YGGCCR 2 cut(s) 76, 181
AdeI CACNNNGTG 1 cut(s) 173
AfaI GTAC 3 cut(s) 99, 219, 543
AfiI CCNNNNNNNGG 1 cut(s) 725
AflIII ACRYGT 1 cut(s) 321
AgsI TTSAA 4 cut(s) 154, 233, 411, 565
AjiI CACGTC 1 cut(s) 322
AjnI CCWGG 1 cut(s) 718
AluBI AGCT 3 cut(s) 24, 146, 512
AluI AGCT 3 cut(s) 24, 146, 512
AoxI GGCC 3 cut(s) 76, 181, 367
ApeKI GCWGC 1 cut(s) 531
AspS9I GGNCC 5 cut(s) 242, 293, 367, 681, 716
AsuHPI GGTGA 1 cut(s) 665
AvaII GGWCC 4 cut(s) 242, 293, 681, 716
BalI TGGCCA 2 cut(s) 78, 183
BanI GGYRCC 1 cut(s) 110
BbsI GAAGAC 2 cut(s) 170, 215
BbvI GCAGC 1 cut(s) 543
BccI CCATC 4 cut(s) 272, 304, 392, 587
BceAI ACGGC 1 cut(s) 139
BciT130I CCWGG 1 cut(s) 720
BfaI CTAG 1 cut(s) 57
BisI GCNGC 1 cut(s) 532
BlsI GCNGC 1 cut(s) 533
Bme1390I CCNGG 1 cut(s) 720
Bme18I GGWCC 4 cut(s) 242, 293, 681, 716
BmgBI CACGTC 1 cut(s) 322
BmgT120I GGNCC 5 cut(s) 242, 293, 367, 681, 716
BmiI GGNNCC 3 cut(s) 112, 422, 682
BmrFI CCNGG 1 cut(s) 720
BmsI GCATC 2 cut(s) 606, 612
BpiI GAAGAC 2 cut(s) 170, 215
BsaAI YACGTR 1 cut(s) 545
BsaWI WCCGGW 1 cut(s) 571
Bsc4I CCNNNNNNNGG 1 cut(s) 725
Bse1I ACTGG 2 cut(s) 184, 655
Bse3DI GCAATG 1 cut(s) 541
BseBI CCWGG 1 cut(s) 720
BseGI GGATG 1 cut(s) 296
BseLI CCNNNNNNNGG 1 cut(s) 725
BseMI GCAATG 1 cut(s) 541
BseNI ACTGG 2 cut(s) 184, 655
BseXI GCAGC 1 cut(s) 543
BshFI GGCC 3 cut(s) 78, 183, 369
BshNI GGYRCC 1 cut(s) 110
BsiSI CCGG 2 cut(s) 117, 572
BslFI GGGAC 1 cut(s) 348
BslI CCNNNNNNNGG 1 cut(s) 725
BsmFI GGGAC 1 cut(s) 348
BsmI GAATGC 2 cut(s) 160, 571
BsnI GGCC 3 cut(s) 78, 183, 369
BspACI CCGC 4 cut(s) 203, 384, 684, 714
BspANI GGCC 3 cut(s) 78, 183, 369
BspLI GGNNCC 3 cut(s) 112, 422, 682
BspT107I GGYRCC 1 cut(s) 110
BsrDI GCAATG 1 cut(s) 541
BsrI ACTGG 2 cut(s) 184, 655
Bst2UI CCWGG 1 cut(s) 720
Bst4CI ACNGT 1 cut(s) 339
Bst6I CTCTTC 2 cut(s) 234, 643
BstBAI YACGTR 1 cut(s) 545
BstC8I GCNNGC 1 cut(s) 344
BstDEI CTNAG 3 cut(s) 20, 92, 305
BstF5I GGATG 1 cut(s) 296
BstMWI GCNNNNNNNGC 2 cut(s) 255, 348
BstNI CCWGG 1 cut(s) 720
BstNSI RCATGY 1 cut(s) 714
BstSCI CCNGG 1 cut(s) 718
BstSNI TACGTA 1 cut(s) 545
BstV1I GCAGC 1 cut(s) 543
BstV2I GAAGAC 2 cut(s) 170, 215
BsuRI GGCC 3 cut(s) 78, 183, 369
BtrI CACGTC 1 cut(s) 322
BtsCI GGATG 1 cut(s) 296
BtsI GCAGTG 1 cut(s) 265
BtsIMutI CAGTG 2 cut(s) 265, 344
Cac8I GCNNGC 1 cut(s) 344
Cfr13I GGNCC 5 cut(s) 242, 293, 367, 681, 716
CsiI ACCWGGT 1 cut(s) 718
Csp6I GTAC 3 cut(s) 98, 218, 542
CviAII CATG 4 cut(s) 159, 704, 711, 725
CviJI RGCY 9 cut(s) 24, 78, 146, 183, 346, 369, 512, 582, 618
CviKI_1 RGCY 9 cut(s) 24, 78, 146, 183, 346, 369, 512, 582, 618
CviQI GTAC 3 cut(s) 98, 218, 542
DdeI CTNAG 3 cut(s) 20, 92, 305
DraIII CACNNNGTG 1 cut(s) 173
EaeI YGGCCR 2 cut(s) 76, 181
Eam1104I CTCTTC 2 cut(s) 234, 643
EarI CTCTTC 2 cut(s) 234, 643
EciI GGCGGA 1 cut(s) 399
Eco105I TACGTA 1 cut(s) 545
Eco47I GGWCC 4 cut(s) 242, 293, 681, 716
EcoO109I RGGNCCY 2 cut(s) 242, 367
EcoRII CCWGG 1 cut(s) 718
EcoT22I ATGCAT 1 cut(s) 160
FaeI CATG 4 cut(s) 162, 707, 714, 728
FaqI GGGAC 1 cut(s) 348
FatI CATG 4 cut(s) 158, 703, 710, 724
FauI CCCGC 1 cut(s) 196
Fnu4HI GCNGC 1 cut(s) 532
FokI GGATG 1 cut(s) 283
Fsp4HI GCNGC 1 cut(s) 532
FspBI CTAG 1 cut(s) 57
GluI GCNGC 1 cut(s) 532
HaeIII GGCC 3 cut(s) 78, 183, 369
HapII CCGG 2 cut(s) 117, 572
Hin1II CATG 4 cut(s) 162, 707, 714, 728
HindIII AAGCTT 1 cut(s) 144
HinfI GANTC 1 cut(s) 635
HpaII CCGG 2 cut(s) 117, 572
HphI GGTGA 1 cut(s) 665
Hpy166II GTNNAC 2 cut(s) 98, 694
Hpy188I TCNGA 2 cut(s) 273, 507
Hpy188III TCNNGA 2 cut(s) 151, 483
Hpy8I GTNNAC 2 cut(s) 98, 694
Hpy99I CGWCG 1 cut(s) 125
HpyAV CCTTC 2 cut(s) 21, 358
HpyCH4III ACNGT 1 cut(s) 339
HpyCH4IV ACGT 4 cut(s) 321, 360, 544, 696
HpyCH4V TGCA 5 cut(s) 158, 249, 327, 569, 668
HpyF10VI GCNNNNNNNGC 2 cut(s) 255, 348
HpyF3I CTNAG 3 cut(s) 20, 92, 305
HpySE526I ACGT 4 cut(s) 321, 360, 544, 696
Hsp92II CATG 4 cut(s) 162, 707, 714, 728
Lsp1109I GCAGC 1 cut(s) 543
LweI GCATC 2 cut(s) 606, 612
MabI ACCWGGT 1 cut(s) 718
MaeI CTAG 1 cut(s) 57
MaeII ACGT 4 cut(s) 321, 360, 544, 696
MaeIII GTNAC 3 cut(s) 622, 697, 706
MboII GAAGA 4 cut(s) 175, 220, 221, 630
MlsI TGGCCA 2 cut(s) 78, 183
MluCI AATT 3 cut(s) 267, 411, 669
MluNI TGGCCA 2 cut(s) 78, 183
MlyI GAGTC 1 cut(s) 629
MnlI CCTC 5 cut(s) 124, 237, 380, 380, 671
Mox20I TGGCCA 2 cut(s) 78, 183
Mph1103I ATGCAT 1 cut(s) 160
MscI TGGCCA 2 cut(s) 78, 183
MseI TTAA 1 cut(s) 672
MslI CAYNNNNRTG 1 cut(s) 564
Msp20I TGGCCA 2 cut(s) 78, 183
MspI CCGG 2 cut(s) 117, 572
MspR9I CCNGG 1 cut(s) 720
Mva1269I GAATGC 2 cut(s) 160, 571
MvaI CCWGG 1 cut(s) 720
MwoI GCNNNNNNNGC 2 cut(s) 255, 348
NlaIII CATG 4 cut(s) 162, 707, 714, 728
NlaIV GGNNCC 3 cut(s) 112, 422, 682
NmuCI GTSAC 1 cut(s) 706
NsiI ATGCAT 1 cut(s) 160
NspI RCATGY 1 cut(s) 714
PctI GAATGC 2 cut(s) 160, 571
PflFI GACNNNGTC 1 cut(s) 720
PflMI CCANNNNNTGG 1 cut(s) 725
PkrI GCNGC 1 cut(s) 533
PleI GAGTC 1 cut(s) 629
PpsI GAGTC 1 cut(s) 629
Ppu21I YACGTR 1 cut(s) 545
PpuMI RGGWCCY 1 cut(s) 242
Psp5II RGGWCCY 1 cut(s) 242
Psp6I CCWGG 1 cut(s) 718
PspGI CCWGG 1 cut(s) 718
PspN4I GGNNCC 3 cut(s) 112, 422, 682
PspPI GGNCC 5 cut(s) 242, 293, 367, 681, 716
PspPPI RGGWCCY 1 cut(s) 242
PsyI GACNNNGTC 1 cut(s) 720
RsaI GTAC 3 cut(s) 99, 219, 543
RsaNI GTAC 3 cut(s) 98, 218, 542
RseI CAYNNNNRTG 1 cut(s) 564
SaqAI TTAA 1 cut(s) 672
SatI GCNGC 1 cut(s) 532
Sau96I GGNCC 5 cut(s) 242, 293, 367, 681, 716
SchI GAGTC 1 cut(s) 629
ScrFI CCNGG 1 cut(s) 720
SexAI ACCWGGT 1 cut(s) 718
SfaNI GCATC 2 cut(s) 606, 612
SinI GGWCC 4 cut(s) 242, 293, 681, 716
SmiMI CAYNNNNRTG 1 cut(s) 564
SnaBI TACGTA 1 cut(s) 545
Sse9I AATT 3 cut(s) 267, 411, 669
SsiI CCGC 4 cut(s) 203, 384, 684, 714
SspI AATATT 1 cut(s) 286
SspMI CTAG 1 cut(s) 57
StyD4I CCNGG 1 cut(s) 718
TaaI ACNGT 1 cut(s) 339
TaiI ACGT 4 cut(s) 324, 363, 547, 699
TaqI TCGA 1 cut(s) 475
TasI AATT 3 cut(s) 267, 411, 669
TatI WGTACW 2 cut(s) 97, 217
Tru1I TTAA 1 cut(s) 672
Tru9I TTAA 1 cut(s) 672
TscAI CASTG 2 cut(s) 265, 344
TseFI GTSAC 1 cut(s) 706
TseI GCWGC 1 cut(s) 531
Tsp45I GTSAC 1 cut(s) 706
TspDTI ATGAA 2 cut(s) 42, 548
TspRI CASTG 2 cut(s) 265, 344
Tth111I GACNNNGTC 1 cut(s) 720
Van91I CCANNNNNTGG 1 cut(s) 725
VpaK11BI GGWCC 4 cut(s) 242, 293, 681, 716
XceI RCATGY 1 cut(s) 714
XspI CTAG 1 cut(s) 57
Zsp2I ATGCAT 1 cut(s) 160
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.