RchiOBHm_Chr2g0110411

Rhamnogalacturonate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
2
OG0000523
Physical Location & Seq
Forward (+)
21893776 .. 21896188
2413 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ48409

Sequence Viewer

Length: 1101 bp
ATGGAAAAAGGTTTTGGGCCTGTCTTTGTGTATCTTAATTCGGCTCCAAGCTCAAAGAATTCCATCCGTATACTCTGGAATGATGCTAAAAAGCAGATGCTTAAAGAAGTCAAGAACTGGCCGTATAATTTCACTCAATCCGAGGACTTTCCTTCTTCCCATCAACGGGGATCAGTTTTGGGCCAATTACTAATACATGATCGATACATCAATGAGAGTTTTTTCCCAGCAAGTTCTGCTTATGTGGGATTGGCTGCACCCGGAGAAGTGGGATCATGGCAAAGGGAAAACAAGGGTTATCAATTTTGGAATCAAGCTGACGAAGAAGGTAGATTCATTATAAAAAATGTGCGACCCGGAAACTACAGTTTTTATGCATGGGTTCCTGGCATTGTTGGGGATTACAAATATGAGATTGATATTACAATTACTCCAGGGTCTAATATCAAATTGGACAATCTTACTTACGAACCTCCAAGAAATGGTCCTACTTTGTGGGAAATTGGCATCCCTGATCGCACTGCTGCCGAATTCTACGTACCAGATCCTTATCCAACTCTTTTGAACAATTTATACACCCAGAATCACACAGAAAATTTTAGGCAATACGGGTTGTGGGCACGTTATGGAGAGCGACACCCTCATAATGATCTTGTGTACAACGTAGCTATCAACAATTACCATGATGATTGGTTCTATGCTCAAGTGACCAGAAATACTGGAAATGAAACCTATGTAGGAACGACGTGGCAAATTCTATTTGAACTTCATAATGTCACAAATCCAGGAAATTATACACTCCAATTGGCATTGGCCTCAGCAAACAATGCAGAATTGCAGGTTCGAATTAACAACAAGAGCGATGAGCAACCTCATTTTTCATCAAAGTTAATCGGAGGGGACAATGCGATAGCAAGACATGGAATTCATGGTTTGTACTGGTTGTTTAGTGTTGAGATACCCAGCTCGCTACTAAAAGAAGGAATCAACACCGTCTATCTTACTCAAGCGAGAGGTGGTGAAACTTTCCAAGGAGTCATGTATGACTACATCAGACTAGAAGCACCTTCATCACACACTGATTCACAAGTAGTGATATAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
CBM-like Rhamnogal_lyase fn3_3

Protein Analysis

366

Amino Acids

41.82

Weight (kDa)

5.67

Isoelectric Point (pI)

31.57

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
fn3_3 PF14686 78 - 151 3e-25 Polysaccharide lyase family 4, domain II
CBM-like PF14683 164 - 353 1e-49 Polysaccharide lyase family 4, domain III
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000523)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G65210 AT2G22620 AT2G22620 AT2G22620 AT2G22620 AT2G22620 AT4G37950 AT4G37950 AT4G38030
fragaria_vesca FvH4_1g03290 FvH4_1g03300 FvH4_1g19194 FvH4_1g19194 FvH4_1g19194 FvH4_1g19194 FvH4_1g19194 FvH4_1g19194 FvH4_1g19200
malus_domestica MD01G1043200.v1.1 MD01G1043300.v1.1 MD02G1298500.v1.1 MD02G1307100.v1.1 MD04G1240500.v1.1 MD12G1256900.v1.1 MD12G1257400.v1.1 MD12G1257500.v1.1 MD15G1308100.v1.1 MD15G1308200.v1.1
prunus_persica Prupe.6G208400_v2.0.a1 Prupe.6G208400_v2.0.a1 Prupe.6G208400_v2.0.a1
pyrus_communis pycom01g07080 pycom15g27240
rosa_chinensis RchiOBHm_Chr2g0088421 RchiOBHm_Chr2g0088461 RchiOBHm_Chr2g0088481 RchiOBHm_Chr2g0110401 RchiOBHm_Chr2g0110411 RchiOBHm_Chr2g0110431
rosa_laevigata RLG00000003093 RLG00000015953 RLG00000015956 RLG00000015959 RLG00000017802 RLG00000017806
rosa_multiflora Rmu_sc0001393.1_g000003 Rmu_sc0001393.1_g000009 Rmu_sc0004733.1_g000013 Rmu_sc0004733.1_g000022
rosa_roxburghii Rroxscaffold_2G00133400 Rroxscaffold_2G00133420 Rroxscaffold_2G00152640 Rroxscaffold_2G00152680
rosa_rugosa Rorug01G0484000 Rorug01G0484200 Rorug01G0484600 Rorug02G0166800 Rorug02G0166900 Rorug02G0167000 Rorug02G0167500 Rorug02G0167600 Rorug02G0167800 Rorug02G0167800 Rorug07G0116100
rosa_samantha Rh2AG038500 Rh2AG038800 Rh2AG039000 Rh2AG219300 Rh2AG219400 Rh2BG038100 Rh2BG038400 Rh2BG228800 Rh2BG229000 Rh2CG039000 Rh2CG039600 Rh2CG221000 Rh2CG221200 Rh2DG038600 Rh2DG038800 Rh2DG225500 Rh2DG225600
rosa_wichuraiana Rw2G003060 Rw2G003080 Rw2G016930 Rw2G016940

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 341
Acc36I ACCTGC 1 cut(s) 829
AccB7I CCANNNNNTGG 1 cut(s) 482
AccI GTMKAC 1 cut(s) 70
AclWI GGATC 3 cut(s) 178, 280, 539
AcoI YGGCCR 1 cut(s) 119
AcsI RAATTY 5 cut(s) 58, 530, 595, 753, 924
AfaI GTAC 3 cut(s) 540, 659, 938
AfiI CCNNNNNNNGG 3 cut(s) 165, 166, 482
AgsI TTSAA 2 cut(s) 565, 764
AjiI CACGTC 1 cut(s) 747
AjnI CCWGG 3 cut(s) 385, 433, 784
AjuI GAANNNNNNNTTGG 1 cut(s) 29
AluBI AGCT 4 cut(s) 51, 317, 668, 966
AluI AGCT 4 cut(s) 51, 317, 668, 966
AlwI GGATC 3 cut(s) 178, 280, 539
AoxI GGCC 4 cut(s) 17, 119, 181, 813
ApeKI GCWGC 2 cut(s) 254, 524
ApoI RAATTY 5 cut(s) 58, 530, 595, 753, 924
AspS9I GGNCC 3 cut(s) 17, 181, 485
AsuC2I CCSGG 2 cut(s) 261, 357
AsuHPI GGTGA 1 cut(s) 1031
AsuII TTCGAA 1 cut(s) 844
AvaII GGWCC 1 cut(s) 485
BaeGI GKGCMC 1 cut(s) 622
BbvCI CCTCAGC 1 cut(s) 817
BbvI GCAGC 2 cut(s) 241, 511
BccI CCATC 2 cut(s) 71, 168
BceAI ACGGC 1 cut(s) 106
BciT130I CCWGG 3 cut(s) 387, 435, 786
BcnI CCSGG 2 cut(s) 261, 357
BfaI CTAG 1 cut(s) 1058
BfmI CTRYAG 1 cut(s) 364
BfuAI ACCTGC 1 cut(s) 829
BisI GCNGC 2 cut(s) 255, 525
BlsI GCNGC 2 cut(s) 256, 526
Bme1390I CCNGG 5 cut(s) 261, 357, 387, 435, 786
Bme18I GGWCC 1 cut(s) 485
BmgBI CACGTC 1 cut(s) 747
BmgT120I GGNCC 3 cut(s) 17, 181, 485
BmiI GGNNCC 2 cut(s) 45, 384
BmrFI CCNGG 5 cut(s) 261, 357, 387, 435, 786
BmsI GCATC 3 cut(s) 73, 87, 516
BpmI CTGGAG 1 cut(s) 417
Bpu10I CCTNAGC 1 cut(s) 817
Bpu14I TTCGAA 1 cut(s) 844
BpuEI CTTGAG 2 cut(s) 687, 990
BpuMI CCSGG 2 cut(s) 261, 357
Bsa29I ATCGAT 1 cut(s) 202
BsaAI YACGTR 1 cut(s) 538
BsaBI GATNNNNATC 1 cut(s) 549
BsaJI CCNNGG 3 cut(s) 141, 434, 1030
BsaXI ACNNNNNCTCC 2 cut(s) 415, 445
Bsc4I CCNNNNNNNGG 3 cut(s) 165, 166, 482
Bse1I ACTGG 3 cut(s) 122, 724, 944
Bse8I GATNNNNATC 1 cut(s) 549
BseBI CCWGG 3 cut(s) 387, 435, 786
BseCI ATCGAT 1 cut(s) 202
BseDI CCNNGG 3 cut(s) 141, 434, 1030
BseGI GGATG 2 cut(s) 63, 507
BseJI GATNNNNATC 1 cut(s) 549
BseLI CCNNNNNNNGG 3 cut(s) 165, 166, 482
BseMII CTCAG 1 cut(s) 831
BseNI ACTGG 3 cut(s) 122, 724, 944
BseSI GKGCMC 1 cut(s) 622
BseXI GCAGC 2 cut(s) 241, 511
BseYI CCCAGC 2 cut(s) 226, 962
BsgI GTGCAG 1 cut(s) 240
BshFI GGCC 4 cut(s) 19, 121, 183, 815
BshVI ATCGAT 1 cut(s) 202
BsiSI CCGG 2 cut(s) 261, 357
BslFI GGGAC 1 cut(s) 914
BslI CCNNNNNNNGG 3 cut(s) 165, 166, 482
BsmFI GGGAC 1 cut(s) 914
BsnI GGCC 4 cut(s) 19, 121, 183, 815
Bsp119I TTCGAA 1 cut(s) 844
Bsp1286I GDGCHC 1 cut(s) 622
Bsp1407I TGTACA 1 cut(s) 657
Bsp143I GATC 6 cut(s) 170, 199, 272, 514, 544, 649
BspANI GGCC 4 cut(s) 19, 121, 183, 815
BspCNI CTCAG 1 cut(s) 830
BspDI ATCGAT 1 cut(s) 202
BspLI GGNNCC 2 cut(s) 45, 384
BspMI ACCTGC 1 cut(s) 829
BspPI GGATC 3 cut(s) 178, 280, 539
BspT104I TTCGAA 1 cut(s) 844
BsrGI TGTACA 1 cut(s) 657
BsrI ACTGG 3 cut(s) 122, 724, 944
BssECI CCNNGG 3 cut(s) 141, 434, 1030
BssMI GATC 6 cut(s) 170, 199, 272, 514, 544, 649
BssNAI GTATAC 1 cut(s) 71
BssT1I CCWWGG 1 cut(s) 1030
Bst1107I GTATAC 1 cut(s) 71
Bst2UI CCWGG 3 cut(s) 387, 435, 786
Bst4CI ACNGT 2 cut(s) 368, 994
BstAPI GCANNNNNTGC 2 cut(s) 236, 827
BstAUI TGTACA 1 cut(s) 657
BstBAI YACGTR 1 cut(s) 538
BstBI TTCGAA 1 cut(s) 844
BstC8I GCNNGC 1 cut(s) 968
BstDEI CTNAG 1 cut(s) 817
BstF5I GGATG 2 cut(s) 63, 507
BstKTI GATC 6 cut(s) 173, 202, 275, 517, 547, 652
BstMBI GATC 6 cut(s) 170, 199, 272, 514, 544, 649
BstMWI GCNNNNNNNGC 2 cut(s) 236, 827
BstNI CCWGG 3 cut(s) 387, 435, 786
BstSCI CCNGG 5 cut(s) 259, 355, 385, 433, 784
BstSFI CTRYAG 1 cut(s) 364
BstSLI GKGCMC 1 cut(s) 622
BstSNI TACGTA 1 cut(s) 538
BstV1I GCAGC 2 cut(s) 241, 511
BstX2I RGATCY 1 cut(s) 544
BstYI RGATCY 1 cut(s) 544
BstZ17I GTATAC 1 cut(s) 71
Bsu15I ATCGAT 1 cut(s) 202
BsuRI GGCC 4 cut(s) 19, 121, 183, 815
BsuTUI ATCGAT 1 cut(s) 202
BtgZI GCGATG 1 cut(s) 876
BtrI CACGTC 1 cut(s) 747
BtsCI GGATG 2 cut(s) 63, 507
BtsI GCAGTG 1 cut(s) 519
BtsIMutI CAGTG 2 cut(s) 519, 1077
BveI ACCTGC 1 cut(s) 829
Cac8I GCNNGC 1 cut(s) 968
Cfr13I GGNCC 3 cut(s) 17, 181, 485
ClaI ATCGAT 1 cut(s) 202
Csp6I GTAC 3 cut(s) 539, 658, 937
CviAII CATG 7 cut(s) 197, 276, 378, 683, 920, 929, 1039
CviQI GTAC 3 cut(s) 539, 658, 937
DdeI CTNAG 1 cut(s) 817
DpnI GATC 6 cut(s) 172, 201, 274, 516, 546, 651
DpnII GATC 6 cut(s) 170, 199, 272, 514, 544, 649
EaeI YGGCCR 1 cut(s) 119
Eco105I TACGTA 1 cut(s) 538
Eco130I CCWWGG 1 cut(s) 1030
Eco47I GGWCC 1 cut(s) 485
EcoRI GAATTC 3 cut(s) 58, 530, 924
EcoRII CCWGG 3 cut(s) 385, 433, 784
EcoT14I CCWWGG 1 cut(s) 1030
EcoT22I ATGCAT 1 cut(s) 379
ErhI CCWWGG 1 cut(s) 1030
FaeI CATG 7 cut(s) 200, 279, 381, 686, 923, 932, 1042
FalI AAGNNNNNCTT 2 cut(s) 223, 255
FaqI GGGAC 1 cut(s) 914
FatI CATG 7 cut(s) 196, 275, 377, 682, 919, 928, 1038
FblI GTMKAC 1 cut(s) 70
Fnu4HI GCNGC 2 cut(s) 255, 525
FokI GGATG 2 cut(s) 50, 494
Fsp4HI GCNGC 2 cut(s) 255, 525
FspBI CTAG 1 cut(s) 1058
GluI GCNGC 2 cut(s) 255, 525
GsaI CCCAGC 2 cut(s) 230, 966
GsuI CTGGAG 1 cut(s) 417
HaeIII GGCC 4 cut(s) 19, 121, 183, 815
HapII CCGG 2 cut(s) 261, 357
Hin1II CATG 7 cut(s) 200, 279, 381, 686, 923, 932, 1042
HinfI GANTC 6 cut(s) 310, 333, 583, 984, 1035, 1082
HpaII CCGG 2 cut(s) 261, 357
HphI GGTGA 1 cut(s) 1031
Hpy166II GTNNAC 2 cut(s) 71, 658
Hpy188I TCNGA 3 cut(s) 142, 896, 1055
Hpy188III TCNNGA 2 cut(s) 76, 112
Hpy8I GTNNAC 2 cut(s) 71, 658
Hpy99I CGWCG 1 cut(s) 748
HpyAV CCTTC 4 cut(s) 162, 320, 974, 1077
HpyCH4III ACNGT 2 cut(s) 368, 994
HpyCH4IV ACGT 4 cut(s) 537, 622, 663, 746
HpyCH4V TGCA 4 cut(s) 257, 377, 830, 838
HpyF10VI GCNNNNNNNGC 2 cut(s) 236, 827
HpyF3I CTNAG 1 cut(s) 817
HpySE526I ACGT 4 cut(s) 537, 622, 663, 746
Hsp92II CATG 7 cut(s) 200, 279, 381, 686, 923, 932, 1042
Kzo9I GATC 6 cut(s) 170, 199, 272, 514, 544, 649
LmnI GCTCC 1 cut(s) 49
Lsp1109I GCAGC 2 cut(s) 241, 511
LweI GCATC 3 cut(s) 73, 87, 516
MaeI CTAG 1 cut(s) 1058
MaeII ACGT 4 cut(s) 537, 622, 663, 746
MaeIII GTNAC 2 cut(s) 706, 775
MalI GATC 6 cut(s) 172, 201, 274, 516, 546, 651
MboI GATC 6 cut(s) 170, 199, 272, 514, 544, 649
MboII GAAGA 2 cut(s) 147, 335
MfeI CAATTG 1 cut(s) 803
MflI RGATCY 1 cut(s) 544
MhlI GDGCHC 1 cut(s) 622
MlyI GAGTC 1 cut(s) 1044
MmeI TCCRAC 1 cut(s) 578
MnlI CCTC 7 cut(s) 136, 483, 651, 826, 882, 890, 1007
Mph1103I ATGCAT 1 cut(s) 379
MseI TTAA 4 cut(s) 36, 102, 849, 890
MspI CCGG 2 cut(s) 261, 357
MspR9I CCNGG 5 cut(s) 261, 357, 387, 435, 786
MunI CAATTG 1 cut(s) 803
MvaI CCWGG 3 cut(s) 387, 435, 786
MwoI GCNNNNNNNGC 2 cut(s) 236, 827
NciI CCSGG 2 cut(s) 261, 357
NdeII GATC 6 cut(s) 170, 199, 272, 514, 544, 649
NlaIII CATG 7 cut(s) 200, 279, 381, 686, 923, 932, 1042
NlaIV GGNNCC 2 cut(s) 45, 384
NmuCI GTSAC 2 cut(s) 706, 775
NsiI ATGCAT 1 cut(s) 379
NspV TTCGAA 1 cut(s) 844
PfeI GAWTC 5 cut(s) 310, 333, 583, 984, 1082
PflMI CCANNNNNTGG 1 cut(s) 482
PfoI TCCNGGA 1 cut(s) 784
PkrI GCNGC 2 cut(s) 256, 526
PleI GAGTC 1 cut(s) 1043
PpsI GAGTC 1 cut(s) 1043
Ppu21I YACGTR 1 cut(s) 538
PsiI TTATAA 1 cut(s) 341
Psp6I CCWGG 3 cut(s) 385, 433, 784
PspFI CCCAGC 2 cut(s) 226, 962
PspGI CCWGG 3 cut(s) 385, 433, 784
PspN4I GGNNCC 2 cut(s) 45, 384
PspPI GGNCC 3 cut(s) 17, 181, 485
PsrI GAACNNNNNNTAC 2 cut(s) 557, 589
PsuI RGATCY 1 cut(s) 544
RsaI GTAC 3 cut(s) 540, 659, 938
RsaNI GTAC 3 cut(s) 539, 658, 937
SaqAI TTAA 4 cut(s) 36, 102, 849, 890
SatI GCNGC 2 cut(s) 255, 525
Sau3AI GATC 6 cut(s) 170, 199, 272, 514, 544, 649
Sau96I GGNCC 3 cut(s) 17, 181, 485
SchI GAGTC 1 cut(s) 1044
ScrFI CCNGG 5 cut(s) 261, 357, 387, 435, 786
SduI GDGCHC 1 cut(s) 622
SfaNI GCATC 3 cut(s) 73, 87, 516
SfcI CTRYAG 1 cut(s) 364
SfuI TTCGAA 1 cut(s) 844
SinI GGWCC 1 cut(s) 485
SmlI CTYRAG 2 cut(s) 702, 1005
SmoI CTYRAG 2 cut(s) 702, 1005
SnaBI TACGTA 1 cut(s) 538
SspMI CTAG 1 cut(s) 1058
StyD4I CCNGG 5 cut(s) 259, 355, 385, 433, 784
StyI CCWWGG 1 cut(s) 1030
TaaI ACNGT 2 cut(s) 368, 994
TaiI ACGT 4 cut(s) 540, 625, 666, 749
TaqI TCGA 2 cut(s) 202, 844
TatI WGTACW 2 cut(s) 657, 936
TfiI GAWTC 5 cut(s) 310, 333, 583, 984, 1082
Tru1I TTAA 4 cut(s) 36, 102, 849, 890
Tru9I TTAA 4 cut(s) 36, 102, 849, 890
TscAI CASTG 2 cut(s) 526, 1084
TseFI GTSAC 2 cut(s) 706, 775
TseI GCWGC 2 cut(s) 254, 524
Tsp45I GTSAC 2 cut(s) 706, 775
TspDTI ATGAA 6 cut(s) 325, 741, 758, 870, 917, 1059
TspGWI ACGGA 1 cut(s) 56
TspRI CASTG 2 cut(s) 526, 1084
Van91I CCANNNNNTGG 1 cut(s) 482
VpaK11BI GGWCC 1 cut(s) 485
XapI RAATTY 5 cut(s) 58, 530, 595, 753, 924
XmiI GTMKAC 1 cut(s) 70
XspI CTAG 1 cut(s) 1058
Zsp2I ATGCAT 1 cut(s) 379
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.