RLG00000015956

Rhamnogalacturonate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr4
OG0000523
Physical Location & Seq
Forward (+)
2745687 .. 2746938
1252 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000015956

Sequence Viewer

Length: 1068 bp
ATGAGCAGTCCTGAATTTGAAGGGGAGGTAGTGGATGATAAGTATCAGTACTCGGCCGAGGACAAAGATATCAAGGTGCATGGTTGGATTTCTATTGATGACCAATCACCACCGGTGGGATTTTGGATGATCACACCTAGTGATGAGTTTCGTATAGGTGGTCCTTTCAAGCAGGACCTCACCTCTCACGTTGGACCAACTTCCCTAACTGTGTTTGCTTCTCATCATTATGTTGGTAAAAAAGTTGGGCTGAAATTCCAAGAGGGTGAGGTATGGAAAAAGGTTTTCGGACCTGTATTTATCCATCTTAACTCGGCAGCACGAAACTCAGCTAATGGTCCTTCACCGATCCGTACACTATGGAACAATGCCAAAGATCAAATGGTTGAAGAAGTCAAAAGTTGGCCATACAATTTCATTAGTTCTCACGACTGTCCTTCTTCGGTTCAACGTGGTCTTCCTCGGCCAAGTTTGGCTTACGTAGGATTGGCTGCACCCGGCGAAGTTGGATCATGGCAAAGGGAAAGCAAGGGATACCAATTTTGGACTCAAACCGATGAAAAAGGCTATTTCCTAATTGAAAATATTAGACCCGGTAACTACAATTTGTATGCATCTGTTCCCGGGATAGTTGGAGACTACAAATATGAGGTTGACATTACAATTGAACCAGGAAGTAAAATCCAATTGGCTAGTATTAATTACGAACCTCCGAAAACCGGTCCTACATTGTGGGAAATTGGCATTCCTGATCGCACAGCTATGGAGTTCTACATACCGGATCCATATCCAACTCCCATGAACAAGTTGTACAAGGGGAGTCGGTTGGACAAATTTAGGCAATACGGGTTGTGGACTTGTGGTCACTTTGAACTCAACAATGTGGTCAATCCCGGAAACTATACACTTCAACTGGCCTTAGCCTCAGCCACTTATGCAGAATTGCAAGTTCGGGTTAACAATTTGAATGCCGAACCACGTCTTTTTTCGACAGGGCTATTAGGCGACGACAATGCTATAGCAAGACATATATGGAATTCATGGTTTATACTGGTTATGGAGTATTGA
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

356

Amino Acids

40.12

Weight (kDa)

5.55

Isoelectric Point (pI)

35.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
fn3_3 PF14686 158 - 230 6.5e-25 Polysaccharide lyase family 4, domain II
CBM-like PF14683 243 - 346 1.2e-13 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
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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)
AclWI GGATC 4 cut(s) 343, 517, 776, 789
AcoI YGGCCR 3 cut(s) 54, 404, 464
AcsI RAATTY 4 cut(s) 14, 254, 833, 1036
AdeI CACNNNGTG 1 cut(s) 140
AfaI GTAC 3 cut(s) 50, 355, 812
AfiI CCNNNNNNNGG 2 cut(s) 116, 719
AgeI ACCGGT 2 cut(s) 112, 719
AgsI TTSAA 9 cut(s) 20, 169, 389, 449, 581, 668, 872, 911, 967
AhdI GACNNNNNGTC 1 cut(s) 861
AjiI CACGTC 1 cut(s) 980
AjnI CCWGG 1 cut(s) 670
AluBI AGCT 2 cut(s) 332, 761
AluI AGCT 2 cut(s) 332, 761
Alw26I GTCTC 1 cut(s) 630
AlwI GGATC 4 cut(s) 343, 517, 776, 789
Ama87I CYCGRG 1 cut(s) 623
AoxI GGCC 4 cut(s) 54, 404, 464, 915
ApeKI GCWGC 2 cut(s) 317, 491
ApoI RAATTY 4 cut(s) 14, 254, 833, 1036
AseI ATTAAT 1 cut(s) 699
AsiGI ACCGGT 2 cut(s) 112, 719
AspS9I GGNCC 6 cut(s) 161, 175, 194, 290, 338, 722
AsuC2I CCSGG 5 cut(s) 498, 594, 624, 625, 894
AsuHPI GGTGA 4 cut(s) 99, 172, 278, 336
AvaI CYCGRG 1 cut(s) 623
AvaII GGWCC 6 cut(s) 161, 175, 194, 290, 338, 722
BalI TGGCCA 1 cut(s) 406
BamHI GGATCC 1 cut(s) 781
BbsI GAAGAC 1 cut(s) 449
BbvCI CCTCAGC 1 cut(s) 925
BbvI GCAGC 2 cut(s) 329, 478
BccI CCATC 1 cut(s) 312
BcgI CGANNNNNNTGC 2 cut(s) 995, 1029
BciT130I CCWGG 1 cut(s) 672
BciVI GTATCC 1 cut(s) 527
BclI TGATCA 1 cut(s) 129
BcnI CCSGG 5 cut(s) 498, 594, 624, 625, 894
BcoDI GTCTC 1 cut(s) 630
BfaI CTAG 2 cut(s) 138, 693
BfmI CTRYAG 1 cut(s) 1017
BfuI GTATCC 1 cut(s) 527
BisI GCNGC 2 cut(s) 318, 492
BlsI GCNGC 2 cut(s) 319, 493
BmcAI AGTACT 1 cut(s) 50
Bme1390I CCNGG 6 cut(s) 498, 594, 624, 625, 672, 894
Bme18I GGWCC 6 cut(s) 161, 175, 194, 290, 338, 722
BmeRI GACNNNNNGTC 1 cut(s) 861
BmeT110I CYCGRG 1 cut(s) 623
BmgBI CACGTC 1 cut(s) 980
BmgT120I GGNCC 6 cut(s) 161, 175, 194, 290, 338, 722
BmiI GGNNCC 1 cut(s) 783
BmrFI CCNGG 6 cut(s) 498, 594, 624, 625, 672, 894
BmsI GCATC 1 cut(s) 623
BpiI GAAGAC 1 cut(s) 449
Bpu10I CCTNAGC 2 cut(s) 919, 925
BpuMI CCSGG 5 cut(s) 498, 594, 624, 625, 894
BsaAI YACGTR 1 cut(s) 481
BsaBI GATNNNNATC 2 cut(s) 42, 786
BsaJI CCNNGG 3 cut(s) 57, 461, 623
BsaWI WCCGGW 3 cut(s) 112, 719, 778
Bsc4I CCNNNNNNNGG 2 cut(s) 116, 719
Bse118I RCCGGY 2 cut(s) 112, 719
Bse1I ACTGG 2 cut(s) 918, 1056
Bse8I GATNNNNATC 2 cut(s) 42, 786
BseBI CCWGG 1 cut(s) 672
BseDI CCNNGG 3 cut(s) 57, 461, 623
BseGI GGATG 2 cut(s) 40, 132
BseJI GATNNNNATC 2 cut(s) 42, 786
BseLI CCNNNNNNNGG 2 cut(s) 116, 719
BseMII CTCAG 2 cut(s) 342, 939
BseNI ACTGG 2 cut(s) 918, 1056
BseX3I CGGCCG 1 cut(s) 54
BseXI GCAGC 2 cut(s) 329, 478
BsgI GTGCAG 1 cut(s) 477
Bsh1285I CGRYCG 1 cut(s) 57
BshFI GGCC 4 cut(s) 56, 406, 466, 917
BshTI ACCGGT 2 cut(s) 112, 719
BsiEI CGRYCG 1 cut(s) 57
BsiHKCI CYCGRG 1 cut(s) 623
BsiSI CCGG 7 cut(s) 113, 498, 594, 624, 720, 779, 894
BslI CCNNNNNNNGG 2 cut(s) 116, 719
BsmAI GTCTC 1 cut(s) 630
BsmI GAATGC 2 cut(s) 744, 973
BsnI GGCC 4 cut(s) 56, 406, 466, 917
BsoBI CYCGRG 1 cut(s) 623
Bsp1407I TGTACA 1 cut(s) 810
Bsp143I GATC 6 cut(s) 129, 348, 376, 509, 751, 781
BspANI GGCC 4 cut(s) 56, 406, 466, 917
BspCNI CTCAG 2 cut(s) 341, 938
BspLI GGNNCC 1 cut(s) 783
BspPI GGATC 4 cut(s) 343, 517, 776, 789
BsrFI RCCGGY 2 cut(s) 112, 719
BsrGI TGTACA 1 cut(s) 810
BsrI ACTGG 2 cut(s) 918, 1056
BssAI RCCGGY 2 cut(s) 112, 719
BssECI CCNNGG 3 cut(s) 57, 461, 623
BssMI GATC 6 cut(s) 129, 348, 376, 509, 751, 781
Bst2UI CCWGG 1 cut(s) 672
Bst4CI ACNGT 2 cut(s) 211, 434
BstAUI TGTACA 1 cut(s) 810
BstBAI YACGTR 1 cut(s) 481
BstDEI CTNAG 3 cut(s) 328, 919, 925
BstF5I GGATG 2 cut(s) 40, 132
BstKTI GATC 6 cut(s) 132, 351, 379, 512, 754, 784
BstMAI GTCTC 1 cut(s) 630
BstMBI GATC 6 cut(s) 129, 348, 376, 509, 751, 781
BstMCI CGRYCG 1 cut(s) 57
BstMWI GCNNNNNNNGC 1 cut(s) 935
BstNI CCWGG 1 cut(s) 672
BstSCI CCNGG 6 cut(s) 496, 592, 622, 623, 670, 892
BstSFI CTRYAG 1 cut(s) 1017
BstSNI TACGTA 1 cut(s) 481
BstV1I GCAGC 2 cut(s) 329, 478
BstV2I GAAGAC 1 cut(s) 449
BstX2I RGATCY 1 cut(s) 781
BstYI RGATCY 1 cut(s) 781
BstZI CGGCCG 1 cut(s) 54
BsuI GTATCC 1 cut(s) 527
BsuRI GGCC 4 cut(s) 56, 406, 466, 917
BtrI CACGTC 1 cut(s) 980
BtsCI GGATG 2 cut(s) 40, 132
Cfr10I RCCGGY 2 cut(s) 112, 719
Cfr13I GGNCC 6 cut(s) 161, 175, 194, 290, 338, 722
Cfr9I CCCGGG 1 cut(s) 623
Csp6I GTAC 3 cut(s) 49, 354, 811
CspAI ACCGGT 2 cut(s) 112, 719
CviAII CATG 4 cut(s) 80, 513, 799, 1041
CviQI GTAC 3 cut(s) 49, 354, 811
DdeI CTNAG 3 cut(s) 328, 919, 925
DpnI GATC 6 cut(s) 131, 350, 378, 511, 753, 783
DpnII GATC 6 cut(s) 129, 348, 376, 509, 751, 781
DraIII CACNNNGTG 1 cut(s) 140
DriI GACNNNNNGTC 1 cut(s) 861
EaeI YGGCCR 3 cut(s) 54, 404, 464
EagI CGGCCG 1 cut(s) 54
Eam1105I GACNNNNNGTC 1 cut(s) 861
EclXI CGGCCG 1 cut(s) 54
Eco105I TACGTA 1 cut(s) 481
Eco32I GATATC 1 cut(s) 70
Eco47I GGWCC 6 cut(s) 161, 175, 194, 290, 338, 722
Eco52I CGGCCG 1 cut(s) 54
Eco88I CYCGRG 1 cut(s) 623
EcoO109I RGGNCCY 1 cut(s) 175
EcoRI GAATTC 1 cut(s) 1036
EcoRII CCWGG 1 cut(s) 670
EcoRV GATATC 1 cut(s) 70
EcoT22I ATGCAT 1 cut(s) 616
FaeI CATG 4 cut(s) 83, 516, 802, 1044
FalI AAGNNNNNCTT 2 cut(s) 460, 492
FatI CATG 4 cut(s) 79, 512, 798, 1040
FbaI TGATCA 1 cut(s) 129
Fnu4HI GCNGC 2 cut(s) 318, 492
FokI GGATG 2 cut(s) 47, 139
Fsp4HI GCNGC 2 cut(s) 318, 492
FspBI CTAG 2 cut(s) 138, 693
GluI GCNGC 2 cut(s) 318, 492
HaeIII GGCC 4 cut(s) 56, 406, 466, 917
HapII CCGG 7 cut(s) 113, 498, 594, 624, 720, 779, 894
Hin1II CATG 4 cut(s) 83, 516, 802, 1044
HincII GTYRAC 2 cut(s) 655, 958
HindII GTYRAC 2 cut(s) 655, 958
HinfI GANTC 2 cut(s) 547, 820
HpaI GTTAAC 1 cut(s) 958
HpaII CCGG 7 cut(s) 113, 498, 594, 624, 720, 779, 894
HphI GGTGA 4 cut(s) 99, 172, 278, 336
Hpy166II GTNNAC 4 cut(s) 356, 655, 855, 958
Hpy188I TCNGA 2 cut(s) 290, 714
Hpy188III TCNNGA 3 cut(s) 11, 428, 749
Hpy8I GTNNAC 4 cut(s) 356, 655, 855, 958
Hpy99I CGWCG 1 cut(s) 1010
HpyAV CCTTC 3 cut(s) 14, 351, 447
HpyCH4III ACNGT 2 cut(s) 211, 434
HpyCH4IV ACGT 4 cut(s) 189, 451, 480, 979
HpyCH4V TGCA 5 cut(s) 79, 494, 614, 938, 946
HpyF10VI GCNNNNNNNGC 1 cut(s) 935
HpyF3I CTNAG 3 cut(s) 328, 919, 925
HpySE526I ACGT 4 cut(s) 189, 451, 480, 979
Hsp92II CATG 4 cut(s) 83, 516, 802, 1044
Ksp22I TGATCA 1 cut(s) 129
KspAI GTTAAC 1 cut(s) 958
Kzo9I GATC 6 cut(s) 129, 348, 376, 509, 751, 781
Lsp1109I GCAGC 2 cut(s) 329, 478
LweI GCATC 1 cut(s) 623
MaeI CTAG 2 cut(s) 138, 693
MaeII ACGT 4 cut(s) 189, 451, 480, 979
MaeIII GTNAC 2 cut(s) 596, 863
MalI GATC 6 cut(s) 131, 350, 378, 511, 753, 783
MboI GATC 6 cut(s) 129, 348, 376, 509, 751, 781
MboII GAAGA 3 cut(s) 401, 432, 449
MfeI CAATTG 2 cut(s) 663, 686
MflI RGATCY 1 cut(s) 781
MlsI TGGCCA 1 cut(s) 406
MluNI TGGCCA 1 cut(s) 406
MlyI GAGTC 2 cut(s) 541, 829
MmeI TCCRAC 6 cut(s) 65, 172, 487, 613, 807, 815
Mox20I TGGCCA 1 cut(s) 406
Mph1103I ATGCAT 1 cut(s) 616
MscI TGGCCA 1 cut(s) 406
MseI TTAA 3 cut(s) 309, 699, 957
MslI CAYNNNNRTG 2 cut(s) 228, 761
Msp20I TGGCCA 1 cut(s) 406
MspI CCGG 7 cut(s) 113, 498, 594, 624, 720, 779, 894
MspR9I CCNGG 6 cut(s) 498, 594, 624, 625, 672, 894
MunI CAATTG 2 cut(s) 663, 686
Mva1269I GAATGC 2 cut(s) 744, 973
MvaI CCWGG 1 cut(s) 672
MwoI GCNNNNNNNGC 1 cut(s) 935
NciI CCSGG 5 cut(s) 498, 594, 624, 625, 894
NdeII GATC 6 cut(s) 129, 348, 376, 509, 751, 781
NlaIII CATG 4 cut(s) 83, 516, 802, 1044
NlaIV GGNNCC 1 cut(s) 783
NmeAIII GCCGAG 4 cut(s) 32, 82, 293, 442
NmuCI GTSAC 1 cut(s) 863
NsiI ATGCAT 1 cut(s) 616
PctI GAATGC 2 cut(s) 744, 973
PfoI TCCNGGA 1 cut(s) 892
PinAI ACCGGT 2 cut(s) 112, 719
PkrI GCNGC 2 cut(s) 319, 493
PleI GAGTC 2 cut(s) 541, 828
PpsI GAGTC 2 cut(s) 541, 828
Ppu21I YACGTR 1 cut(s) 481
PpuMI RGGWCCY 1 cut(s) 175
PshBI ATTAAT 1 cut(s) 699
Psp5II RGGWCCY 1 cut(s) 175
Psp6I CCWGG 1 cut(s) 670
PspGI CCWGG 1 cut(s) 670
PspN4I GGNNCC 1 cut(s) 783
PspPI GGNCC 6 cut(s) 161, 175, 194, 290, 338, 722
PspPPI RGGWCCY 1 cut(s) 175
PsrI GAACNNNNNNTAC 2 cut(s) 794, 826
PsuI RGATCY 1 cut(s) 781
RsaI GTAC 3 cut(s) 50, 355, 812
RsaNI GTAC 3 cut(s) 49, 354, 811
RseI CAYNNNNRTG 2 cut(s) 228, 761
SaqAI TTAA 3 cut(s) 309, 699, 957
SatI GCNGC 2 cut(s) 318, 492
Sau3AI GATC 6 cut(s) 129, 348, 376, 509, 751, 781
Sau96I GGNCC 6 cut(s) 161, 175, 194, 290, 338, 722
ScaI AGTACT 1 cut(s) 50
SchI GAGTC 2 cut(s) 541, 829
ScrFI CCNGG 6 cut(s) 498, 594, 624, 625, 672, 894
SfaNI GCATC 1 cut(s) 623
SfcI CTRYAG 1 cut(s) 1017
SgrAI CRCCGGYG 1 cut(s) 112
SinI GGWCC 6 cut(s) 161, 175, 194, 290, 338, 722
SmaI CCCGGG 1 cut(s) 625
SmiMI CAYNNNNRTG 2 cut(s) 228, 761
SnaBI TACGTA 1 cut(s) 481
SspI AATATT 1 cut(s) 586
SspMI CTAG 2 cut(s) 138, 693
StyD4I CCNGG 6 cut(s) 496, 592, 622, 623, 670, 892
TaaI ACNGT 2 cut(s) 211, 434
TaiI ACGT 4 cut(s) 192, 454, 483, 982
TaqI TCGA 1 cut(s) 989
TatI WGTACW 2 cut(s) 48, 810
Tru1I TTAA 3 cut(s) 309, 699, 957
Tru9I TTAA 3 cut(s) 309, 699, 957
TseFI GTSAC 1 cut(s) 863
TseI GCWGC 2 cut(s) 317, 491
Tsp45I GTSAC 1 cut(s) 863
TspDTI ATGAA 4 cut(s) 406, 573, 815, 1029
TspGWI ACGGA 1 cut(s) 341
TspMI CCCGGG 1 cut(s) 623
VpaK11BI GGWCC 6 cut(s) 161, 175, 194, 290, 338, 722
VspI ATTAAT 1 cut(s) 699
XapI RAATTY 4 cut(s) 14, 254, 833, 1036
XcmI CCANNNNNNNNNTGG 1 cut(s) 379
XmaI CCCGGG 1 cut(s) 623
XspI CTAG 2 cut(s) 138, 693
ZrmI AGTACT 1 cut(s) 50
Zsp2I ATGCAT 1 cut(s) 616
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.