Rh2AG039000

Rhamnogalacturonate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2A
OG0000523
Physical Location & Seq
Forward (+)
3088619 .. 3089461
843 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2AG039000.1

Sequence Viewer

Length: 843 bp
ATGGGTGGTCCTTTCAAGCAGGACCTCACCTCTCACGTTGGACCAACTTGCCTAACTGGGTTTGCTTCTCATCATTATGTTGGTAAAGAAGTTGGGCTGACATTCCAAGAGGGTGAGGTACGGAAAAAGGTTTTCGGACCTGTCTTTATCTATCTTAACTCGGCAGCACGAAACTCAGATAATAGTCCTTCAACGATCCATACACTATGGAACAATGCCAAAGATCAAATGCTTGAAGAAGTCAAAACTTGGCCATACAATTTCATTAGTTCTCACGACTTTCCTTCTTCAGATCAACGTGGATCAGTTTCGGGCCAGTTACTAGTACATAATCGATACACTGAAAGTCTTCCAAGGACAAGTTTGGCTTACGTAGGATTGGCTGCACCCGGAGAAGTTGGATCATGGCAAAGGGAGAGCAAGGGATACCAATTTTGGACTCAAACCGATGAAAAAGGCTATTTCCTCATTGAAAATATTAGACCCGGTAGCTATATTTTGTATGCATCTGTTCCGGGGATAGTTGGAGACTACAAATATGAGGTTGACATTACAATTGAACCAGGAAGTAAAATCCAATTGGCTAGTGTTACTTACAAACCTCCGAGAACCGGTACCGGTCCTACATTGTGGGAAATTGGCATTCCTGATCGCACAGCTGCGGAGTTCTACATACCGGATCCATATCCAACTCTCATGAACAAGTTGTACAAGGGGAGTCGGTTGGACAAGTTTAGGCAGTACGGGTTGTGGTCACGTTATTATGAGCGTTACCTTAACAAGACCTCATCTACCTTGTTGGTGCTAACAATTACCGTGAGGATTGGTTTTATGCTCAAGTGA
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

280

Amino Acids

31.68

Weight (kDa)

8.9

Isoelectric Point (pI)

30.86

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
fn3_3 PF14686 123 - 194 1.1e-23 Polysaccharide lyase family 4, domain II
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)
Acc65I GGTACC 1 cut(s) 614
AccB1I GGYRCC 1 cut(s) 614
AciI CCGC 1 cut(s) 662
AclWI GGATC 5 cut(s) 190, 310, 409, 674, 687
AcoI YGGCCR 1 cut(s) 251
AcuI CTGAAG 1 cut(s) 273
AfaI GTAC 5 cut(s) 120, 327, 616, 710, 743
AfiI CCNNNNNNNGG 1 cut(s) 611
AgeI ACCGGT 2 cut(s) 611, 617
AgsI TTSAA 5 cut(s) 16, 192, 236, 473, 560
AhlI ACTAGT 1 cut(s) 322
AjnI CCWGG 1 cut(s) 562
AluBI AGCT 2 cut(s) 492, 659
AluI AGCT 2 cut(s) 492, 659
Alw26I GTCTC 1 cut(s) 522
AlwI GGATC 5 cut(s) 190, 310, 409, 674, 687
AoxI GGCC 2 cut(s) 251, 313
ApeKI GCWGC 3 cut(s) 164, 383, 659
AsiGI ACCGGT 2 cut(s) 611, 617
Asp700I GAANNNNTTC 1 cut(s) 348
Asp718I GGTACC 1 cut(s) 614
AspS9I GGNCC 6 cut(s) 8, 22, 41, 137, 313, 620
AsuC2I CCSGG 3 cut(s) 390, 486, 516
AsuHPI GGTGA 2 cut(s) 19, 125
AvaII GGWCC 5 cut(s) 8, 22, 41, 137, 620
BalI TGGCCA 1 cut(s) 253
BamHI GGATCC 1 cut(s) 679
BanI GGYRCC 1 cut(s) 614
BbsI GAAGAC 1 cut(s) 341
BbvI GCAGC 3 cut(s) 176, 370, 646
BciT130I CCWGG 1 cut(s) 564
BciVI GTATCC 1 cut(s) 419
BcnI CCSGG 3 cut(s) 390, 486, 516
BcoDI GTCTC 1 cut(s) 522
BcuI ACTAGT 1 cut(s) 322
BfaI CTAG 2 cut(s) 323, 585
BfuI GTATCC 1 cut(s) 419
BisI GCNGC 3 cut(s) 165, 384, 660
BlsI GCNGC 3 cut(s) 166, 385, 661
Bme1390I CCNGG 4 cut(s) 390, 486, 516, 564
Bme18I GGWCC 5 cut(s) 8, 22, 41, 137, 620
BmgT120I GGNCC 6 cut(s) 8, 22, 41, 137, 313, 620
BmiI GGNNCC 2 cut(s) 616, 681
BmrFI CCNGG 4 cut(s) 390, 486, 516, 564
BmrI ACTGGG 1 cut(s) 66
BmsI GCATC 1 cut(s) 515
BmuI ACTGGG 1 cut(s) 66
BpiI GAAGAC 1 cut(s) 341
BpuEI CTTGAG 1 cut(s) 821
BpuMI CCSGG 3 cut(s) 390, 486, 516
Bsa29I ATCGAT 1 cut(s) 334
BsaAI YACGTR 1 cut(s) 373
BsaBI GATNNNNATC 1 cut(s) 684
BsaJI CCNNGG 2 cut(s) 353, 515
BsaWI WCCGGW 3 cut(s) 611, 617, 676
Bsc4I CCNNNNNNNGG 1 cut(s) 611
Bse118I RCCGGY 2 cut(s) 611, 617
Bse1I ACTGG 2 cut(s) 61, 316
Bse8I GATNNNNATC 1 cut(s) 684
BseBI CCWGG 1 cut(s) 564
BseCI ATCGAT 1 cut(s) 334
BseDI CCNNGG 2 cut(s) 353, 515
BseJI GATNNNNATC 1 cut(s) 684
BseLI CCNNNNNNNGG 1 cut(s) 611
BseMII CTCAG 1 cut(s) 189
BseNI ACTGG 2 cut(s) 61, 316
BseXI GCAGC 3 cut(s) 176, 370, 646
BsgI GTGCAG 1 cut(s) 369
BshFI GGCC 2 cut(s) 253, 315
BshNI GGYRCC 1 cut(s) 614
BshTI ACCGGT 2 cut(s) 611, 617
BshVI ATCGAT 1 cut(s) 334
BsiSI CCGG 6 cut(s) 390, 486, 515, 612, 618, 677
BslI CCNNNNNNNGG 1 cut(s) 611
BsmAI GTCTC 1 cut(s) 522
BsmI GAATGC 1 cut(s) 642
BsnI GGCC 2 cut(s) 253, 315
Bsp1407I TGTACA 1 cut(s) 708
Bsp143I GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
BspACI CCGC 1 cut(s) 662
BspANI GGCC 2 cut(s) 253, 315
BspCNI CTCAG 1 cut(s) 188
BspDI ATCGAT 1 cut(s) 334
BspHI TCATGA 1 cut(s) 696
BspLI GGNNCC 2 cut(s) 616, 681
BspPI GGATC 5 cut(s) 190, 310, 409, 674, 687
BspT107I GGYRCC 1 cut(s) 614
BsrFI RCCGGY 2 cut(s) 611, 617
BsrGI TGTACA 1 cut(s) 708
BsrI ACTGG 2 cut(s) 61, 316
BssAI RCCGGY 2 cut(s) 611, 617
BssECI CCNNGG 2 cut(s) 353, 515
BssMI GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
BssT1I CCWWGG 1 cut(s) 353
Bst2UI CCWGG 1 cut(s) 564
Bst4CI ACNGT 1 cut(s) 817
BstAUI TGTACA 1 cut(s) 708
BstBAI YACGTR 1 cut(s) 373
BstDEI CTNAG 1 cut(s) 175
BstKTI GATC 7 cut(s) 198, 226, 295, 305, 404, 652, 682
BstMAI GTCTC 1 cut(s) 522
BstMBI GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
BstNI CCWGG 1 cut(s) 564
BstSCI CCNGG 4 cut(s) 388, 484, 514, 562
BstSNI TACGTA 1 cut(s) 373
BstV1I GCAGC 3 cut(s) 176, 370, 646
BstV2I GAAGAC 1 cut(s) 341
BstX2I RGATCY 1 cut(s) 679
BstYI RGATCY 1 cut(s) 679
Bsu15I ATCGAT 1 cut(s) 334
BsuI GTATCC 1 cut(s) 419
BsuRI GGCC 2 cut(s) 253, 315
BsuTUI ATCGAT 1 cut(s) 334
BtsIMutI CAGTG 1 cut(s) 339
CciI TCATGA 1 cut(s) 696
Cfr10I RCCGGY 2 cut(s) 611, 617
Cfr13I GGNCC 6 cut(s) 8, 22, 41, 137, 313, 620
ClaI ATCGAT 1 cut(s) 334
Csp6I GTAC 5 cut(s) 119, 326, 615, 709, 742
CspAI ACCGGT 2 cut(s) 611, 617
CviAII CATG 2 cut(s) 405, 697
CviJI RGCY 9 cut(s) 97, 253, 315, 368, 383, 459, 492, 584, 659
CviKI_1 RGCY 9 cut(s) 97, 253, 315, 368, 383, 459, 492, 584, 659
CviQI GTAC 5 cut(s) 119, 326, 615, 709, 742
DdeI CTNAG 1 cut(s) 175
DpnI GATC 7 cut(s) 197, 225, 294, 304, 403, 651, 681
DpnII GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
EaeI YGGCCR 1 cut(s) 251
Eco105I TACGTA 1 cut(s) 373
Eco130I CCWWGG 1 cut(s) 353
Eco47I GGWCC 5 cut(s) 8, 22, 41, 137, 620
Eco57I CTGAAG 1 cut(s) 273
EcoO109I RGGNCCY 1 cut(s) 22
EcoRII CCWGG 1 cut(s) 562
EcoT14I CCWWGG 1 cut(s) 353
EcoT22I ATGCAT 1 cut(s) 508
ErhI CCWWGG 1 cut(s) 353
FaeI CATG 2 cut(s) 408, 700
FalI AAGNNNNNCTT 2 cut(s) 352, 384
FatI CATG 2 cut(s) 404, 696
Fnu4HI GCNGC 3 cut(s) 165, 384, 660
Fsp4HI GCNGC 3 cut(s) 165, 384, 660
FspBI CTAG 2 cut(s) 323, 585
GluI GCNGC 3 cut(s) 165, 384, 660
HaeIII GGCC 2 cut(s) 253, 315
HapII CCGG 6 cut(s) 390, 486, 515, 612, 618, 677
Hin1II CATG 2 cut(s) 408, 700
HincII GTYRAC 1 cut(s) 547
HindII GTYRAC 1 cut(s) 547
HinfI GANTC 2 cut(s) 439, 718
HpaII CCGG 6 cut(s) 390, 486, 515, 612, 618, 677
HphI GGTGA 2 cut(s) 19, 125
Hpy166II GTNNAC 1 cut(s) 547
Hpy188I TCNGA 4 cut(s) 137, 178, 292, 606
Hpy188III TCNNGA 3 cut(s) 275, 647, 697
Hpy8I GTNNAC 1 cut(s) 547
HpyAV CCTTC 2 cut(s) 198, 294
HpyCH4III ACNGT 1 cut(s) 817
HpyCH4IV ACGT 4 cut(s) 36, 298, 372, 757
HpyCH4V TGCA 2 cut(s) 386, 506
HpyF3I CTNAG 1 cut(s) 175
HpySE526I ACGT 4 cut(s) 36, 298, 372, 757
Hsp92II CATG 2 cut(s) 408, 700
KpnI GGTACC 1 cut(s) 618
Kzo9I GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
Lsp1109I GCAGC 3 cut(s) 176, 370, 646
LweI GCATC 1 cut(s) 515
MaeI CTAG 2 cut(s) 323, 585
MaeII ACGT 4 cut(s) 36, 298, 372, 757
MaeIII GTNAC 4 cut(s) 318, 589, 753, 770
MalI GATC 7 cut(s) 197, 225, 294, 304, 403, 651, 681
MboI GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
MboII GAAGA 3 cut(s) 248, 279, 341
MfeI CAATTG 2 cut(s) 555, 578
MflI RGATCY 1 cut(s) 679
MlsI TGGCCA 1 cut(s) 253
MluCI AATT 6 cut(s) 259, 431, 555, 578, 636, 810
MluNI TGGCCA 1 cut(s) 253
MlyI GAGTC 2 cut(s) 433, 727
MmeI TCCRAC 5 cut(s) 19, 379, 505, 705, 713
MnlI CCTC 9 cut(s) 35, 40, 103, 109, 476, 535, 612, 796, 813
Mox20I TGGCCA 1 cut(s) 253
Mph1103I ATGCAT 1 cut(s) 508
MroXI GAANNNNTTC 1 cut(s) 348
MscI TGGCCA 1 cut(s) 253
MseI TTAA 2 cut(s) 156, 777
MslI CAYNNNNRTG 1 cut(s) 75
Msp20I TGGCCA 1 cut(s) 253
MspA1I CMGCKG 1 cut(s) 659
MspI CCGG 6 cut(s) 390, 486, 515, 612, 618, 677
MspR9I CCNGG 4 cut(s) 390, 486, 516, 564
MunI CAATTG 2 cut(s) 555, 578
Mva1269I GAATGC 1 cut(s) 642
MvaI CCWGG 1 cut(s) 564
NciI CCSGG 3 cut(s) 390, 486, 516
NdeII GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
NlaIII CATG 2 cut(s) 408, 700
NlaIV GGNNCC 2 cut(s) 616, 681
NmeAIII GCCGAG 1 cut(s) 140
NmuCI GTSAC 1 cut(s) 753
NsiI ATGCAT 1 cut(s) 508
PagI TCATGA 1 cut(s) 696
PctI GAATGC 1 cut(s) 642
PdmI GAANNNNTTC 1 cut(s) 348
PinAI ACCGGT 2 cut(s) 611, 617
PkrI GCNGC 3 cut(s) 166, 385, 661
PleI GAGTC 2 cut(s) 433, 726
PpsI GAGTC 2 cut(s) 433, 726
Ppu21I YACGTR 1 cut(s) 373
PpuMI RGGWCCY 1 cut(s) 22
Psp5II RGGWCCY 1 cut(s) 22
Psp6I CCWGG 1 cut(s) 562
PspGI CCWGG 1 cut(s) 562
PspN4I GGNNCC 2 cut(s) 616, 681
PspPI GGNCC 6 cut(s) 8, 22, 41, 137, 313, 620
PspPPI RGGWCCY 1 cut(s) 22
PsrI GAACNNNNNNTAC 2 cut(s) 692, 724
PsuI RGATCY 1 cut(s) 679
PvuII CAGCTG 1 cut(s) 659
RsaI GTAC 5 cut(s) 120, 327, 616, 710, 743
RsaNI GTAC 5 cut(s) 119, 326, 615, 709, 742
RseI CAYNNNNRTG 1 cut(s) 75
SaqAI TTAA 2 cut(s) 156, 777
SatI GCNGC 3 cut(s) 165, 384, 660
Sau3AI GATC 7 cut(s) 195, 223, 292, 302, 401, 649, 679
Sau96I GGNCC 6 cut(s) 8, 22, 41, 137, 313, 620
SchI GAGTC 2 cut(s) 433, 727
ScrFI CCNGG 4 cut(s) 390, 486, 516, 564
SfaNI GCATC 1 cut(s) 515
SinI GGWCC 5 cut(s) 8, 22, 41, 137, 620
SmiMI CAYNNNNRTG 1 cut(s) 75
SmlI CTYRAG 1 cut(s) 836
SmoI CTYRAG 1 cut(s) 836
SnaBI TACGTA 1 cut(s) 373
SpeI ACTAGT 1 cut(s) 322
Sse9I AATT 6 cut(s) 259, 431, 555, 578, 636, 810
SsiI CCGC 1 cut(s) 662
SspI AATATT 1 cut(s) 478
SspMI CTAG 2 cut(s) 323, 585
StyD4I CCNGG 4 cut(s) 388, 484, 514, 562
StyI CCWWGG 1 cut(s) 353
TaaI ACNGT 1 cut(s) 817
TaiI ACGT 4 cut(s) 39, 301, 375, 760
TaqI TCGA 1 cut(s) 334
TasI AATT 6 cut(s) 259, 431, 555, 578, 636, 810
TatI WGTACW 2 cut(s) 325, 708
Tru1I TTAA 2 cut(s) 156, 777
Tru9I TTAA 2 cut(s) 156, 777
TscAI CASTG 1 cut(s) 346
TseFI GTSAC 1 cut(s) 753
TseI GCWGC 3 cut(s) 164, 383, 659
Tsp45I GTSAC 1 cut(s) 753
TspDTI ATGAA 3 cut(s) 253, 465, 713
TspGWI ACGGA 1 cut(s) 136
TspRI CASTG 1 cut(s) 346
VpaK11BI GGWCC 5 cut(s) 8, 22, 41, 137, 620
XmnI GAANNNNTTC 1 cut(s) 348
XspI CTAG 2 cut(s) 323, 585
Zsp2I ATGCAT 1 cut(s) 508
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.