RchiOBHm_Chr2g0088461

Rhamnogalacturonate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
2
OG0000523
Physical Location & Seq
Forward (+)
3002952 .. 3003475
524 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ46378

Sequence Viewer

Length: 444 bp
ATGAACAAGTTGTACAAGGGGAGTCGGTTGGACAAGTTTAGGCAATACGGGTTGTGGTCACGTTATTATGAGCATTACCCTAACAATGACCTCATCTACCTTGTTGGAACTACATGGCGGATACAGTTTGAACCCAACAATGTGGTCAATCCCGGAAACTACACACTTCAACTGGCCTTGGCATCAGCCACTTATGCAGAATTGCAAGTTCGGGTTAACAATTTGAATGTCAAACCACCTCTTTTTTCGACAGGGCTAATAGGTGACGACAATGCTATTGCAAGACATGGAATTCATGGCTTATACTGGTTATGGAGTATTGATGTACCGTGCACTCTACTACGCGAAGGAAGCAACACCATCTATCTTACTCAGTCCAGAGATGGCAATTCACCTTTCCAAGGAGTCATGTATGATTATATAAGACTAGCTAAGAGACCATAA
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

147

Amino Acids

17.01

Weight (kDa)

9.21

Isoelectric Point (pI)

40.13

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CBM-like PF14683 19 - 143 2.1e-30 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)
AccII CGCG 1 cut(s) 345
AciI CCGC 1 cut(s) 118
AcsI RAATTY 1 cut(s) 291
AfaI GTAC 2 cut(s) 14, 327
AfiI CCNNNNNNNGG 1 cut(s) 401
AgsI TTSAA 3 cut(s) 131, 170, 226
AluBI AGCT 1 cut(s) 431
AluI AGCT 1 cut(s) 431
Alw21I GWGCWC 1 cut(s) 335
Alw26I GTCTC 1 cut(s) 430
Alw44I GTGCAC 1 cut(s) 331
AoxI GGCC 1 cut(s) 174
ApaLI GTGCAC 1 cut(s) 331
ApoI RAATTY 1 cut(s) 291
AsuC2I CCSGG 1 cut(s) 153
AsuHPI GGTGA 2 cut(s) 275, 384
BaeGI GKGCMC 1 cut(s) 335
Bbv12I GWGCWC 1 cut(s) 335
BccI CCATC 2 cut(s) 368, 377
BciVI GTATCC 1 cut(s) 114
BcnI CCSGG 1 cut(s) 153
BcoDI GTCTC 1 cut(s) 430
BfaI CTAG 1 cut(s) 428
BfuI GTATCC 1 cut(s) 114
Bme1390I CCNGG 1 cut(s) 153
BmrFI CCNGG 1 cut(s) 153
BmsI GCATC 1 cut(s) 191
BpuMI CCSGG 1 cut(s) 153
BsaI GGTCTC 1 cut(s) 430
BsaJI CCNNGG 2 cut(s) 177, 400
Bsc4I CCNNNNNNNGG 1 cut(s) 401
Bse1I ACTGG 2 cut(s) 177, 311
BseDI CCNNGG 2 cut(s) 177, 400
BseLI CCNNNNNNNGG 1 cut(s) 401
BseMII CTCAG 1 cut(s) 386
BseNI ACTGG 2 cut(s) 177, 311
BseSI GKGCMC 1 cut(s) 335
Bsh1236I CGCG 1 cut(s) 345
BshFI GGCC 1 cut(s) 176
BsiHKAI GWGCWC 1 cut(s) 335
BsiSI CCGG 1 cut(s) 153
BslI CCNNNNNNNGG 1 cut(s) 401
BsmAI GTCTC 1 cut(s) 430
BsnI GGCC 1 cut(s) 176
Bso31I GGTCTC 1 cut(s) 430
Bsp1286I GDGCHC 1 cut(s) 335
Bsp1407I TGTACA 1 cut(s) 12
BspACI CCGC 1 cut(s) 118
BspANI GGCC 1 cut(s) 176
BspCNI CTCAG 1 cut(s) 385
BspFNI CGCG 1 cut(s) 345
BspTNI GGTCTC 1 cut(s) 430
BsrGI TGTACA 1 cut(s) 12
BsrI ACTGG 2 cut(s) 177, 311
BssECI CCNNGG 2 cut(s) 177, 400
BssT1I CCWWGG 2 cut(s) 177, 400
Bst4CI ACNGT 2 cut(s) 126, 330
BstAUI TGTACA 1 cut(s) 12
BstDEI CTNAG 2 cut(s) 372, 432
BstENI CCTNNNNNAGG 1 cut(s) 399
BstFNI CGCG 1 cut(s) 345
BstMAI GTCTC 1 cut(s) 430
BstMWI GCNNNNNNNGC 2 cut(s) 194, 351
BstSCI CCNGG 1 cut(s) 151
BstSLI GKGCMC 1 cut(s) 335
BstUI CGCG 1 cut(s) 345
BstXI CCANNNNNNTGG 1 cut(s) 142
BsuI GTATCC 1 cut(s) 114
BsuRI GGCC 1 cut(s) 176
Csp6I GTAC 2 cut(s) 13, 326
CviAII CATG 4 cut(s) 114, 287, 296, 409
CviJI RGCY 5 cut(s) 176, 188, 256, 300, 431
CviKI_1 RGCY 5 cut(s) 176, 188, 256, 300, 431
CviQI GTAC 2 cut(s) 13, 326
DdeI CTNAG 2 cut(s) 372, 432
EciI GGCGGA 1 cut(s) 133
Eco130I CCWWGG 2 cut(s) 177, 400
Eco31I GGTCTC 1 cut(s) 430
EcoNI CCTNNNNNAGG 1 cut(s) 399
EcoRI GAATTC 1 cut(s) 291
EcoT14I CCWWGG 2 cut(s) 177, 400
ErhI CCWWGG 2 cut(s) 177, 400
FaeI CATG 4 cut(s) 117, 290, 299, 412
FatI CATG 4 cut(s) 113, 286, 295, 408
FspBI CTAG 1 cut(s) 428
HaeIII GGCC 1 cut(s) 176
HapII CCGG 1 cut(s) 153
Hin1II CATG 4 cut(s) 117, 290, 299, 412
HincII GTYRAC 1 cut(s) 217
HindII GTYRAC 1 cut(s) 217
HinfI GANTC 2 cut(s) 22, 405
HpaI GTTAAC 1 cut(s) 217
HpaII CCGG 1 cut(s) 153
HphI GGTGA 2 cut(s) 275, 384
Hpy166II GTNNAC 2 cut(s) 217, 333
Hpy188III TCNNGA 1 cut(s) 378
Hpy8I GTNNAC 2 cut(s) 217, 333
HpyAV CCTTC 1 cut(s) 341
HpyCH4III ACNGT 2 cut(s) 126, 330
HpyCH4IV ACGT 1 cut(s) 61
HpyCH4V TGCA 4 cut(s) 197, 205, 281, 333
HpyF10VI GCNNNNNNNGC 2 cut(s) 194, 351
HpyF3I CTNAG 2 cut(s) 372, 432
HpySE526I ACGT 1 cut(s) 61
Hsp92II CATG 4 cut(s) 117, 290, 299, 412
KspAI GTTAAC 1 cut(s) 217
LpnPI CCDG 5 cut(s) 158, 166, 237, 292, 391
LweI GCATC 1 cut(s) 191
MaeI CTAG 1 cut(s) 428
MaeII ACGT 1 cut(s) 61
MaeIII GTNAC 2 cut(s) 57, 263
MhlI GDGCHC 1 cut(s) 335
MluCI AATT 4 cut(s) 200, 220, 291, 388
MlyI GAGTC 2 cut(s) 31, 414
MmeI TCCRAC 2 cut(s) 9, 85
MnlI CCTC 2 cut(s) 101, 249
MseI TTAA 1 cut(s) 216
MspI CCGG 1 cut(s) 153
MspR9I CCNGG 1 cut(s) 153
MvnI CGCG 1 cut(s) 345
MwoI GCNNNNNNNGC 2 cut(s) 194, 351
NciI CCSGG 1 cut(s) 153
NlaIII CATG 4 cut(s) 117, 290, 299, 412
NmuCI GTSAC 2 cut(s) 57, 263
PfoI TCCNGGA 1 cut(s) 151
PleI GAGTC 2 cut(s) 30, 413
PpsI GAGTC 2 cut(s) 30, 413
PsrI GAACNNNNNNTAC 1 cut(s) 28
RsaI GTAC 2 cut(s) 14, 327
RsaNI GTAC 2 cut(s) 13, 326
SaqAI TTAA 1 cut(s) 216
SchI GAGTC 2 cut(s) 31, 414
ScrFI CCNGG 1 cut(s) 153
SduI GDGCHC 1 cut(s) 335
SetI ASST 7 cut(s) 64, 93, 102, 241, 265, 397, 433
SfaNI GCATC 1 cut(s) 191
Sse9I AATT 4 cut(s) 200, 220, 291, 388
SsiI CCGC 1 cut(s) 118
SspMI CTAG 1 cut(s) 428
StyD4I CCNGG 1 cut(s) 151
StyI CCWWGG 2 cut(s) 177, 400
TaaI ACNGT 2 cut(s) 126, 330
TaiI ACGT 1 cut(s) 64
TaqI TCGA 1 cut(s) 248
TasI AATT 4 cut(s) 200, 220, 291, 388
TatI WGTACW 1 cut(s) 12
Tru1I TTAA 1 cut(s) 216
Tru9I TTAA 1 cut(s) 216
TseFI GTSAC 2 cut(s) 57, 263
Tsp45I GTSAC 2 cut(s) 57, 263
TspDTI ATGAA 2 cut(s) 17, 284
VneI GTGCAC 1 cut(s) 331
XagI CCTNNNNNAGG 1 cut(s) 399
XapI RAATTY 1 cut(s) 291
XspI CTAG 1 cut(s) 428
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.