MD02G1298500.v1.1

Rhamnogalacturonate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr02
OG0000523
Physical Location & Seq
Reverse (-)
35410048 .. 35415046
4999 bp
Loading structure...
UTR
Exon/CDS
Intron
MD02G1298500.v1.1.491

Sequence Viewer

Length: 342 bp
ATGGCAAATTTTATTTCAACTTCAAAATTAATGAACACCGGAGATTATACACTCCAGTTGGCATTGGCCTCAGCAAACGGTGCAGAACTGCAGGTTCGATTGAACGACCAGAGCCCCAACGACCGACATCATTTTACAACTAGGCTAATAATAGGGAAGGACAATGCTATTGCAAGGCATGGAATTCATGGTTTGTACCAGCTGTTCAGTGTTGTTGTGCCAAGCTTTCGACTACGAGAAGGAAACAACACTATCTATCTTACTCAGTCCAGAAGTGCAAATGGCCCTTTCTCAGGTATCATGTACGACTATATCCGACTAGAAGGATCTCCTCCGAAGTGA
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

114

Amino Acids

12.58

Weight (kDa)

9.52

Isoelectric Point (pI)

38.88

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CBM-like PF14683 9 - 107 1.6e-24 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)
Acc36I ACCTGC 1 cut(s) 82
AclWI GGATC 1 cut(s) 334
AcsI RAATTY 2 cut(s) 7, 183
AfaI GTAC 2 cut(s) 197, 305
AfiI CCNNNNNNNGG 1 cut(s) 293
AgsI TTSAA 3 cut(s) 18, 24, 103
AluBI AGCT 2 cut(s) 202, 225
AluI AGCT 2 cut(s) 202, 225
AlwI GGATC 1 cut(s) 334
AoxI GGCC 2 cut(s) 66, 283
ApoI RAATTY 2 cut(s) 7, 183
AseI ATTAAT 1 cut(s) 29
AspS9I GGNCC 1 cut(s) 284
BanII GRGCYC 1 cut(s) 116
BbvCI CCTCAGC 1 cut(s) 70
BfaI CTAG 2 cut(s) 141, 320
BfmI CTRYAG 1 cut(s) 89
BfuAI ACCTGC 1 cut(s) 82
BmgT120I GGNCC 1 cut(s) 284
BpmI CTGGAG 1 cut(s) 38
Bpu10I CCTNAGC 1 cut(s) 70
BsaWI WCCGGW 1 cut(s) 38
Bsc4I CCNNNNNNNGG 1 cut(s) 293
Bse1I ACTGG 1 cut(s) 55
BseLI CCNNNNNNNGG 1 cut(s) 293
BseMII CTCAG 3 cut(s) 84, 278, 306
BseNI ACTGG 1 cut(s) 55
BseRI GAGGAG 1 cut(s) 321
BsgI GTGCAG 1 cut(s) 102
Bsh1285I CGRYCG 1 cut(s) 124
BshFI GGCC 2 cut(s) 68, 285
BsiEI CGRYCG 1 cut(s) 124
BsiSI CCGG 1 cut(s) 39
BslI CCNNNNNNNGG 1 cut(s) 293
BsnI GGCC 2 cut(s) 68, 285
Bsp1286I GDGCHC 1 cut(s) 116
Bsp143I GATC 1 cut(s) 326
BspANI GGCC 2 cut(s) 68, 285
BspCNI CTCAG 3 cut(s) 83, 277, 305
BspMAI CTGCAG 1 cut(s) 93
BspMI ACCTGC 1 cut(s) 82
BspPI GGATC 1 cut(s) 334
BsrI ACTGG 1 cut(s) 55
BssMI GATC 1 cut(s) 326
Bst4CI ACNGT 1 cut(s) 80
BstAPI GCANNNNNTGC 1 cut(s) 80
BstDEI CTNAG 3 cut(s) 70, 264, 292
BstENI CCTNNNNNAGG 1 cut(s) 291
BstKTI GATC 1 cut(s) 329
BstMBI GATC 1 cut(s) 326
BstMCI CGRYCG 1 cut(s) 124
BstMWI GCNNNNNNNGC 1 cut(s) 80
BstSFI CTRYAG 1 cut(s) 89
BstX2I RGATCY 1 cut(s) 326
BstYI RGATCY 1 cut(s) 326
BsuRI GGCC 2 cut(s) 68, 285
BtsIMutI CAGTG 1 cut(s) 214
BveI ACCTGC 1 cut(s) 82
Cfr13I GGNCC 1 cut(s) 284
Csp6I GTAC 2 cut(s) 196, 304
CviAII CATG 3 cut(s) 179, 188, 301
CviJI RGCY 6 cut(s) 68, 114, 145, 202, 225, 285
CviKI_1 RGCY 6 cut(s) 68, 114, 145, 202, 225, 285
CviQI GTAC 2 cut(s) 196, 304
DdeI CTNAG 3 cut(s) 70, 264, 292
DpnI GATC 1 cut(s) 328
DpnII GATC 1 cut(s) 326
Eco24I GRGCYC 1 cut(s) 116
EcoNI CCTNNNNNAGG 1 cut(s) 291
EcoRI GAATTC 1 cut(s) 183
EcoT38I GRGCYC 1 cut(s) 116
FaeI CATG 3 cut(s) 182, 191, 304
FaiI YATR 5 cut(s) 48, 180, 189, 302, 312
FatI CATG 3 cut(s) 178, 187, 300
FriOI GRGCYC 1 cut(s) 116
FspBI CTAG 2 cut(s) 141, 320
GsuI CTGGAG 1 cut(s) 38
HaeIII GGCC 2 cut(s) 68, 285
HapII CCGG 1 cut(s) 39
Hin1II CATG 3 cut(s) 182, 191, 304
HindIII AAGCTT 1 cut(s) 223
HpaII CCGG 1 cut(s) 39
Hpy188I TCNGA 2 cut(s) 317, 336
Hpy188III TCNNGA 1 cut(s) 270
HpyAV CCTTC 3 cut(s) 151, 233, 317
HpyCH4III ACNGT 1 cut(s) 80
HpyCH4V TGCA 4 cut(s) 83, 91, 173, 278
HpyF10VI GCNNNNNNNGC 1 cut(s) 80
HpyF3I CTNAG 3 cut(s) 70, 264, 292
Hsp92II CATG 3 cut(s) 182, 191, 304
Kzo9I GATC 1 cut(s) 326
LpnPI CCDG 7 cut(s) 52, 68, 77, 122, 212, 279, 283
MaeI CTAG 2 cut(s) 141, 320
MalI GATC 1 cut(s) 328
MboI GATC 1 cut(s) 326
MflI RGATCY 1 cut(s) 326
MhlI GDGCHC 1 cut(s) 116
MluCI AATT 3 cut(s) 7, 26, 183
MmeI TCCRAC 1 cut(s) 340
MnlI CCTC 2 cut(s) 79, 342
MseI TTAA 1 cut(s) 29
MspA1I CMGCKG 1 cut(s) 202
MspI CCGG 1 cut(s) 39
MwoI GCNNNNNNNGC 1 cut(s) 80
NdeII GATC 1 cut(s) 326
NlaIII CATG 3 cut(s) 182, 191, 304
PshBI ATTAAT 1 cut(s) 29
PspPI GGNCC 1 cut(s) 284
PsrI GAACNNNNNNTAC 2 cut(s) 188, 220
PstI CTGCAG 1 cut(s) 93
PsuI RGATCY 1 cut(s) 326
PvuII CAGCTG 1 cut(s) 202
RsaI GTAC 2 cut(s) 197, 305
RsaNI GTAC 2 cut(s) 196, 304
SaqAI TTAA 1 cut(s) 29
Sau3AI GATC 1 cut(s) 326
Sau96I GGNCC 1 cut(s) 284
SduI GDGCHC 1 cut(s) 116
SetI ASST 4 cut(s) 96, 204, 227, 298
SfcI CTRYAG 1 cut(s) 89
Sse9I AATT 3 cut(s) 7, 26, 183
SspMI CTAG 2 cut(s) 141, 320
TaaI ACNGT 1 cut(s) 80
TaqI TCGA 2 cut(s) 97, 229
TaqII GACCGA 1 cut(s) 138
TasI AATT 3 cut(s) 7, 26, 183
Tru1I TTAA 1 cut(s) 29
Tru9I TTAA 1 cut(s) 29
TscAI CASTG 1 cut(s) 214
TspDTI ATGAA 2 cut(s) 47, 176
TspRI CASTG 1 cut(s) 214
VspI ATTAAT 1 cut(s) 29
XagI CCTNNNNNAGG 1 cut(s) 291
XapI RAATTY 2 cut(s) 7, 183
XspI CTAG 2 cut(s) 141, 320
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.