MD12G1257500.v1.1

Rhamnogalacturonate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr12
OG0000523
Physical Location & Seq
Reverse (-)
32476305 .. 32477409
1105 bp
Loading structure...
UTR
Exon/CDS
Intron
MD12G1257500.v1.1.491

Sequence Viewer

Length: 948 bp
ATGCTAACACAGCAAACTCATAACACCGTGGAGCTGAACAAAGGCATTGTCCGAGTCACTTTTTCAAATCCCAGAGGAGATGTCATTGGAATTGAATACAAGGGAATAGACAACTTGCTCGAAATCAAAAACCTCCCAAGCAATAGAGGTTATTGGGATCTTGTATGGAAAAATGGCTTGGACAGACTACAAGGAACAACATTTAAGATTGTTACATTGACGGCAGACCAAATAGAGATTTCTTTTAATAAAACTTATGATGATTCCCTCGGTGATTGGACGCTACCCTTAAATCCGAAGATCGCGACAGAGACCACGTTCAGACCCTTGCCTTTAACTAATCCAAGAAATCCCGAGCTTAATGGAGAGGTGGATGACAAATACCAATACTCCAGCAACGTCAAAGACATTAAGGTTCACGGTTGGATTAGCACTGACGATGCTATAGGGCTTTGGATGATCACACCTAGTACTGAGTTTCGTTCAGCGGGGCCGTTCAAGCAGGAACTTACCTCTCATGTCGGACCAACTACCCTTACTGTGTTTCTTAGTAGTCACTACCTCGGGAAAGATGTTGGATTGACCTTTGCAGAAGGTGAGGCATGGAAGAAGGTTTTCGGGCCCCTTTTTGTGTATCTTAACTCAGATGTTCGAAGCTCGAATGCGTCCTTCTCTCTGTGGGAAAATGCAAAAGAACAGATGTATGAAGAAGTAAAGAGTTGGCTATACAATTTCACTCAGTCTGAAGACTTTCCTAGTTCCGACGGACGTGGCTCAGTTTCTGGTCAATTACTAATACGGGATTCGCACATCAACGAGAGCCTAGTCTCAGCAAGTTATGCTTATGTGGGATTGGCTGCACGCGGATACGCGGGATCATGGCAAACGGAAGAATTGGGGATTGGGGTTACTCGGAAGAATTGGGCAAAGTTCTTCAATATATTTTGA
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

316

Amino Acids

35.49

Weight (kDa)

5.35

Isoelectric Point (pI)

34.87

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Rhamnogal_lyase PF06045 6 - 98 6.1e-28 Rhamnogalacturonate lyase family
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 3 cut(s) 305, 864, 872
AciI CCGC 3 cut(s) 488, 864, 872
AclWI GGATC 2 cut(s) 165, 883
AcuI CTGAAG 1 cut(s) 765
AfaI GTAC 1 cut(s) 472
AgsI TTSAA 4 cut(s) 66, 95, 499, 937
AjiI CACGTC 1 cut(s) 770
AjuI GAANNNNNNNTTGG 4 cut(s) 161, 193, 885, 917
AluBI AGCT 3 cut(s) 34, 358, 657
AluI AGCT 3 cut(s) 34, 358, 657
Alw26I GTCTC 2 cut(s) 305, 832
AlwI GGATC 2 cut(s) 165, 883
AlwNI CAGNNNCTG 1 cut(s) 782
Ama87I CYCGRG 2 cut(s) 353, 563
AoxI GGCC 2 cut(s) 491, 620
ApaI GGGCCC 1 cut(s) 624
ApeKI GCWGC 1 cut(s) 857
ArsI GACNNNNNNTTYG 2 cut(s) 33, 65
Asp700I GAANNNNTTC 2 cut(s) 614, 750
AspS9I GGNCC 4 cut(s) 491, 524, 620, 621
AsuHPI GGTGA 2 cut(s) 284, 608
AsuII TTCGAA 1 cut(s) 652
AvaI CYCGRG 2 cut(s) 353, 563
AvaII GGWCC 1 cut(s) 524
BaeGI GKGCMC 1 cut(s) 624
BanII GRGCYC 1 cut(s) 624
BbsI GAAGAC 1 cut(s) 753
BbvI GCAGC 1 cut(s) 844
BceAI ACGGC 2 cut(s) 237, 478
BciVI GTATCC 1 cut(s) 860
BclI TGATCA 1 cut(s) 459
BcoDI GTCTC 2 cut(s) 305, 832
BfaI CTAG 3 cut(s) 468, 756, 824
BfmI CTRYAG 1 cut(s) 444
BfuI GTATCC 1 cut(s) 860
BisI GCNGC 1 cut(s) 858
BlsI GCNGC 1 cut(s) 859
BmcAI AGTACT 1 cut(s) 472
Bme18I GGWCC 1 cut(s) 524
BmeT110I CYCGRG 2 cut(s) 353, 563
BmgBI CACGTC 1 cut(s) 770
BmgT120I GGNCC 4 cut(s) 491, 524, 620, 621
BmiI GGNNCC 3 cut(s) 492, 622, 623
BmsI GCATC 1 cut(s) 430
BpiI GAAGAC 1 cut(s) 753
BpmI CTGGAG 1 cut(s) 376
Bpu14I TTCGAA 1 cut(s) 652
BsaI GGTCTC 1 cut(s) 305
BsaJI CCNNGG 3 cut(s) 27, 268, 562
BsaXI ACNNNNNCTCC 2 cut(s) 374, 404
BseDI CCNNGG 3 cut(s) 27, 268, 562
BseGI GGATG 2 cut(s) 379, 462
BseMII CTCAG 5 cut(s) 465, 657, 752, 789, 843
BseRI GAGGAG 1 cut(s) 90
BseSI GKGCMC 1 cut(s) 624
BseXI GCAGC 1 cut(s) 844
BsgI GTGCAG 1 cut(s) 843
Bsh1236I CGCG 3 cut(s) 305, 864, 872
BshFI GGCC 2 cut(s) 493, 622
BsiHKCI CYCGRG 2 cut(s) 353, 563
BsmAI GTCTC 2 cut(s) 305, 832
BsmI GAATGC 1 cut(s) 667
BsnI GGCC 2 cut(s) 493, 622
Bso31I GGTCTC 1 cut(s) 305
BsoBI CYCGRG 2 cut(s) 353, 563
Bsp119I TTCGAA 1 cut(s) 652
Bsp120I GGGCCC 1 cut(s) 620
Bsp1286I GDGCHC 1 cut(s) 624
Bsp143I GATC 4 cut(s) 157, 300, 459, 875
Bsp68I TCGCGA 1 cut(s) 305
BspACI CCGC 3 cut(s) 488, 864, 872
BspANI GGCC 2 cut(s) 493, 622
BspCNI CTCAG 5 cut(s) 466, 656, 751, 788, 842
BspFNI CGCG 3 cut(s) 305, 864, 872
BspLI GGNNCC 3 cut(s) 492, 622, 623
BspPI GGATC 2 cut(s) 165, 883
BspT104I TTCGAA 1 cut(s) 652
BspTNI GGTCTC 1 cut(s) 305
BssECI CCNNGG 3 cut(s) 27, 268, 562
BssMI GATC 4 cut(s) 157, 300, 459, 875
Bst4CI ACNGT 3 cut(s) 28, 422, 541
BstAPI GCANNNNNTGC 1 cut(s) 839
BstBI TTCGAA 1 cut(s) 652
BstC8I GCNNGC 1 cut(s) 862
BstDEI CTNAG 6 cut(s) 474, 548, 643, 738, 775, 829
BstDSI CCRYGG 1 cut(s) 27
BstF5I GGATG 2 cut(s) 379, 462
BstFNI CGCG 3 cut(s) 305, 864, 872
BstKTI GATC 4 cut(s) 160, 303, 462, 878
BstMAI GTCTC 2 cut(s) 305, 832
BstMBI GATC 4 cut(s) 157, 300, 459, 875
BstMWI GCNNNNNNNGC 3 cut(s) 10, 499, 839
BstSFI CTRYAG 1 cut(s) 444
BstSLI GKGCMC 1 cut(s) 624
BstUI CGCG 3 cut(s) 305, 864, 872
BstV1I GCAGC 1 cut(s) 844
BstV2I GAAGAC 1 cut(s) 753
BstX2I RGATCY 1 cut(s) 157
BstYI RGATCY 1 cut(s) 157
BsuI GTATCC 1 cut(s) 860
BsuRI GGCC 2 cut(s) 493, 622
BtgI CCRYGG 1 cut(s) 27
BtrI CACGTC 1 cut(s) 770
BtsCI GGATG 2 cut(s) 379, 462
BtsIMutI CAGTG 1 cut(s) 432
BtuMI TCGCGA 1 cut(s) 305
Cac8I GCNNGC 1 cut(s) 862
CaiI CAGNNNCTG 1 cut(s) 782
Cfr13I GGNCC 4 cut(s) 491, 524, 620, 621
CseI GACGC 2 cut(s) 289, 654
Csp6I GTAC 1 cut(s) 471
CviAII CATG 3 cut(s) 518, 603, 879
CviQI GTAC 1 cut(s) 471
DdeI CTNAG 6 cut(s) 474, 548, 643, 738, 775, 829
DpnI GATC 4 cut(s) 159, 302, 461, 877
DpnII GATC 4 cut(s) 157, 300, 459, 875
Eco24I GRGCYC 1 cut(s) 624
Eco31I GGTCTC 1 cut(s) 305
Eco47I GGWCC 1 cut(s) 524
Eco57I CTGAAG 1 cut(s) 765
Eco88I CYCGRG 2 cut(s) 353, 563
EcoO109I RGGNCCY 1 cut(s) 621
EcoT38I GRGCYC 1 cut(s) 624
FaeI CATG 3 cut(s) 521, 606, 882
FalI AAGNNNNNCTT 2 cut(s) 826, 858
FatI CATG 3 cut(s) 517, 602, 878
FauI CCCGC 2 cut(s) 481, 865
FbaI TGATCA 1 cut(s) 459
Fnu4HI GCNGC 1 cut(s) 858
FokI GGATG 2 cut(s) 386, 469
FriOI GRGCYC 1 cut(s) 624
Fsp4HI GCNGC 1 cut(s) 858
FspBI CTAG 3 cut(s) 468, 756, 824
GluI GCNGC 1 cut(s) 858
GsuI CTGGAG 1 cut(s) 376
HaeIII GGCC 2 cut(s) 493, 622
HgaI GACGC 2 cut(s) 289, 654
Hin1II CATG 3 cut(s) 521, 606, 882
HinfI GANTC 3 cut(s) 54, 263, 803
HphI GGTGA 2 cut(s) 284, 608
Hpy166II GTNNAC 1 cut(s) 418
Hpy188I TCNGA 8 cut(s) 53, 297, 323, 524, 646, 745, 763, 915
Hpy188III TCNNGA 3 cut(s) 304, 353, 565
Hpy8I GTNNAC 1 cut(s) 418
Hpy99I CGWCG 1 cut(s) 767
HpyAV CCTTC 3 cut(s) 587, 604, 679
HpyCH4III ACNGT 3 cut(s) 28, 422, 541
HpyCH4IV ACGT 3 cut(s) 317, 399, 769
HpyCH4V TGCA 3 cut(s) 590, 689, 860
HpyF10VI GCNNNNNNNGC 3 cut(s) 10, 499, 839
HpyF3I CTNAG 6 cut(s) 474, 548, 643, 738, 775, 829
HpySE526I ACGT 3 cut(s) 317, 399, 769
Hsp92II CATG 3 cut(s) 521, 606, 882
Ksp22I TGATCA 1 cut(s) 459
Kzo9I GATC 4 cut(s) 157, 300, 459, 875
LmnI GCTCC 1 cut(s) 31
LpnPI CCDG 4 cut(s) 85, 406, 488, 768
Lsp1109I GCAGC 1 cut(s) 844
LweI GCATC 1 cut(s) 430
MaeI CTAG 3 cut(s) 468, 756, 824
MaeII ACGT 3 cut(s) 317, 399, 769
MaeIII GTNAC 4 cut(s) 55, 211, 554, 907
MalI GATC 4 cut(s) 159, 302, 461, 877
MboI GATC 4 cut(s) 157, 300, 459, 875
MboII GAAGA 7 cut(s) 310, 619, 719, 758, 902, 925, 928
MflI RGATCY 1 cut(s) 157
MhlI GDGCHC 1 cut(s) 624
MluCI AATT 5 cut(s) 90, 730, 788, 893, 919
MlyI GAGTC 1 cut(s) 63
MmeI TCCRAC 4 cut(s) 404, 502, 556, 786
MnlI CCTC 8 cut(s) 68, 140, 143, 278, 361, 523, 572, 592
MroXI GAANNNNTTC 2 cut(s) 614, 750
MseI TTAA 7 cut(s) 204, 246, 290, 335, 360, 411, 639
MspA1I CMGCKG 1 cut(s) 488
Mva1269I GAATGC 1 cut(s) 667
MvnI CGCG 3 cut(s) 305, 864, 872
MwoI GCNNNNNNNGC 3 cut(s) 10, 499, 839
NdeII GATC 4 cut(s) 157, 300, 459, 875
NlaIII CATG 3 cut(s) 521, 606, 882
NlaIV GGNNCC 3 cut(s) 492, 622, 623
NmuCI GTSAC 2 cut(s) 55, 554
NruI TCGCGA 1 cut(s) 305
NspV TTCGAA 1 cut(s) 652
PctI GAATGC 1 cut(s) 667
PdmI GAANNNNTTC 2 cut(s) 614, 750
PfeI GAWTC 2 cut(s) 263, 803
PkrI GCNGC 1 cut(s) 859
PleI GAGTC 1 cut(s) 62
PpsI GAGTC 1 cut(s) 62
PspN4I GGNNCC 3 cut(s) 492, 622, 623
PspOMI GGGCCC 1 cut(s) 620
PspPI GGNCC 4 cut(s) 491, 524, 620, 621
PstNI CAGNNNCTG 1 cut(s) 782
PsuI RGATCY 1 cut(s) 157
RruI TCGCGA 1 cut(s) 305
RsaI GTAC 1 cut(s) 472
RsaNI GTAC 1 cut(s) 471
SaqAI TTAA 7 cut(s) 204, 246, 290, 335, 360, 411, 639
SatI GCNGC 1 cut(s) 858
Sau3AI GATC 4 cut(s) 157, 300, 459, 875
Sau96I GGNCC 4 cut(s) 491, 524, 620, 621
ScaI AGTACT 1 cut(s) 472
SchI GAGTC 1 cut(s) 63
SduI GDGCHC 1 cut(s) 624
SfaNI GCATC 1 cut(s) 430
SfcI CTRYAG 1 cut(s) 444
SfuI TTCGAA 1 cut(s) 652
SinI GGWCC 1 cut(s) 524
Sse9I AATT 5 cut(s) 90, 730, 788, 893, 919
SsiI CCGC 3 cut(s) 488, 864, 872
SspMI CTAG 3 cut(s) 468, 756, 824
TaaI ACNGT 3 cut(s) 28, 422, 541
TaiI ACGT 3 cut(s) 320, 402, 772
TaqI TCGA 3 cut(s) 120, 652, 659
TasI AATT 5 cut(s) 90, 730, 788, 893, 919
TatI WGTACW 1 cut(s) 470
TfiI GAWTC 2 cut(s) 263, 803
Tru1I TTAA 7 cut(s) 204, 246, 290, 335, 360, 411, 639
Tru9I TTAA 7 cut(s) 204, 246, 290, 335, 360, 411, 639
TscAI CASTG 1 cut(s) 439
TseFI GTSAC 2 cut(s) 55, 554
TseI GCWGC 1 cut(s) 857
Tsp45I GTSAC 2 cut(s) 55, 554
TspDTI ATGAA 1 cut(s) 720
TspGWI ACGGA 2 cut(s) 780, 902
TspRI CASTG 1 cut(s) 439
VpaK11BI GGWCC 1 cut(s) 524
XmnI GAANNNNTTC 2 cut(s) 614, 750
XspI CTAG 3 cut(s) 468, 756, 824
ZrmI AGTACT 1 cut(s) 472
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.