Rh4DG316200

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0013798
Physical Location & Seq
Forward (+)
53900904 .. 53901892
989 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4DG316200.1

Sequence Viewer

Length: 825 bp
ATGACCATCACGCTGAAAGAGGAGCTGATGATGAACTCGTTCAAGACCATCGACGGCCGAGGAGCCAATGTACACATCGCCGGCGGGCCTTGCATTACTATTCAATACGTCACCAATATCATAATCCACGGCTTGAACATCCACGACTGCAAGCAAGGCGGGAATGCTTATGTTAGAGACTCTCCTAGCCATTATGGGTGGAGGACTTTGTCTGACGGAGACGGGGTTTCGATTTTCGGGGGAAGCCATGTTTGGGTGGATCATTGCTCTCTCTCGAACTGCCGTGATGGTCTCATTGATGCGATTCATGGCTCTACGGCTATTACGATTTCCAACAATTACATGACGCACCATAACAAGGTCATGTTGTTGGGTCACAGTGACACCTACACGCAGGACAAGAACATGCAGGTCACTATTGCGTTCAATCACTTTGGAGAAGGCCTTGTTCAAAGGATGCCAAGGTGCAGGCATGGAAATTTTCATGTGGTGAACAATGACTATACGCATTGGGAAATGTATGCAATTGGGGGTAGTGCTTCTCCAACTATCAACAGCCAAGGGAATAGGTTTCTTGCACCTAATGATAGATTTAACAAAGAGGTGACTAAACATGAGGAAGCACCACAGAATGAGTGGAGCAAATGGAACTGGAGGTCTTCAGGGGATTTACTGCTGAATGGTGCATTTTTCACAGCGTCTGGTGCCGGAGCTTCTTCGAGTTACGCCAAGGCTTCGAGTTTGGGTGCAAGGCCATCTTCCCTAGTGAGCTCAATCACAGCTGGTGCTGGTTCACTCAAATGTAAGAAGGGCTCGCGTTGCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00040 ko02024 map00040 map02024
Pfam Domains
Protein Families
Pec_lyase_C

Protein Analysis

274

Amino Acids

29.89

Weight (kDa)

8.45

Isoelectric Point (pI)

33.55

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 7 - 207 3.5e-21 Pectate lyase
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: OG0013798)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G67750
fragaria_vesca FvH4_4g25110
malus_domestica MD13G1106200.v1.1 MD16G1106400.v1.1
prunus_persica Prupe.1G239900_v2.0.a1 Prupe.1G239900_v2.0.a1
pyrus_communis pycom13g09220 pycom16g09060
rosa_chinensis RchiOBHm_Chr4g0432291
rosa_laevigata RLG00000006855
rosa_multiflora Rmu_sc0001084.1_g000044
rosa_roxburghii Rroxscaffold_5G00373750
rosa_rugosa Rorug04G0256800
rosa_samantha Rh4BG320700 Rh4CG335900 Rh4DG316200
rosa_wichuraiana Rw4G027220

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 400
AccB1I GGYRCC 1 cut(s) 704
AccII CGCG 1 cut(s) 817
AciI CCGC 2 cut(s) 84, 159
AclWI GGATC 1 cut(s) 267
AcoI YGGCCR 1 cut(s) 55
AcsI RAATTY 1 cut(s) 478
AcuI CTGAAG 1 cut(s) 645
AfaI GTAC 1 cut(s) 72
AfiI CCNNNNNNNGG 2 cut(s) 253, 358
AgsI TTSAA 5 cut(s) 43, 104, 136, 427, 452
AjuI GAANNNNNNNTTGG 2 cut(s) 235, 267
AluBI AGCT 4 cut(s) 25, 713, 771, 782
AluI AGCT 4 cut(s) 25, 713, 771, 782
Alw21I GWGCWC 1 cut(s) 773
Alw26I GTCTC 3 cut(s) 171, 213, 296
AlwI GGATC 1 cut(s) 267
AlwNI CAGNNNCTG 1 cut(s) 701
AoxI GGCC 4 cut(s) 55, 86, 442, 752
ApoI RAATTY 1 cut(s) 478
Asp700I GAANNNNTTC 1 cut(s) 38
AspS9I GGNCC 1 cut(s) 86
AsuHPI GGTGA 3 cut(s) 103, 502, 616
BanI GGYRCC 1 cut(s) 704
BanII GRGCYC 2 cut(s) 773, 815
BbsI GAAGAC 1 cut(s) 651
Bbv12I GWGCWC 1 cut(s) 773
BccI CCATC 4 cut(s) 14, 56, 281, 763
BceAI ACGGC 4 cut(s) 70, 145, 267, 333
BcoDI GTCTC 3 cut(s) 171, 213, 296
BfaI CTAG 2 cut(s) 186, 764
BfuAI ACCTGC 1 cut(s) 400
BmgT120I GGNCC 1 cut(s) 86
BmiI GGNNCC 2 cut(s) 64, 706
BmsI GCATC 2 cut(s) 289, 447
BpiI GAAGAC 1 cut(s) 651
BpmI CTGGAG 1 cut(s) 673
BsaI GGTCTC 1 cut(s) 296
BsaJI CCNNGG 5 cut(s) 58, 127, 461, 559, 729
BsaXI ACNNNNNCTCC 4 cut(s) 54, 84, 210, 240
Bsc4I CCNNNNNNNGG 2 cut(s) 253, 358
Bse118I RCCGGY 1 cut(s) 80
Bse1I ACTGG 1 cut(s) 656
Bse3DI GCAATG 1 cut(s) 262
BseDI CCNNGG 5 cut(s) 58, 127, 461, 559, 729
BseGI GGATG 2 cut(s) 138, 462
BseLI CCNNNNNNNGG 2 cut(s) 253, 358
BseMI GCAATG 1 cut(s) 262
BseNI ACTGG 1 cut(s) 656
BseRI GAGGAG 2 cut(s) 35, 75
BseX3I CGGCCG 1 cut(s) 55
BsgI GTGCAG 1 cut(s) 487
Bsh1236I CGCG 1 cut(s) 817
Bsh1285I CGRYCG 1 cut(s) 58
BshFI GGCC 4 cut(s) 57, 88, 444, 754
BshNI GGYRCC 1 cut(s) 704
BsiEI CGRYCG 1 cut(s) 58
BsiHKAI GWGCWC 1 cut(s) 773
BsiSI CCGG 2 cut(s) 81, 708
BslI CCNNNNNNNGG 2 cut(s) 253, 358
BsmAI GTCTC 3 cut(s) 171, 213, 296
BsmBI CGTCTC 1 cut(s) 213
BsmI GAATGC 1 cut(s) 169
BsnI GGCC 4 cut(s) 57, 88, 444, 754
Bso31I GGTCTC 1 cut(s) 296
Bsp1286I GDGCHC 2 cut(s) 773, 815
Bsp1407I TGTACA 1 cut(s) 70
Bsp143I GATC 1 cut(s) 259
BspACI CCGC 2 cut(s) 84, 159
BspANI GGCC 4 cut(s) 57, 88, 444, 754
BspFNI CGCG 1 cut(s) 817
BspLI GGNNCC 2 cut(s) 64, 706
BspMI ACCTGC 1 cut(s) 400
BspPI GGATC 1 cut(s) 267
BspT107I GGYRCC 1 cut(s) 704
BspTNI GGTCTC 1 cut(s) 296
BsrDI GCAATG 1 cut(s) 262
BsrFI RCCGGY 1 cut(s) 80
BsrGI TGTACA 1 cut(s) 70
BsrI ACTGG 1 cut(s) 656
BssAI RCCGGY 1 cut(s) 80
BssECI CCNNGG 5 cut(s) 58, 127, 461, 559, 729
BssMI GATC 1 cut(s) 259
BssT1I CCWWGG 3 cut(s) 461, 559, 729
Bst4CI ACNGT 1 cut(s) 380
BstAUI TGTACA 1 cut(s) 70
BstC8I GCNNGC 5 cut(s) 82, 86, 152, 470, 815
BstDSI CCRYGG 1 cut(s) 127
BstF5I GGATG 2 cut(s) 138, 462
BstFNI CGCG 1 cut(s) 817
BstKTI GATC 1 cut(s) 262
BstMAI GTCTC 3 cut(s) 171, 213, 296
BstMBI GATC 1 cut(s) 259
BstMCI CGRYCG 1 cut(s) 58
BstMWI GCNNNNNNNGC 4 cut(s) 90, 156, 704, 819
BstNSI RCATGY 1 cut(s) 409
BstUI CGCG 1 cut(s) 817
BstV2I GAAGAC 1 cut(s) 651
BstZI CGGCCG 1 cut(s) 55
BsuRI GGCC 4 cut(s) 57, 88, 444, 754
BtgI CCRYGG 1 cut(s) 127
BtgZI GCGATG 1 cut(s) 61
BtsCI GGATG 2 cut(s) 138, 462
BtsIMutI CAGTG 1 cut(s) 385
BveI ACCTGC 1 cut(s) 400
Cac8I GCNNGC 5 cut(s) 82, 86, 152, 470, 815
CaiI CAGNNNCTG 1 cut(s) 701
Cfr10I RCCGGY 1 cut(s) 80
Cfr13I GGNCC 1 cut(s) 86
CseI GACGC 2 cut(s) 355, 687
Csp6I GTAC 1 cut(s) 71
CviAII CATG 8 cut(s) 248, 308, 343, 364, 406, 473, 485, 614
CviQI GTAC 1 cut(s) 71
DpnI GATC 1 cut(s) 261
DpnII GATC 1 cut(s) 259
EaeI YGGCCR 1 cut(s) 55
EagI CGGCCG 1 cut(s) 55
Ecl136II GAGCTC 1 cut(s) 771
EclXI CGGCCG 1 cut(s) 55
Eco130I CCWWGG 3 cut(s) 461, 559, 729
Eco147I AGGCCT 1 cut(s) 444
Eco24I GRGCYC 2 cut(s) 773, 815
Eco31I GGTCTC 1 cut(s) 296
Eco52I CGGCCG 1 cut(s) 55
Eco53kI GAGCTC 1 cut(s) 771
Eco57I CTGAAG 1 cut(s) 645
EcoICRI GAGCTC 1 cut(s) 771
EcoT14I CCWWGG 3 cut(s) 461, 559, 729
EcoT38I GRGCYC 2 cut(s) 773, 815
ErhI CCWWGG 3 cut(s) 461, 559, 729
Esp3I CGTCTC 1 cut(s) 213
FaeI CATG 8 cut(s) 251, 311, 346, 367, 409, 476, 488, 617
FalI AAGNNNNNCTT 2 cut(s) 742, 774
FatI CATG 8 cut(s) 247, 307, 342, 363, 405, 472, 484, 613
FauI CCCGC 2 cut(s) 77, 152
FokI GGATG 2 cut(s) 125, 469
FriOI GRGCYC 2 cut(s) 773, 815
FspBI CTAG 2 cut(s) 186, 764
GsuI CTGGAG 1 cut(s) 673
HaeIII GGCC 4 cut(s) 57, 88, 444, 754
HapII CCGG 2 cut(s) 81, 708
HgaI GACGC 2 cut(s) 355, 687
Hin1II CATG 8 cut(s) 251, 311, 346, 367, 409, 476, 488, 617
HinfI GANTC 2 cut(s) 179, 304
HpaII CCGG 2 cut(s) 81, 708
HphI GGTGA 3 cut(s) 103, 502, 616
Hpy166II GTNNAC 3 cut(s) 73, 493, 794
Hpy188I TCNGA 1 cut(s) 214
Hpy188III TCNNGA 2 cut(s) 43, 274
Hpy8I GTNNAC 3 cut(s) 73, 493, 794
Hpy99I CGWCG 1 cut(s) 56
HpyAV CCTTC 2 cut(s) 434, 802
HpyCH4III ACNGT 1 cut(s) 380
HpyCH4IV ACGT 1 cut(s) 108
HpyCH4V TGCA 8 cut(s) 93, 150, 409, 468, 524, 578, 686, 749
HpyF10VI GCNNNNNNNGC 4 cut(s) 90, 156, 704, 819
HpySE526I ACGT 1 cut(s) 108
Hsp92II CATG 8 cut(s) 251, 311, 346, 367, 409, 476, 488, 617
KroI GCCGGC 1 cut(s) 80
KroNI GCCGGC 1 cut(s) 82
Kzo9I GATC 1 cut(s) 259
LmnI GCTCC 4 cut(s) 22, 62, 639, 710
LweI GCATC 2 cut(s) 289, 447
MaeI CTAG 2 cut(s) 186, 764
MaeII ACGT 1 cut(s) 108
MaeIII GTNAC 6 cut(s) 109, 374, 380, 412, 604, 722
MalI GATC 1 cut(s) 261
MboI GATC 1 cut(s) 259
MboII GAAGA 3 cut(s) 651, 708, 750
MfeI CAATTG 1 cut(s) 525
MhlI GDGCHC 2 cut(s) 773, 815
MluCI AATT 3 cut(s) 337, 478, 525
MlyI GAGTC 1 cut(s) 173
MmeI TCCRAC 2 cut(s) 357, 569
MnlI CCTC 6 cut(s) 13, 53, 195, 595, 610, 648
MreI CGCCGGCG 1 cut(s) 80
MroNI GCCGGC 1 cut(s) 80
MroXI GAANNNNTTC 1 cut(s) 38
MseI TTAA 1 cut(s) 594
MslI CAYNNNNRTG 1 cut(s) 799
MspA1I CMGCKG 1 cut(s) 782
MspI CCGG 2 cut(s) 81, 708
MunI CAATTG 1 cut(s) 525
Mva1269I GAATGC 1 cut(s) 169
MvnI CGCG 1 cut(s) 817
MwoI GCNNNNNNNGC 4 cut(s) 90, 156, 704, 819
NaeI GCCGGC 1 cut(s) 82
NdeII GATC 1 cut(s) 259
NgoMIV GCCGGC 1 cut(s) 80
NlaIII CATG 8 cut(s) 251, 311, 346, 367, 409, 476, 488, 617
NlaIV GGNNCC 2 cut(s) 64, 706
NmeAIII GCCGAG 1 cut(s) 83
NmuCI GTSAC 5 cut(s) 109, 374, 380, 412, 604
NspI RCATGY 1 cut(s) 409
PceI AGGCCT 1 cut(s) 444
PcsI WCGNNNNNNNCGW 1 cut(s) 323
PctI GAATGC 1 cut(s) 169
PdiI GCCGGC 1 cut(s) 82
PdmI GAANNNNTTC 1 cut(s) 38
PfeI GAWTC 1 cut(s) 304
PflFI GACNNNGTC 1 cut(s) 208
PleI GAGTC 1 cut(s) 173
PpsI GAGTC 1 cut(s) 173
Psp124BI GAGCTC 1 cut(s) 773
PspN4I GGNNCC 2 cut(s) 64, 706
PspPI GGNCC 1 cut(s) 86
PstNI CAGNNNCTG 1 cut(s) 701
PsyI GACNNNGTC 1 cut(s) 208
PvuII CAGCTG 1 cut(s) 782
RsaI GTAC 1 cut(s) 72
RsaNI GTAC 1 cut(s) 71
RseI CAYNNNNRTG 1 cut(s) 799
SacI GAGCTC 1 cut(s) 773
SaqAI TTAA 1 cut(s) 594
Sau3AI GATC 1 cut(s) 259
Sau96I GGNCC 1 cut(s) 86
SchI GAGTC 1 cut(s) 173
SduI GDGCHC 2 cut(s) 773, 815
SfaNI GCATC 2 cut(s) 289, 447
SgrAI CRCCGGYG 1 cut(s) 80
SmiMI CAYNNNNRTG 1 cut(s) 799
Sse9I AATT 3 cut(s) 337, 478, 525
SseBI AGGCCT 1 cut(s) 444
SsiI CCGC 2 cut(s) 84, 159
SspMI CTAG 2 cut(s) 186, 764
SstI GAGCTC 1 cut(s) 773
StuI AGGCCT 1 cut(s) 444
StyI CCWWGG 3 cut(s) 461, 559, 729
TaaI ACNGT 1 cut(s) 380
TaiI ACGT 1 cut(s) 111
TaqI TCGA 5 cut(s) 51, 230, 275, 719, 737
TasI AATT 3 cut(s) 337, 478, 525
TatI WGTACW 1 cut(s) 70
TfiI GAWTC 1 cut(s) 304
Tru1I TTAA 1 cut(s) 594
Tru9I TTAA 1 cut(s) 594
TscAI CASTG 1 cut(s) 385
TseFI GTSAC 5 cut(s) 109, 374, 380, 412, 604
Tsp45I GTSAC 5 cut(s) 109, 374, 380, 412, 604
TspDTI ATGAA 3 cut(s) 47, 296, 473
TspGWI ACGGA 1 cut(s) 231
TspRI CASTG 1 cut(s) 385
Tth111I GACNNNGTC 1 cut(s) 208
XapI RAATTY 1 cut(s) 478
XceI RCATGY 1 cut(s) 409
XcmI CCANNNNNNNNNTGG 1 cut(s) 633
XmnI GAANNNNTTC 1 cut(s) 38
XspI CTAG 2 cut(s) 186, 764
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.