Rroxscaffold_5G00373750

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0013798
Physical Location & Seq
Forward (+)
54883481 .. 54885091
1611 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00373750.1

Sequence Viewer

Length: 483 bp
ATGACGCACCATAACAAGGTCATGTTGTTGGGTCACAGTGACACCTACACGCAGGACAAGAACATGCAGGTCACTATTGCGTTCAATCACTTCGGAGAAGGCCTTGTTCAAAGGATGCCGAGGTGTAGGCATGGAAATTTTCATGTGGTGAACAATGACTATACACACTGGGAAATGTATGCAATTGGGGGTAGTGCTTCTCCAACTATCAACAGCCAAGGGAATAGGTTTCTTGCACCTAATGATAGATTTAACAAAGAGGTGACCAAACATGAGGATGCACCACAGAATGAGTGGAGCAATTGGAACTGGAGGTCTTCAGGGGATTTACTGCTGAATGGTGCATTTTTCACAGCGTCTGGTGCCGGAGCTTCTTCGAGTTACGCCAAGGCTTCGAGTTTGGGTGCAAGGCCATCTTCCCTGGTGAGCTCAATCACAGCTGGTGCTGGTTCACTCAAATGTAAGAAGGGCTCGCGTTGCTGA
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

160

Amino Acids

17.54

Weight (kDa)

9.3

Isoelectric Point (pI)

30.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 2 - 130 5.2e-12 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
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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) 58
AccB1I GGYRCC 1 cut(s) 362
AccII CGCG 1 cut(s) 475
AcsI RAATTY 1 cut(s) 136
AcuI CTGAAG 1 cut(s) 303
AfiI CCNNNNNNNGG 1 cut(s) 16
AgsI TTSAA 2 cut(s) 85, 110
AjnI CCWGG 1 cut(s) 420
AluBI AGCT 3 cut(s) 371, 429, 440
AluI AGCT 3 cut(s) 371, 429, 440
Alw21I GWGCWC 1 cut(s) 431
AlwNI CAGNNNCTG 1 cut(s) 359
AoxI GGCC 2 cut(s) 100, 410
ApoI RAATTY 1 cut(s) 136
AsuHPI GGTGA 3 cut(s) 160, 274, 436
BanI GGYRCC 1 cut(s) 362
BanII GRGCYC 2 cut(s) 431, 473
BbsI GAAGAC 1 cut(s) 309
Bbv12I GWGCWC 1 cut(s) 431
BccI CCATC 1 cut(s) 421
BciT130I CCWGG 1 cut(s) 422
BfuAI ACCTGC 1 cut(s) 58
Bme1390I CCNGG 1 cut(s) 422
BmiI GGNNCC 1 cut(s) 364
BmrFI CCNGG 1 cut(s) 422
BmrI ACTGGG 1 cut(s) 178
BmsI GCATC 2 cut(s) 105, 268
BmuI ACTGGG 1 cut(s) 178
BpiI GAAGAC 1 cut(s) 309
BpmI CTGGAG 1 cut(s) 331
BsaJI CCNNGG 4 cut(s) 119, 217, 387, 420
Bsc4I CCNNNNNNNGG 1 cut(s) 16
Bse1I ACTGG 2 cut(s) 173, 314
BseBI CCWGG 1 cut(s) 422
BseDI CCNNGG 4 cut(s) 119, 217, 387, 420
BseGI GGATG 2 cut(s) 120, 283
BseLI CCNNNNNNNGG 1 cut(s) 16
BseNI ACTGG 2 cut(s) 173, 314
Bsh1236I CGCG 1 cut(s) 475
BshFI GGCC 2 cut(s) 102, 412
BshNI GGYRCC 1 cut(s) 362
BsiHKAI GWGCWC 1 cut(s) 431
BsiSI CCGG 1 cut(s) 366
BslI CCNNNNNNNGG 1 cut(s) 16
BsnI GGCC 2 cut(s) 102, 412
Bsp1286I GDGCHC 2 cut(s) 431, 473
BspANI GGCC 2 cut(s) 102, 412
BspFNI CGCG 1 cut(s) 475
BspLI GGNNCC 1 cut(s) 364
BspMI ACCTGC 1 cut(s) 58
BspT107I GGYRCC 1 cut(s) 362
BsrI ACTGG 2 cut(s) 173, 314
BssECI CCNNGG 4 cut(s) 119, 217, 387, 420
BssT1I CCWWGG 2 cut(s) 217, 387
Bst2UI CCWGG 1 cut(s) 422
Bst4CI ACNGT 1 cut(s) 38
BstC8I GCNNGC 1 cut(s) 473
BstEII GGTNACC 1 cut(s) 262
BstF5I GGATG 2 cut(s) 120, 283
BstFNI CGCG 1 cut(s) 475
BstMWI GCNNNNNNNGC 2 cut(s) 362, 477
BstNI CCWGG 1 cut(s) 422
BstNSI RCATGY 1 cut(s) 67
BstPI GGTNACC 1 cut(s) 262
BstSCI CCNGG 1 cut(s) 420
BstUI CGCG 1 cut(s) 475
BstV2I GAAGAC 1 cut(s) 309
BsuRI GGCC 2 cut(s) 102, 412
BtsCI GGATG 2 cut(s) 120, 283
BtsIMutI CAGTG 2 cut(s) 43, 166
BveI ACCTGC 1 cut(s) 58
Cac8I GCNNGC 1 cut(s) 473
CaiI CAGNNNCTG 1 cut(s) 359
CseI GACGC 2 cut(s) 13, 345
CviAII CATG 5 cut(s) 22, 64, 131, 143, 272
CviJI RGCY 8 cut(s) 102, 216, 371, 392, 412, 429, 440, 471
CviKI_1 RGCY 8 cut(s) 102, 216, 371, 392, 412, 429, 440, 471
Ecl136II GAGCTC 1 cut(s) 429
Eco130I CCWWGG 2 cut(s) 217, 387
Eco147I AGGCCT 1 cut(s) 102
Eco24I GRGCYC 2 cut(s) 431, 473
Eco53kI GAGCTC 1 cut(s) 429
Eco57I CTGAAG 1 cut(s) 303
Eco91I GGTNACC 1 cut(s) 262
EcoICRI GAGCTC 1 cut(s) 429
EcoO65I GGTNACC 1 cut(s) 262
EcoRII CCWGG 1 cut(s) 420
EcoT14I CCWWGG 2 cut(s) 217, 387
EcoT38I GRGCYC 2 cut(s) 431, 473
ErhI CCWWGG 2 cut(s) 217, 387
FaeI CATG 5 cut(s) 25, 67, 134, 146, 275
FaiI YATR 8 cut(s) 12, 23, 65, 132, 144, 162, 180, 273
FalI AAGNNNNNCTT 2 cut(s) 400, 432
FatI CATG 5 cut(s) 21, 63, 130, 142, 271
FokI GGATG 2 cut(s) 127, 290
FriOI GRGCYC 2 cut(s) 431, 473
GsuI CTGGAG 1 cut(s) 331
HaeIII GGCC 2 cut(s) 102, 412
HapII CCGG 1 cut(s) 366
HgaI GACGC 2 cut(s) 13, 345
Hin1II CATG 5 cut(s) 25, 67, 134, 146, 275
HpaII CCGG 1 cut(s) 366
HphI GGTGA 3 cut(s) 160, 274, 436
Hpy166II GTNNAC 2 cut(s) 151, 452
Hpy188I TCNGA 1 cut(s) 95
Hpy8I GTNNAC 2 cut(s) 151, 452
HpyAV CCTTC 2 cut(s) 92, 460
HpyCH4III ACNGT 1 cut(s) 38
HpyCH4V TGCA 6 cut(s) 67, 182, 236, 281, 344, 407
HpyF10VI GCNNNNNNNGC 2 cut(s) 362, 477
Hsp92II CATG 5 cut(s) 25, 67, 134, 146, 275
LmnI GCTCC 2 cut(s) 297, 368
LweI GCATC 2 cut(s) 105, 268
MaeIII GTNAC 5 cut(s) 32, 38, 70, 262, 380
MboII GAAGA 3 cut(s) 309, 366, 408
MfeI CAATTG 2 cut(s) 183, 301
MhlI GDGCHC 2 cut(s) 431, 473
MluCI AATT 3 cut(s) 136, 183, 301
MmeI TCCRAC 1 cut(s) 227
MnlI CCTC 4 cut(s) 114, 253, 268, 306
MseI TTAA 1 cut(s) 252
MslI CAYNNNNRTG 2 cut(s) 276, 457
MspA1I CMGCKG 1 cut(s) 440
MspI CCGG 1 cut(s) 366
MspR9I CCNGG 1 cut(s) 422
MunI CAATTG 2 cut(s) 183, 301
MvaI CCWGG 1 cut(s) 422
MvnI CGCG 1 cut(s) 475
MwoI GCNNNNNNNGC 2 cut(s) 362, 477
NlaIII CATG 5 cut(s) 25, 67, 134, 146, 275
NlaIV GGNNCC 1 cut(s) 364
NmeAIII GCCGAG 1 cut(s) 144
NmuCI GTSAC 4 cut(s) 32, 38, 70, 262
NspI RCATGY 1 cut(s) 67
PceI AGGCCT 1 cut(s) 102
Psp124BI GAGCTC 1 cut(s) 431
Psp6I CCWGG 1 cut(s) 420
PspEI GGTNACC 1 cut(s) 262
PspGI CCWGG 1 cut(s) 420
PspN4I GGNNCC 1 cut(s) 364
PstNI CAGNNNCTG 1 cut(s) 359
PvuII CAGCTG 1 cut(s) 440
RseI CAYNNNNRTG 2 cut(s) 276, 457
SacI GAGCTC 1 cut(s) 431
SaqAI TTAA 1 cut(s) 252
ScrFI CCNGG 1 cut(s) 422
SduI GDGCHC 2 cut(s) 431, 473
SfaNI GCATC 2 cut(s) 105, 268
SmiMI CAYNNNNRTG 2 cut(s) 276, 457
Sse9I AATT 3 cut(s) 136, 183, 301
SseBI AGGCCT 1 cut(s) 102
SstI GAGCTC 1 cut(s) 431
StuI AGGCCT 1 cut(s) 102
StyD4I CCNGG 1 cut(s) 420
StyI CCWWGG 2 cut(s) 217, 387
TaaI ACNGT 1 cut(s) 38
TaqI TCGA 2 cut(s) 377, 395
TasI AATT 3 cut(s) 136, 183, 301
Tru1I TTAA 1 cut(s) 252
Tru9I TTAA 1 cut(s) 252
TscAI CASTG 2 cut(s) 43, 173
TseFI GTSAC 4 cut(s) 32, 38, 70, 262
Tsp45I GTSAC 4 cut(s) 32, 38, 70, 262
TspDTI ATGAA 1 cut(s) 131
TspRI CASTG 2 cut(s) 43, 173
XapI RAATTY 1 cut(s) 136
XceI RCATGY 1 cut(s) 67
XcmI CCANNNNNNNNNTGG 1 cut(s) 291
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.