Rroxscaffold_1G00073370

Pectate lyase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0009756
Physical Location & Seq
Reverse (-)
94243070 .. 94244221
1152 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00073370.1

Sequence Viewer

Length: 822 bp
ATGGTTATCACCCTCAAGAATGAGCTCATTATGAATAGTTTCAAGACCATAGACGGTAGAGGGGCTAAAGTAGAGATTGCATATGGACCATGCATAACTGTGCAGGGTATTAGTCATGTTATTATCCATGGAATAAGTATTCATGATTGTAAGCCGGGGAAGTCCGGCATGGTTAGGAGCACTCCTACACATGTCGGGCGGCGCCTAGGGTGCGACGGTGATTCCATTAGTATCTTTGCTTCTTCGCATGTTTGGGTTGACCATTGCTTTTTGGCACATGGCGCTGATGGCCTCATTGATATCACCCATGCTTCCACGGCAGTCACCGTCACTAACAACTATTTCTCCCAGCACGACAAGGTGATGCTGCTTGGACACAATGATAAATTTACTGCAGATAAAATTATGAAGGTCACAATAGCCTTTAACCGTTTTGGGGCAGGCCTAATTGAAAGGATGCCAAGGGTCAGATTTGGCTATGCCCATGTTGCCAACAATAGATATGATGAGTGGAAGATGTACGCCATTGGTGGCAGTGCTAATCCAACCATTTTCAGTGAAGGCAACTACTTCATAGCTCCTGAAAATCATGATGCCAAACAGGTTACGAAAAGAGAGGCCTACGATGGTTGGAAGAGTTGGAAATGGAGATCTTCTAATGATGTGCTTCAAAATGGAGCTTATTTTATTCAATCTGGATGGGGAAGTTGTTATCCAATGTACACTCGAACACAGAAGTTCAAGGTCTCTCCAGGATCGATGGTTCCTGCTTTGACTTCAAATGCAGGTCCACTGCACTGCATTGTTGGTAAAGCATGTTGA
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

273

Amino Acids

30.16

Weight (kDa)

9.11

Isoelectric Point (pI)

28.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pectate_lyase_4 PF00544 11 - 205 3.2e-25 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: OG0009756)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G11920 AT1G30350 AT4G22080 AT4G22090
fragaria_vesca FvH4_3g01680
malus_domestica MD00G1202500.v1.1 MD05G1350000.v1.1 MD10G1324800.v1.1
prunus_persica Prupe.4G017400_v2.0.a1 Prupe.4G020600_v2.0.a1
pyrus_communis pycom10g27510
rosa_chinensis RchiOBHm_Chr5g0002531
rosa_laevigata RLG00000031037
rosa_multiflora Rmu_sc0010731.1_g000004
rosa_roxburghii Rroxscaffold_1G00073370
rosa_rugosa Rorug04G0396700
rosa_samantha Rh5AG020100 Rh5BG022800 Rh5CG022100 Rh5DG021200
rosa_wichuraiana Rw5G001850

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 776
AccB1I GGYRCC 1 cut(s) 201
AciI CCGC 1 cut(s) 199
AclWI GGATC 1 cut(s) 763
AcsI RAATTY 1 cut(s) 386
AcyI GRCGYC 1 cut(s) 202
AfaI GTAC 2 cut(s) 521, 722
AfiI CCNNNNNNNGG 1 cut(s) 436
AflIII ACRYGT 1 cut(s) 190
AgsI TTSAA 6 cut(s) 43, 452, 671, 692, 742, 780
AjnI CCWGG 1 cut(s) 751
AloI GAACNNNNNNTCC 2 cut(s) 747, 779
AluBI AGCT 3 cut(s) 25, 578, 680
AluI AGCT 3 cut(s) 25, 578, 680
Alw21I GWGCWC 2 cut(s) 27, 182
Alw26I GTCTC 1 cut(s) 751
AlwI GGATC 1 cut(s) 763
AoxI GGCC 3 cut(s) 289, 442, 618
ApeKI GCWGC 1 cut(s) 367
ApoI RAATTY 1 cut(s) 386
Asp700I GAANNNNTTC 1 cut(s) 38
AspA2I CCTAGG 1 cut(s) 205
AspLEI GCGC 2 cut(s) 204, 284
AspS9I GGNCC 2 cut(s) 86, 788
AsuC2I CCSGG 1 cut(s) 156
AsuHPI GGTGA 4 cut(s) 230, 295, 316, 373
AvaII GGWCC 2 cut(s) 86, 788
AvrII CCTAGG 1 cut(s) 205
BanI GGYRCC 1 cut(s) 201
BanII GRGCYC 1 cut(s) 27
BarI GAAGNNNNNNTAC 2 cut(s) 223, 255
Bbv12I GWGCWC 2 cut(s) 27, 182
BbvI GCAGC 1 cut(s) 354
BccI CCATC 4 cut(s) 281, 620, 693, 754
BceAI ACGGC 1 cut(s) 333
BciT130I CCWGG 1 cut(s) 753
BcnI CCSGG 1 cut(s) 156
BcoDI GTCTC 1 cut(s) 751
BfaI CTAG 1 cut(s) 206
BfmI CTRYAG 1 cut(s) 393
BfoI RGCGCY 2 cut(s) 205, 285
BfuAI ACCTGC 1 cut(s) 776
BglII AGATCT 1 cut(s) 650
BisI GCNGC 2 cut(s) 200, 368
BlnI CCTAGG 1 cut(s) 205
BlsI GCNGC 2 cut(s) 201, 369
Bme1390I CCNGG 2 cut(s) 156, 753
Bme18I GGWCC 2 cut(s) 86, 788
BmgT120I GGNCC 2 cut(s) 86, 788
BmiI GGNNCC 2 cut(s) 203, 765
BmrFI CCNGG 2 cut(s) 156, 753
BmsI GCATC 3 cut(s) 354, 447, 583
BpmI CTGGAG 1 cut(s) 735
BpuMI CCSGG 1 cut(s) 156
Bsa29I ATCGAT 1 cut(s) 758
BsaHI GRCGYC 1 cut(s) 202
BsaI GGTCTC 1 cut(s) 751
BsaJI CCNNGG 5 cut(s) 127, 155, 205, 315, 461
BsaXI ACNNNNNCTCC 2 cut(s) 329, 359
Bsc4I CCNNNNNNNGG 1 cut(s) 436
Bse3DI GCAATG 1 cut(s) 262
BseBI CCWGG 1 cut(s) 753
BseCI ATCGAT 1 cut(s) 758
BseDI CCNNGG 5 cut(s) 127, 155, 205, 315, 461
BseGI GGATG 2 cut(s) 462, 704
BseLI CCNNNNNNNGG 1 cut(s) 436
BseMI GCAATG 1 cut(s) 262
BseXI GCAGC 1 cut(s) 354
BseYI CCCAGC 1 cut(s) 348
BsgI GTGCAG 2 cut(s) 122, 779
BshFI GGCC 3 cut(s) 291, 444, 620
BshNI GGYRCC 1 cut(s) 201
BshVI ATCGAT 1 cut(s) 758
BsiHKAI GWGCWC 2 cut(s) 27, 182
BsiSI CCGG 2 cut(s) 155, 165
BslI CCNNNNNNNGG 1 cut(s) 436
BsmAI GTCTC 1 cut(s) 751
BsnI GGCC 3 cut(s) 291, 444, 620
Bso31I GGTCTC 1 cut(s) 751
Bsp1286I GDGCHC 2 cut(s) 27, 182
Bsp1407I TGTACA 1 cut(s) 720
Bsp143I GATC 2 cut(s) 650, 755
Bsp19I CCATGG 1 cut(s) 127
BspACI CCGC 1 cut(s) 199
BspANI GGCC 3 cut(s) 291, 444, 620
BspDI ATCGAT 1 cut(s) 758
BspHI TCATGA 2 cut(s) 142, 589
BspLI GGNNCC 2 cut(s) 203, 765
BspMAI CTGCAG 1 cut(s) 397
BspMI ACCTGC 1 cut(s) 776
BspPI GGATC 1 cut(s) 763
BspT107I GGYRCC 1 cut(s) 201
BspTNI GGTCTC 1 cut(s) 751
BsrDI GCAATG 1 cut(s) 262
BsrGI TGTACA 1 cut(s) 720
BssECI CCNNGG 5 cut(s) 127, 155, 205, 315, 461
BssMI GATC 2 cut(s) 650, 755
BssNI GRCGYC 1 cut(s) 202
BssT1I CCWWGG 3 cut(s) 127, 205, 461
Bst2UI CCWGG 1 cut(s) 753
Bst4CI ACNGT 5 cut(s) 56, 100, 218, 328, 431
Bst6I CTCTTC 1 cut(s) 629
BstACI GRCGYC 1 cut(s) 202
BstAUI TGTACA 1 cut(s) 720
BstC8I GCNNGC 1 cut(s) 442
BstDSI CCRYGG 2 cut(s) 127, 315
BstF5I GGATG 2 cut(s) 462, 704
BstH2I RGCGCY 2 cut(s) 205, 285
BstHHI GCGC 2 cut(s) 204, 284
BstKTI GATC 2 cut(s) 653, 758
BstMAI GTCTC 1 cut(s) 751
BstMBI GATC 2 cut(s) 650, 755
BstMWI GCNNNNNNNGC 5 cut(s) 210, 281, 288, 317, 488
BstNI CCWGG 1 cut(s) 753
BstNSI RCATGY 3 cut(s) 194, 251, 819
BstSCI CCNGG 2 cut(s) 154, 751
BstSFI CTRYAG 1 cut(s) 393
BstV1I GCAGC 1 cut(s) 354
BstX2I RGATCY 1 cut(s) 650
BstYI RGATCY 1 cut(s) 650
Bsu15I ATCGAT 1 cut(s) 758
BsuRI GGCC 3 cut(s) 291, 444, 620
BsuTUI ATCGAT 1 cut(s) 758
BtgI CCRYGG 2 cut(s) 127, 315
BtsCI GGATG 2 cut(s) 462, 704
BtsI GCAGTG 3 cut(s) 541, 791, 796
BtsIMutI CAGTG 4 cut(s) 541, 562, 791, 796
BveI ACCTGC 1 cut(s) 776
Cac8I GCNNGC 1 cut(s) 442
CciI TCATGA 2 cut(s) 142, 589
CfoI GCGC 2 cut(s) 204, 284
Cfr13I GGNCC 2 cut(s) 86, 788
ClaI ATCGAT 1 cut(s) 758
Csp6I GTAC 2 cut(s) 520, 721
CviQI GTAC 2 cut(s) 520, 721
DinI GGCGCC 1 cut(s) 203
DpnI GATC 2 cut(s) 652, 757
DpnII GATC 2 cut(s) 650, 755
Eam1104I CTCTTC 1 cut(s) 629
EarI CTCTTC 1 cut(s) 629
Ecl136II GAGCTC 1 cut(s) 25
Eco130I CCWWGG 3 cut(s) 127, 205, 461
Eco147I AGGCCT 2 cut(s) 444, 620
Eco24I GRGCYC 1 cut(s) 27
Eco31I GGTCTC 1 cut(s) 751
Eco32I GATATC 1 cut(s) 301
Eco47I GGWCC 2 cut(s) 86, 788
Eco53kI GAGCTC 1 cut(s) 25
EcoICRI GAGCTC 1 cut(s) 25
EcoRII CCWGG 1 cut(s) 751
EcoRV GATATC 1 cut(s) 301
EcoT14I CCWWGG 3 cut(s) 127, 205, 461
EcoT22I ATGCAT 1 cut(s) 95
EcoT38I GRGCYC 1 cut(s) 27
EgeI GGCGCC 1 cut(s) 203
EheI GGCGCC 1 cut(s) 203
ErhI CCWWGG 3 cut(s) 127, 205, 461
FauNDI CATATG 1 cut(s) 82
Fnu4HI GCNGC 2 cut(s) 200, 368
FokI GGATG 2 cut(s) 469, 711
FriOI GRGCYC 1 cut(s) 27
Fsp4HI GCNGC 2 cut(s) 200, 368
FspBI CTAG 1 cut(s) 206
GlaI GCGC 2 cut(s) 203, 283
GluI GCNGC 2 cut(s) 200, 368
GsaI CCCAGC 1 cut(s) 352
GsuI CTGGAG 1 cut(s) 735
HaeII RGCGCY 2 cut(s) 205, 285
HaeIII GGCC 3 cut(s) 291, 444, 620
HapII CCGG 2 cut(s) 155, 165
HhaI GCGC 2 cut(s) 204, 284
Hin1I GRCGYC 1 cut(s) 202
Hin6I GCGC 2 cut(s) 202, 282
HinP1I GCGC 2 cut(s) 202, 282
HincII GTYRAC 1 cut(s) 259
HindII GTYRAC 1 cut(s) 259
HinfI GANTC 1 cut(s) 221
HpaII CCGG 2 cut(s) 155, 165
HphI GGTGA 4 cut(s) 230, 295, 316, 373
Hpy166II GTNNAC 3 cut(s) 259, 723, 791
Hpy188I TCNGA 1 cut(s) 470
Hpy188III TCNNGA 6 cut(s) 16, 43, 143, 581, 590, 696
Hpy8I GTNNAC 3 cut(s) 259, 723, 791
Hpy99I CGWCG 1 cut(s) 218
HpyAV CCTTC 2 cut(s) 403, 554
HpyCH4III ACNGT 5 cut(s) 56, 100, 218, 328, 431
HpyCH4V TGCA 7 cut(s) 80, 93, 103, 395, 785, 796, 801
HpyF10VI GCNNNNNNNGC 5 cut(s) 210, 281, 288, 317, 488
Hsp92I GRCGYC 1 cut(s) 202
HspAI GCGC 2 cut(s) 202, 282
KasI GGCGCC 1 cut(s) 201
Kzo9I GATC 2 cut(s) 650, 755
LmnI GCTCC 3 cut(s) 177, 583, 677
Lsp1109I GCAGC 1 cut(s) 354
LweI GCATC 3 cut(s) 354, 447, 583
MaeI CTAG 1 cut(s) 206
MaeIII GTNAC 4 cut(s) 322, 328, 412, 604
MalI GATC 2 cut(s) 652, 757
MboI GATC 2 cut(s) 650, 755
MboII GAAGA 4 cut(s) 234, 526, 645, 646
MflI RGATCY 1 cut(s) 650
MhlI GDGCHC 2 cut(s) 27, 182
MluCI AATT 3 cut(s) 386, 402, 447
Mly113I GGCGCC 1 cut(s) 202
MmeI TCCRAC 3 cut(s) 569, 611, 620
MnlI CCTC 4 cut(s) 23, 53, 302, 610
Mph1103I ATGCAT 1 cut(s) 95
MroXI GAANNNNTTC 1 cut(s) 38
MseI TTAA 1 cut(s) 426
MslI CAYNNNNRTG 1 cut(s) 98
MspI CCGG 2 cut(s) 155, 165
MspR9I CCNGG 2 cut(s) 156, 753
MvaI CCWGG 1 cut(s) 753
MwoI GCNNNNNNNGC 5 cut(s) 210, 281, 288, 317, 488
NarI GGCGCC 1 cut(s) 202
NciI CCSGG 1 cut(s) 156
NcoI CCATGG 1 cut(s) 127
NdeI CATATG 1 cut(s) 82
NdeII GATC 2 cut(s) 650, 755
NlaIV GGNNCC 2 cut(s) 203, 765
NmuCI GTSAC 3 cut(s) 322, 328, 412
NsiI ATGCAT 1 cut(s) 95
NspI RCATGY 3 cut(s) 194, 251, 819
PagI TCATGA 2 cut(s) 142, 589
PceI AGGCCT 2 cut(s) 444, 620
PciI ACATGT 1 cut(s) 190
PdmI GAANNNNTTC 1 cut(s) 38
PfeI GAWTC 1 cut(s) 221
PfoI TCCNGGA 1 cut(s) 751
PkrI GCNGC 2 cut(s) 201, 369
PluTI GGCGCC 1 cut(s) 205
PscI ACATGT 1 cut(s) 190
Psp124BI GAGCTC 1 cut(s) 27
Psp6I CCWGG 1 cut(s) 751
PspFI CCCAGC 1 cut(s) 348
PspGI CCWGG 1 cut(s) 751
PspN4I GGNNCC 2 cut(s) 203, 765
PspPI GGNCC 2 cut(s) 86, 788
PstI CTGCAG 1 cut(s) 397
PsuI RGATCY 1 cut(s) 650
RsaI GTAC 2 cut(s) 521, 722
RsaNI GTAC 2 cut(s) 520, 721
RseI CAYNNNNRTG 1 cut(s) 98
SacI GAGCTC 1 cut(s) 27
SaqAI TTAA 1 cut(s) 426
SatI GCNGC 2 cut(s) 200, 368
Sau3AI GATC 2 cut(s) 650, 755
Sau96I GGNCC 2 cut(s) 86, 788
ScrFI CCNGG 2 cut(s) 156, 753
SduI GDGCHC 2 cut(s) 27, 182
SetI ASST 8 cut(s) 27, 363, 414, 580, 606, 682, 747, 790
SfaNI GCATC 3 cut(s) 354, 447, 583
SfcI CTRYAG 1 cut(s) 393
SfoI GGCGCC 1 cut(s) 203
SinI GGWCC 2 cut(s) 86, 788
SmiMI CAYNNNNRTG 1 cut(s) 98
SmlI CTYRAG 1 cut(s) 14
SmoI CTYRAG 1 cut(s) 14
Sse9I AATT 3 cut(s) 386, 402, 447
SseBI AGGCCT 2 cut(s) 444, 620
SsiI CCGC 1 cut(s) 199
SspDI GGCGCC 1 cut(s) 201
SspMI CTAG 1 cut(s) 206
SstI GAGCTC 1 cut(s) 27
StuI AGGCCT 2 cut(s) 444, 620
StyD4I CCNGG 2 cut(s) 154, 751
StyI CCWWGG 3 cut(s) 127, 205, 461
TaaI ACNGT 5 cut(s) 56, 100, 218, 328, 431
TaqI TCGA 2 cut(s) 727, 758
TasI AATT 3 cut(s) 386, 402, 447
TatI WGTACW 1 cut(s) 720
TauI GCSGC 1 cut(s) 202
TfiI GAWTC 1 cut(s) 221
Tru1I TTAA 1 cut(s) 426
Tru9I TTAA 1 cut(s) 426
TscAI CASTG 4 cut(s) 541, 562, 798, 803
TseFI GTSAC 3 cut(s) 322, 328, 412
TseI GCWGC 1 cut(s) 367
Tsp45I GTSAC 3 cut(s) 322, 328, 412
TspDTI ATGAA 4 cut(s) 47, 131, 422, 562
TspRI CASTG 4 cut(s) 541, 562, 798, 803
VpaK11BI GGWCC 2 cut(s) 86, 788
XapI RAATTY 1 cut(s) 386
XceI RCATGY 3 cut(s) 194, 251, 819
XmaJI CCTAGG 1 cut(s) 205
XmnI GAANNNNTTC 1 cut(s) 38
XspI CTAG 1 cut(s) 206
Zsp2I ATGCAT 1 cut(s) 95
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.