Rroxscaffold_1G00062140

LSM domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0017944
Physical Location & Seq
Forward (+)
84165652 .. 84166017
366 bp
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UTR
Exon/CDS
Intron
Rroxscaffold_1G00062140.1

Sequence Viewer

Length: 366 bp
ATGGAACAAGAAGCAGCGGAATCACTGATTCAGGTGGCGGGCTCAGAAGGGTCGAACCCAAATAGCTCAGACGGGTCGGACCACCCAGCTTGCTCGGAGGCCGTGACCCGCGTCAAGAAGCTTCTTTTCCGGCGAATGCTGGTTGGGATCAAAGACGGCCGCTTTTTCTTGGGGACCTTTCACTGCATTGACAAACAGGGTAACATCATTCTTCAAGACTCTGTGGAGTATCGGAGCACTCGCCGGAATTCGCCTTCTCCGATGGAGCAGCGGTGCCTCGGTCTGATTCTCATCCCTAGCTCTTGTCGTGTCTCTTGCCATGTTGGGTGCTCCATTGAAGAACAAATGAGTCTGCTTTTGGTCTAG
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
LSM

Protein Analysis

121

Amino Acids

13.31

Weight (kDa)

6.28

Isoelectric Point (pI)

79.42

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
LSM PF01423 39 - 99 7.2e-08 LSM domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0017944)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G18372 AT4G18372
fragaria_vesca FvH4_3g05282
malus_domestica MD05G1281500.v1.1
prunus_persica Prupe.4G083100_v2.0.a1
rosa_chinensis RchiOBHm_Chr5g0014441
rosa_laevigata RLG00000032110
rosa_multiflora Rmu_sc0031709.1_g000002 Rmu_ssc0000422.1_g000033
rosa_roxburghii Rroxscaffold_1G00062140
rosa_wichuraiana Rw5G009820

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 273
AccII CGCG 1 cut(s) 111
AciI CCGC 5 cut(s) 17, 38, 109, 160, 271
AclWI GGATC 1 cut(s) 155
AcoI YGGCCR 1 cut(s) 157
AcsI RAATTY 1 cut(s) 247
AgsI TTSAA 2 cut(s) 215, 338
AluBI AGCT 4 cut(s) 66, 89, 121, 300
AluI AGCT 4 cut(s) 66, 89, 121, 300
Alw21I GWGCWC 2 cut(s) 239, 332
Alw26I GTCTC 1 cut(s) 316
AlwI GGATC 1 cut(s) 155
AoxI GGCC 2 cut(s) 99, 157
ApeKI GCWGC 2 cut(s) 14, 268
ApoI RAATTY 1 cut(s) 247
AspS9I GGNCC 2 cut(s) 79, 174
AvaII GGWCC 2 cut(s) 79, 174
BanI GGYRCC 1 cut(s) 273
BanII GRGCYC 1 cut(s) 44
Bbv12I GWGCWC 2 cut(s) 239, 332
BbvI GCAGC 2 cut(s) 26, 280
BccI CCATC 1 cut(s) 256
BceAI ACGGC 2 cut(s) 86, 172
BcoDI GTCTC 1 cut(s) 316
BfaI CTAG 2 cut(s) 297, 364
BisI GCNGC 3 cut(s) 15, 160, 269
BlsI GCNGC 3 cut(s) 16, 161, 270
Bme18I GGWCC 2 cut(s) 79, 174
BmgT120I GGNCC 2 cut(s) 79, 174
BmiI GGNNCC 2 cut(s) 175, 275
BoxI GACNNNNGTC 1 cut(s) 110
BsaBI GATNNNNATC 1 cut(s) 290
BsaJI CCNNGG 1 cut(s) 277
BsaXI ACNNNNNCTCC 2 cut(s) 257, 287
Bse8I GATNNNNATC 1 cut(s) 290
BseDI CCNNGG 1 cut(s) 277
BseGI GGATG 1 cut(s) 291
BseJI GATNNNNATC 1 cut(s) 290
BseMII CTCAG 2 cut(s) 57, 81
BseX3I CGGCCG 1 cut(s) 157
BseXI GCAGC 2 cut(s) 26, 280
BseYI CCCAGC 1 cut(s) 85
Bsh1236I CGCG 1 cut(s) 111
Bsh1285I CGRYCG 1 cut(s) 160
BshFI GGCC 2 cut(s) 101, 159
BshNI GGYRCC 1 cut(s) 273
BsiEI CGRYCG 1 cut(s) 160
BsiHKAI GWGCWC 2 cut(s) 239, 332
BsiSI CCGG 2 cut(s) 130, 244
BslFI GGGAC 1 cut(s) 187
BsmAI GTCTC 1 cut(s) 316
BsmFI GGGAC 1 cut(s) 187
BsmI GAATGC 1 cut(s) 141
BsnI GGCC 2 cut(s) 101, 159
Bsp1286I GDGCHC 3 cut(s) 44, 239, 332
Bsp143I GATC 1 cut(s) 147
BspACI CCGC 5 cut(s) 17, 38, 109, 160, 271
BspANI GGCC 2 cut(s) 101, 159
BspCNI CTCAG 2 cut(s) 56, 80
BspFNI CGCG 1 cut(s) 111
BspLI GGNNCC 2 cut(s) 175, 275
BspPI GGATC 1 cut(s) 155
BspT107I GGYRCC 1 cut(s) 273
BssECI CCNNGG 1 cut(s) 277
BssMI GATC 1 cut(s) 147
BstC8I GCNNGC 2 cut(s) 40, 91
BstDEI CTNAG 2 cut(s) 43, 67
BstF5I GGATG 1 cut(s) 291
BstFNI CGCG 1 cut(s) 111
BstKTI GATC 1 cut(s) 150
BstMAI GTCTC 1 cut(s) 316
BstMBI GATC 1 cut(s) 147
BstMCI CGRYCG 1 cut(s) 160
BstPAI GACNNNNGTC 1 cut(s) 110
BstUI CGCG 1 cut(s) 111
BstV1I GCAGC 2 cut(s) 26, 280
BstZI CGGCCG 1 cut(s) 157
BsuRI GGCC 2 cut(s) 101, 159
BtsCI GGATG 1 cut(s) 291
BtsI GCAGTG 1 cut(s) 181
BtsIMutI CAGTG 2 cut(s) 23, 181
Cac8I GCNNGC 2 cut(s) 40, 91
Cfr13I GGNCC 2 cut(s) 79, 174
CseI GACGC 1 cut(s) 100
CspCI CAANNNNNGTGG 2 cut(s) 71, 106
CviAII CATG 1 cut(s) 320
CviJI RGCY 7 cut(s) 42, 66, 89, 101, 121, 159, 300
CviKI_1 RGCY 7 cut(s) 42, 66, 89, 101, 121, 159, 300
DdeI CTNAG 2 cut(s) 43, 67
DpnI GATC 1 cut(s) 149
DpnII GATC 1 cut(s) 147
EaeI YGGCCR 1 cut(s) 157
EagI CGGCCG 1 cut(s) 157
EclXI CGGCCG 1 cut(s) 157
Eco24I GRGCYC 1 cut(s) 44
Eco47I GGWCC 2 cut(s) 79, 174
Eco52I CGGCCG 1 cut(s) 157
EcoO109I RGGNCCY 1 cut(s) 174
EcoRI GAATTC 1 cut(s) 247
EcoT38I GRGCYC 1 cut(s) 44
FaeI CATG 1 cut(s) 323
FaiI YATR 1 cut(s) 321
FaqI GGGAC 1 cut(s) 187
FatI CATG 1 cut(s) 319
FauI CCCGC 2 cut(s) 31, 116
Fnu4HI GCNGC 3 cut(s) 15, 160, 269
FokI GGATG 1 cut(s) 278
FriOI GRGCYC 1 cut(s) 44
Fsp4HI GCNGC 3 cut(s) 15, 160, 269
FspBI CTAG 2 cut(s) 297, 364
GluI GCNGC 3 cut(s) 15, 160, 269
GsaI CCCAGC 1 cut(s) 89
HaeIII GGCC 2 cut(s) 101, 159
HapII CCGG 2 cut(s) 130, 244
HgaI GACGC 1 cut(s) 100
Hin1II CATG 1 cut(s) 323
HindIII AAGCTT 1 cut(s) 119
HinfI GANTC 5 cut(s) 20, 28, 218, 286, 349
HpaII CCGG 2 cut(s) 130, 244
Hpy188I TCNGA 7 cut(s) 46, 70, 79, 97, 234, 261, 285
Hpy188III TCNNGA 2 cut(s) 115, 215
HpyAV CCTTC 2 cut(s) 41, 264
HpyCH4V TGCA 1 cut(s) 186
HpyF3I CTNAG 2 cut(s) 43, 67
Hsp92II CATG 1 cut(s) 323
Kzo9I GATC 1 cut(s) 147
LmnI GCTCC 3 cut(s) 234, 265, 335
LpnPI CCDG 6 cut(s) 17, 99, 125, 143, 182, 257
Lsp1109I GCAGC 2 cut(s) 26, 280
MaeI CTAG 2 cut(s) 297, 364
MaeIII GTNAC 2 cut(s) 103, 200
MalI GATC 1 cut(s) 149
MboI GATC 1 cut(s) 147
MboII GAAGA 2 cut(s) 203, 350
MhlI GDGCHC 3 cut(s) 44, 239, 332
MluCI AATT 1 cut(s) 247
MlyI GAGTC 2 cut(s) 212, 358
MmeI TCCRAC 1 cut(s) 57
MnlI CCTC 2 cut(s) 91, 287
MspA1I CMGCKG 2 cut(s) 17, 271
MspI CCGG 2 cut(s) 130, 244
Mva1269I GAATGC 1 cut(s) 141
MvnI CGCG 1 cut(s) 111
NdeII GATC 1 cut(s) 147
NlaIII CATG 1 cut(s) 323
NlaIV GGNNCC 2 cut(s) 175, 275
NmuCI GTSAC 1 cut(s) 103
PcsI WCGNNNNNNNCGW 1 cut(s) 257
PctI GAATGC 1 cut(s) 141
PfeI GAWTC 3 cut(s) 20, 28, 286
PkrI GCNGC 3 cut(s) 16, 161, 270
PleI GAGTC 2 cut(s) 212, 357
PpsI GAGTC 2 cut(s) 212, 357
PpuMI RGGWCCY 1 cut(s) 174
PshAI GACNNNNGTC 1 cut(s) 110
Psp5II RGGWCCY 1 cut(s) 174
PspFI CCCAGC 1 cut(s) 85
PspN4I GGNNCC 2 cut(s) 175, 275
PspPI GGNCC 2 cut(s) 79, 174
PspPPI RGGWCCY 1 cut(s) 174
SatI GCNGC 3 cut(s) 15, 160, 269
Sau3AI GATC 1 cut(s) 147
Sau96I GGNCC 2 cut(s) 79, 174
SchI GAGTC 2 cut(s) 212, 358
SduI GDGCHC 3 cut(s) 44, 239, 332
SetI ASST 6 cut(s) 36, 68, 91, 123, 179, 302
SinI GGWCC 2 cut(s) 79, 174
Sse9I AATT 1 cut(s) 247
SsiI CCGC 5 cut(s) 17, 38, 109, 160, 271
SspMI CTAG 2 cut(s) 297, 364
TaqI TCGA 1 cut(s) 53
TaqII GACCGA 1 cut(s) 269
TasI AATT 1 cut(s) 247
TauI GCSGC 1 cut(s) 162
TfiI GAWTC 3 cut(s) 20, 28, 286
TscAI CASTG 2 cut(s) 30, 188
TseFI GTSAC 1 cut(s) 103
TseI GCWGC 2 cut(s) 14, 268
Tsp45I GTSAC 1 cut(s) 103
TspRI CASTG 2 cut(s) 30, 188
VpaK11BI GGWCC 2 cut(s) 79, 174
XapI RAATTY 1 cut(s) 247
XspI CTAG 2 cut(s) 297, 364
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.