Rroxscaffold_4G00280440

PAM68-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0013185
Physical Location & Seq
Forward (+)
3006588 .. 3007127
540 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00280440.1

Sequence Viewer

Length: 540 bp
ATGAGAACTCTGATCTTTCAGTCACAACCATCTTTCCATCTTTCTCAGTCTTCTCCATGGAAGCCCAAAAGCCCAGCCCTCCACCCAACAAGTCTCCAAAGCCTACCACTCCCCAAAAGAACACATCATATTCAGCCACATGCCAATGCAAAAGGGTTTGGCAATAACACACCAATCACCATGAAAGAAAAACCCACAAGTAAAAACCCTAAGAATGATGATGACGATGAGGAGATTCCGCAGGTCGTAACGGAGAGGATGCTGGTGAGGATTGTGGCGGCAGTCGGGCTGCCTCTGGCTACCGGCATAGCTTTTCTGAACGTTTTCGAATTCATTAAGGAGAGGCACTTGTTGGATGTGCCGGTTTGGCTTCCTTTCTTGACGACGTTGTTGACCTTTGGGACGTCAGCGCTTGGGATTGCTTATGGGGCTCTGTCTACGAGTTGGGATGCAGAGAAGAAGGGTTCCATTCTTGGTTTTGAAGAAGCTCAGAAGAATTGGGTTGATATGTGGAGGGAGGAAGATGAGGGTAGTTCATAG

Protein Analysis

179

Amino Acids

19.99

Weight (kDa)

6.3

Isoelectric Point (pI)

46.89

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DUF3464 PF11947 39 - 173 3.7e-41 Photosynthesis affected mutant 68
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: OG0013185)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G52780
fragaria_vesca FvH4_7g30320
malus_domestica MD01G1209300.v1.1 MD07G1279500.v1.1
prunus_persica Prupe.2G301700_v2.0.a1
pyrus_communis pycom01g21970 pycom07g25420
rosa_chinensis RchiOBHm_Chr1g0378471
rosa_laevigata RLG00000026434
rosa_multiflora Rmu_sc0008712.1_g000014 Rmu_sc0028132.1_g000001
rosa_roxburghii Rroxscaffold_4G00280440
rosa_rugosa Rorug01G0409100
rosa_samantha Rh1AG430400 Rh1BG388300 Rh1CG401700 Rh1DG419300
rosa_wichuraiana Rw1G037700

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 407
Acc36I ACCTGC 1 cut(s) 232
AccI GTMKAC 1 cut(s) 437
AciI CCGC 2 cut(s) 239, 278
AclI AACGTT 1 cut(s) 321
AcsI RAATTY 1 cut(s) 329
AcyI GRCGYC 1 cut(s) 404
AfeI AGCGCT 1 cut(s) 411
AgsI TTSAA 1 cut(s) 482
AluBI AGCT 2 cut(s) 311, 488
AluI AGCT 2 cut(s) 311, 488
Alw26I GTCTC 1 cut(s) 98
Aor51HI AGCGCT 1 cut(s) 411
ApeKI GCWGC 1 cut(s) 289
ApoI RAATTY 1 cut(s) 329
Asp700I GAANNNNTTC 1 cut(s) 323
AspLEI GCGC 1 cut(s) 412
AsuHPI GGTGA 2 cut(s) 169, 277
AsuII TTCGAA 1 cut(s) 327
BanII GRGCYC 1 cut(s) 433
BbsI GAAGAC 1 cut(s) 42
BbvI GCAGC 1 cut(s) 276
BccI CCATC 2 cut(s) 37, 45
BcoDI GTCTC 1 cut(s) 98
BfoI RGCGCY 1 cut(s) 413
BfuAI ACCTGC 1 cut(s) 232
BglI GCCNNNNNGGC 1 cut(s) 367
BisI GCNGC 2 cut(s) 279, 290
BlsI GCNGC 2 cut(s) 280, 291
BmiI GGNNCC 1 cut(s) 466
BmsI GCATC 2 cut(s) 249, 439
BpiI GAAGAC 1 cut(s) 42
Bpu14I TTCGAA 1 cut(s) 327
BsaHI GRCGYC 1 cut(s) 404
BsaJI CCNNGG 1 cut(s) 56
Bse118I RCCGGY 2 cut(s) 302, 361
BseDI CCNNGG 1 cut(s) 56
BseGI GGATG 3 cut(s) 264, 361, 454
BseMII CTCAG 2 cut(s) 59, 503
BseRI GAGGAG 1 cut(s) 245
BseXI GCAGC 1 cut(s) 276
BseYI CCCAGC 1 cut(s) 73
BsiSI CCGG 2 cut(s) 303, 362
BslFI GGGAC 1 cut(s) 415
BsmAI GTCTC 1 cut(s) 98
BsmFI GGGAC 1 cut(s) 415
Bsp119I TTCGAA 1 cut(s) 327
Bsp1286I GDGCHC 1 cut(s) 433
Bsp143I GATC 1 cut(s) 12
Bsp19I CCATGG 1 cut(s) 56
BspACI CCGC 2 cut(s) 239, 278
BspCNI CTCAG 2 cut(s) 58, 502
BspLI GGNNCC 1 cut(s) 466
BspMI ACCTGC 1 cut(s) 232
BspT104I TTCGAA 1 cut(s) 327
BsrFI RCCGGY 2 cut(s) 302, 361
BssAI RCCGGY 2 cut(s) 302, 361
BssECI CCNNGG 1 cut(s) 56
BssMI GATC 1 cut(s) 12
BssNI GRCGYC 1 cut(s) 404
BssT1I CCWWGG 1 cut(s) 56
BstACI GRCGYC 1 cut(s) 404
BstBI TTCGAA 1 cut(s) 327
BstDEI CTNAG 3 cut(s) 45, 210, 489
BstDSI CCRYGG 1 cut(s) 56
BstF5I GGATG 3 cut(s) 264, 361, 454
BstH2I RGCGCY 1 cut(s) 413
BstHHI GCGC 1 cut(s) 412
BstKTI GATC 1 cut(s) 15
BstMAI GTCTC 1 cut(s) 98
BstMBI GATC 1 cut(s) 12
BstMWI GCNNNNNNNGC 2 cut(s) 367, 428
BstNSI RCATGY 1 cut(s) 143
BstV1I GCAGC 1 cut(s) 276
BstV2I GAAGAC 1 cut(s) 42
BtgI CCRYGG 1 cut(s) 56
BtsCI GGATG 3 cut(s) 264, 361, 454
BveI ACCTGC 1 cut(s) 232
CfoI GCGC 1 cut(s) 412
Cfr10I RCCGGY 2 cut(s) 302, 361
CviAII CATG 3 cut(s) 57, 140, 181
DdeI CTNAG 3 cut(s) 45, 210, 489
DpnI GATC 1 cut(s) 14
DpnII GATC 1 cut(s) 12
Eco130I CCWWGG 1 cut(s) 56
Eco24I GRGCYC 1 cut(s) 433
Eco47III AGCGCT 1 cut(s) 411
EcoRI GAATTC 1 cut(s) 329
EcoT14I CCWWGG 1 cut(s) 56
EcoT38I GRGCYC 1 cut(s) 433
ErhI CCWWGG 1 cut(s) 56
FaeI CATG 3 cut(s) 60, 143, 184
FaiI YATR 8 cut(s) 58, 129, 141, 182, 308, 426, 509, 538
FaqI GGGAC 1 cut(s) 415
FatI CATG 3 cut(s) 56, 139, 180
FblI GTMKAC 1 cut(s) 437
Fnu4HI GCNGC 2 cut(s) 279, 290
FokI GGATG 3 cut(s) 271, 368, 461
FriOI GRGCYC 1 cut(s) 433
Fsp4HI GCNGC 2 cut(s) 279, 290
GlaI GCGC 1 cut(s) 411
GluI GCNGC 2 cut(s) 279, 290
GsaI CCCAGC 1 cut(s) 77
HaeII RGCGCY 1 cut(s) 413
HapII CCGG 2 cut(s) 303, 362
HhaI GCGC 1 cut(s) 412
Hin1I GRCGYC 1 cut(s) 404
Hin1II CATG 3 cut(s) 60, 143, 184
Hin6I GCGC 1 cut(s) 410
HinP1I GCGC 1 cut(s) 410
HincII GTYRAC 1 cut(s) 393
HindII GTYRAC 1 cut(s) 393
HinfI GANTC 1 cut(s) 235
HpaII CCGG 2 cut(s) 303, 362
HphI GGTGA 2 cut(s) 169, 277
Hpy166II GTNNAC 2 cut(s) 393, 438
Hpy188I TCNGA 3 cut(s) 12, 318, 492
Hpy188III TCNNGA 1 cut(s) 379
Hpy8I GTNNAC 2 cut(s) 393, 438
Hpy99I CGWCG 1 cut(s) 388
HpyAV CCTTC 1 cut(s) 454
HpyCH4IV ACGT 3 cut(s) 321, 386, 404
HpyCH4V TGCA 2 cut(s) 149, 452
HpyF10VI GCNNNNNNNGC 2 cut(s) 367, 428
HpyF3I CTNAG 3 cut(s) 45, 210, 489
HpySE526I ACGT 3 cut(s) 321, 386, 404
Hsp92I GRCGYC 1 cut(s) 404
Hsp92II CATG 3 cut(s) 60, 143, 184
HspAI GCGC 1 cut(s) 410
Kzo9I GATC 1 cut(s) 12
LpnPI CCDG 6 cut(s) 87, 227, 248, 281, 316, 375
Lsp1109I GCAGC 1 cut(s) 276
LweI GCATC 2 cut(s) 249, 439
MaeII ACGT 3 cut(s) 321, 386, 404
MaeIII GTNAC 2 cut(s) 21, 247
MalI GATC 1 cut(s) 14
MboI GATC 1 cut(s) 12
MboII GAAGA 5 cut(s) 42, 469, 494, 505, 533
MhlI GDGCHC 1 cut(s) 433
MluCI AATT 2 cut(s) 329, 496
MmeI TCCRAC 1 cut(s) 333
MnlI CCTC 9 cut(s) 89, 223, 249, 261, 303, 336, 507, 511, 520
MroXI GAANNNNTTC 1 cut(s) 323
MseI TTAA 1 cut(s) 336
MslI CAYNNNNRTG 1 cut(s) 144
MspI CCGG 2 cut(s) 303, 362
MwoI GCNNNNNNNGC 2 cut(s) 367, 428
NcoI CCATGG 1 cut(s) 56
NdeII GATC 1 cut(s) 12
NlaIII CATG 3 cut(s) 60, 143, 184
NlaIV GGNNCC 1 cut(s) 466
NmuCI GTSAC 1 cut(s) 21
NspI RCATGY 1 cut(s) 143
NspV TTCGAA 1 cut(s) 327
PdmI GAANNNNTTC 1 cut(s) 323
PfeI GAWTC 1 cut(s) 235
PkrI GCNGC 2 cut(s) 280, 291
Psp1406I AACGTT 1 cut(s) 321
PspFI CCCAGC 1 cut(s) 73
PspN4I GGNNCC 1 cut(s) 466
RseI CAYNNNNRTG 1 cut(s) 144
SaqAI TTAA 1 cut(s) 336
SatI GCNGC 2 cut(s) 279, 290
Sau3AI GATC 1 cut(s) 12
SduI GDGCHC 1 cut(s) 433
SetI ASST 7 cut(s) 246, 313, 324, 389, 398, 407, 490
SfaNI GCATC 2 cut(s) 249, 439
SfuI TTCGAA 1 cut(s) 327
SmiMI CAYNNNNRTG 1 cut(s) 144
Sse9I AATT 2 cut(s) 329, 496
SsiI CCGC 2 cut(s) 239, 278
StyI CCWWGG 1 cut(s) 56
TaiI ACGT 3 cut(s) 324, 389, 407
TaqI TCGA 1 cut(s) 327
TasI AATT 2 cut(s) 329, 496
TauI GCSGC 1 cut(s) 281
TfiI GAWTC 1 cut(s) 235
Tru1I TTAA 1 cut(s) 336
Tru9I TTAA 1 cut(s) 336
TseFI GTSAC 1 cut(s) 21
TseI GCWGC 1 cut(s) 289
Tsp45I GTSAC 1 cut(s) 21
TspDTI ATGAA 3 cut(s) 197, 322, 525
TspGWI ACGGA 1 cut(s) 266
XapI RAATTY 1 cut(s) 329
XceI RCATGY 1 cut(s) 143
XmiI GTMKAC 1 cut(s) 437
XmnI GAANNNNTTC 1 cut(s) 323
ZraI GACGTC 1 cut(s) 405
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.