Rh5DG304400

Ycf4

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0019580
Physical Location & Seq
Reverse (-)
38373270 .. 38374496
1227 bp
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UTR
Exon/CDS
Intron
Rh5DG304400.1

Sequence Viewer

Length: 555 bp
ATGAGTTGGCGATCAGAACGTATATGGATAGAACTTATAGCGGGATCTCGAAAAATAAGTAATTTCAGTTGGGCCCTTATTCTTTTTTTAGGTTCATTAGGGTTTGTATTGGTTGGAACCTCCAGTTATTTTGGTAGGAATTTTATATCTTTATTTCCTTCTCAGCAAATAAATTTTTTTCCACAGGGGATCGTGATGTCTTTCTATGGGATCGCGGGTCTTTTTATTAGCTCCTACTTGTGGTGCACAATTTCGTGGAATGTAGGTAGTGGTTATGATCGATTCGATATAAAAGAGGGTATAGTGTGTATTTTTCGTTGGGGATTTCCTGGAAAAAACCGTCGCATATTTCTGCGATTCCTTATGAAAGATATTCAGTCCATCAGAATAGAAAATAAAGAGGGTCTTTTTGCTCGTCGGGTCCTTTATATGGAAATCAGAGGCCAGGGGGCCATTCCCTTGACGCGTACTGATGAGAATTTGACTCCACGAGAAATTGAGCAAAAAGCTGCTGAATTGGCCTATTTCTTGCGCGTACCAAATGAAGTATTTTGA

Protein Analysis

184

Amino Acids

21.38

Weight (kDa)

9.74

Isoelectric Point (pI)

54.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ycf4 PF02392 7 - 174 3.5e-72 Ycf4
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: OG0019580)

Species Orthologous Gene IDs
arabidopsis_thaliana ATCG00520
malus_domestica MD15G1388400.v1.1
pyrus_communis pycom02g25860
rosa_chinensis RchiOBHm_Chr5g0042981 RchiOBHm_CPg0502091
rosa_samantha Rh5BG294600 Rh5DG304400

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 3 cut(s) 215, 466, 534
AciI CCGC 2 cut(s) 41, 215
AclWI GGATC 3 cut(s) 52, 197, 218
AcsI RAATTY 3 cut(s) 139, 172, 478
AfaI GTAC 2 cut(s) 469, 537
AfiI CCNNNNNNNGG 2 cut(s) 240, 430
AflIII ACRYGT 1 cut(s) 464
AjnI CCWGG 2 cut(s) 328, 444
AluBI AGCT 2 cut(s) 231, 509
AluI AGCT 2 cut(s) 231, 509
Alw21I GWGCWC 1 cut(s) 248
Alw44I GTGCAC 1 cut(s) 244
AlwI GGATC 3 cut(s) 52, 197, 218
AoxI GGCC 4 cut(s) 72, 442, 450, 519
ApaI GGGCCC 1 cut(s) 76
ApaLI GTGCAC 1 cut(s) 244
ApeKI GCWGC 1 cut(s) 509
ApoI RAATTY 3 cut(s) 139, 172, 478
AspLEI GCGC 1 cut(s) 534
AspS9I GGNCC 4 cut(s) 72, 73, 421, 450
AvaII GGWCC 1 cut(s) 421
BaeGI GKGCMC 2 cut(s) 76, 248
BanII GRGCYC 1 cut(s) 76
BauI CACGAG 1 cut(s) 489
Bbv12I GWGCWC 1 cut(s) 248
BbvI GCAGC 1 cut(s) 496
BccI CCATC 1 cut(s) 389
BciT130I CCWGG 2 cut(s) 330, 446
BisI GCNGC 1 cut(s) 510
BlsI GCNGC 1 cut(s) 511
Bme1390I CCNGG 2 cut(s) 330, 446
Bme18I GGWCC 1 cut(s) 421
BmgT120I GGNCC 4 cut(s) 72, 73, 421, 450
BmiI GGNNCC 4 cut(s) 74, 118, 422, 451
BmrFI CCNGG 2 cut(s) 330, 446
BpmI CTGGAG 1 cut(s) 106
Bsa29I ATCGAT 1 cut(s) 280
BsaJI CCNNGG 1 cut(s) 445
Bsc4I CCNNNNNNNGG 2 cut(s) 240, 430
Bse1I ACTGG 1 cut(s) 123
BseBI CCWGG 2 cut(s) 330, 446
BseCI ATCGAT 1 cut(s) 280
BseDI CCNNGG 1 cut(s) 445
BseLI CCNNNNNNNGG 2 cut(s) 240, 430
BseMII CTCAG 1 cut(s) 176
BseNI ACTGG 1 cut(s) 123
BseSI GKGCMC 2 cut(s) 76, 248
BseXI GCAGC 1 cut(s) 496
Bsh1236I CGCG 3 cut(s) 215, 466, 534
BshFI GGCC 4 cut(s) 74, 444, 452, 521
BshVI ATCGAT 1 cut(s) 280
BsiHKAI GWGCWC 1 cut(s) 248
BslI CCNNNNNNNGG 2 cut(s) 240, 430
BsnI GGCC 4 cut(s) 74, 444, 452, 521
Bsp120I GGGCCC 1 cut(s) 72
Bsp1286I GDGCHC 2 cut(s) 76, 248
Bsp143I GATC 5 cut(s) 11, 44, 189, 210, 277
BspACI CCGC 2 cut(s) 41, 215
BspANI GGCC 4 cut(s) 74, 444, 452, 521
BspCNI CTCAG 1 cut(s) 175
BspDI ATCGAT 1 cut(s) 280
BspFNI CGCG 3 cut(s) 215, 466, 534
BspLI GGNNCC 4 cut(s) 74, 118, 422, 451
BspPI GGATC 3 cut(s) 52, 197, 218
BsrI ACTGG 1 cut(s) 123
BssECI CCNNGG 1 cut(s) 445
BssMI GATC 5 cut(s) 11, 44, 189, 210, 277
BssSI CACGAG 1 cut(s) 489
Bst2BI CACGAG 1 cut(s) 489
Bst2UI CCWGG 2 cut(s) 330, 446
Bst4CI ACNGT 1 cut(s) 341
BstDEI CTNAG 1 cut(s) 162
BstFNI CGCG 3 cut(s) 215, 466, 534
BstHHI GCGC 1 cut(s) 534
BstKTI GATC 5 cut(s) 14, 47, 192, 213, 280
BstMBI GATC 5 cut(s) 11, 44, 189, 210, 277
BstMWI GCNNNNNNNGC 1 cut(s) 518
BstNI CCWGG 2 cut(s) 330, 446
BstSCI CCNGG 2 cut(s) 328, 444
BstSLI GKGCMC 2 cut(s) 76, 248
BstUI CGCG 3 cut(s) 215, 466, 534
BstV1I GCAGC 1 cut(s) 496
BstX2I RGATCY 1 cut(s) 44
BstYI RGATCY 1 cut(s) 44
Bsu15I ATCGAT 1 cut(s) 280
BsuRI GGCC 4 cut(s) 74, 444, 452, 521
BsuTUI ATCGAT 1 cut(s) 280
CfoI GCGC 1 cut(s) 534
Cfr13I GGNCC 4 cut(s) 72, 73, 421, 450
ClaI ATCGAT 1 cut(s) 280
CseI GACGC 1 cut(s) 472
Csp6I GTAC 2 cut(s) 468, 536
CviJI RGCY 6 cut(s) 74, 231, 444, 452, 509, 521
CviKI_1 RGCY 6 cut(s) 74, 231, 444, 452, 509, 521
CviQI GTAC 2 cut(s) 468, 536
DdeI CTNAG 1 cut(s) 162
DpnI GATC 5 cut(s) 13, 46, 191, 212, 279
DpnII GATC 5 cut(s) 11, 44, 189, 210, 277
Eco24I GRGCYC 1 cut(s) 76
Eco47I GGWCC 1 cut(s) 421
EcoO109I RGGNCCY 2 cut(s) 73, 421
EcoRII CCWGG 2 cut(s) 328, 444
EcoT38I GRGCYC 1 cut(s) 76
FalI AAGNNNNNCTT 2 cut(s) 390, 422
FauI CCCGC 2 cut(s) 34, 208
Fnu4HI GCNGC 1 cut(s) 510
FriOI GRGCYC 1 cut(s) 76
Fsp4HI GCNGC 1 cut(s) 510
GlaI GCGC 1 cut(s) 533
GluI GCNGC 1 cut(s) 510
GsuI CTGGAG 1 cut(s) 106
HaeIII GGCC 4 cut(s) 74, 444, 452, 521
HgaI GACGC 1 cut(s) 472
HhaI GCGC 1 cut(s) 534
Hin6I GCGC 1 cut(s) 532
HinP1I GCGC 1 cut(s) 532
HinfI GANTC 3 cut(s) 282, 357, 484
Hpy166II GTNNAC 1 cut(s) 246
Hpy188I TCNGA 3 cut(s) 16, 386, 440
Hpy188III TCNNGA 2 cut(s) 48, 193
Hpy8I GTNNAC 1 cut(s) 246
Hpy99I CGWCG 2 cut(s) 345, 420
HpyAV CCTTC 1 cut(s) 168
HpyCH4III ACNGT 1 cut(s) 341
HpyCH4IV ACGT 1 cut(s) 19
HpyCH4V TGCA 1 cut(s) 246
HpyF10VI GCNNNNNNNGC 1 cut(s) 518
HpyF3I CTNAG 1 cut(s) 162
HpySE526I ACGT 1 cut(s) 19
HspAI GCGC 1 cut(s) 532
Kzo9I GATC 5 cut(s) 11, 44, 189, 210, 277
LmnI GCTCC 1 cut(s) 236
LpnPI CCDG 6 cut(s) 136, 170, 315, 342, 431, 458
Lsp1109I GCAGC 1 cut(s) 496
MaeII ACGT 1 cut(s) 19
MalI GATC 5 cut(s) 13, 46, 191, 212, 279
MboI GATC 5 cut(s) 11, 44, 189, 210, 277
MflI RGATCY 1 cut(s) 44
MhlI GDGCHC 2 cut(s) 76, 248
MluCI AATT 7 cut(s) 61, 139, 172, 249, 478, 495, 515
MluI ACGCGT 1 cut(s) 464
MlyI GAGTC 1 cut(s) 478
MmeI TCCRAC 1 cut(s) 94
MnlI CCTC 4 cut(s) 130, 289, 394, 434
MspR9I CCNGG 2 cut(s) 330, 446
MvaI CCWGG 2 cut(s) 330, 446
MvnI CGCG 3 cut(s) 215, 466, 534
MwoI GCNNNNNNNGC 1 cut(s) 518
NdeII GATC 5 cut(s) 11, 44, 189, 210, 277
NlaIV GGNNCC 4 cut(s) 74, 118, 422, 451
PfeI GAWTC 2 cut(s) 282, 357
PfoI TCCNGGA 1 cut(s) 328
PkrI GCNGC 1 cut(s) 511
PleI GAGTC 1 cut(s) 478
PpsI GAGTC 1 cut(s) 478
PpuMI RGGWCCY 1 cut(s) 421
Psp5II RGGWCCY 1 cut(s) 421
Psp6I CCWGG 2 cut(s) 328, 444
PspGI CCWGG 2 cut(s) 328, 444
PspN4I GGNNCC 4 cut(s) 74, 118, 422, 451
PspOMI GGGCCC 1 cut(s) 72
PspPI GGNCC 4 cut(s) 72, 73, 421, 450
PspPPI RGGWCCY 1 cut(s) 421
PsuI RGATCY 1 cut(s) 44
RsaI GTAC 2 cut(s) 469, 537
RsaNI GTAC 2 cut(s) 468, 536
SatI GCNGC 1 cut(s) 510
Sau3AI GATC 5 cut(s) 11, 44, 189, 210, 277
Sau96I GGNCC 4 cut(s) 72, 73, 421, 450
SchI GAGTC 1 cut(s) 478
ScrFI CCNGG 2 cut(s) 330, 446
SduI GDGCHC 2 cut(s) 76, 248
SetI ASST 6 cut(s) 22, 94, 122, 233, 268, 511
SinI GGWCC 1 cut(s) 421
Sse9I AATT 7 cut(s) 61, 139, 172, 249, 478, 495, 515
SsiI CCGC 2 cut(s) 41, 215
StyD4I CCNGG 2 cut(s) 328, 444
TaaI ACNGT 1 cut(s) 341
TaiI ACGT 1 cut(s) 22
TaqI TCGA 3 cut(s) 49, 280, 285
TasI AATT 7 cut(s) 61, 139, 172, 249, 478, 495, 515
TfiI GAWTC 2 cut(s) 282, 357
TseI GCWGC 1 cut(s) 509
TspDTI ATGAA 2 cut(s) 84, 380
VneI GTGCAC 1 cut(s) 244
VpaK11BI GGWCC 1 cut(s) 421
XapI RAATTY 3 cut(s) 139, 172, 478
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.