Rh5DG476400

The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0019216
Physical Location & Seq
Reverse (-)
75252392 .. 75253067
676 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG476400.1

Sequence Viewer

Length: 519 bp
ATGGAGACTAGTGGAGTAGTGGAGCATATGAAGCCAACTGGAAATGAAGCAAGCGAGTCCTCTCATATTGCACAGAGTACTAAGTTCAAATTCTATTGGCTGAAAATGAGCACTTGTCTATTACACAAAAACACTCGCTACAATTTCAGCATCTCTCGAATGGCTTCTTCAGCAATGGCTCTCTCCTCCCCTTCCCTAGCTGGCCAAGCTGTGAAGCTCAGTTCCTCCATATCTAATTTCCTCGGTGAGGGCCGAATCACCATGCGCAAAACCGCAGCCAAGTCCAAAATCGTATCATCTGGCAGCCCATGGTACGGTGCAGACCGTGTTAAGTATTTGGGCCCATTCTTCGGTGAGGCCCCATCTTCCCTCATCGGAGAGTTTCCTGGGGATTACGGTTGGGACACTGCTGGGCTATCAGCGGATCCCGAGACTTTTGCCAAAAACCGTGAGCTTGAGGTCATCTTGGGCTGTGTTTTCCCCGAACTCCTAGCCCGCTATGGAGTCAACTTCGGCTAG

Protein Analysis

172

Amino Acids

18.68

Weight (kDa)

8.87

Isoelectric Point (pI)

37.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Chloroa_b-bind PF00504 121 - 155 3.3e-07 Chlorophyll A-B binding protein
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: OG0019216)

Species Orthologous Gene IDs
fragaria_vesca FvH4_3g37620
rosa_chinensis RchiOBHm_Chr5g0067741
rosa_multiflora Rmu_sc0000230.1_g000003
rosa_roxburghii Rroxscaffold_1G00013520 Rroxscaffold_2G00104610
rosa_samantha Rh3CG308600 Rh5AG445100 Rh5DG476400

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 266
AciI CCGC 3 cut(s) 273, 422, 496
AclWI GGATC 2 cut(s) 419, 432
AcoI YGGCCR 1 cut(s) 202
AcsI RAATTY 1 cut(s) 89
AcuI CTGAAG 1 cut(s) 153
AfaI GTAC 2 cut(s) 79, 314
AfiI CCNNNNNNNGG 3 cut(s) 247, 314, 350
AgsI TTSAA 1 cut(s) 88
AhlI ACTAGT 1 cut(s) 8
AjnI CCWGG 1 cut(s) 385
AluBI AGCT 4 cut(s) 200, 209, 217, 454
AluI AGCT 4 cut(s) 200, 209, 217, 454
Alw21I GWGCWC 1 cut(s) 113
Alw26I GTCTC 1 cut(s) 425
AlwI GGATC 2 cut(s) 419, 432
Ama87I CYCGRG 1 cut(s) 428
AoxI GGCC 4 cut(s) 202, 250, 340, 357
ApaI GGGCCC 1 cut(s) 344
ApeKI GCWGC 2 cut(s) 275, 303
ApoI RAATTY 1 cut(s) 89
Asp700I GAANNNNTTC 1 cut(s) 163
AspLEI GCGC 1 cut(s) 267
AspS9I GGNCC 4 cut(s) 250, 340, 341, 358
AsuHPI GGTGA 3 cut(s) 250, 257, 365
AvaI CYCGRG 1 cut(s) 428
BaeGI GKGCMC 1 cut(s) 344
BalI TGGCCA 1 cut(s) 204
BamHI GGATCC 1 cut(s) 424
BanII GRGCYC 1 cut(s) 344
Bbv12I GWGCWC 1 cut(s) 113
BbvI GCAGC 2 cut(s) 287, 315
BccI CCATC 1 cut(s) 370
BcgI CGANNNNNNTGC 2 cut(s) 419, 453
BciT130I CCWGG 1 cut(s) 387
BcoDI GTCTC 1 cut(s) 425
BcuI ACTAGT 1 cut(s) 8
BfaI CTAG 4 cut(s) 9, 197, 491, 517
BisI GCNGC 2 cut(s) 276, 304
BlsI GCNGC 2 cut(s) 277, 305
BmcAI AGTACT 1 cut(s) 79
Bme1390I CCNGG 1 cut(s) 387
BmeT110I CYCGRG 1 cut(s) 428
BmgT120I GGNCC 4 cut(s) 250, 340, 341, 358
BmiI GGNNCC 3 cut(s) 342, 360, 426
BmrFI CCNGG 1 cut(s) 387
BmsI GCATC 1 cut(s) 159
BpuEI CTTGAG 1 cut(s) 476
BsaJI CCNNGG 3 cut(s) 241, 308, 386
Bsc4I CCNNNNNNNGG 3 cut(s) 247, 314, 350
Bse1I ACTGG 1 cut(s) 43
Bse3DI GCAATG 1 cut(s) 180
BseBI CCWGG 1 cut(s) 387
BseDI CCNNGG 3 cut(s) 241, 308, 386
BseLI CCNNNNNNNGG 3 cut(s) 247, 314, 350
BseMI GCAATG 1 cut(s) 180
BseMII CTCAG 1 cut(s) 232
BseNI ACTGG 1 cut(s) 43
BseRI GAGGAG 1 cut(s) 175
BseSI GKGCMC 1 cut(s) 344
BseXI GCAGC 2 cut(s) 287, 315
BseYI CCCAGC 1 cut(s) 410
BsgI GTGCAG 1 cut(s) 339
BshFI GGCC 4 cut(s) 204, 252, 342, 359
BsiHKAI GWGCWC 1 cut(s) 113
BsiHKCI CYCGRG 1 cut(s) 428
BslFI GGGAC 1 cut(s) 416
BslI CCNNNNNNNGG 3 cut(s) 247, 314, 350
BsmAI GTCTC 1 cut(s) 425
BsmFI GGGAC 1 cut(s) 416
BsnI GGCC 4 cut(s) 204, 252, 342, 359
BsoBI CYCGRG 1 cut(s) 428
Bsp120I GGGCCC 1 cut(s) 340
Bsp1286I GDGCHC 2 cut(s) 113, 344
Bsp143I GATC 1 cut(s) 424
Bsp19I CCATGG 1 cut(s) 308
BspACI CCGC 3 cut(s) 273, 422, 496
BspANI GGCC 4 cut(s) 204, 252, 342, 359
BspCNI CTCAG 1 cut(s) 231
BspLI GGNNCC 3 cut(s) 342, 360, 426
BspPI GGATC 2 cut(s) 419, 432
BsrDI GCAATG 1 cut(s) 180
BsrI ACTGG 1 cut(s) 43
BssECI CCNNGG 3 cut(s) 241, 308, 386
BssMI GATC 1 cut(s) 424
BssT1I CCWWGG 1 cut(s) 308
Bst2UI CCWGG 1 cut(s) 387
Bst4CI ACNGT 4 cut(s) 317, 326, 398, 449
BstC8I GCNNGC 3 cut(s) 52, 202, 496
BstDEI CTNAG 2 cut(s) 81, 218
BstDSI CCRYGG 1 cut(s) 308
BstENI CCTNNNNNAGG 1 cut(s) 245
BstHHI GCGC 1 cut(s) 267
BstKTI GATC 1 cut(s) 427
BstMAI GTCTC 1 cut(s) 425
BstMBI GATC 1 cut(s) 424
BstMWI GCNNNNNNNGC 3 cut(s) 31, 170, 206
BstNI CCWGG 1 cut(s) 387
BstSCI CCNGG 1 cut(s) 385
BstSLI GKGCMC 1 cut(s) 344
BstV1I GCAGC 2 cut(s) 287, 315
BstX2I RGATCY 1 cut(s) 424
BstYI RGATCY 1 cut(s) 424
BsuRI GGCC 4 cut(s) 204, 252, 342, 359
BtgI CCRYGG 1 cut(s) 308
BtsI GCAGTG 1 cut(s) 405
BtsIMutI CAGTG 1 cut(s) 405
Cac8I GCNNGC 3 cut(s) 52, 202, 496
CfoI GCGC 1 cut(s) 267
Cfr13I GGNCC 4 cut(s) 250, 340, 341, 358
Csp6I GTAC 2 cut(s) 78, 313
CviAII CATG 2 cut(s) 262, 309
CviQI GTAC 2 cut(s) 78, 313
DdeI CTNAG 2 cut(s) 81, 218
DpnI GATC 1 cut(s) 426
DpnII GATC 1 cut(s) 424
EaeI YGGCCR 1 cut(s) 202
Eco130I CCWWGG 1 cut(s) 308
Eco24I GRGCYC 1 cut(s) 344
Eco57I CTGAAG 1 cut(s) 153
Eco88I CYCGRG 1 cut(s) 428
EcoNI CCTNNNNNAGG 1 cut(s) 245
EcoO109I RGGNCCY 1 cut(s) 358
EcoRII CCWGG 1 cut(s) 385
EcoT14I CCWWGG 1 cut(s) 308
EcoT38I GRGCYC 1 cut(s) 344
ErhI CCWWGG 1 cut(s) 308
FaeI CATG 2 cut(s) 265, 312
FaiI YATR 7 cut(s) 27, 29, 66, 230, 263, 310, 501
FaqI GGGAC 1 cut(s) 416
FatI CATG 2 cut(s) 261, 308
FauI CCCGC 1 cut(s) 503
FauNDI CATATG 1 cut(s) 27
Fnu4HI GCNGC 2 cut(s) 276, 304
FriOI GRGCYC 1 cut(s) 344
Fsp4HI GCNGC 2 cut(s) 276, 304
FspBI CTAG 4 cut(s) 9, 197, 491, 517
FspI TGCGCA 1 cut(s) 266
GlaI GCGC 1 cut(s) 266
GluI GCNGC 2 cut(s) 276, 304
GsaI CCCAGC 1 cut(s) 414
HaeIII GGCC 4 cut(s) 204, 252, 342, 359
HhaI GCGC 1 cut(s) 267
Hin1II CATG 2 cut(s) 265, 312
Hin6I GCGC 1 cut(s) 265
HinP1I GCGC 1 cut(s) 265
HincII GTYRAC 1 cut(s) 508
HindII GTYRAC 1 cut(s) 508
HinfI GANTC 3 cut(s) 56, 255, 504
HphI GGTGA 3 cut(s) 250, 257, 365
Hpy166II GTNNAC 1 cut(s) 508
Hpy188I TCNGA 1 cut(s) 377
Hpy188III TCNNGA 2 cut(s) 156, 428
Hpy8I GTNNAC 1 cut(s) 508
HpyAV CCTTC 1 cut(s) 201
HpyCH4III ACNGT 4 cut(s) 317, 326, 398, 449
HpyCH4V TGCA 2 cut(s) 71, 320
HpyF10VI GCNNNNNNNGC 3 cut(s) 31, 170, 206
HpyF3I CTNAG 2 cut(s) 81, 218
Hsp92II CATG 2 cut(s) 265, 312
HspAI GCGC 1 cut(s) 265
Kzo9I GATC 1 cut(s) 424
LmnI GCTCC 1 cut(s) 22
LpnPI CCDG 6 cut(s) 24, 186, 285, 372, 396, 399
Lsp1109I GCAGC 2 cut(s) 287, 315
LweI GCATC 1 cut(s) 159
MaeI CTAG 4 cut(s) 9, 197, 491, 517
MalI GATC 1 cut(s) 426
MboI GATC 1 cut(s) 424
MboII GAAGA 3 cut(s) 159, 340, 357
MflI RGATCY 1 cut(s) 424
MhlI GDGCHC 2 cut(s) 113, 344
MlsI TGGCCA 1 cut(s) 204
MluCI AATT 3 cut(s) 89, 142, 235
MluNI TGGCCA 1 cut(s) 204
MlyI GAGTC 2 cut(s) 65, 513
MnlI CCTC 8 cut(s) 70, 196, 235, 241, 251, 349, 380, 451
Mox20I TGGCCA 1 cut(s) 204
MroXI GAANNNNTTC 1 cut(s) 163
MscI TGGCCA 1 cut(s) 204
MseI TTAA 1 cut(s) 330
Msp20I TGGCCA 1 cut(s) 204
MspA1I CMGCKG 1 cut(s) 422
MspR9I CCNGG 1 cut(s) 387
MvaI CCWGG 1 cut(s) 387
MwoI GCNNNNNNNGC 3 cut(s) 31, 170, 206
NcoI CCATGG 1 cut(s) 308
NdeI CATATG 1 cut(s) 27
NdeII GATC 1 cut(s) 424
NlaIII CATG 2 cut(s) 265, 312
NlaIV GGNNCC 3 cut(s) 342, 360, 426
NsbI TGCGCA 1 cut(s) 266
PdmI GAANNNNTTC 1 cut(s) 163
PfeI GAWTC 1 cut(s) 255
PkrI GCNGC 2 cut(s) 277, 305
PleI GAGTC 2 cut(s) 64, 512
PpsI GAGTC 2 cut(s) 64, 512
Psp6I CCWGG 1 cut(s) 385
PspFI CCCAGC 1 cut(s) 410
PspGI CCWGG 1 cut(s) 385
PspN4I GGNNCC 3 cut(s) 342, 360, 426
PspOMI GGGCCC 1 cut(s) 340
PspPI GGNCC 4 cut(s) 250, 340, 341, 358
PsuI RGATCY 1 cut(s) 424
RsaI GTAC 2 cut(s) 79, 314
RsaNI GTAC 2 cut(s) 78, 313
SaqAI TTAA 1 cut(s) 330
SatI GCNGC 2 cut(s) 276, 304
Sau3AI GATC 1 cut(s) 424
Sau96I GGNCC 4 cut(s) 250, 340, 341, 358
ScaI AGTACT 1 cut(s) 79
SchI GAGTC 2 cut(s) 65, 513
ScrFI CCNGG 1 cut(s) 387
SduI GDGCHC 2 cut(s) 113, 344
SetI ASST 5 cut(s) 202, 211, 219, 456, 462
SfaNI GCATC 1 cut(s) 159
SmlI CTYRAG 1 cut(s) 455
SmoI CTYRAG 1 cut(s) 455
SpeI ACTAGT 1 cut(s) 8
Sse9I AATT 3 cut(s) 89, 142, 235
SsiI CCGC 3 cut(s) 273, 422, 496
SspMI CTAG 4 cut(s) 9, 197, 491, 517
StyD4I CCNGG 1 cut(s) 385
StyI CCWWGG 1 cut(s) 308
TaaI ACNGT 4 cut(s) 317, 326, 398, 449
TaqI TCGA 1 cut(s) 157
TasI AATT 3 cut(s) 89, 142, 235
TatI WGTACW 1 cut(s) 77
TfiI GAWTC 1 cut(s) 255
Tru1I TTAA 1 cut(s) 330
Tru9I TTAA 1 cut(s) 330
TscAI CASTG 1 cut(s) 412
TseI GCWGC 2 cut(s) 275, 303
TspDTI ATGAA 2 cut(s) 44, 60
TspRI CASTG 1 cut(s) 412
XagI CCTNNNNNAGG 1 cut(s) 245
XapI RAATTY 1 cut(s) 89
XmnI GAANNNNTTC 1 cut(s) 163
XspI CTAG 4 cut(s) 9, 197, 491, 517
ZrmI AGTACT 1 cut(s) 79
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.