Rh5AG281200

One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light- driven water plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0018721
Physical Location & Seq
Reverse (-)
38142277 .. 38144775
2499 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG281200.1

Sequence Viewer

Length: 591 bp
ATGAAAACCTTATATTCCCTGAGGAGGTTCTACCCCGTGGAAACGCTCTTTAATGGAACTTTAGAAATAGCTGGTCGTGACCAAGAAACCACCGGTTTCGCTTGGTGGGCCGGGAATGCCCGACTTATCAATTTATCCGGTAAACTACTGGGGGCCCATGTCGCCCATGTCGGATTAATTGTATTCTGGGCCGGAGCAATGAACCTATTGGAAGTGGCTCATTTCGTACTAGAGAAGCCTATGTATGAACAAGGATTAATTTTACTTCCCCACCTAGCTACTCTAGGTTGGGGGTTAGGTCCGGGTGGGGAAGTTCTAGACACCTTTCCATACTTTGTGTCTGGAGTACTTCACTTAATTTCCTCTGCAGTATTGGGCTTTGGCGGTATTTATCATGCACTTCTGGGACCCGAGACTCTTGAAGAATCTTTTCCATTTTCCGGTTATGTATGGAAAGATAGAAATAAAATGACTACAATTTTGGGTATTCACTTAATCTTGTTAGGCATAGGTGCTTTTCTTCTAGTATTCAAGTATTGTATTTGGTTATTTACTAAAATTCCCTTTTGGCGGAGAAGGGTGGATCGTTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00195 ko01100 map00195 map01100
Pfam Domains
Protein Families
PSII

Protein Analysis

196

Amino Acids

22.0

Weight (kDa)

8.71

Isoelectric Point (pI)

31.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PSII PF00421 31 - 181 5.6e-45 Photosystem II 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: OG0018721)

Species Orthologous Gene IDs
arabidopsis_thaliana ATCG00280
rosa_laevigata RLG00000022754
rosa_multiflora Rmu_sc0006153.1_g000042
rosa_roxburghii Rroxscaffold_7G00181930
rosa_rugosa RorugMtG0000600
rosa_samantha Rh1BG017200 Rh5AG281200 Rh7DG262700
rosa_wichuraiana Rw0G001310

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 2 cut(s) 384, 571
AcsI RAATTY 1 cut(s) 558
AfaI GTAC 2 cut(s) 228, 348
AfiI CCNNNNNNNGG 3 cut(s) 24, 440, 570
AgeI ACCGGT 1 cut(s) 92
AgsI TTSAA 2 cut(s) 422, 532
AluBI AGCT 2 cut(s) 71, 278
AluI AGCT 2 cut(s) 71, 278
Alw26I GTCTC 1 cut(s) 407
Ama87I CYCGRG 1 cut(s) 410
AoxI GGCC 3 cut(s) 108, 153, 189
ApaI GGGCCC 1 cut(s) 157
ApoI RAATTY 1 cut(s) 558
ArsI GACNNNNNNTTYG 2 cut(s) 463, 495
AseI ATTAAT 2 cut(s) 176, 257
AsiGI ACCGGT 1 cut(s) 92
Asp700I GAANNNNTTC 1 cut(s) 429
AspS9I GGNCC 6 cut(s) 108, 153, 154, 189, 299, 407
AsuC2I CCSGG 2 cut(s) 112, 303
AvaI CYCGRG 1 cut(s) 410
AvaII GGWCC 2 cut(s) 299, 407
AxyI CCTNAGG 1 cut(s) 20
BaeGI GKGCMC 1 cut(s) 157
BanII GRGCYC 1 cut(s) 157
BcnI CCSGG 2 cut(s) 112, 303
BcoDI GTCTC 1 cut(s) 407
BfaI CTAG 5 cut(s) 230, 275, 284, 317, 524
BfmI CTRYAG 1 cut(s) 366
BmcAI AGTACT 1 cut(s) 348
Bme1390I CCNGG 2 cut(s) 112, 303
Bme18I GGWCC 2 cut(s) 299, 407
BmeT110I CYCGRG 1 cut(s) 410
BmgT120I GGNCC 6 cut(s) 108, 153, 154, 189, 299, 407
BmiI GGNNCC 4 cut(s) 154, 155, 408, 409
BmrFI CCNGG 2 cut(s) 112, 303
BmrI ACTGGG 1 cut(s) 158
BmuI ACTGGG 1 cut(s) 158
BpmI CTGGAG 1 cut(s) 363
BpuMI CCSGG 2 cut(s) 112, 303
BsaJI CCNNGG 1 cut(s) 36
BsaWI WCCGGW 3 cut(s) 92, 137, 440
Bsc4I CCNNNNNNNGG 3 cut(s) 24, 440, 570
Bse118I RCCGGY 1 cut(s) 92
Bse1I ACTGG 1 cut(s) 153
Bse21I CCTNAGG 1 cut(s) 20
Bse3DI GCAATG 1 cut(s) 204
BseDI CCNNGG 1 cut(s) 36
BseLI CCNNNNNNNGG 3 cut(s) 24, 440, 570
BseMI GCAATG 1 cut(s) 204
BseMII CTCAG 1 cut(s) 11
BseNI ACTGG 1 cut(s) 153
BseRI GAGGAG 1 cut(s) 37
BseSI GKGCMC 1 cut(s) 157
BshFI GGCC 3 cut(s) 110, 155, 191
BshTI ACCGGT 1 cut(s) 92
BsiHKCI CYCGRG 1 cut(s) 410
BsiSI CCGG 6 cut(s) 93, 111, 138, 192, 302, 441
BslFI GGGAC 1 cut(s) 420
BslI CCNNNNNNNGG 3 cut(s) 24, 440, 570
BsmAI GTCTC 1 cut(s) 407
BsmFI GGGAC 1 cut(s) 420
BsmI GAATGC 1 cut(s) 121
BsnI GGCC 3 cut(s) 110, 155, 191
BsoBI CYCGRG 1 cut(s) 410
Bsp120I GGGCCC 1 cut(s) 153
Bsp1286I GDGCHC 1 cut(s) 157
Bsp143I GATC 1 cut(s) 583
BspACI CCGC 2 cut(s) 384, 571
BspANI GGCC 3 cut(s) 110, 155, 191
BspCNI CTCAG 1 cut(s) 12
BspLI GGNNCC 4 cut(s) 154, 155, 408, 409
BspMAI CTGCAG 1 cut(s) 370
BsrDI GCAATG 1 cut(s) 204
BsrFI RCCGGY 1 cut(s) 92
BsrI ACTGG 1 cut(s) 153
BssAI RCCGGY 1 cut(s) 92
BssECI CCNNGG 1 cut(s) 36
BssMI GATC 1 cut(s) 583
BstDEI CTNAG 1 cut(s) 20
BstDSI CCRYGG 1 cut(s) 36
BstKTI GATC 1 cut(s) 586
BstMAI GTCTC 1 cut(s) 407
BstMBI GATC 1 cut(s) 583
BstMWI GCNNNNNNNGC 3 cut(s) 107, 116, 161
BstSCI CCNGG 2 cut(s) 110, 301
BstSFI CTRYAG 1 cut(s) 366
BstSLI GKGCMC 1 cut(s) 157
Bsu36I CCTNAGG 1 cut(s) 20
BsuRI GGCC 3 cut(s) 110, 155, 191
BtgI CCRYGG 1 cut(s) 36
Cfr10I RCCGGY 1 cut(s) 92
Cfr13I GGNCC 6 cut(s) 108, 153, 154, 189, 299, 407
Csp6I GTAC 2 cut(s) 227, 347
CspAI ACCGGT 1 cut(s) 92
CviAII CATG 3 cut(s) 158, 167, 395
CviJI RGCY 8 cut(s) 71, 110, 155, 191, 218, 238, 278, 378
CviKI_1 RGCY 8 cut(s) 71, 110, 155, 191, 218, 238, 278, 378
CviQI GTAC 2 cut(s) 227, 347
DdeI CTNAG 1 cut(s) 20
DpnI GATC 1 cut(s) 585
DpnII GATC 1 cut(s) 583
EciI GGCGGA 1 cut(s) 586
Eco24I GRGCYC 1 cut(s) 157
Eco47I GGWCC 2 cut(s) 299, 407
Eco81I CCTNAGG 1 cut(s) 20
Eco88I CYCGRG 1 cut(s) 410
EcoO109I RGGNCCY 2 cut(s) 153, 407
EcoT38I GRGCYC 1 cut(s) 157
FaeI CATG 3 cut(s) 161, 170, 398
FaqI GGGAC 1 cut(s) 420
FatI CATG 3 cut(s) 157, 166, 394
FriOI GRGCYC 1 cut(s) 157
FspBI CTAG 5 cut(s) 230, 275, 284, 317, 524
GsuI CTGGAG 1 cut(s) 363
HaeIII GGCC 3 cut(s) 110, 155, 191
HapII CCGG 6 cut(s) 93, 111, 138, 192, 302, 441
Hin1II CATG 3 cut(s) 161, 170, 398
HinfI GANTC 2 cut(s) 415, 425
HpaII CCGG 6 cut(s) 93, 111, 138, 192, 302, 441
Hpy166II GTNNAC 1 cut(s) 143
Hpy188I TCNGA 1 cut(s) 173
Hpy188III TCNNGA 4 cut(s) 77, 317, 342, 419
Hpy8I GTNNAC 1 cut(s) 143
HpyAV CCTTC 1 cut(s) 570
HpyCH4V TGCA 2 cut(s) 368, 398
HpyF10VI GCNNNNNNNGC 3 cut(s) 107, 116, 161
HpyF3I CTNAG 1 cut(s) 20
Hsp92II CATG 3 cut(s) 161, 170, 398
KflI GGGWCCC 1 cut(s) 407
Kzo9I GATC 1 cut(s) 583
LmnI GCTCC 1 cut(s) 194
MaeI CTAG 5 cut(s) 230, 275, 284, 317, 524
MaeIII GTNAC 1 cut(s) 77
MalI GATC 1 cut(s) 585
MboI GATC 1 cut(s) 583
MboII GAAGA 2 cut(s) 434, 512
MhlI GDGCHC 1 cut(s) 157
MluCI AATT 6 cut(s) 130, 177, 258, 357, 477, 558
MlyI GAGTC 1 cut(s) 409
MmeI TCCRAC 1 cut(s) 151
MnlI CCTC 3 cut(s) 15, 18, 373
MroXI GAANNNNTTC 1 cut(s) 429
MseI TTAA 5 cut(s) 51, 176, 257, 356, 494
MspI CCGG 6 cut(s) 93, 111, 138, 192, 302, 441
MspR9I CCNGG 2 cut(s) 112, 303
Mva1269I GAATGC 1 cut(s) 121
MwoI GCNNNNNNNGC 3 cut(s) 107, 116, 161
NciI CCSGG 2 cut(s) 112, 303
NdeII GATC 1 cut(s) 583
NlaIII CATG 3 cut(s) 161, 170, 398
NlaIV GGNNCC 4 cut(s) 154, 155, 408, 409
NmuCI GTSAC 1 cut(s) 77
PctI GAATGC 1 cut(s) 121
PdmI GAANNNNTTC 1 cut(s) 429
PfeI GAWTC 1 cut(s) 425
PinAI ACCGGT 1 cut(s) 92
PleI GAGTC 1 cut(s) 409
PpsI GAGTC 1 cut(s) 409
PpuMI RGGWCCY 1 cut(s) 407
PshBI ATTAAT 2 cut(s) 176, 257
Psp5II RGGWCCY 1 cut(s) 407
PspN4I GGNNCC 4 cut(s) 154, 155, 408, 409
PspOMI GGGCCC 1 cut(s) 153
PspPI GGNCC 6 cut(s) 108, 153, 154, 189, 299, 407
PspPPI RGGWCCY 1 cut(s) 407
PstI CTGCAG 1 cut(s) 370
RsaI GTAC 2 cut(s) 228, 348
RsaNI GTAC 2 cut(s) 227, 347
SaqAI TTAA 5 cut(s) 51, 176, 257, 356, 494
Sau3AI GATC 1 cut(s) 583
Sau96I GGNCC 6 cut(s) 108, 153, 154, 189, 299, 407
ScaI AGTACT 1 cut(s) 348
SchI GAGTC 1 cut(s) 409
ScrFI CCNGG 2 cut(s) 112, 303
SduI GDGCHC 1 cut(s) 157
SfcI CTRYAG 1 cut(s) 366
SinI GGWCC 2 cut(s) 299, 407
Sse9I AATT 6 cut(s) 130, 177, 258, 357, 477, 558
SsiI CCGC 2 cut(s) 384, 571
SspMI CTAG 5 cut(s) 230, 275, 284, 317, 524
StyD4I CCNGG 2 cut(s) 110, 301
TasI AATT 6 cut(s) 130, 177, 258, 357, 477, 558
TatI WGTACW 1 cut(s) 346
TfiI GAWTC 1 cut(s) 425
Tru1I TTAA 5 cut(s) 51, 176, 257, 356, 494
Tru9I TTAA 5 cut(s) 51, 176, 257, 356, 494
TseFI GTSAC 1 cut(s) 77
Tsp45I GTSAC 1 cut(s) 77
TspDTI ATGAA 3 cut(s) 17, 215, 261
VpaK11BI GGWCC 2 cut(s) 299, 407
VspI ATTAAT 2 cut(s) 176, 257
XapI RAATTY 1 cut(s) 558
XbaI TCTAGA 1 cut(s) 316
XmnI GAANNNNTTC 1 cut(s) 429
XspI CTAG 5 cut(s) 230, 275, 284, 317, 524
ZrmI AGTACT 1 cut(s) 348
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.