RchiOBHm_Chr3g0490211

Required for ribosome biogenesis. Part of a complex which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0012386
Physical Location & Seq
Forward (+)
36897318 .. 36899570
2253 bp
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UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 564 bp
ATGCGACCTCCCAGAGGTGGCGGTAGTTTCAGAGGCAACCGCGGTGGCGGAGGTTTCAGAGGCCGCGGCGGCGGAGACTTCAGAGGTGGCCGTGGTGGCTTCCGCGACGAAGGCCCTCCTTCGGAAGTGGTAGAGGTTTCAACGTTTGTTCATGCATGTGAGGGTGATGCTGTCACAAAGCTCACACATGAGAAGATACCCTATTTCAATGCCCCAATCTATCTGCAGAACAAGACTCAGATAGGCAAAGTCGATGAAATTTTTGGCCCAATTAATGAATCTTACTTCTCGGTCAAAGTGATGGAAGGCATTGTGGCAACTTCATATTCACAGGGTGATAAGTTCTATATTGACCCAGCGAAGCTTCTTCCTCTTGCAAGATTTCTTCCACAGCCCAAGGGACAGAAACCAGCTTTTTCTCGAGGTGGAGGACGTGGAGGCAGGGGACCTCCAAGGGGTGGCGGCAGAGGTGGAGTTTATCGTGGCAGGGGACCTCCAAGGGGGGGTGGCAGAGGACCCCCGAGGGGTGGGCGTGGTGGCTTCAGGGGCAGAGGGAGATTTTAG

Protein Analysis

187

Amino Acids

19.81

Weight (kDa)

11.15

Isoelectric Point (pI)

29.64

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Gar1 PF04410 43 - 129 7.9e-28 Gar1/Naf1 RNA binding region
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0012386)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G03920 AT5G18180
fragaria_vesca FvH4_1g30320
malus_domestica MD00G1189600.v1.1 MD05G1045500.v1.1
prunus_persica Prupe.8G064800_v2.0.a1
pyrus_communis pycom05g03790 pycom10g03750
rosa_chinensis RchiOBHm_Chr3g0490211
rosa_laevigata RLG00000022895
rosa_multiflora Rmu_sc0018339.1_g000001 Rmu_sc0019534.1_g000007
rosa_roxburghii Rroxscaffold_6G00393700
rosa_rugosa Rorug03G0243000
rosa_samantha Rh3AG291400 Rh3BG328400 Rh3CG325400 Rh3DG324700
rosa_wichuraiana Rw3G025790

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 458
AccII CGCG 3 cut(s) 42, 66, 105
AclI AACGTT 1 cut(s) 143
AcoI YGGCCR 1 cut(s) 88
AcsI RAATTY 1 cut(s) 258
AcuI CTGAAG 2 cut(s) 64, 526
AdeI CACNNNGTG 1 cut(s) 335
AfiI CCNNNNNNNGG 9 cut(s) 14, 17, 121, 455, 458, 500, 503, 524, 527
AgsI TTSAA 2 cut(s) 141, 208
AjiI CACGTC 1 cut(s) 434
AluBI AGCT 3 cut(s) 181, 364, 413
AluI AGCT 3 cut(s) 181, 364, 413
Alw26I GTCTC 1 cut(s) 69
Ama87I CYCGRG 2 cut(s) 420, 520
AoxI GGCC 4 cut(s) 61, 88, 112, 265
ApoI RAATTY 1 cut(s) 258
AseI ATTAAT 1 cut(s) 273
AspS9I GGNCC 5 cut(s) 113, 266, 446, 491, 515
AsuHPI GGTGA 2 cut(s) 176, 347
AvaI CYCGRG 2 cut(s) 420, 520
AvaII GGWCC 3 cut(s) 446, 491, 515
BccI CCATC 1 cut(s) 295
BceAI ACGGC 1 cut(s) 75
BcoDI GTCTC 1 cut(s) 69
BfmI CTRYAG 1 cut(s) 224
BglI GCCNNNNNGGC 2 cut(s) 69, 96
BisI GCNGC 4 cut(s) 64, 67, 70, 463
BlsI GCNGC 4 cut(s) 65, 68, 71, 464
Bme18I GGWCC 3 cut(s) 446, 491, 515
BmeT110I CYCGRG 2 cut(s) 420, 520
BmgBI CACGTC 1 cut(s) 434
BmgT120I GGNCC 5 cut(s) 113, 266, 446, 491, 515
BmiI GGNNCC 3 cut(s) 447, 492, 517
BmsI GCATC 1 cut(s) 157
BsaJI CCNNGG 7 cut(s) 40, 64, 91, 396, 452, 497, 521
Bsc4I CCNNNNNNNGG 9 cut(s) 14, 17, 121, 455, 458, 500, 503, 524, 527
BseDI CCNNGG 7 cut(s) 40, 64, 91, 396, 452, 497, 521
BseLI CCNNNNNNNGG 9 cut(s) 14, 17, 121, 455, 458, 500, 503, 524, 527
BseMII CTCAG 1 cut(s) 251
BseYI CCCAGC 1 cut(s) 355
Bsh1236I CGCG 3 cut(s) 42, 66, 105
BshFI GGCC 4 cut(s) 63, 90, 114, 267
BsiHKCI CYCGRG 2 cut(s) 420, 520
BslFI GGGAC 3 cut(s) 414, 459, 504
BslI CCNNNNNNNGG 9 cut(s) 14, 17, 121, 455, 458, 500, 503, 524, 527
BsmAI GTCTC 1 cut(s) 69
BsmFI GGGAC 3 cut(s) 414, 459, 504
BsnI GGCC 4 cut(s) 63, 90, 114, 267
BsoBI CYCGRG 2 cut(s) 420, 520
BspANI GGCC 4 cut(s) 63, 90, 114, 267
BspCNI CTCAG 1 cut(s) 250
BspFNI CGCG 3 cut(s) 42, 66, 105
BspLI GGNNCC 3 cut(s) 447, 492, 517
BspMAI CTGCAG 1 cut(s) 228
BssECI CCNNGG 7 cut(s) 40, 64, 91, 396, 452, 497, 521
BssT1I CCWWGG 3 cut(s) 396, 452, 497
BstDEI CTNAG 1 cut(s) 237
BstDSI CCRYGG 3 cut(s) 40, 64, 91
BstENI CCTNNNNNAGG 1 cut(s) 12
BstFNI CGCG 3 cut(s) 42, 66, 105
BstMAI GTCTC 1 cut(s) 69
BstMWI GCNNNNNNNGC 4 cut(s) 69, 96, 111, 546
BstNSI RCATGY 1 cut(s) 159
BstSFI CTRYAG 1 cut(s) 224
BstUI CGCG 3 cut(s) 42, 66, 105
BsuRI GGCC 4 cut(s) 63, 90, 114, 267
BtgI CCRYGG 3 cut(s) 40, 64, 91
BtrI CACGTC 1 cut(s) 434
Cfr13I GGNCC 5 cut(s) 113, 266, 446, 491, 515
Cfr42I CCGCGG 2 cut(s) 43, 67
CspCI CAANNNNNGTGG 2 cut(s) 25, 60
CviAII CATG 3 cut(s) 152, 156, 188
DdeI CTNAG 1 cut(s) 237
DraIII CACNNNGTG 1 cut(s) 335
EaeI YGGCCR 1 cut(s) 88
EciI GGCGGA 2 cut(s) 63, 87
Eco130I CCWWGG 3 cut(s) 396, 452, 497
Eco47I GGWCC 3 cut(s) 446, 491, 515
Eco57I CTGAAG 2 cut(s) 64, 526
Eco88I CYCGRG 2 cut(s) 420, 520
EcoNI CCTNNNNNAGG 1 cut(s) 12
EcoO109I RGGNCCY 4 cut(s) 113, 446, 491, 515
EcoT14I CCWWGG 3 cut(s) 396, 452, 497
EcoT22I ATGCAT 1 cut(s) 157
ErhI CCWWGG 3 cut(s) 396, 452, 497
FaeI CATG 3 cut(s) 155, 159, 191
FaiI YATR 5 cut(s) 153, 157, 189, 325, 348
FaqI GGGAC 3 cut(s) 414, 459, 504
FatI CATG 3 cut(s) 151, 155, 187
Fnu4HI GCNGC 4 cut(s) 64, 67, 70, 463
Fsp4HI GCNGC 4 cut(s) 64, 67, 70, 463
GluI GCNGC 4 cut(s) 64, 67, 70, 463
GsaI CCCAGC 1 cut(s) 359
HaeIII GGCC 4 cut(s) 63, 90, 114, 267
Hin1II CATG 3 cut(s) 155, 159, 191
HindIII AAGCTT 1 cut(s) 362
HinfI GANTC 2 cut(s) 235, 278
HphI GGTGA 2 cut(s) 176, 347
Hpy188I TCNGA 5 cut(s) 32, 59, 83, 124, 240
Hpy188III TCNNGA 1 cut(s) 420
Hpy99I CGWCG 1 cut(s) 110
HpyAV CCTTC 3 cut(s) 104, 129, 299
HpyCH4IV ACGT 2 cut(s) 143, 433
HpyCH4V TGCA 3 cut(s) 155, 226, 377
HpyF10VI GCNNNNNNNGC 4 cut(s) 69, 96, 111, 546
HpyF3I CTNAG 1 cut(s) 237
HpySE526I ACGT 2 cut(s) 143, 433
Hsp92II CATG 3 cut(s) 155, 159, 191
KspI CCGCGG 2 cut(s) 43, 67
LpnPI CCDG 7 cut(s) 25, 317, 369, 423, 427, 472, 529
LweI GCATC 1 cut(s) 157
MaeII ACGT 2 cut(s) 143, 433
MaeIII GTNAC 1 cut(s) 172
MboII GAAGA 3 cut(s) 205, 359, 377
MluCI AATT 2 cut(s) 258, 270
MlyI GAGTC 1 cut(s) 229
Mph1103I ATGCAT 1 cut(s) 157
MseI TTAA 1 cut(s) 273
MslI CAYNNNNRTG 1 cut(s) 156
MspA1I CMGCKG 2 cut(s) 42, 66
MvnI CGCG 3 cut(s) 42, 66, 105
MwoI GCNNNNNNNGC 4 cut(s) 69, 96, 111, 546
NlaIII CATG 3 cut(s) 155, 159, 191
NlaIV GGNNCC 3 cut(s) 447, 492, 517
NmuCI GTSAC 1 cut(s) 172
NsiI ATGCAT 1 cut(s) 157
NspI RCATGY 1 cut(s) 159
PaeR7I CTCGAG 1 cut(s) 420
PfeI GAWTC 1 cut(s) 278
PflMI CCANNNNNTGG 1 cut(s) 458
PkrI GCNGC 4 cut(s) 65, 68, 71, 464
PleI GAGTC 1 cut(s) 229
PpsI GAGTC 1 cut(s) 229
PpuMI RGGWCCY 3 cut(s) 446, 491, 515
PshBI ATTAAT 1 cut(s) 273
Psp1406I AACGTT 1 cut(s) 143
Psp5II RGGWCCY 3 cut(s) 446, 491, 515
PspFI CCCAGC 1 cut(s) 355
PspN4I GGNNCC 3 cut(s) 447, 492, 517
PspPI GGNCC 5 cut(s) 113, 266, 446, 491, 515
PspPPI RGGWCCY 3 cut(s) 446, 491, 515
PstI CTGCAG 1 cut(s) 228
RseI CAYNNNNRTG 1 cut(s) 156
SacII CCGCGG 2 cut(s) 43, 67
SaqAI TTAA 1 cut(s) 273
SatI GCNGC 4 cut(s) 64, 67, 70, 463
Sau96I GGNCC 5 cut(s) 113, 266, 446, 491, 515
SchI GAGTC 1 cut(s) 229
SfaNI GCATC 1 cut(s) 157
SfcI CTRYAG 1 cut(s) 224
Sfr274I CTCGAG 1 cut(s) 420
Sfr303I CCGCGG 2 cut(s) 43, 67
SgrBI CCGCGG 2 cut(s) 43, 67
SinI GGWCC 3 cut(s) 446, 491, 515
SlaI CTCGAG 1 cut(s) 420
SmiMI CAYNNNNRTG 1 cut(s) 156
SmlI CTYRAG 1 cut(s) 420
SmoI CTYRAG 1 cut(s) 420
Sse9I AATT 2 cut(s) 258, 270
StyI CCWWGG 3 cut(s) 396, 452, 497
TaiI ACGT 2 cut(s) 146, 436
TaqI TCGA 2 cut(s) 252, 421
TaqII GACCGA 1 cut(s) 280
TasI AATT 2 cut(s) 258, 270
TauI GCSGC 4 cut(s) 66, 69, 72, 465
TfiI GAWTC 1 cut(s) 278
Tru1I TTAA 1 cut(s) 273
Tru9I TTAA 1 cut(s) 273
TseFI GTSAC 1 cut(s) 172
Tsp45I GTSAC 1 cut(s) 172
TspDTI ATGAA 4 cut(s) 140, 270, 291, 312
Van91I CCANNNNNTGG 1 cut(s) 458
VpaK11BI GGWCC 3 cut(s) 446, 491, 515
VspI ATTAAT 1 cut(s) 273
XagI CCTNNNNNAGG 1 cut(s) 12
XapI RAATTY 1 cut(s) 258
XceI RCATGY 1 cut(s) 159
XhoI CTCGAG 1 cut(s) 420
Zsp2I ATGCAT 1 cut(s) 157
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.