Rh5DG236400

Encoded by

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0017395
Physical Location & Seq
Reverse (-)
26975458 .. 26976335
878 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG236400.1

Sequence Viewer

Length: 660 bp
ATGGCGACGGCGCTTCTGTCTGAGATTACCGCGCTCATTCCGATCAAGCTCGACTTCTCTCGACCTTATCAGGTGTGGAGGTACGCGATGACGGCCGTTCTTGAGTCCAGGAACTTGATGGGGTATGTTGATTCGACAACTGATCTAAAGGGGCATTCGTCCGAGTCAGATGACGTGCGTATGTGGTGTTCTGATGGAGAGCTCAGTAATTGGGAGGAGGCTGAAGACAGGGTGGTAATGGCTGTGATAAACGCGACGCTTGCCCCTTCAGTTCTTGCTCGAGTCATCAGGTGCGTGTCGGCCCGAAGCCTTTGGCTTGAGCTTGAGGAAATCTTCACAAAGATGGAACCTTTTCATGTCAAGTGTCTTTACAACAAGCTGAGCAACCTGGTTTATAAAAGTGGGCAGACGGTGGAGGGTTTTGTTGGAGAAGTTGAGAGTATCTGGTTCGATATGGTTTCTAGAGATGCTGCAATTCCAGAGGCTGAAATGGTGGATCTTGTTCTGAGTCGCTTCCCATTTCCCATCTCTAATGGAGAAGAATTCCAGCGTCCTCGAAGCCTGAGACAATTATATGCCTTGCTTCTGCAAGAGACAATTGTCCAAGACGGAAGGACCAAAGCTGAGACCGAGGCTGTTCTGTTCAGCCATTATATCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Retrotran_gag_2 Retrotran_gag_3

Protein Analysis

219

Amino Acids

24.94

Weight (kDa)

4.8

Isoelectric Point (pI)

47.25

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 30 - 173 9.8e-13 gag-polypeptide of LTR copia-type
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: OG0017395)

Species Orthologous Gene IDs
malus_domestica MD11G1266200.v1.1
rosa_chinensis RchiOBHm_Chr5g0033261
rosa_multiflora Rmu_sc0006239.1_g000005
rosa_roxburghii Rroxscaffold_1G00046720 Rroxscaffold_1G00046730
rosa_rugosa Rorug05G0138200 Rorug05G0138200
rosa_samantha Rh5AG230000 Rh5BG230900 Rh5CG258900 Rh5DG236000 Rh5DG236400
rosa_wichuraiana Rw5G021030

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 396
AccII CGCG 3 cut(s) 32, 86, 254
AciI CCGC 1 cut(s) 30
AclWI GGATC 1 cut(s) 504
AcoI YGGCCR 1 cut(s) 93
AcsI RAATTY 1 cut(s) 542
AcuI CTGAAG 2 cut(s) 243, 252
AfaI GTAC 1 cut(s) 83
AjiI CACGTC 1 cut(s) 175
AjnI CCWGG 2 cut(s) 107, 387
AluBI AGCT 5 cut(s) 49, 202, 322, 379, 623
AluI AGCT 5 cut(s) 49, 202, 322, 379, 623
Alw21I GWGCWC 1 cut(s) 204
Alw26I GTCTC 3 cut(s) 559, 587, 620
AlwI GGATC 1 cut(s) 504
AlwNI CAGNNNCTG 1 cut(s) 485
Ama87I CYCGRG 1 cut(s) 279
AoxI GGCC 2 cut(s) 93, 300
ApeKI GCWGC 1 cut(s) 470
ApoI RAATTY 1 cut(s) 542
Asp700I GAANNNNTTC 1 cut(s) 351
AspLEI GCGC 2 cut(s) 13, 34
AspS9I GGNCC 2 cut(s) 301, 615
AvaI CYCGRG 1 cut(s) 279
AvaII GGWCC 1 cut(s) 615
BanII GRGCYC 1 cut(s) 204
BbsI GAAGAC 1 cut(s) 231
Bbv12I GWGCWC 1 cut(s) 204
BbvI GCAGC 1 cut(s) 457
BccI CCATC 4 cut(s) 112, 188, 337, 533
BceAI ACGGC 3 cut(s) 24, 80, 108
BciT130I CCWGG 2 cut(s) 109, 389
BcoDI GTCTC 3 cut(s) 559, 587, 620
BfaI CTAG 1 cut(s) 462
BfoI RGCGCY 1 cut(s) 14
BisI GCNGC 1 cut(s) 471
BlpI GCTNAGC 1 cut(s) 380
BlsI GCNGC 1 cut(s) 472
Bme1390I CCNGG 2 cut(s) 109, 389
Bme18I GGWCC 1 cut(s) 615
BmeT110I CYCGRG 1 cut(s) 279
BmgBI CACGTC 1 cut(s) 175
BmgT120I GGNCC 2 cut(s) 301, 615
BmiI GGNNCC 1 cut(s) 348
BmrFI CCNGG 2 cut(s) 109, 389
BmsI GCATC 1 cut(s) 457
BoxI GACNNNNGTC 1 cut(s) 599
BpiI GAAGAC 1 cut(s) 231
Bpu1102I GCTNAGC 1 cut(s) 380
BpuEI CTTGAG 3 cut(s) 122, 338, 344
BsaI GGTCTC 1 cut(s) 620
BsaJI CCNNGG 1 cut(s) 630
BseBI CCWGG 2 cut(s) 109, 389
BseDI CCNNGG 1 cut(s) 630
BseMII CTCAG 6 cut(s) 12, 217, 371, 497, 554, 615
BseRI GAGGAG 1 cut(s) 230
BseX3I CGGCCG 1 cut(s) 93
BseXI GCAGC 1 cut(s) 457
Bsh1236I CGCG 3 cut(s) 32, 86, 254
Bsh1285I CGRYCG 1 cut(s) 96
BshFI GGCC 2 cut(s) 95, 302
BsiEI CGRYCG 1 cut(s) 96
BsiHKAI GWGCWC 1 cut(s) 204
BsiHKCI CYCGRG 1 cut(s) 279
BsmAI GTCTC 3 cut(s) 559, 587, 620
BsmI GAATGC 1 cut(s) 154
BsnI GGCC 2 cut(s) 95, 302
Bso31I GGTCTC 1 cut(s) 620
BsoBI CYCGRG 1 cut(s) 279
Bsp1286I GDGCHC 1 cut(s) 204
Bsp143I GATC 3 cut(s) 42, 142, 496
Bsp1720I GCTNAGC 1 cut(s) 380
BspACI CCGC 1 cut(s) 30
BspANI GGCC 2 cut(s) 95, 302
BspCNI CTCAG 6 cut(s) 13, 216, 372, 498, 555, 616
BspFNI CGCG 3 cut(s) 32, 86, 254
BspLI GGNNCC 1 cut(s) 348
BspPI GGATC 1 cut(s) 504
BspTNI GGTCTC 1 cut(s) 620
BssECI CCNNGG 1 cut(s) 630
BssMI GATC 3 cut(s) 42, 142, 496
Bst2UI CCWGG 2 cut(s) 109, 389
Bst4CI ACNGT 1 cut(s) 412
BstC8I GCNNGC 1 cut(s) 261
BstDEI CTNAG 6 cut(s) 21, 203, 380, 506, 563, 624
BstFNI CGCG 3 cut(s) 32, 86, 254
BstH2I RGCGCY 1 cut(s) 14
BstHHI GCGC 2 cut(s) 13, 34
BstKTI GATC 3 cut(s) 45, 145, 499
BstMAI GTCTC 3 cut(s) 559, 587, 620
BstMBI GATC 3 cut(s) 42, 142, 496
BstMCI CGRYCG 1 cut(s) 96
BstMWI GCNNNNNNNGC 2 cut(s) 92, 260
BstNI CCWGG 2 cut(s) 109, 389
BstPAI GACNNNNGTC 1 cut(s) 599
BstSCI CCNGG 2 cut(s) 107, 387
BstUI CGCG 3 cut(s) 32, 86, 254
BstV1I GCAGC 1 cut(s) 457
BstV2I GAAGAC 1 cut(s) 231
BstX2I RGATCY 1 cut(s) 496
BstYI RGATCY 1 cut(s) 496
BstZI CGGCCG 1 cut(s) 93
BsuRI GGCC 2 cut(s) 95, 302
BtgZI GCGATG 1 cut(s) 101
BtrI CACGTC 1 cut(s) 175
Cac8I GCNNGC 1 cut(s) 261
CaiI CAGNNNCTG 1 cut(s) 485
CfoI GCGC 2 cut(s) 13, 34
Cfr13I GGNCC 2 cut(s) 301, 615
CseI GACGC 2 cut(s) 265, 539
CsiI ACCWGGT 1 cut(s) 387
Csp6I GTAC 1 cut(s) 82
CviAII CATG 1 cut(s) 356
CviQI GTAC 1 cut(s) 82
DdeI CTNAG 6 cut(s) 21, 203, 380, 506, 563, 624
DpnI GATC 3 cut(s) 44, 144, 498
DpnII GATC 3 cut(s) 42, 142, 496
EaeI YGGCCR 1 cut(s) 93
EagI CGGCCG 1 cut(s) 93
Ecl136II GAGCTC 1 cut(s) 202
EclXI CGGCCG 1 cut(s) 93
Eco24I GRGCYC 1 cut(s) 204
Eco31I GGTCTC 1 cut(s) 620
Eco47I GGWCC 1 cut(s) 615
Eco52I CGGCCG 1 cut(s) 93
Eco53kI GAGCTC 1 cut(s) 202
Eco57I CTGAAG 2 cut(s) 243, 252
Eco88I CYCGRG 1 cut(s) 279
EcoICRI GAGCTC 1 cut(s) 202
EcoRI GAATTC 1 cut(s) 542
EcoRII CCWGG 2 cut(s) 107, 387
EcoT38I GRGCYC 1 cut(s) 204
FaeI CATG 1 cut(s) 359
FaiI YATR 8 cut(s) 126, 182, 357, 396, 455, 574, 576, 654
FalI AAGNNNNNCTT 2 cut(s) 38, 70
FatI CATG 1 cut(s) 355
Fnu4HI GCNGC 1 cut(s) 471
FriOI GRGCYC 1 cut(s) 204
Fsp4HI GCNGC 1 cut(s) 471
FspBI CTAG 1 cut(s) 462
GlaI GCGC 2 cut(s) 12, 33
GluI GCNGC 1 cut(s) 471
HaeII RGCGCY 1 cut(s) 14
HaeIII GGCC 2 cut(s) 95, 302
HgaI GACGC 2 cut(s) 265, 539
HhaI GCGC 2 cut(s) 13, 34
Hin1II CATG 1 cut(s) 359
Hin6I GCGC 2 cut(s) 11, 32
HinP1I GCGC 2 cut(s) 11, 32
HinfI GANTC 5 cut(s) 104, 131, 164, 282, 508
Hpy188I TCNGA 7 cut(s) 22, 42, 163, 169, 193, 507, 659
Hpy188III TCNNGA 4 cut(s) 60, 101, 462, 479
Hpy99I CGWCG 2 cut(s) 10, 259
HpyAV CCTTC 2 cut(s) 276, 606
HpyCH4III ACNGT 1 cut(s) 412
HpyCH4IV ACGT 1 cut(s) 174
HpyCH4V TGCA 2 cut(s) 473, 589
HpyF10VI GCNNNNNNNGC 2 cut(s) 92, 260
HpyF3I CTNAG 6 cut(s) 21, 203, 380, 506, 563, 624
HpySE526I ACGT 1 cut(s) 174
Hsp92II CATG 1 cut(s) 359
HspAI GCGC 2 cut(s) 11, 32
Kzo9I GATC 3 cut(s) 42, 142, 496
Lsp1109I GCAGC 1 cut(s) 457
LweI GCATC 1 cut(s) 457
MabI ACCWGGT 1 cut(s) 387
MaeI CTAG 1 cut(s) 462
MaeII ACGT 1 cut(s) 174
MalI GATC 3 cut(s) 44, 144, 498
MboI GATC 3 cut(s) 42, 142, 496
MboII GAAGA 3 cut(s) 236, 325, 551
MfeI CAATTG 1 cut(s) 597
MflI RGATCY 1 cut(s) 496
MhlI GDGCHC 1 cut(s) 204
MluCI AATT 5 cut(s) 208, 474, 542, 569, 597
MlyI GAGTC 4 cut(s) 113, 173, 291, 517
MmeI TCCRAC 1 cut(s) 406
MnlI CCTC 8 cut(s) 72, 208, 211, 319, 409, 475, 564, 625
MroXI GAANNNNTTC 1 cut(s) 351
MslI CAYNNNNRTG 1 cut(s) 341
MspR9I CCNGG 2 cut(s) 109, 389
MunI CAATTG 1 cut(s) 597
Mva1269I GAATGC 1 cut(s) 154
MvaI CCWGG 2 cut(s) 109, 389
MvnI CGCG 3 cut(s) 32, 86, 254
MwoI GCNNNNNNNGC 2 cut(s) 92, 260
NdeII GATC 3 cut(s) 42, 142, 496
NlaIII CATG 1 cut(s) 359
NlaIV GGNNCC 1 cut(s) 348
PaeR7I CTCGAG 1 cut(s) 279
PctI GAATGC 1 cut(s) 154
PdmI GAANNNNTTC 1 cut(s) 351
PfeI GAWTC 1 cut(s) 131
PfoI TCCNGGA 1 cut(s) 107
PkrI GCNGC 1 cut(s) 472
PleI GAGTC 4 cut(s) 112, 172, 290, 516
PpsI GAGTC 4 cut(s) 112, 172, 290, 516
PshAI GACNNNNGTC 1 cut(s) 599
PsiI TTATAA 1 cut(s) 396
Psp124BI GAGCTC 1 cut(s) 204
Psp6I CCWGG 2 cut(s) 107, 387
PspGI CCWGG 2 cut(s) 107, 387
PspN4I GGNNCC 1 cut(s) 348
PspPI GGNCC 2 cut(s) 301, 615
PspXI VCTCGAGB 1 cut(s) 279
PsrI GAACNNNNNNTAC 2 cut(s) 172, 204
PstNI CAGNNNCTG 1 cut(s) 485
PsuI RGATCY 1 cut(s) 496
RsaI GTAC 1 cut(s) 83
RsaNI GTAC 1 cut(s) 82
RseI CAYNNNNRTG 1 cut(s) 341
SacI GAGCTC 1 cut(s) 204
SatI GCNGC 1 cut(s) 471
Sau3AI GATC 3 cut(s) 42, 142, 496
Sau96I GGNCC 2 cut(s) 301, 615
SchI GAGTC 4 cut(s) 113, 173, 291, 517
ScrFI CCNGG 2 cut(s) 109, 389
SduI GDGCHC 1 cut(s) 204
SexAI ACCWGGT 1 cut(s) 387
SfaNI GCATC 1 cut(s) 457
Sfr274I CTCGAG 1 cut(s) 279
SinI GGWCC 1 cut(s) 615
SlaI CTCGAG 1 cut(s) 279
SmiMI CAYNNNNRTG 1 cut(s) 341
SmlI CTYRAG 4 cut(s) 101, 279, 317, 323
SmoI CTYRAG 4 cut(s) 101, 279, 317, 323
Sse9I AATT 5 cut(s) 208, 474, 542, 569, 597
SsiI CCGC 1 cut(s) 30
SspMI CTAG 1 cut(s) 462
SstI GAGCTC 1 cut(s) 204
StyD4I CCNGG 2 cut(s) 107, 387
TaaI ACNGT 1 cut(s) 412
TaiI ACGT 1 cut(s) 177
TaqI TCGA 6 cut(s) 51, 61, 134, 280, 450, 556
TaqII GACCGA 1 cut(s) 644
TasI AATT 5 cut(s) 208, 474, 542, 569, 597
TfiI GAWTC 1 cut(s) 131
TseI GCWGC 1 cut(s) 470
TspDTI ATGAA 1 cut(s) 344
TspGWI ACGGA 1 cut(s) 624
VpaK11BI GGWCC 1 cut(s) 615
XapI RAATTY 1 cut(s) 542
XbaI TCTAGA 1 cut(s) 461
XcmI CCANNNNNNNNNTGG 1 cut(s) 115
XhoI CTCGAG 1 cut(s) 279
XmnI GAANNNNTTC 1 cut(s) 351
XspI CTAG 1 cut(s) 462
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.