Rw5G039910

T=7 icosahedral viral capsid

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000976
Physical Location & Seq
Reverse (-)
70523122 .. 70524066
945 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G039910.1

Sequence Viewer

Length: 945 bp
ATGCAAAATTTCAATCCAGGAAAGGAAAGGAATCTCCTTCCCTACCAGGATATAGAAATGGAAGAAGGAGAGAGCTCCAAAACTTCCATCATTCGAGAAAAAGGAAAGATTAAACTTCCTATACAGAAGGCCCCTACGGGTAGAAATGGAGAAAGAAATTCTCAAAGATTTGTCCCAGAGGAGAAGATACCCAGAGTACCAATTTCCAACTATGGAATTTGGCTAGATCTGGATAAAGCTCTAGACAAGAGAAAAACTCTTGACCAATGGGTAGACAGCCTGATGATGGCCTCTGCTCTTACCCTTGGAAAATTTGAAGCTCCTGATCTTCAGATGTACTTTGAAACTACTCTCATCGGGGTAGCAAAAAAGTATTACTTCTCTTTCAAAGAGACAGCCAGAGGAAAAGAGTGGCTGGAAGAAATCAAGACTTCAAAGTCTCCGTATGATTTTGTAGTACCCCTGTACGATCAGTTCTGTGGAGATCTCTCAAATTTGAGTGAAAAAGCCAAAGAAATGGCAAAATCTAATATCTATGCTCTCAAGATATGTGACATGAGATATTTCGAAGAATACCGGAATGAGTTTCAGGAATACTACTGTACAATTGGTGAACTAGAGAATACTGATCTAGTTAATCTGTTGCACAGAAAGCTCCCTGAACCATGGAGAACAGCTGTGAGAGAAAGCATAGCTGAGAAACCAATTGAAAGATTTTCAGTTGGAGGAATTGCCGACAGAATCAGGCAATTACTGAAAGAGCAATGCAAAGCCAATCTTAGAGCTAAGATGGCCAGGAAGCAACTCAGAGGAGTTGAAAATTTCTGCTATGGAATATTGGATATGCCCACAAACTGGGGATGTCATGAAGCAAAGTTCCACAGAAAGAAGAAAGAAAAATATTACTCTAAAAAATTCAAAAAGAGTAATCAGAAGAAGAATTGA
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
No domains found.

Protein Analysis

314

Amino Acids

36.9

Weight (kDa)

9.26

Isoelectric Point (pI)

34.69

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Caulimovir_coat_dom PF22909 171 - 277 1.5e-08 Caulimovirus coat protein, conserved domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000976)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g24112 FvH4_4g10003
rosa_chinensis RchiOBHm_Chr3g0487531 RchiOBHm_Chr5g0034781 RchiOBHm_Chr6g0277631
rosa_laevigata RLG00000021184
rosa_multiflora Rmu_sc0000144.1_g000006 Rmu_sc0000161.1_g000054 Rmu_sc0000383.1_g000008 Rmu_sc0000420.1_g000038 Rmu_sc0000429.1_g000090 Rmu_sc0000429.1_g000091 Rmu_sc0000453.1_g000018 Rmu_sc0000458.1_g000020 Rmu_sc0000483.1_g000003 Rmu_sc0000531.1_g000007 Rmu_sc0000595.1_g000055 Rmu_sc0000768.1_g000022 Rmu_sc0000855.1_g000012 Rmu_sc0000974.1_g000020 Rmu_sc0001018.1_g000020 Rmu_sc0001265.1_g000003 Rmu_sc0001407.1_g000004 Rmu_sc0001694.1_g000007 Rmu_sc0001785.1_g000004 Rmu_sc0001847.1_g000011 Rmu_sc0002148.1_g000003 Rmu_sc0002316.1_g000089 Rmu_sc0002501.1_g000027 Rmu_sc0002521.1_g000031 Rmu_sc0002845.1_g000028 Rmu_sc0003315.1_g000022 Rmu_sc0003371.1_g000015 Rmu_sc0003386.1_g000006 Rmu_sc0003415.1_g000012 Rmu_sc0003467.1_g000010 Rmu_sc0003583.1_g000002 Rmu_sc0003832.1_g000032 Rmu_sc0004094.1_g000040 Rmu_sc0004286.1_g000014 Rmu_sc0004344.1_g000014 Rmu_sc0004798.1_g000005 Rmu_sc0004846.1_g000001 Rmu_sc0005362.1_g000001 Rmu_sc0005481.1_g000002 Rmu_sc0006498.1_g000005 Rmu_sc0006968.1_g000011 Rmu_sc0007369.1_g000004 Rmu_sc0007727.1_g000016 Rmu_sc0008681.1_g000002 Rmu_sc0010278.1_g000009 Rmu_sc0011015.1_g000002 Rmu_sc0011611.1_g000004 Rmu_sc0012216.1_g000005 Rmu_sc0013333.1_g000001 Rmu_sc0016916.1_g000001 Rmu_sc0024220.1_g000001 Rmu_sc0036248.1_g000001 Rmu_sc0037776.1_g000001 Rmu_ssc0000052.1_g000014
rosa_samantha Rh4CG090000
rosa_wichuraiana Rw2G035730 Rw5G039910

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 436
AccB7I CCANNNNNTGG 1 cut(s) 855
AccI GTMKAC 1 cut(s) 273
AcoI YGGCCR 1 cut(s) 792
AcsI RAATTY 7 cut(s) 7, 157, 216, 311, 493, 820, 914
AcuI CTGAAG 1 cut(s) 314
AfaI GTAC 5 cut(s) 198, 338, 459, 467, 604
AfiI CCNNNNNNNGG 2 cut(s) 286, 855
AgsI TTSAA 8 cut(s) 13, 317, 344, 388, 435, 710, 818, 919
AjnI CCWGG 3 cut(s) 16, 45, 794
AluBI AGCT 7 cut(s) 75, 239, 320, 655, 677, 695, 785
AluI AGCT 7 cut(s) 75, 239, 320, 655, 677, 695, 785
Alw21I GWGCWC 1 cut(s) 77
Alw26I GTCTC 2 cut(s) 386, 444
AoxI GGCC 3 cut(s) 129, 288, 792
ApoI RAATTY 7 cut(s) 7, 157, 216, 311, 493, 820, 914
AspS9I GGNCC 1 cut(s) 130
AsuHPI GGTGA 1 cut(s) 623
AsuII TTCGAA 1 cut(s) 567
BalI TGGCCA 1 cut(s) 794
BanII GRGCYC 1 cut(s) 77
Bbv12I GWGCWC 1 cut(s) 77
BccI CCATC 3 cut(s) 95, 280, 784
BciT130I CCWGG 3 cut(s) 18, 47, 796
BcoDI GTCTC 2 cut(s) 386, 444
BfaI CTAG 4 cut(s) 224, 242, 617, 632
BglII AGATCT 2 cut(s) 226, 484
Bme1390I CCNGG 3 cut(s) 18, 47, 796
BmgT120I GGNCC 1 cut(s) 130
BmiI GGNNCC 1 cut(s) 132
BmrFI CCNGG 3 cut(s) 18, 47, 796
BmrI ACTGGG 1 cut(s) 865
BmuI ACTGGG 1 cut(s) 865
BplI GAGNNNNNCTC 2 cut(s) 241, 273
Bpu14I TTCGAA 1 cut(s) 567
BpuEI CTTGAG 1 cut(s) 527
BsaJI CCNNGG 2 cut(s) 304, 665
BsaWI WCCGGW 1 cut(s) 576
Bsc4I CCNNNNNNNGG 2 cut(s) 286, 855
Bse1I ACTGG 1 cut(s) 860
Bse3DI GCAATG 1 cut(s) 770
BseBI CCWGG 3 cut(s) 18, 47, 796
BseDI CCNNGG 2 cut(s) 304, 665
BseGI GGATG 1 cut(s) 866
BseLI CCNNNNNNNGG 2 cut(s) 286, 855
BseMI GCAATG 1 cut(s) 770
BseMII CTCAG 2 cut(s) 687, 820
BseNI ACTGG 1 cut(s) 860
BseRI GAGGAG 2 cut(s) 194, 825
BshFI GGCC 3 cut(s) 131, 290, 794
BsiHKAI GWGCWC 1 cut(s) 77
BsiSI CCGG 1 cut(s) 577
BslFI GGGAC 1 cut(s) 158
BslI CCNNNNNNNGG 2 cut(s) 286, 855
BsmAI GTCTC 2 cut(s) 386, 444
BsmFI GGGAC 1 cut(s) 158
BsnI GGCC 3 cut(s) 131, 290, 794
Bsp119I TTCGAA 1 cut(s) 567
Bsp1286I GDGCHC 1 cut(s) 77
Bsp1407I TGTACA 1 cut(s) 602
Bsp143I GATC 5 cut(s) 226, 325, 469, 484, 628
Bsp19I CCATGG 1 cut(s) 665
BspANI GGCC 3 cut(s) 131, 290, 794
BspCNI CTCAG 2 cut(s) 688, 819
BspHI TCATGA 1 cut(s) 865
BspLI GGNNCC 1 cut(s) 132
BspT104I TTCGAA 1 cut(s) 567
BsrDI GCAATG 1 cut(s) 770
BsrGI TGTACA 1 cut(s) 602
BsrI ACTGG 1 cut(s) 860
BssECI CCNNGG 2 cut(s) 304, 665
BssMI GATC 5 cut(s) 226, 325, 469, 484, 628
BssT1I CCWWGG 2 cut(s) 304, 665
Bst2UI CCWGG 3 cut(s) 18, 47, 796
Bst4CI ACNGT 1 cut(s) 602
BstAUI TGTACA 1 cut(s) 602
BstBI TTCGAA 1 cut(s) 567
BstDEI CTNAG 4 cut(s) 696, 779, 786, 806
BstDSI CCRYGG 1 cut(s) 665
BstF5I GGATG 1 cut(s) 866
BstKTI GATC 5 cut(s) 229, 328, 472, 487, 631
BstMAI GTCTC 2 cut(s) 386, 444
BstMBI GATC 5 cut(s) 226, 325, 469, 484, 628
BstMWI GCNNNNNNNGC 2 cut(s) 652, 791
BstNI CCWGG 3 cut(s) 18, 47, 796
BstSCI CCNGG 3 cut(s) 16, 45, 794
BstX2I RGATCY 2 cut(s) 226, 484
BstXI CCANNNNNNTGG 1 cut(s) 517
BstYI RGATCY 2 cut(s) 226, 484
BsuRI GGCC 3 cut(s) 131, 290, 794
BtgI CCRYGG 1 cut(s) 665
BtsCI GGATG 1 cut(s) 866
CciI TCATGA 1 cut(s) 865
Cfr13I GGNCC 1 cut(s) 130
Csp6I GTAC 5 cut(s) 197, 337, 458, 466, 603
CviAII CATG 3 cut(s) 556, 666, 866
CviQI GTAC 5 cut(s) 197, 337, 458, 466, 603
DdeI CTNAG 4 cut(s) 696, 779, 786, 806
DpnI GATC 5 cut(s) 228, 327, 471, 486, 630
DpnII GATC 5 cut(s) 226, 325, 469, 484, 628
DrdI GACNNNNNNGTC 1 cut(s) 436
DseDI GACNNNNNNGTC 1 cut(s) 436
EaeI YGGCCR 1 cut(s) 792
Ecl136II GAGCTC 1 cut(s) 75
Eco130I CCWWGG 2 cut(s) 304, 665
Eco24I GRGCYC 1 cut(s) 77
Eco53kI GAGCTC 1 cut(s) 75
Eco57I CTGAAG 1 cut(s) 314
EcoICRI GAGCTC 1 cut(s) 75
EcoO109I RGGNCCY 1 cut(s) 130
EcoRII CCWGG 3 cut(s) 16, 45, 794
EcoT14I CCWWGG 2 cut(s) 304, 665
EcoT38I GRGCYC 1 cut(s) 77
ErhI CCWWGG 2 cut(s) 304, 665
FaeI CATG 3 cut(s) 559, 669, 869
FalI AAGNNNNNCTT 4 cut(s) 362, 394, 762, 794
FaqI GGGAC 1 cut(s) 158
FatI CATG 3 cut(s) 555, 665, 865
FblI GTMKAC 1 cut(s) 273
FokI GGATG 1 cut(s) 873
FriOI GRGCYC 1 cut(s) 77
FspBI CTAG 4 cut(s) 224, 242, 617, 632
HaeIII GGCC 3 cut(s) 131, 290, 794
HapII CCGG 1 cut(s) 577
Hin1II CATG 3 cut(s) 559, 669, 869
HinfI GANTC 2 cut(s) 31, 741
HpaII CCGG 1 cut(s) 577
HphI GGTGA 1 cut(s) 623
Hpy166II GTNNAC 2 cut(s) 274, 614
Hpy188I TCNGA 3 cut(s) 333, 809, 933
Hpy188III TCNNGA 9 cut(s) 95, 230, 242, 260, 323, 427, 544, 590, 866
Hpy8I GTNNAC 2 cut(s) 274, 614
HpyAV CCTTC 3 cut(s) 47, 59, 121
HpyCH4III ACNGT 1 cut(s) 602
HpyCH4V TGCA 3 cut(s) 4, 646, 768
HpyF10VI GCNNNNNNNGC 2 cut(s) 652, 791
HpyF3I CTNAG 4 cut(s) 696, 779, 786, 806
Hsp92II CATG 3 cut(s) 559, 669, 869
Kzo9I GATC 5 cut(s) 226, 325, 469, 484, 628
LmnI GCTCC 3 cut(s) 80, 325, 660
MaeI CTAG 4 cut(s) 224, 242, 617, 632
MaeIII GTNAC 1 cut(s) 551
MalI GATC 5 cut(s) 228, 327, 471, 486, 630
MboI GATC 5 cut(s) 226, 325, 469, 484, 628
MboII GAAGA 6 cut(s) 74, 196, 320, 431, 581, 901
MfeI CAATTG 2 cut(s) 606, 705
MflI RGATCY 2 cut(s) 226, 484
MhlI GDGCHC 1 cut(s) 77
MlsI TGGCCA 1 cut(s) 794
MluNI TGGCCA 1 cut(s) 794
MmeI TCCRAC 2 cut(s) 231, 703
MnlI CCTC 5 cut(s) 172, 301, 395, 719, 803
Mox20I TGGCCA 1 cut(s) 794
MscI TGGCCA 1 cut(s) 794
MseI TTAA 2 cut(s) 111, 636
Msp20I TGGCCA 1 cut(s) 794
MspA1I CMGCKG 1 cut(s) 677
MspI CCGG 1 cut(s) 577
MspR9I CCNGG 3 cut(s) 18, 47, 796
MunI CAATTG 2 cut(s) 606, 705
MvaI CCWGG 3 cut(s) 18, 47, 796
MwoI GCNNNNNNNGC 2 cut(s) 652, 791
NcoI CCATGG 1 cut(s) 665
NdeII GATC 5 cut(s) 226, 325, 469, 484, 628
NlaIII CATG 3 cut(s) 559, 669, 869
NlaIV GGNNCC 1 cut(s) 132
NmuCI GTSAC 1 cut(s) 551
NspV TTCGAA 1 cut(s) 567
PagI TCATGA 1 cut(s) 865
PfeI GAWTC 2 cut(s) 31, 741
PflMI CCANNNNNTGG 1 cut(s) 855
PfoI TCCNGGA 1 cut(s) 16
Psp124BI GAGCTC 1 cut(s) 77
Psp6I CCWGG 3 cut(s) 16, 45, 794
PspGI CCWGG 3 cut(s) 16, 45, 794
PspN4I GGNNCC 1 cut(s) 132
PspPI GGNCC 1 cut(s) 130
PsrI GAACNNNNNNTAC 2 cut(s) 458, 490
PsuI RGATCY 2 cut(s) 226, 484
PvuII CAGCTG 1 cut(s) 677
RsaI GTAC 5 cut(s) 198, 338, 459, 467, 604
RsaNI GTAC 5 cut(s) 197, 337, 458, 466, 603
SacI GAGCTC 1 cut(s) 77
SaqAI TTAA 2 cut(s) 111, 636
Sau3AI GATC 5 cut(s) 226, 325, 469, 484, 628
Sau96I GGNCC 1 cut(s) 130
ScrFI CCNGG 3 cut(s) 18, 47, 796
SduI GDGCHC 1 cut(s) 77
SetI ASST 7 cut(s) 77, 241, 322, 657, 679, 697, 787
SfuI TTCGAA 1 cut(s) 567
SmlI CTYRAG 1 cut(s) 542
SmoI CTYRAG 1 cut(s) 542
SspI AATATT 2 cut(s) 837, 902
SspMI CTAG 4 cut(s) 224, 242, 617, 632
SstI GAGCTC 1 cut(s) 77
StyD4I CCNGG 3 cut(s) 16, 45, 794
StyI CCWWGG 2 cut(s) 304, 665
TaaI ACNGT 1 cut(s) 602
TaqI TCGA 2 cut(s) 94, 567
TatI WGTACW 2 cut(s) 336, 602
TfiI GAWTC 2 cut(s) 31, 741
Tru1I TTAA 2 cut(s) 111, 636
Tru9I TTAA 2 cut(s) 111, 636
TseFI GTSAC 1 cut(s) 551
Tsp45I GTSAC 1 cut(s) 551
TspDTI ATGAA 1 cut(s) 882
TspGWI ACGGA 1 cut(s) 432
Van91I CCANNNNNTGG 1 cut(s) 855
XapI RAATTY 7 cut(s) 7, 157, 216, 311, 493, 820, 914
XbaI TCTAGA 1 cut(s) 241
XmiI GTMKAC 1 cut(s) 273
XspI CTAG 4 cut(s) 224, 242, 617, 632
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.