Rh6AG284900

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6A
OG0000414
Physical Location & Seq
Forward (+)
48104404 .. 48109483
5080 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6AG284900.1

Sequence Viewer

Length: 780 bp
ATGTTGTCTCTGATCTTGGATATCTTACGGACACCGGAGCCGTACCGTGTGTCCCTAGCTGTACACCAGCTTGTCGGGGAGGCTGACAACTGGTGGGATACCGTCCGTAGCCTACGGACTGTTGCTGATTTAACTTGGGCAGAGTTCGAGCAACTCTTTCTGGAGAGGTTCTTTCCACCTGTTCTGAAGGCACAGAAGATCAGTGAGTTCTTTGCTCTGACCCAAGGAAACAAGACCACTCATGAGTATGTTGTGGCCTTCACACGACTACTTAAGTACGTGCCAGCAATCGCCAATGACGATCAGATGAAGAAACAGAGGTTCATGGCGGGACTCCGAGACTCGATTCGACGTGAGTTACGCTCGGACACTACCTTGAGCTACAGTGAGACAGTAGCCGCCGCCTACGCCATCGAGGCTGATGAAGCTGCATACCCAAGACGTGGGGATGGTCAGGGAAGCTCTCACCCACGGAAGAATCACTGGGTGCACCGGAGGAAGCCCCGAGGAGGAAACTTCCAAGGAAATGCCAGTTCCAGCAGTAGCAGTGGATCTTCAGGAAGACGGGGCCCTGCACCCTACACTTGTTTTGCTTGTGGCCAACCTGGACACACCAAGGTTCGCTGCCCGTTTGTTAACAACTCACAAGGAGCGTGTTCTGGCTCGGGATTCCAGAATCCGAGGCCAGCTCAGTCACTATCGACTCAGATATCACCAGCACCATATCGACCACCGAACCCTACTCAGCAGCAGTACCAACAACCTCAGCGCTGGCAGTGA
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
Retrotrans_gag zf-CCHC

Protein Analysis

259

Amino Acids

29.1

Weight (kDa)

9.75

Isoelectric Point (pI)

53.65

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 13 - 139 1.7e-10 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 19 - 114 4.7e-22 Retrotransposon gag 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000414)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g15941 FvH4_1g22181 FvH4_3g31442 FvH4_4g06832 FvH4_5g15722 FvH4_6g30661 FvH4_7g13761
rosa_chinensis RchiOBHm_Chr3g0478271 RchiOBHm_Chr4g0421141
rosa_laevigata RLG00000002038 RLG00000016047 RLG00000021902 RLG00000024696 RLG00000027779 RLG00000033727 RLG00000035621
rosa_multiflora Rmu_sc0000125.1_g000007 Rmu_sc0000221.1_g000019 Rmu_sc0000221.1_g000020 Rmu_sc0000338.1_g000006 Rmu_sc0000429.1_g000059 Rmu_sc0000429.1_g000060 Rmu_sc0000429.1_g000061 Rmu_sc0000543.1_g000046 Rmu_sc0000689.1_g000008 Rmu_sc0000689.1_g000009 Rmu_sc0001436.1_g000002 Rmu_sc0001634.1_g000004 Rmu_sc0001782.1_g000025 Rmu_sc0002206.1_g000012 Rmu_sc0002985.1_g000008 Rmu_sc0002985.1_g000009 Rmu_sc0003044.1_g000040 Rmu_sc0003044.1_g000041 Rmu_sc0003044.1_g000042 Rmu_sc0003275.1_g000010 Rmu_sc0003561.1_g000002 Rmu_sc0003850.1_g000001 Rmu_sc0003850.1_g000002 Rmu_sc0004092.1_g000039 Rmu_sc0004311.1_g000003 Rmu_sc0004443.1_g000016 Rmu_sc0004542.1_g000002 Rmu_sc0004873.1_g000001 Rmu_sc0005757.1_g000002 Rmu_sc0005964.1_g000004 Rmu_sc0006598.1_g000014 Rmu_sc0006598.1_g000015 Rmu_sc0006889.1_g000023 Rmu_sc0007059.1_g000007 Rmu_sc0007390.1_g000014 Rmu_sc0008085.1_g000015 Rmu_sc0009948.1_g000001 Rmu_sc0010235.1_g000005 Rmu_sc0010665.1_g000022 Rmu_sc0011183.1_g000001 Rmu_sc0021637.1_g000001 Rmu_ssc0000242.1_g000016 Rmu_ssc0000317.1_g000003 Rmu_ssc0000317.1_g000004 Rmu_ssc0000432.1_g000093 Rmu_ssc0000432.1_g000095
rosa_roxburghii Rroxscaffold_1G00024670 Rroxscaffold_1G00047120 Rroxscaffold_4G00283230 Rroxscaffold_5G00365300 Rroxscaffold_7G00192220
rosa_rugosa Rorug03G0325200 Rorug06G0093800 Rorug07G0209800
rosa_samantha Rh1AG084000 Rh1AG202300 Rh1AG294200 Rh1BG259000 Rh2AG357500 Rh2AG389500 Rh2CG376700 Rh2CG468700 Rh2DG441200 Rh2DG504700 Rh2DG505700 Rh3BG359700 Rh3DG120200 Rh4BG161300 Rh4CG087000 Rh5BG550100 Rh5CG573000 Rh6AG284900 Rh6AG426700 Rh7DG285400
rosa_wichuraiana Rw1G030090 Rw2G030600 Rw3G018220 Rw3G027930 Rw4G000900 Rw6G003680 Rw6G036920 Rw6G043190 Rw7G020880

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 443
AciI CCGC 3 cut(s) 329, 399, 402
AclWI GGATC 1 cut(s) 559
AcoI YGGCCR 1 cut(s) 598
AcuI CTGAAG 2 cut(s) 206, 540
AdeI CACNNNGTG 1 cut(s) 487
AfaI GTAC 4 cut(s) 44, 63, 278, 755
AfeI AGCGCT 1 cut(s) 770
AfiI CCNNNNNNNGG 2 cut(s) 443, 509
AflII CTTAAG 1 cut(s) 272
AjiI CACGTC 2 cut(s) 353, 443
AjnI CCWGG 1 cut(s) 604
AluBI AGCT 6 cut(s) 59, 70, 381, 428, 462, 689
AluI AGCT 6 cut(s) 59, 70, 381, 428, 462, 689
Alw21I GWGCWC 1 cut(s) 492
Alw26I GTCTC 3 cut(s) 12, 333, 383
Alw44I GTGCAC 1 cut(s) 488
AlwI GGATC 1 cut(s) 559
Ama87I CYCGRG 2 cut(s) 504, 664
Aor51HI AGCGCT 1 cut(s) 770
AoxI GGCC 4 cut(s) 255, 568, 598, 683
ApaI GGGCCC 1 cut(s) 572
ApaLI GTGCAC 1 cut(s) 488
ApeKI GCWGC 3 cut(s) 428, 624, 748
AspLEI GCGC 1 cut(s) 771
AspS9I GGNCC 2 cut(s) 568, 569
AsuHPI GGTGA 2 cut(s) 458, 705
AvaI CYCGRG 2 cut(s) 504, 664
BaeGI GKGCMC 2 cut(s) 492, 572
BalI TGGCCA 1 cut(s) 600
BanII GRGCYC 1 cut(s) 572
BbsI GAAGAC 1 cut(s) 568
Bbv12I GWGCWC 1 cut(s) 492
BbvCI CCTCAGC 1 cut(s) 765
BbvI GCAGC 3 cut(s) 415, 611, 760
BccI CCATC 2 cut(s) 419, 443
BceAI ACGGC 1 cut(s) 25
BciT130I CCWGG 1 cut(s) 606
BciVI GTATCC 1 cut(s) 91
BcoDI GTCTC 3 cut(s) 12, 333, 383
BfaI CTAG 1 cut(s) 56
BfmI CTRYAG 1 cut(s) 382
BfoI RGCGCY 1 cut(s) 772
BfrI CTTAAG 1 cut(s) 272
BfuI GTATCC 1 cut(s) 91
BglI GCCNNNNNGGC 1 cut(s) 416
BisI GCNGC 5 cut(s) 399, 402, 429, 625, 749
BlsI GCNGC 5 cut(s) 400, 403, 430, 626, 750
Bme1390I CCNGG 1 cut(s) 606
BmeT110I CYCGRG 2 cut(s) 504, 664
BmgBI CACGTC 2 cut(s) 353, 443
BmgT120I GGNCC 2 cut(s) 568, 569
BmiI GGNNCC 3 cut(s) 39, 569, 570
BmrFI CCNGG 1 cut(s) 606
BmrI ACTGGG 1 cut(s) 493
BmuI ACTGGG 1 cut(s) 493
BpiI GAAGAC 1 cut(s) 568
BplI GAGNNNNNCTC 4 cut(s) 347, 379, 673, 705
BpmI CTGGAG 1 cut(s) 182
Bpu10I CCTNAGC 1 cut(s) 765
BpuEI CTTGAG 1 cut(s) 397
BsaAI YACGTR 1 cut(s) 280
BsaJI CCNNGG 6 cut(s) 223, 470, 505, 520, 615, 680
BsaWI WCCGGW 2 cut(s) 34, 492
Bsc4I CCNNNNNNNGG 2 cut(s) 443, 509
Bse1I ACTGG 3 cut(s) 95, 488, 531
BseBI CCWGG 1 cut(s) 606
BseDI CCNNGG 6 cut(s) 223, 470, 505, 520, 615, 680
BseGI GGATG 1 cut(s) 454
BseLI CCNNNNNNNGG 2 cut(s) 443, 509
BseMII CTCAG 4 cut(s) 704, 719, 758, 779
BseNI ACTGG 3 cut(s) 95, 488, 531
BseRI GAGGAG 1 cut(s) 522
BseSI GKGCMC 2 cut(s) 492, 572
BseXI GCAGC 3 cut(s) 415, 611, 760
BsgI GTGCAG 1 cut(s) 558
BshFI GGCC 4 cut(s) 257, 570, 600, 685
BsiHKAI GWGCWC 1 cut(s) 492
BsiHKCI CYCGRG 2 cut(s) 504, 664
BsiSI CCGG 2 cut(s) 35, 493
BslFI GGGAC 2 cut(s) 37, 345
BslI CCNNNNNNNGG 2 cut(s) 443, 509
BsmAI GTCTC 3 cut(s) 12, 333, 383
BsmFI GGGAC 2 cut(s) 37, 345
BsnI GGCC 4 cut(s) 257, 570, 600, 685
BsoBI CYCGRG 2 cut(s) 504, 664
Bsp120I GGGCCC 1 cut(s) 568
Bsp1286I GDGCHC 2 cut(s) 492, 572
Bsp1407I TGTACA 1 cut(s) 61
Bsp143I GATC 4 cut(s) 12, 198, 301, 551
BspACI CCGC 3 cut(s) 329, 399, 402
BspANI GGCC 4 cut(s) 257, 570, 600, 685
BspCNI CTCAG 4 cut(s) 703, 718, 757, 778
BspHI TCATGA 1 cut(s) 241
BspLI GGNNCC 3 cut(s) 39, 569, 570
BspPI GGATC 1 cut(s) 559
BspTI CTTAAG 1 cut(s) 272
BsrGI TGTACA 1 cut(s) 61
BsrI ACTGG 3 cut(s) 95, 488, 531
BssECI CCNNGG 6 cut(s) 223, 470, 505, 520, 615, 680
BssMI GATC 4 cut(s) 12, 198, 301, 551
BssT1I CCWWGG 3 cut(s) 223, 520, 615
Bst2UI CCWGG 1 cut(s) 606
Bst4CI ACNGT 5 cut(s) 47, 103, 121, 386, 394
BstAFI CTTAAG 1 cut(s) 272
BstAUI TGTACA 1 cut(s) 61
BstBAI YACGTR 1 cut(s) 280
BstC8I GCNNGC 3 cut(s) 285, 687, 773
BstDEI CTNAG 4 cut(s) 690, 705, 744, 765
BstDSI CCRYGG 1 cut(s) 470
BstF5I GGATG 1 cut(s) 454
BstH2I RGCGCY 1 cut(s) 772
BstHHI GCGC 1 cut(s) 771
BstKTI GATC 4 cut(s) 15, 201, 304, 554
BstMAI GTCTC 3 cut(s) 12, 333, 383
BstMBI GATC 4 cut(s) 12, 198, 301, 551
BstMWI GCNNNNNNNGC 3 cut(s) 407, 416, 425
BstNI CCWGG 1 cut(s) 606
BstSCI CCNGG 1 cut(s) 604
BstSFI CTRYAG 1 cut(s) 382
BstSLI GKGCMC 2 cut(s) 492, 572
BstV1I GCAGC 3 cut(s) 415, 611, 760
BstV2I GAAGAC 1 cut(s) 568
BstX2I RGATCY 1 cut(s) 551
BstYI RGATCY 1 cut(s) 551
BsuI GTATCC 1 cut(s) 91
BsuRI GGCC 4 cut(s) 257, 570, 600, 685
BtgI CCRYGG 1 cut(s) 470
BtrI CACGTC 2 cut(s) 353, 443
BtsCI GGATG 1 cut(s) 454
BtsI GCAGTG 1 cut(s) 553
BtsIMutI CAGTG 4 cut(s) 208, 391, 481, 553
Cac8I GCNNGC 3 cut(s) 285, 687, 773
CciI TCATGA 1 cut(s) 241
CfoI GCGC 1 cut(s) 771
Cfr13I GGNCC 2 cut(s) 568, 569
Csp6I GTAC 4 cut(s) 43, 62, 277, 754
CviAII CATG 2 cut(s) 242, 325
CviQI GTAC 4 cut(s) 43, 62, 277, 754
DdeI CTNAG 4 cut(s) 690, 705, 744, 765
DpnI GATC 4 cut(s) 14, 200, 303, 553
DpnII GATC 4 cut(s) 12, 198, 301, 551
DraIII CACNNNGTG 1 cut(s) 487
EaeI YGGCCR 1 cut(s) 598
Eco130I CCWWGG 3 cut(s) 223, 520, 615
Eco24I GRGCYC 1 cut(s) 572
Eco32I GATATC 2 cut(s) 22, 711
Eco47III AGCGCT 1 cut(s) 770
Eco57I CTGAAG 2 cut(s) 206, 540
Eco88I CYCGRG 2 cut(s) 504, 664
EcoO109I RGGNCCY 2 cut(s) 568, 569
EcoRII CCWGG 1 cut(s) 604
EcoRV GATATC 2 cut(s) 22, 711
EcoT14I CCWWGG 3 cut(s) 223, 520, 615
EcoT38I GRGCYC 1 cut(s) 572
ErhI CCWWGG 3 cut(s) 223, 520, 615
FaeI CATG 2 cut(s) 245, 328
FaiI YATR 5 cut(s) 243, 249, 326, 433, 724
FaqI GGGAC 2 cut(s) 37, 345
FatI CATG 2 cut(s) 241, 324
FauI CCCGC 1 cut(s) 322
Fnu4HI GCNGC 5 cut(s) 399, 402, 429, 625, 749
FokI GGATG 1 cut(s) 461
FriOI GRGCYC 1 cut(s) 572
Fsp4HI GCNGC 5 cut(s) 399, 402, 429, 625, 749
FspBI CTAG 1 cut(s) 56
GlaI GCGC 1 cut(s) 770
GluI GCNGC 5 cut(s) 399, 402, 429, 625, 749
GsuI CTGGAG 1 cut(s) 182
HaeII RGCGCY 1 cut(s) 772
HaeIII GGCC 4 cut(s) 257, 570, 600, 685
HapII CCGG 2 cut(s) 35, 493
HhaI GCGC 1 cut(s) 771
Hin1II CATG 2 cut(s) 245, 328
Hin6I GCGC 1 cut(s) 769
HinP1I GCGC 1 cut(s) 769
HincII GTYRAC 1 cut(s) 637
HindII GTYRAC 1 cut(s) 637
HinfI GANTC 7 cut(s) 333, 341, 346, 478, 669, 676, 703
HpaI GTTAAC 1 cut(s) 637
HpaII CCGG 2 cut(s) 35, 493
HphI GGTGA 2 cut(s) 458, 705
Hpy166II GTNNAC 3 cut(s) 64, 490, 637
Hpy188I TCNGA 8 cut(s) 12, 186, 219, 306, 338, 367, 681, 708
Hpy188III TCNNGA 5 cut(s) 161, 242, 558, 666, 673
Hpy8I GTNNAC 3 cut(s) 64, 490, 637
Hpy99I CGWCG 1 cut(s) 354
HpyAV CCTTC 2 cut(s) 181, 268
HpyCH4III ACNGT 5 cut(s) 47, 103, 121, 386, 394
HpyCH4IV ACGT 3 cut(s) 279, 352, 442
HpyCH4V TGCA 3 cut(s) 431, 490, 575
HpyF10VI GCNNNNNNNGC 3 cut(s) 407, 416, 425
HpyF3I CTNAG 4 cut(s) 690, 705, 744, 765
HpySE526I ACGT 3 cut(s) 279, 352, 442
Hsp92II CATG 2 cut(s) 245, 328
HspAI GCGC 1 cut(s) 769
KspAI GTTAAC 1 cut(s) 637
Kzo9I GATC 4 cut(s) 12, 198, 301, 551
LmnI GCTCC 2 cut(s) 37, 650
Lsp1109I GCAGC 3 cut(s) 415, 611, 760
MaeI CTAG 1 cut(s) 56
MaeII ACGT 3 cut(s) 279, 352, 442
MaeIII GTNAC 2 cut(s) 357, 693
MalI GATC 4 cut(s) 14, 200, 303, 553
MboI GATC 4 cut(s) 12, 198, 301, 551
MboII GAAGA 5 cut(s) 208, 322, 487, 546, 573
MflI RGATCY 1 cut(s) 551
MhlI GDGCHC 2 cut(s) 492, 572
MlsI TGGCCA 1 cut(s) 600
MluNI TGGCCA 1 cut(s) 600
MlyI GAGTC 3 cut(s) 327, 335, 697
MnlI CCTC 9 cut(s) 73, 159, 312, 409, 489, 500, 503, 675, 774
Mox20I TGGCCA 1 cut(s) 600
MscI TGGCCA 1 cut(s) 600
MseI TTAA 3 cut(s) 131, 273, 636
MslI CAYNNNNRTG 1 cut(s) 246
Msp20I TGGCCA 1 cut(s) 600
MspCI CTTAAG 1 cut(s) 272
MspI CCGG 2 cut(s) 35, 493
MspR9I CCNGG 1 cut(s) 606
MvaI CCWGG 1 cut(s) 606
MwoI GCNNNNNNNGC 3 cut(s) 407, 416, 425
NdeII GATC 4 cut(s) 12, 198, 301, 551
NlaIII CATG 2 cut(s) 245, 328
NlaIV GGNNCC 3 cut(s) 39, 569, 570
NmuCI GTSAC 1 cut(s) 693
PagI TCATGA 1 cut(s) 241
PcsI WCGNNNNNNNCGW 1 cut(s) 297
PfeI GAWTC 4 cut(s) 346, 478, 669, 676
PflMI CCANNNNNTGG 1 cut(s) 443
PkrI GCNGC 5 cut(s) 400, 403, 430, 626, 750
PleI GAGTC 3 cut(s) 327, 335, 697
PpsI GAGTC 3 cut(s) 327, 335, 697
Ppu21I YACGTR 1 cut(s) 280
Psp6I CCWGG 1 cut(s) 604
PspGI CCWGG 1 cut(s) 604
PspN4I GGNNCC 3 cut(s) 39, 569, 570
PspOMI GGGCCC 1 cut(s) 568
PspPI GGNCC 2 cut(s) 568, 569
PsuI RGATCY 1 cut(s) 551
RsaI GTAC 4 cut(s) 44, 63, 278, 755
RsaNI GTAC 4 cut(s) 43, 62, 277, 754
RseI CAYNNNNRTG 1 cut(s) 246
SaqAI TTAA 3 cut(s) 131, 273, 636
SatI GCNGC 5 cut(s) 399, 402, 429, 625, 749
Sau3AI GATC 4 cut(s) 12, 198, 301, 551
Sau96I GGNCC 2 cut(s) 568, 569
SchI GAGTC 3 cut(s) 327, 335, 697
ScrFI CCNGG 1 cut(s) 606
SduI GDGCHC 2 cut(s) 492, 572
SfcI CTRYAG 1 cut(s) 382
SmiMI CAYNNNNRTG 1 cut(s) 246
SmlI CTYRAG 2 cut(s) 272, 376
SmoI CTYRAG 2 cut(s) 272, 376
SsiI CCGC 3 cut(s) 329, 399, 402
SspMI CTAG 1 cut(s) 56
StyD4I CCNGG 1 cut(s) 604
StyI CCWWGG 3 cut(s) 223, 520, 615
TaaI ACNGT 5 cut(s) 47, 103, 121, 386, 394
TaiI ACGT 3 cut(s) 282, 355, 445
TaqI TCGA 6 cut(s) 147, 344, 349, 414, 701, 727
TatI WGTACW 1 cut(s) 61
TauI GCSGC 2 cut(s) 401, 404
TfiI GAWTC 4 cut(s) 346, 478, 669, 676
Tru1I TTAA 3 cut(s) 131, 273, 636
Tru9I TTAA 3 cut(s) 131, 273, 636
TscAI CASTG 4 cut(s) 208, 391, 488, 553
TseFI GTSAC 1 cut(s) 693
TseI GCWGC 3 cut(s) 428, 624, 748
Tsp45I GTSAC 1 cut(s) 693
TspDTI ATGAA 3 cut(s) 313, 323, 438
TspGWI ACGGA 4 cut(s) 43, 95, 130, 487
TspRI CASTG 4 cut(s) 208, 391, 488, 553
Van91I CCANNNNNTGG 1 cut(s) 443
Vha464I CTTAAG 1 cut(s) 272
VneI GTGCAC 1 cut(s) 488
XspI CTAG 1 cut(s) 56
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.