Rroxscaffold_2G00094160

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0000370
Physical Location & Seq
Forward (+)
15462801 .. 15475811
13011 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00094160.1

Sequence Viewer

Length: 822 bp
ATGGTGTCGAAGGGAGTAATTTTCTTCTTGAGGTTGGCTGTGAGGAGGTACTTTGACTCCTGGGTCGGTGTGGATGAAGTGTCGTTGATATGGCGTTATTTTCGGGGACTACATGTTTTACTCTCGGTGTTTTCTTATTATCAATATGGTAGTGACTTGCTCTTGCATGTGGCTTGGTTGGTTTGGGACACAGTGTTGATGAAGGGGAAGTGGCTTCTCCTCAAATCTCGCTTCCTTGCTCTAGCTCGTCGGCGACAACATGGATGTGTTGCCAATACGGCGGAGAATCGTGCCTCTTTTCGACAACTTGGATCTGGAAATTTTACACGTTCAAAACCAGGAATTATTGTGTTTTGCTCCTTAGGTGATGGACTCACGAGGAGGCGAGCTAGGGGTCGAGGTAGACCCGGAGGCGGGGGTAGAGCCCGAGGTAGGGGCGGGGATTCCTCCTCTGTTGAGGAGGTGTTCGAGAATGATGTCGAGGCATCGAACGTTGAGTACTGTTCCACTGTTGTGGAGGTTGCGAATCTTGTGGATCCCACTCGTTTGTCGAAATTGGCAAAGGAGATCTCGAGGCCGGGAGGAGTTCCATTCCGAGGAGGTACGGATCACATGTTAGCGGATCAATGGATCGAGAACATGAAGACCTACTTCGAGATGGTCGTCTGCGACGACATTGAGAAGAGAAGATTGCTGCGTTTATGCTCCCGAGGCGATGCACGAGTATGGTGGAGCGGCACGCAGAGAGTTATGGATGTGTCCACCGTGACTTGGAATGGTTTTGTGGAACTGTTCGGAAGAAGTACTTTCCGCCTTCGGTGA
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
RVP_2 Retrotrans_gag zf-CCHC

Protein Analysis

273

Amino Acids

31.09

Weight (kDa)

10.1

Isoelectric Point (pI)

37.01

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this 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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 62
AccBSI CCGCTC 1 cut(s) 735
AccI GTMKAC 1 cut(s) 403
AciI CCGC 6 cut(s) 281, 414, 438, 620, 735, 811
AclI AACGTT 1 cut(s) 492
AclWI GGATC 6 cut(s) 319, 530, 543, 615, 630, 638
AcsI RAATTY 1 cut(s) 319
AfaI GTAC 4 cut(s) 50, 500, 604, 805
AfiI CCNNNNNNNGG 6 cut(s) 413, 414, 432, 433, 596, 771
AflIII ACRYGT 3 cut(s) 112, 326, 612
AgsI TTSAA 1 cut(s) 333
AjnI CCWGG 2 cut(s) 59, 337
AleI CACNNNNGTG 1 cut(s) 512
AluBI AGCT 2 cut(s) 245, 389
AluI AGCT 2 cut(s) 245, 389
AlwI GGATC 6 cut(s) 319, 530, 543, 615, 630, 638
Ama87I CYCGRG 3 cut(s) 426, 571, 708
AoxI GGCC 1 cut(s) 575
ApeKI GCWGC 1 cut(s) 694
ApoI RAATTY 1 cut(s) 319
AsuC2I CCSGG 2 cut(s) 408, 579
AsuHPI GGTGA 1 cut(s) 377
AvaI CYCGRG 3 cut(s) 426, 571, 708
AxyI CCTNAGG 1 cut(s) 361
BamHI GGATCC 1 cut(s) 535
BanII GRGCYC 1 cut(s) 427
BauI CACGAG 2 cut(s) 376, 720
BbsI GAAGAC 1 cut(s) 650
BbvI GCAGC 1 cut(s) 681
BccI CCATC 2 cut(s) 362, 652
BceAI ACGGC 1 cut(s) 294
BciT130I CCWGG 2 cut(s) 61, 339
BcnI CCSGG 2 cut(s) 408, 579
BfaI CTAG 2 cut(s) 242, 390
BglI GCCNNNNNGGC 1 cut(s) 278
BglII AGATCT 1 cut(s) 567
BisI GCNGC 2 cut(s) 695, 736
BlsI GCNGC 2 cut(s) 696, 737
BmcAI AGTACT 2 cut(s) 500, 805
Bme1390I CCNGG 4 cut(s) 61, 339, 408, 579
BmeT110I CYCGRG 3 cut(s) 426, 571, 708
BmiI GGNNCC 1 cut(s) 537
BmrFI CCNGG 4 cut(s) 61, 339, 408, 579
BmsI GCATC 2 cut(s) 494, 706
BpiI GAAGAC 1 cut(s) 650
BpuEI CTTGAG 1 cut(s) 49
BpuMI CCSGG 2 cut(s) 408, 579
BsaJI CCNNGG 4 cut(s) 60, 427, 595, 709
BsaXI ACNNNNNCTCC 2 cut(s) 41, 71
Bsc4I CCNNNNNNNGG 6 cut(s) 413, 414, 432, 433, 596, 771
Bse21I CCTNAGG 1 cut(s) 361
BseBI CCWGG 2 cut(s) 61, 339
BseDI CCNNGG 4 cut(s) 60, 427, 595, 709
BseGI GGATG 3 cut(s) 79, 269, 760
BseLI CCNNNNNNNGG 6 cut(s) 413, 414, 432, 433, 596, 771
BseRI GAGGAG 7 cut(s) 58, 209, 394, 439, 473, 597, 612
BseXI GCAGC 1 cut(s) 681
BshFI GGCC 1 cut(s) 577
BsiHKCI CYCGRG 3 cut(s) 426, 571, 708
BsiSI CCGG 2 cut(s) 408, 578
BslFI GGGAC 2 cut(s) 120, 200
BslI CCNNNNNNNGG 6 cut(s) 413, 414, 432, 433, 596, 771
BsmFI GGGAC 2 cut(s) 120, 200
BsnI GGCC 1 cut(s) 577
BsoBI CYCGRG 3 cut(s) 426, 571, 708
Bsp1286I GDGCHC 1 cut(s) 427
Bsp143I GATC 6 cut(s) 311, 535, 567, 607, 622, 630
BspACI CCGC 6 cut(s) 281, 414, 438, 620, 735, 811
BspANI GGCC 1 cut(s) 577
BspLI GGNNCC 1 cut(s) 537
BspPI GGATC 6 cut(s) 319, 530, 543, 615, 630, 638
BsrBI CCGCTC 1 cut(s) 735
BssECI CCNNGG 4 cut(s) 60, 427, 595, 709
BssMI GATC 6 cut(s) 311, 535, 567, 607, 622, 630
BssSI CACGAG 2 cut(s) 376, 720
Bst2BI CACGAG 2 cut(s) 376, 720
Bst2UI CCWGG 2 cut(s) 61, 339
Bst4CI ACNGT 5 cut(s) 193, 503, 511, 766, 792
Bst6I CTCTTC 1 cut(s) 677
BstC8I GCNNGC 2 cut(s) 387, 740
BstDEI CTNAG 1 cut(s) 361
BstF5I GGATG 3 cut(s) 79, 269, 760
BstKTI GATC 6 cut(s) 314, 538, 570, 610, 625, 633
BstMBI GATC 6 cut(s) 311, 535, 567, 607, 622, 630
BstMWI GCNNNNNNNGC 2 cut(s) 278, 711
BstNI CCWGG 2 cut(s) 61, 339
BstNSI RCATGY 3 cut(s) 116, 170, 616
BstSCI CCNGG 4 cut(s) 59, 337, 406, 577
BstV1I GCAGC 1 cut(s) 681
BstV2I GAAGAC 1 cut(s) 650
BstX2I RGATCY 3 cut(s) 311, 535, 567
BstXI CCANNNNNNTGG 1 cut(s) 514
BstYI RGATCY 3 cut(s) 311, 535, 567
Bsu36I CCTNAGG 1 cut(s) 361
BsuRI GGCC 1 cut(s) 577
BtgZI GCGATG 1 cut(s) 729
BtsCI GGATG 3 cut(s) 79, 269, 760
BtsIMutI CAGTG 2 cut(s) 198, 507
Cac8I GCNNGC 2 cut(s) 387, 740
Csp6I GTAC 4 cut(s) 49, 499, 603, 804
CviAII CATG 5 cut(s) 113, 167, 260, 613, 640
CviJI RGCY 7 cut(s) 38, 173, 214, 245, 389, 425, 577
CviKI_1 RGCY 7 cut(s) 38, 173, 214, 245, 389, 425, 577
CviQI GTAC 4 cut(s) 49, 499, 603, 804
DdeI CTNAG 1 cut(s) 361
DpnI GATC 6 cut(s) 313, 537, 569, 609, 624, 632
DpnII GATC 6 cut(s) 311, 535, 567, 607, 622, 630
DrdI GACNNNNNNGTC 1 cut(s) 62
DseDI GACNNNNNNGTC 1 cut(s) 62
Eam1104I CTCTTC 1 cut(s) 677
EarI CTCTTC 1 cut(s) 677
EciI GGCGGA 2 cut(s) 296, 800
Eco24I GRGCYC 1 cut(s) 427
Eco81I CCTNAGG 1 cut(s) 361
Eco88I CYCGRG 3 cut(s) 426, 571, 708
EcoRII CCWGG 2 cut(s) 59, 337
EcoT38I GRGCYC 1 cut(s) 427
FaeI CATG 5 cut(s) 116, 170, 263, 616, 643
FalI AAGNNNNNCTT 4 cut(s) 635, 667, 790, 822
FaqI GGGAC 2 cut(s) 120, 200
FatI CATG 5 cut(s) 112, 166, 259, 612, 639
FauI CCCGC 2 cut(s) 407, 431
FblI GTMKAC 1 cut(s) 403
Fnu4HI GCNGC 2 cut(s) 695, 736
FokI GGATG 3 cut(s) 86, 276, 767
FriOI GRGCYC 1 cut(s) 427
Fsp4HI GCNGC 2 cut(s) 695, 736
FspBI CTAG 2 cut(s) 242, 390
GluI GCNGC 2 cut(s) 695, 736
HaeIII GGCC 1 cut(s) 577
HapII CCGG 2 cut(s) 408, 578
Hin1II CATG 5 cut(s) 116, 170, 263, 616, 643
HinfI GANTC 5 cut(s) 56, 286, 372, 443, 526
HpaII CCGG 2 cut(s) 408, 578
HphI GGTGA 1 cut(s) 377
Hpy166II GTNNAC 2 cut(s) 404, 762
Hpy188I TCNGA 2 cut(s) 596, 797
Hpy188III TCNNGA 8 cut(s) 28, 315, 376, 469, 571, 634, 655, 708
Hpy8I GTNNAC 2 cut(s) 404, 762
Hpy99I CGWCG 2 cut(s) 252, 674
HpyAV CCTTC 2 cut(s) 4, 196
HpyCH4III ACNGT 5 cut(s) 193, 503, 511, 766, 792
HpyCH4IV ACGT 2 cut(s) 328, 492
HpyCH4V TGCA 2 cut(s) 166, 719
HpyF10VI GCNNNNNNNGC 2 cut(s) 278, 711
HpyF3I CTNAG 1 cut(s) 361
HpySE526I ACGT 2 cut(s) 328, 492
Hsp92II CATG 5 cut(s) 116, 170, 263, 616, 643
Kzo9I GATC 6 cut(s) 311, 535, 567, 607, 622, 630
LmnI GCTCC 3 cut(s) 362, 710, 732
LpnPI CCDG 7 cut(s) 46, 73, 300, 324, 351, 421, 591
Lsp1109I GCAGC 1 cut(s) 681
LweI GCATC 2 cut(s) 494, 706
MaeI CTAG 2 cut(s) 242, 390
MaeII ACGT 2 cut(s) 328, 492
MaeIII GTNAC 2 cut(s) 152, 766
MalI GATC 6 cut(s) 313, 537, 569, 609, 624, 632
MbiI CCGCTC 1 cut(s) 735
MboI GATC 6 cut(s) 311, 535, 567, 607, 622, 630
MboII GAAGA 5 cut(s) 16, 655, 694, 699, 810
MflI RGATCY 3 cut(s) 311, 535, 567
MhlI GDGCHC 1 cut(s) 427
MluCI AATT 4 cut(s) 18, 319, 342, 554
MlyI GAGTC 2 cut(s) 50, 366
MslI CAYNNNNRTG 3 cut(s) 264, 512, 724
MspI CCGG 2 cut(s) 408, 578
MspR9I CCNGG 4 cut(s) 61, 339, 408, 579
MvaI CCWGG 2 cut(s) 61, 339
MwoI GCNNNNNNNGC 2 cut(s) 278, 711
NciI CCSGG 2 cut(s) 408, 579
NdeII GATC 6 cut(s) 311, 535, 567, 607, 622, 630
NlaIII CATG 5 cut(s) 116, 170, 263, 616, 643
NlaIV GGNNCC 1 cut(s) 537
NmuCI GTSAC 2 cut(s) 152, 766
NspI RCATGY 3 cut(s) 116, 170, 616
OliI CACNNNNGTG 1 cut(s) 512
PaeR7I CTCGAG 1 cut(s) 571
PciI ACATGT 2 cut(s) 112, 612
PcsI WCGNNNNNNNCGW 2 cut(s) 660, 669
PfeI GAWTC 3 cut(s) 286, 443, 526
PkrI GCNGC 2 cut(s) 696, 737
PleI GAGTC 2 cut(s) 50, 366
PpsI GAGTC 2 cut(s) 50, 366
PscI ACATGT 2 cut(s) 112, 612
Psp1406I AACGTT 1 cut(s) 492
Psp6I CCWGG 2 cut(s) 59, 337
PspGI CCWGG 2 cut(s) 59, 337
PspN4I GGNNCC 1 cut(s) 537
PsrI GAACNNNNNNTAC 2 cut(s) 482, 514
PsuI RGATCY 3 cut(s) 311, 535, 567
RsaI GTAC 4 cut(s) 50, 500, 604, 805
RsaNI GTAC 4 cut(s) 49, 499, 603, 804
RseI CAYNNNNRTG 3 cut(s) 264, 512, 724
SatI GCNGC 2 cut(s) 695, 736
Sau3AI GATC 6 cut(s) 311, 535, 567, 607, 622, 630
ScaI AGTACT 2 cut(s) 500, 805
SchI GAGTC 2 cut(s) 50, 366
ScrFI CCNGG 4 cut(s) 61, 339, 408, 579
SduI GDGCHC 1 cut(s) 427
SfaNI GCATC 2 cut(s) 494, 706
Sfr274I CTCGAG 1 cut(s) 571
SlaI CTCGAG 1 cut(s) 571
SmiMI CAYNNNNRTG 3 cut(s) 264, 512, 724
SmlI CTYRAG 2 cut(s) 28, 571
SmoI CTYRAG 2 cut(s) 28, 571
Sse9I AATT 4 cut(s) 18, 319, 342, 554
SsiI CCGC 6 cut(s) 281, 414, 438, 620, 735, 811
SspMI CTAG 2 cut(s) 242, 390
StyD4I CCNGG 4 cut(s) 59, 337, 406, 577
TaaI ACNGT 5 cut(s) 193, 503, 511, 766, 792
TaiI ACGT 2 cut(s) 331, 495
TasI AATT 4 cut(s) 18, 319, 342, 554
TatI WGTACW 2 cut(s) 498, 803
TauI GCSGC 1 cut(s) 738
TfiI GAWTC 3 cut(s) 286, 443, 526
TscAI CASTG 2 cut(s) 198, 514
TseFI GTSAC 2 cut(s) 152, 766
TseI GCWGC 1 cut(s) 694
Tsp45I GTSAC 2 cut(s) 152, 766
TspDTI ATGAA 3 cut(s) 90, 215, 656
TspGWI ACGGA 1 cut(s) 620
TspRI CASTG 2 cut(s) 198, 514
XapI RAATTY 1 cut(s) 319
XceI RCATGY 3 cut(s) 116, 170, 616
XhoI CTCGAG 1 cut(s) 571
XmiI GTMKAC 1 cut(s) 403
XspI CTAG 2 cut(s) 242, 390
ZrmI AGTACT 2 cut(s) 500, 805
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.