Rw4G017340

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0000370
Physical Location & Seq
Reverse (-)
38973502 .. 38974443
942 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G017340.1

Sequence Viewer

Length: 942 bp
ATGGATCCTCTGAGAGGCAGAGCTAGAGGCCGAGGTAGGCCCCGAGGAGGGGGCAGAGCTAGAAGTAGAGGCACCGTCCCTCCTGTGGAGGAGTTCTACGAGGAGGAGGTGGAGGTACTGTATGTGGTGCCTGTTCCACTTATCGTTGATGTAGGTGAGGCCATTCGCTTAGCTAAACTGGCTAAGGAGATTTTTAGGCTGGGAGCGACCTTGTTCAAGGGAGGTACGGATCACATGTTGGCCGATGAGTGGATCGAGAATATGGAGACGTACTTCGAGATGGTCATCTGCACTGAGATCGAGAAGAGGAAGATAGATGCGCATCTTCTTCAGGGTGAGGCAACACAGAGGGCAGTAGATGTGTCCACCTTGACTTGGGAGGGTTTTGTGGGACTCTTCTGGGACATGTACTTTCCGCCTGCAGTGAGGGAGCAGTTGGGGCTTGAGTTCATTGCTCTAGTTCAGGGGGATATGAGCATCAGAGACTATGAGGCACGGTTATCCCAGTTGTATCGATTCGTCCCACAGATAGACGCAAAGGCCCTGGCCAAGAAGTTTCTGCGGGGACTGAAGTATGAGATCAGGCAGATTATGTACCCCCTTATGTTGCCTACGAAGGAGGGCAAGATGCATGTAAGTGAGACCTTGGCCTTGAGAGATTCCCAGGGAAAGGGGAAGGCAGTTGCCTGGAGTAGTAGTTCTACGGGTTATCGAGGCGGGTCTTGGAAGAGACAGCGAACTCAGCATCAGGCTCCAGCTAGAGTGGCAACTGCACCCGTTAGGGCTACACCTATCAGGCAGGTAGCACCAGCCGCACCTCTAACATGTTTCCACTGCGGCGAGGTAGGCCATGTTTCCAGAGCGTGCACGAGGCCGAAGAGCATGACATGCTTTAGATGTGGACAAGCAGGGCATTTCACTAGACAATGTACCCAACCTTAG
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

313

Amino Acids

35.19

Weight (kDa)

9.41

Isoelectric Point (pI)

46.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 121 - 191 8.3e-11 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: 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)
Acc16I TGCGCA 1 cut(s) 321
Acc36I ACCTGC 1 cut(s) 790
AccB1I GGYRCC 2 cut(s) 71, 127
AciI CCGC 5 cut(s) 416, 562, 717, 813, 837
AclWI GGATC 3 cut(s) 12, 237, 260
AcoI YGGCCR 2 cut(s) 240, 546
AcuI CTGAAG 2 cut(s) 314, 590
AfaI GTAC 6 cut(s) 117, 226, 272, 410, 596, 931
AfiI CCNNNNNNNGG 8 cut(s) 14, 47, 48, 49, 85, 249, 375, 670
AflIII ACRYGT 3 cut(s) 234, 405, 824
AgsI TTSAA 1 cut(s) 217
AjnI CCWGG 3 cut(s) 543, 663, 686
AloI GAACNNNNNNTCC 2 cut(s) 682, 714
AluBI AGCT 4 cut(s) 23, 59, 173, 758
AluI AGCT 4 cut(s) 23, 59, 173, 758
Alw21I GWGCWC 1 cut(s) 869
Alw26I GTCTC 4 cut(s) 260, 477, 635, 724
Alw44I GTGCAC 1 cut(s) 865
AlwI GGATC 3 cut(s) 12, 237, 260
Ama87I CYCGRG 1 cut(s) 42
AoxI GGCC 9 cut(s) 28, 38, 159, 240, 540, 546, 648, 847, 872
ApaLI GTGCAC 1 cut(s) 865
AspLEI GCGC 1 cut(s) 322
AspS9I GGNCC 2 cut(s) 39, 541
AsuHPI GGTGA 2 cut(s) 167, 347
AvaI CYCGRG 1 cut(s) 42
BaeGI GKGCMC 1 cut(s) 869
BalI TGGCCA 1 cut(s) 548
BamHI GGATCC 1 cut(s) 4
BanI GGYRCC 2 cut(s) 71, 127
BauI CACGAG 1 cut(s) 868
Bbv12I GWGCWC 1 cut(s) 869
BccI CCATC 1 cut(s) 274
BcgI CGANNNNNNTGC 2 cut(s) 280, 314
BciT130I CCWGG 3 cut(s) 545, 665, 688
BcoDI GTCTC 4 cut(s) 260, 477, 635, 724
BfaI CTAG 5 cut(s) 24, 60, 458, 759, 921
BfmI CTRYAG 1 cut(s) 420
BfuAI ACCTGC 1 cut(s) 790
BisI GCNGC 2 cut(s) 813, 838
BlpI GCTNAGC 1 cut(s) 169
BlsI GCNGC 2 cut(s) 814, 839
Bme1390I CCNGG 3 cut(s) 545, 665, 688
BmeT110I CYCGRG 1 cut(s) 42
BmgT120I GGNCC 2 cut(s) 39, 541
BmiI GGNNCC 5 cut(s) 6, 41, 73, 129, 753
BmrFI CCNGG 3 cut(s) 545, 665, 688
BmrI ACTGGG 1 cut(s) 499
BmsI GCATC 5 cut(s) 307, 331, 486, 618, 754
BmuI ACTGGG 1 cut(s) 499
BpmI CTGGAG 2 cut(s) 709, 738
Bpu10I CCTNAGC 1 cut(s) 183
Bpu1102I GCTNAGC 1 cut(s) 169
BpuEI CTTGAG 2 cut(s) 464, 673
Bsa29I ATCGAT 1 cut(s) 514
BsaBI GATNNNNATC 2 cut(s) 284, 321
BsaI GGTCTC 1 cut(s) 635
BsaJI CCNNGG 6 cut(s) 31, 43, 543, 645, 663, 664
BsaXI ACNNNNNCTCC 6 cut(s) 64, 94, 104, 134, 682, 712
Bsc4I CCNNNNNNNGG 8 cut(s) 14, 47, 48, 49, 85, 249, 375, 670
Bse1I ACTGG 2 cut(s) 183, 505
Bse3DI GCAATG 1 cut(s) 450
Bse8I GATNNNNATC 2 cut(s) 284, 321
BseBI CCWGG 3 cut(s) 545, 665, 688
BseCI ATCGAT 1 cut(s) 514
BseDI CCNNGG 6 cut(s) 31, 43, 543, 645, 663, 664
BseJI GATNNNNATC 2 cut(s) 284, 321
BseLI CCNNNNNNNGG 8 cut(s) 14, 47, 48, 49, 85, 249, 375, 670
BseMI GCAATG 1 cut(s) 450
BseMII CTCAG 2 cut(s) 285, 755
BseNI ACTGG 2 cut(s) 183, 505
BseRI GAGGAG 4 cut(s) 60, 104, 116, 119
BseSI GKGCMC 1 cut(s) 869
BseYI CCCAGC 1 cut(s) 199
BsgI GTGCAG 2 cut(s) 274, 756
BshFI GGCC 9 cut(s) 30, 40, 161, 242, 542, 548, 650, 849, 874
BshNI GGYRCC 2 cut(s) 71, 127
BshVI ATCGAT 1 cut(s) 514
BsiHKAI GWGCWC 1 cut(s) 869
BsiHKCI CYCGRG 1 cut(s) 42
BslFI GGGAC 5 cut(s) 62, 405, 416, 506, 579
BslI CCNNNNNNNGG 8 cut(s) 14, 47, 48, 49, 85, 249, 375, 670
BsmAI GTCTC 4 cut(s) 260, 477, 635, 724
BsmBI CGTCTC 1 cut(s) 260
BsmFI GGGAC 5 cut(s) 62, 405, 416, 506, 579
BsnI GGCC 9 cut(s) 30, 40, 161, 242, 542, 548, 650, 849, 874
Bso31I GGTCTC 1 cut(s) 635
BsoBI CYCGRG 1 cut(s) 42
Bsp1286I GDGCHC 1 cut(s) 869
Bsp143I GATC 5 cut(s) 4, 229, 252, 297, 579
Bsp1720I GCTNAGC 1 cut(s) 169
BspACI CCGC 5 cut(s) 416, 562, 717, 813, 837
BspANI GGCC 9 cut(s) 30, 40, 161, 242, 542, 548, 650, 849, 874
BspCNI CTCAG 2 cut(s) 286, 754
BspDI ATCGAT 1 cut(s) 514
BspLI GGNNCC 5 cut(s) 6, 41, 73, 129, 753
BspMAI CTGCAG 1 cut(s) 424
BspMI ACCTGC 1 cut(s) 790
BspPI GGATC 3 cut(s) 12, 237, 260
BspQI GCTCTTC 1 cut(s) 872
BspT107I GGYRCC 2 cut(s) 71, 127
BspTNI GGTCTC 1 cut(s) 635
BsrDI GCAATG 1 cut(s) 450
BsrI ACTGG 2 cut(s) 183, 505
BssECI CCNNGG 6 cut(s) 31, 43, 543, 645, 663, 664
BssMI GATC 5 cut(s) 4, 229, 252, 297, 579
BssSI CACGAG 1 cut(s) 868
BssT1I CCWWGG 1 cut(s) 645
Bst2BI CACGAG 1 cut(s) 868
Bst2UI CCWGG 3 cut(s) 545, 665, 688
Bst4CI ACNGT 3 cut(s) 76, 120, 498
Bst6I CTCTTC 4 cut(s) 299, 401, 722, 872
BstAPI GCANNNNNTGC 1 cut(s) 888
BstC8I GCNNGC 2 cut(s) 420, 865
BstDEI CTNAG 6 cut(s) 11, 169, 183, 294, 741, 939
BstENI CCTNNNNNAGG 1 cut(s) 12
BstHHI GCGC 1 cut(s) 322
BstKTI GATC 5 cut(s) 7, 232, 255, 300, 582
BstMAI GTCTC 4 cut(s) 260, 477, 635, 724
BstMBI GATC 5 cut(s) 4, 229, 252, 297, 579
BstMWI GCNNNNNNNGC 7 cut(s) 179, 439, 742, 764, 812, 846, 888
BstNI CCWGG 3 cut(s) 545, 665, 688
BstNSI RCATGY 5 cut(s) 238, 409, 635, 828, 891
BstSCI CCNGG 3 cut(s) 543, 663, 686
BstSFI CTRYAG 1 cut(s) 420
BstSLI GKGCMC 1 cut(s) 869
BstX2I RGATCY 1 cut(s) 4
BstYI RGATCY 1 cut(s) 4
Bsu15I ATCGAT 1 cut(s) 514
BsuRI GGCC 9 cut(s) 30, 40, 161, 242, 542, 548, 650, 849, 874
BsuTUI ATCGAT 1 cut(s) 514
BtsI GCAGTG 2 cut(s) 429, 832
BtsIMutI CAGTG 3 cut(s) 291, 429, 832
BveI ACCTGC 1 cut(s) 790
Cac8I GCNNGC 2 cut(s) 420, 865
CfoI GCGC 1 cut(s) 322
Cfr13I GGNCC 2 cut(s) 39, 541
ClaI ATCGAT 1 cut(s) 514
CseI GACGC 1 cut(s) 542
Csp6I GTAC 6 cut(s) 116, 225, 271, 409, 595, 930
CviAII CATG 7 cut(s) 235, 406, 632, 825, 851, 883, 888
CviQI GTAC 6 cut(s) 116, 225, 271, 409, 595, 930
DdeI CTNAG 6 cut(s) 11, 169, 183, 294, 741, 939
DpnI GATC 5 cut(s) 6, 231, 254, 299, 581
DpnII GATC 5 cut(s) 4, 229, 252, 297, 579
EaeI YGGCCR 2 cut(s) 240, 546
Eam1104I CTCTTC 4 cut(s) 299, 401, 722, 872
EarI CTCTTC 4 cut(s) 299, 401, 722, 872
EciI GGCGGA 1 cut(s) 405
Eco130I CCWWGG 1 cut(s) 645
Eco31I GGTCTC 1 cut(s) 635
Eco57I CTGAAG 2 cut(s) 314, 590
Eco88I CYCGRG 1 cut(s) 42
EcoNI CCTNNNNNAGG 1 cut(s) 12
EcoO109I RGGNCCY 2 cut(s) 39, 541
EcoRII CCWGG 3 cut(s) 543, 663, 686
EcoT14I CCWWGG 1 cut(s) 645
EcoT22I ATGCAT 1 cut(s) 633
ErhI CCWWGG 1 cut(s) 645
Esp3I CGTCTC 1 cut(s) 260
FaeI CATG 7 cut(s) 238, 409, 635, 828, 854, 886, 891
FaqI GGGAC 5 cut(s) 62, 405, 416, 506, 579
FatI CATG 7 cut(s) 234, 405, 631, 824, 850, 882, 887
FauI CCCGC 2 cut(s) 555, 710
Fnu4HI GCNGC 2 cut(s) 813, 838
Fsp4HI GCNGC 2 cut(s) 813, 838
FspAI RTGCGCAY 1 cut(s) 321
FspBI CTAG 5 cut(s) 24, 60, 458, 759, 921
FspI TGCGCA 1 cut(s) 321
GlaI GCGC 1 cut(s) 321
GluI GCNGC 2 cut(s) 813, 838
GsaI CCCAGC 1 cut(s) 203
GsuI CTGGAG 2 cut(s) 709, 738
HaeIII GGCC 9 cut(s) 30, 40, 161, 242, 542, 548, 650, 849, 874
HgaI GACGC 1 cut(s) 542
HhaI GCGC 1 cut(s) 322
Hin1II CATG 7 cut(s) 238, 409, 635, 828, 854, 886, 891
Hin6I GCGC 1 cut(s) 320
HinP1I GCGC 1 cut(s) 320
HinfI GANTC 3 cut(s) 393, 516, 659
HphI GGTGA 2 cut(s) 167, 347
Hpy166II GTNNAC 3 cut(s) 366, 867, 902
Hpy188I TCNGA 2 cut(s) 12, 482
Hpy188III TCNNGA 4 cut(s) 256, 277, 301, 858
Hpy8I GTNNAC 3 cut(s) 366, 867, 902
HpyAV CCTTC 2 cut(s) 610, 670
HpyCH4III ACNGT 3 cut(s) 76, 120, 498
HpyCH4IV ACGT 1 cut(s) 269
HpyCH4V TGCA 5 cut(s) 291, 422, 631, 773, 867
HpyF10VI GCNNNNNNNGC 7 cut(s) 179, 439, 742, 764, 812, 846, 888
HpyF3I CTNAG 6 cut(s) 11, 169, 183, 294, 741, 939
HpySE526I ACGT 1 cut(s) 269
Hsp92II CATG 7 cut(s) 238, 409, 635, 828, 854, 886, 891
HspAI GCGC 1 cut(s) 320
Kzo9I GATC 5 cut(s) 4, 229, 252, 297, 579
LguI GCTCTTC 1 cut(s) 872
LmnI GCTCC 3 cut(s) 203, 430, 757
LweI GCATC 5 cut(s) 307, 331, 486, 618, 754
MaeI CTAG 5 cut(s) 24, 60, 458, 759, 921
MaeII ACGT 1 cut(s) 269
MalI GATC 5 cut(s) 6, 231, 254, 299, 581
MboI GATC 5 cut(s) 4, 229, 252, 297, 579
MboII GAAGA 7 cut(s) 316, 317, 320, 322, 388, 739, 889
MflI RGATCY 1 cut(s) 4
MhlI GDGCHC 1 cut(s) 869
MlsI TGGCCA 1 cut(s) 548
MluNI TGGCCA 1 cut(s) 548
MlyI GAGTC 1 cut(s) 387
Mox20I TGGCCA 1 cut(s) 548
Mph1103I ATGCAT 1 cut(s) 633
MscI TGGCCA 1 cut(s) 548
MslI CAYNNNNRTG 1 cut(s) 636
Msp20I TGGCCA 1 cut(s) 548
MspR9I CCNGG 3 cut(s) 545, 665, 688
MvaI CCWGG 3 cut(s) 545, 665, 688
MwoI GCNNNNNNNGC 7 cut(s) 179, 439, 742, 764, 812, 846, 888
NdeII GATC 5 cut(s) 4, 229, 252, 297, 579
NlaIII CATG 7 cut(s) 238, 409, 635, 828, 854, 886, 891
NlaIV GGNNCC 5 cut(s) 6, 41, 73, 129, 753
NmeAIII GCCGAG 1 cut(s) 56
NsbI TGCGCA 1 cut(s) 321
NsiI ATGCAT 1 cut(s) 633
NspI RCATGY 5 cut(s) 238, 409, 635, 828, 891
PasI CCCWGGG 1 cut(s) 664
PciI ACATGT 3 cut(s) 234, 405, 824
PciSI GCTCTTC 1 cut(s) 872
PfeI GAWTC 2 cut(s) 516, 659
PkrI GCNGC 2 cut(s) 814, 839
PleI GAGTC 1 cut(s) 387
PpsI GAGTC 1 cut(s) 387
PscI ACATGT 3 cut(s) 234, 405, 824
Psp6I CCWGG 3 cut(s) 543, 663, 686
PspFI CCCAGC 1 cut(s) 199
PspGI CCWGG 3 cut(s) 543, 663, 686
PspN4I GGNNCC 5 cut(s) 6, 41, 73, 129, 753
PspPI GGNCC 2 cut(s) 39, 541
PstI CTGCAG 1 cut(s) 424
PsuI RGATCY 1 cut(s) 4
RsaI GTAC 6 cut(s) 117, 226, 272, 410, 596, 931
RsaNI GTAC 6 cut(s) 116, 225, 271, 409, 595, 930
RseI CAYNNNNRTG 1 cut(s) 636
SapI GCTCTTC 1 cut(s) 872
SatI GCNGC 2 cut(s) 813, 838
Sau3AI GATC 5 cut(s) 4, 229, 252, 297, 579
Sau96I GGNCC 2 cut(s) 39, 541
SchI GAGTC 1 cut(s) 387
ScrFI CCNGG 3 cut(s) 545, 665, 688
SduI GDGCHC 1 cut(s) 869
SfaNI GCATC 5 cut(s) 307, 331, 486, 618, 754
SfcI CTRYAG 1 cut(s) 420
SmiMI CAYNNNNRTG 1 cut(s) 636
SmlI CTYRAG 2 cut(s) 443, 652
SmoI CTYRAG 2 cut(s) 443, 652
SsiI CCGC 5 cut(s) 416, 562, 717, 813, 837
SspMI CTAG 5 cut(s) 24, 60, 458, 759, 921
StyD4I CCNGG 3 cut(s) 543, 663, 686
StyI CCWWGG 1 cut(s) 645
TaaI ACNGT 3 cut(s) 76, 120, 498
TaiI ACGT 1 cut(s) 272
TaqI TCGA 5 cut(s) 255, 276, 300, 514, 712
TatI WGTACW 1 cut(s) 408
TauI GCSGC 2 cut(s) 815, 840
TfiI GAWTC 2 cut(s) 516, 659
TscAI CASTG 3 cut(s) 298, 429, 839
TspDTI ATGAA 1 cut(s) 439
TspGWI ACGGA 1 cut(s) 242
TspRI CASTG 3 cut(s) 298, 429, 839
VneI GTGCAC 1 cut(s) 865
XagI CCTNNNNNAGG 1 cut(s) 12
XceI RCATGY 5 cut(s) 238, 409, 635, 828, 891
XspI CTAG 5 cut(s) 24, 60, 458, 759, 921
Zsp2I ATGCAT 1 cut(s) 633
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.