Rh7BG186600

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr7B
OG0000370
Physical Location & Seq
Forward (+)
15006200 .. 15029175
22976 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh7BG186600.1

Sequence Viewer

Length: 978 bp
ATGGAGGCAAACCAAGTCGGTGGAAGGCTAGGACGGCTAGTAACATATATAAAGAGTATAGGGGCAACAAAATTTACTGGAGGGAAACCTCACGAGGCTGAAGAATGGATTTACAATCTGGAAATCCACTTTGAAATGATGGACTGTACCCAAGTAGAGCTACGAAGAATGGCTACTTGTCTTTTAGAAGGAGATGCTCGTTTCTGGTGGGACACAGTCAAACGTGTCACACTCCCTGCAACAATGGAACTCATGGAATGGGCTGTCTTCAAAGAGAAATTTCTGGAAAAATATTTTCCACAAGTTGAGAAAGACAAGAAAGAATTAGAGTTTATTCAACTTACCCAAGGAAAGATGACTGTGATTGAGTACGAGACCAAGTTCACTAAACTTTCTCGTTTTGCTCCACACATGGTAGATACCGACGATAAAAAGGCAAGACGATTCATTGGAGGACTGAATTCCAATATTCGAAGAATGGTCACTCAACGTGGAATCACGTACGAGGAAGCTGTGGACAAAGCCCTAACTCAAGAGGAAGAAAATCAAAAGTACCGCACGGAGAAAGAGCGAGAGAATGGTTTCCGAGGAAAAAGAAGTCATCCAATGTCTAATCAGAAAAGCGAACAACCATGGAAGAAGCAGAAAGGGAGAGACTCATCAACTGAAAAAGGAAAGGAGGTGGCAAGAGGGCCAAATTGGTGTTTCAACTGTGGGGAAACGGGACACATGTCTAATGCTTGTCCAAAGCCACGTCGCATTCCAGGATCTTGTTTCAATTGTGGAAAGGTGGGACATTTCTCAAAACAGTGCAATGCACCGAGGCGAAACAATAACCCACCACCTCGTCCTGTCCAGCTAAATGCCATAGCTTGTGAGAACATCGTGATGGAAGGATCTCTCGTCATCGATTGTCGCTTCTGTCCGTCCTGTCAGAGCACTCTGTTGAATGCTACTTTGAGGGTCGTGAACGCATGA
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

325

Amino Acids

37.4

Weight (kDa)

9.13

Isoelectric Point (pI)

42.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 24 - 184 1.7e-07 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 56 - 154 2.6e-21 Retrotransposon gag protein
zf-CCHC PF00098 235 - 250 5.9e-06 Zinc knuckle
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)
AciI CCGC 1 cut(s) 556
AclWI GGATC 2 cut(s) 775, 904
AcsI RAATTY 3 cut(s) 71, 278, 460
AcuI CTGAAG 1 cut(s) 120
AfaI GTAC 4 cut(s) 148, 371, 503, 554
AflIII ACRYGT 2 cut(s) 223, 729
AgsI TTSAA 6 cut(s) 134, 271, 338, 709, 778, 949
AjiI CACGTC 1 cut(s) 755
AjnI CCWGG 1 cut(s) 763
AluBI AGCT 4 cut(s) 160, 512, 859, 872
AluI AGCT 4 cut(s) 160, 512, 859, 872
Alw21I GWGCWC 1 cut(s) 941
Alw26I GTCTC 2 cut(s) 368, 648
AlwI GGATC 2 cut(s) 775, 904
AoxI GGCC 1 cut(s) 692
ApoI RAATTY 3 cut(s) 71, 278, 460
Asp700I GAANNNNTTC 1 cut(s) 581
AspS9I GGNCC 1 cut(s) 692
AsuII TTCGAA 1 cut(s) 472
BarI GAAGNNNNNNTAC 2 cut(s) 157, 189
BauI CACGAG 1 cut(s) 92
BbsI GAAGAC 1 cut(s) 259
Bbv12I GWGCWC 1 cut(s) 941
BccI CCATC 2 cut(s) 133, 883
BceAI ACGGC 1 cut(s) 50
BciT130I CCWGG 1 cut(s) 765
BcoDI GTCTC 2 cut(s) 368, 648
BfaI CTAG 2 cut(s) 29, 38
Bme1390I CCNGG 1 cut(s) 765
BmgBI CACGTC 1 cut(s) 755
BmgT120I GGNCC 1 cut(s) 692
BmrFI CCNGG 1 cut(s) 765
BmsI GCATC 1 cut(s) 184
BoxI GACNNNNGTC 1 cut(s) 730
BpiI GAAGAC 1 cut(s) 259
BpmI CTGGAG 1 cut(s) 99
Bpu14I TTCGAA 1 cut(s) 472
BpuEI CTTGAG 1 cut(s) 516
Bsa29I ATCGAT 1 cut(s) 909
BsaAI YACGTR 1 cut(s) 501
BsaI GGTCTC 1 cut(s) 368
BsaJI CCNNGG 4 cut(s) 346, 586, 632, 821
Bse1I ACTGG 1 cut(s) 82
Bse3DI GCAATG 1 cut(s) 820
BseBI CCWGG 1 cut(s) 765
BseCI ATCGAT 1 cut(s) 909
BseDI CCNNGG 4 cut(s) 346, 586, 632, 821
BseGI GGATG 1 cut(s) 601
BseMI GCAATG 1 cut(s) 820
BseNI ACTGG 1 cut(s) 82
BshFI GGCC 1 cut(s) 694
BshVI ATCGAT 1 cut(s) 909
BsiHKAI GWGCWC 1 cut(s) 941
BsiWI CGTACG 1 cut(s) 501
BslFI GGGAC 3 cut(s) 224, 738, 807
BsmAI GTCTC 2 cut(s) 368, 648
BsmFI GGGAC 3 cut(s) 224, 738, 807
BsmI GAATGC 2 cut(s) 759, 955
BsnI GGCC 1 cut(s) 694
Bso31I GGTCTC 1 cut(s) 368
Bsp119I TTCGAA 1 cut(s) 472
Bsp1286I GDGCHC 1 cut(s) 941
Bsp143I GATC 2 cut(s) 767, 896
Bsp19I CCATGG 1 cut(s) 632
BspACI CCGC 1 cut(s) 556
BspANI GGCC 1 cut(s) 694
BspDI ATCGAT 1 cut(s) 909
BspPI GGATC 2 cut(s) 775, 904
BspT104I TTCGAA 1 cut(s) 472
BspTNI GGTCTC 1 cut(s) 368
BsrDI GCAATG 1 cut(s) 820
BsrI ACTGG 1 cut(s) 82
BssECI CCNNGG 4 cut(s) 346, 586, 632, 821
BssMI GATC 2 cut(s) 767, 896
BssSI CACGAG 1 cut(s) 92
BssT1I CCWWGG 2 cut(s) 346, 632
Bst2BI CACGAG 1 cut(s) 92
Bst2UI CCWGG 1 cut(s) 765
Bst4CI ACNGT 5 cut(s) 146, 217, 361, 713, 810
BstBAI YACGTR 1 cut(s) 501
BstBI TTCGAA 1 cut(s) 472
BstDSI CCRYGG 1 cut(s) 632
BstF5I GGATG 1 cut(s) 601
BstKTI GATC 2 cut(s) 770, 899
BstMAI GTCTC 2 cut(s) 368, 648
BstMBI GATC 2 cut(s) 767, 896
BstMWI GCNNNNNNNGC 1 cut(s) 34
BstNI CCWGG 1 cut(s) 765
BstNSI RCATGY 1 cut(s) 733
BstPAI GACNNNNGTC 1 cut(s) 730
BstSCI CCNGG 1 cut(s) 763
BstV2I GAAGAC 1 cut(s) 259
BstX2I RGATCY 2 cut(s) 767, 896
BstXI CCANNNNNNTGG 1 cut(s) 20
BstYI RGATCY 2 cut(s) 767, 896
Bsu15I ATCGAT 1 cut(s) 909
BsuRI GGCC 1 cut(s) 694
BsuTUI ATCGAT 1 cut(s) 909
BtgI CCRYGG 1 cut(s) 632
BtrI CACGTC 1 cut(s) 755
BtsCI GGATG 1 cut(s) 601
BtsIMutI CAGTG 1 cut(s) 815
Cfr13I GGNCC 1 cut(s) 692
ClaI ATCGAT 1 cut(s) 909
Csp6I GTAC 4 cut(s) 147, 370, 502, 553
CviAII CATG 5 cut(s) 253, 412, 633, 730, 975
CviQI GTAC 4 cut(s) 147, 370, 502, 553
DpnI GATC 2 cut(s) 769, 898
DpnII GATC 2 cut(s) 767, 896
Eco130I CCWWGG 2 cut(s) 346, 632
Eco31I GGTCTC 1 cut(s) 368
Eco57I CTGAAG 1 cut(s) 120
EcoRI GAATTC 1 cut(s) 460
EcoRII CCWGG 1 cut(s) 763
EcoT14I CCWWGG 2 cut(s) 346, 632
ErhI CCWWGG 2 cut(s) 346, 632
FaeI CATG 5 cut(s) 256, 415, 636, 733, 978
FaqI GGGAC 3 cut(s) 224, 738, 807
FatI CATG 5 cut(s) 252, 411, 632, 729, 974
FokI GGATG 1 cut(s) 588
FspBI CTAG 2 cut(s) 29, 38
GsuI CTGGAG 1 cut(s) 99
HaeIII GGCC 1 cut(s) 694
Hin1II CATG 5 cut(s) 256, 415, 636, 733, 978
HinfI GANTC 3 cut(s) 444, 495, 656
Hpy166II GTNNAC 3 cut(s) 384, 517, 970
Hpy188I TCNGA 3 cut(s) 587, 618, 936
Hpy188III TCNNGA 6 cut(s) 92, 119, 284, 533, 886, 967
Hpy8I GTNNAC 3 cut(s) 384, 517, 970
Hpy99I CGWCG 2 cut(s) 428, 759
HpyAV CCTTC 3 cut(s) 18, 182, 887
HpyCH4III ACNGT 5 cut(s) 146, 217, 361, 713, 810
HpyCH4IV ACGT 4 cut(s) 223, 490, 500, 754
HpyCH4V TGCA 3 cut(s) 239, 813, 818
HpyF10VI GCNNNNNNNGC 1 cut(s) 34
HpySE526I ACGT 4 cut(s) 223, 490, 500, 754
Hsp92II CATG 5 cut(s) 256, 415, 636, 733, 978
Kzo9I GATC 2 cut(s) 767, 896
LmnI GCTCC 1 cut(s) 409
LweI GCATC 1 cut(s) 184
MaeI CTAG 2 cut(s) 29, 38
MaeII ACGT 4 cut(s) 223, 490, 500, 754
MaeIII GTNAC 3 cut(s) 40, 226, 481
MalI GATC 2 cut(s) 769, 898
MboI GATC 2 cut(s) 767, 896
MboII GAAGA 6 cut(s) 113, 177, 259, 486, 551, 649
MfeI CAATTG 1 cut(s) 778
MflI RGATCY 2 cut(s) 767, 896
MhlI GDGCHC 1 cut(s) 941
MluCI AATT 6 cut(s) 71, 278, 323, 460, 697, 778
MlyI GAGTC 1 cut(s) 650
MroXI GAANNNNTTC 1 cut(s) 581
MslI CAYNNNNRTG 1 cut(s) 887
MspR9I CCNGG 1 cut(s) 765
MunI CAATTG 1 cut(s) 778
Mva1269I GAATGC 2 cut(s) 759, 955
MvaI CCWGG 1 cut(s) 765
MwoI GCNNNNNNNGC 1 cut(s) 34
NcoI CCATGG 1 cut(s) 632
NdeII GATC 2 cut(s) 767, 896
NlaIII CATG 5 cut(s) 256, 415, 636, 733, 978
NmuCI GTSAC 2 cut(s) 226, 481
NspI RCATGY 1 cut(s) 733
NspV TTCGAA 1 cut(s) 472
PciI ACATGT 1 cut(s) 729
PctI GAATGC 2 cut(s) 759, 955
PdmI GAANNNNTTC 1 cut(s) 581
PfeI GAWTC 2 cut(s) 444, 495
Pfl23II CGTACG 1 cut(s) 501
PflFI GACNNNGTC 1 cut(s) 215
PfoI TCCNGGA 1 cut(s) 763
PleI GAGTC 1 cut(s) 650
PpsI GAGTC 1 cut(s) 650
Ppu21I YACGTR 1 cut(s) 501
PscI ACATGT 1 cut(s) 729
PshAI GACNNNNGTC 1 cut(s) 730
Psp6I CCWGG 1 cut(s) 763
PspGI CCWGG 1 cut(s) 763
PspLI CGTACG 1 cut(s) 501
PspPI GGNCC 1 cut(s) 692
PsuI RGATCY 2 cut(s) 767, 896
PsyI GACNNNGTC 1 cut(s) 215
RsaI GTAC 4 cut(s) 148, 371, 503, 554
RsaNI GTAC 4 cut(s) 147, 370, 502, 553
RseI CAYNNNNRTG 1 cut(s) 887
Sau3AI GATC 2 cut(s) 767, 896
Sau96I GGNCC 1 cut(s) 692
SchI GAGTC 1 cut(s) 650
ScrFI CCNGG 1 cut(s) 765
SduI GDGCHC 1 cut(s) 941
SfaNI GCATC 1 cut(s) 184
SfuI TTCGAA 1 cut(s) 472
SmiMI CAYNNNNRTG 1 cut(s) 887
SmlI CTYRAG 1 cut(s) 531
SmoI CTYRAG 1 cut(s) 531
Sse9I AATT 6 cut(s) 71, 278, 323, 460, 697, 778
SsiI CCGC 1 cut(s) 556
SspI AATATT 2 cut(s) 293, 469
SspMI CTAG 2 cut(s) 29, 38
StyD4I CCNGG 1 cut(s) 763
StyI CCWWGG 2 cut(s) 346, 632
TaaI ACNGT 5 cut(s) 146, 217, 361, 713, 810
TaiI ACGT 4 cut(s) 226, 493, 503, 757
TaqI TCGA 2 cut(s) 472, 909
TasI AATT 6 cut(s) 71, 278, 323, 460, 697, 778
TfiI GAWTC 2 cut(s) 444, 495
TscAI CASTG 1 cut(s) 815
TseFI GTSAC 2 cut(s) 226, 481
Tsp45I GTSAC 2 cut(s) 226, 481
TspDTI ATGAA 1 cut(s) 436
TspGWI ACGGA 2 cut(s) 575, 915
TspRI CASTG 1 cut(s) 815
Tth111I GACNNNGTC 1 cut(s) 215
XapI RAATTY 3 cut(s) 71, 278, 460
XceI RCATGY 1 cut(s) 733
XmnI GAANNNNTTC 1 cut(s) 581
XspI CTAG 2 cut(s) 29, 38
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.