Rroxscaffold_3G00229110

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000370
Physical Location & Seq
Forward (+)
13619581 .. 13620516
936 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00229110.1

Sequence Viewer

Length: 936 bp
ATGGCCGATAGAAGAAATCCACCTGTCGACGCGGACGAATTCGTCGAAGCCTTCGCAAGAAGGATGGAGGCAAATCAAGTCGGTGGGAGGCTAGGACGACTAGTAACACACATAAGGAATCTAGGAGCAAGGAAATTTACTGGAGGGAAACCTCACGAGGCTGAAGAATGGATTTACAATCTGGAGATCCACTTTGAAATGATGGACTGTACCCAAGTAGAGTTACGAAGAGTGGCTACTTGTCTTTTAGAAGGAGATGCTCGTTTACGGTGGGACACGGTCAAACGTGTCACACTCCCTGCAGCAATGGAACTCATGGAATGGGCTGTCTTCAAAGAGAAATTTCTGGAAAAATATTTTCCACAAGTTGAGAGAGACAAGAAAGAATTAGAGTTTATTCAACTTACCCAAGGAAAGATGACTGTGATTGAATATGAGACCAAGTTCACTAAACTTTCTCGTTTTGCTCCACACATGGTAGATACCGATGATAAAAAGGCAAGACGATTCATTGGAGGACTGAATTCCAATATTCGAAGAATGGTCACTCAACGTGGAATCACGTACGAGGAAGTCGTGGACAAAGCCCTAACTCAAGAGGAAGAAAATCAAAAATACCGCATGGAGAAGGAGCGAGAGAATAGCTTCCGTGGAAAGAGAAGTCATCCAATGTCTAACCAGAAAAGCGGGCAACCATGGAAGCAGCAAACAAGGAGAGACGCATTTCAAAAGCCGACAACATTAAAAGGAAAGGAGGTAGCAAGAGGCCCAATTCGGTGTTACAACTGTGGAGAAATGGGGCACATGTCTAATGCTTGCCCAAAGCCACGTCGCCTTCCGGGATCTTGTTACAATTGTGGCAAGATGGGACATTTCTCAAATCGGTGCGATGCACCGAGGCAAAAAAATAACCCACCACCTCGTCTGTTCGGCTAA
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

311

Amino Acids

36.3

Weight (kDa)

9.56

Isoelectric Point (pI)

44.47

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 78 - 175 8.8e-19 Retrotransposon gag protein
zf-CCHC PF00098 259 - 275 3e-07 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)
AasI GACNNNNNNGTC 1 cut(s) 41
AccI GTMKAC 1 cut(s) 27
AccII CGCG 1 cut(s) 32
AciI CCGC 3 cut(s) 32, 619, 687
AclWI GGATC 2 cut(s) 181, 850
AcoI YGGCCR 1 cut(s) 3
AcsI RAATTY 4 cut(s) 38, 134, 341, 523
AcuI CTGAAG 1 cut(s) 183
AfaI GTAC 2 cut(s) 211, 566
AflIII ACRYGT 2 cut(s) 286, 804
AgsI TTSAA 5 cut(s) 197, 334, 401, 431, 728
AhlI ACTAGT 1 cut(s) 100
AjiI CACGTC 1 cut(s) 830
AluBI AGCT 1 cut(s) 645
AluI AGCT 1 cut(s) 645
Alw26I GTCTC 3 cut(s) 369, 431, 711
AlwI GGATC 2 cut(s) 181, 850
AoxI GGCC 2 cut(s) 3, 766
ApeKI GCWGC 2 cut(s) 302, 703
ApoI RAATTY 4 cut(s) 38, 134, 341, 523
Asp700I GAANNNNTTC 1 cut(s) 644
AspS9I GGNCC 1 cut(s) 767
AsuC2I CCSGG 1 cut(s) 840
AsuII TTCGAA 1 cut(s) 535
BaeGI GKGCMC 1 cut(s) 804
BarI GAAGNNNNNNTAC 2 cut(s) 220, 252
BauI CACGAG 1 cut(s) 155
BbsI GAAGAC 1 cut(s) 322
BbvI GCAGC 2 cut(s) 314, 715
BccI CCATC 3 cut(s) 58, 196, 859
BcnI CCSGG 1 cut(s) 840
BcoDI GTCTC 3 cut(s) 369, 431, 711
BcuI ACTAGT 1 cut(s) 100
BfaI CTAG 3 cut(s) 92, 101, 122
BfmI CTRYAG 1 cut(s) 300
BisI GCNGC 2 cut(s) 303, 704
BlsI GCNGC 2 cut(s) 304, 705
Bme1390I CCNGG 1 cut(s) 840
BmgBI CACGTC 1 cut(s) 830
BmgT120I GGNCC 1 cut(s) 767
BmrFI CCNGG 1 cut(s) 840
BmsI GCATC 2 cut(s) 247, 880
BpiI GAAGAC 1 cut(s) 322
BpmI CTGGAG 2 cut(s) 162, 203
Bpu14I TTCGAA 1 cut(s) 535
BpuEI CTTGAG 1 cut(s) 579
BpuMI CCSGG 1 cut(s) 840
BsaAI YACGTR 1 cut(s) 564
BsaI GGTCTC 1 cut(s) 431
BsaJI CCNNGG 4 cut(s) 409, 649, 695, 896
Bse1I ACTGG 1 cut(s) 145
Bse3DI GCAATG 1 cut(s) 312
BseDI CCNNGG 4 cut(s) 409, 649, 695, 896
BseGI GGATG 2 cut(s) 69, 664
BseMI GCAATG 1 cut(s) 312
BseNI ACTGG 1 cut(s) 145
BseSI GKGCMC 1 cut(s) 804
BseXI GCAGC 2 cut(s) 314, 715
Bsh1236I CGCG 1 cut(s) 32
BshFI GGCC 2 cut(s) 5, 768
BsiSI CCGG 1 cut(s) 839
BsiWI CGTACG 1 cut(s) 564
BslFI GGGAC 2 cut(s) 287, 882
BsmAI GTCTC 3 cut(s) 369, 431, 711
BsmBI CGTCTC 1 cut(s) 711
BsmFI GGGAC 2 cut(s) 287, 882
BsnI GGCC 2 cut(s) 5, 768
Bso31I GGTCTC 1 cut(s) 431
Bsp119I TTCGAA 1 cut(s) 535
Bsp1286I GDGCHC 1 cut(s) 804
Bsp143I GATC 2 cut(s) 186, 842
Bsp19I CCATGG 1 cut(s) 695
BspACI CCGC 3 cut(s) 32, 619, 687
BspANI GGCC 2 cut(s) 5, 768
BspFNI CGCG 1 cut(s) 32
BspMAI CTGCAG 1 cut(s) 304
BspPI GGATC 2 cut(s) 181, 850
BspT104I TTCGAA 1 cut(s) 535
BspTNI GGTCTC 1 cut(s) 431
BsrDI GCAATG 1 cut(s) 312
BsrI ACTGG 1 cut(s) 145
BssECI CCNNGG 4 cut(s) 409, 649, 695, 896
BssMI GATC 2 cut(s) 186, 842
BssSI CACGAG 1 cut(s) 155
BssT1I CCWWGG 2 cut(s) 409, 695
Bst2BI CACGAG 1 cut(s) 155
Bst4CI ACNGT 5 cut(s) 209, 270, 280, 424, 788
Bst6I CTCTTC 1 cut(s) 223
BstBAI YACGTR 1 cut(s) 564
BstBI TTCGAA 1 cut(s) 535
BstC8I GCNNGC 2 cut(s) 689, 817
BstDSI CCRYGG 2 cut(s) 649, 695
BstF5I GGATG 2 cut(s) 69, 664
BstFNI CGCG 1 cut(s) 32
BstKTI GATC 2 cut(s) 189, 845
BstMAI GTCTC 3 cut(s) 369, 431, 711
BstMBI GATC 2 cut(s) 186, 842
BstNSI RCATGY 1 cut(s) 808
BstSCI CCNGG 1 cut(s) 838
BstSFI CTRYAG 1 cut(s) 300
BstSLI GKGCMC 1 cut(s) 804
BstUI CGCG 1 cut(s) 32
BstV1I GCAGC 2 cut(s) 314, 715
BstV2I GAAGAC 1 cut(s) 322
BstX2I RGATCY 2 cut(s) 186, 842
BstYI RGATCY 2 cut(s) 186, 842
BsuRI GGCC 2 cut(s) 5, 768
BtgI CCRYGG 2 cut(s) 649, 695
BtgZI GCGATG 1 cut(s) 903
BtrI CACGTC 1 cut(s) 830
BtsCI GGATG 2 cut(s) 69, 664
Cac8I GCNNGC 2 cut(s) 689, 817
Cfr13I GGNCC 1 cut(s) 767
CseI GACGC 2 cut(s) 38, 728
Csp6I GTAC 2 cut(s) 210, 565
CviAII CATG 5 cut(s) 316, 475, 622, 696, 805
CviQI GTAC 2 cut(s) 210, 565
DpnI GATC 2 cut(s) 188, 844
DpnII GATC 2 cut(s) 186, 842
DrdI GACNNNNNNGTC 1 cut(s) 41
DseDI GACNNNNNNGTC 1 cut(s) 41
EaeI YGGCCR 1 cut(s) 3
Eam1104I CTCTTC 1 cut(s) 223
EarI CTCTTC 1 cut(s) 223
Eco130I CCWWGG 2 cut(s) 409, 695
Eco31I GGTCTC 1 cut(s) 431
Eco57I CTGAAG 1 cut(s) 183
EcoRI GAATTC 2 cut(s) 38, 523
EcoT14I CCWWGG 2 cut(s) 409, 695
ErhI CCWWGG 2 cut(s) 409, 695
Esp3I CGTCTC 1 cut(s) 711
FaeI CATG 5 cut(s) 319, 478, 625, 699, 808
FaiI YATR 7 cut(s) 113, 317, 435, 476, 623, 697, 806
FaqI GGGAC 2 cut(s) 287, 882
FatI CATG 5 cut(s) 315, 474, 621, 695, 804
FauI CCCGC 1 cut(s) 680
FblI GTMKAC 1 cut(s) 27
Fnu4HI GCNGC 2 cut(s) 303, 704
FokI GGATG 2 cut(s) 76, 651
Fsp4HI GCNGC 2 cut(s) 303, 704
FspBI CTAG 3 cut(s) 92, 101, 122
GluI GCNGC 2 cut(s) 303, 704
GsuI CTGGAG 2 cut(s) 162, 203
HaeIII GGCC 2 cut(s) 5, 768
HapII CCGG 1 cut(s) 839
HgaI GACGC 2 cut(s) 38, 728
Hin1II CATG 5 cut(s) 319, 478, 625, 699, 808
HincII GTYRAC 1 cut(s) 28
HindII GTYRAC 1 cut(s) 28
HinfI GANTC 3 cut(s) 118, 507, 558
HpaII CCGG 1 cut(s) 839
Hpy166II GTNNAC 4 cut(s) 28, 266, 447, 580
Hpy188III TCNNGA 4 cut(s) 155, 182, 347, 596
Hpy8I GTNNAC 4 cut(s) 28, 266, 447, 580
Hpy99I CGWCG 3 cut(s) 32, 47, 834
HpyAV CCTTC 5 cut(s) 54, 61, 245, 622, 845
HpyCH4III ACNGT 5 cut(s) 209, 270, 280, 424, 788
HpyCH4IV ACGT 4 cut(s) 286, 553, 563, 829
HpyCH4V TGCA 2 cut(s) 302, 893
HpySE526I ACGT 4 cut(s) 286, 553, 563, 829
Hsp92II CATG 5 cut(s) 319, 478, 625, 699, 808
Kzo9I GATC 2 cut(s) 186, 842
LmnI GCTCC 3 cut(s) 125, 472, 631
LpnPI CCDG 7 cut(s) 36, 126, 167, 312, 332, 692, 852
Lsp1109I GCAGC 2 cut(s) 314, 715
LweI GCATC 2 cut(s) 247, 880
MaeI CTAG 3 cut(s) 92, 101, 122
MaeII ACGT 4 cut(s) 286, 553, 563, 829
MaeIII GTNAC 6 cut(s) 103, 222, 289, 544, 779, 848
MalI GATC 2 cut(s) 188, 844
MboI GATC 2 cut(s) 186, 842
MboII GAAGA 6 cut(s) 24, 176, 240, 322, 549, 614
MfeI CAATTG 1 cut(s) 853
MflI RGATCY 2 cut(s) 186, 842
MhlI GDGCHC 1 cut(s) 804
MluCI AATT 7 cut(s) 38, 134, 341, 386, 523, 771, 853
MroXI GAANNNNTTC 1 cut(s) 644
MseI TTAA 1 cut(s) 743
MspI CCGG 1 cut(s) 839
MspR9I CCNGG 1 cut(s) 840
MunI CAATTG 1 cut(s) 853
MvnI CGCG 1 cut(s) 32
NciI CCSGG 1 cut(s) 840
NcoI CCATGG 1 cut(s) 695
NdeII GATC 2 cut(s) 186, 842
NlaIII CATG 5 cut(s) 319, 478, 625, 699, 808
NmuCI GTSAC 2 cut(s) 289, 544
NspI RCATGY 1 cut(s) 808
NspV TTCGAA 1 cut(s) 535
PciI ACATGT 1 cut(s) 804
PcsI WCGNNNNNNNCGW 3 cut(s) 33, 42, 573
PdmI GAANNNNTTC 1 cut(s) 644
PfeI GAWTC 3 cut(s) 118, 507, 558
Pfl23II CGTACG 1 cut(s) 564
PflFI GACNNNGTC 1 cut(s) 278
PfoI TCCNGGA 1 cut(s) 838
PkrI GCNGC 2 cut(s) 304, 705
Ppu21I YACGTR 1 cut(s) 564
PscI ACATGT 1 cut(s) 804
PspLI CGTACG 1 cut(s) 564
PspPI GGNCC 1 cut(s) 767
PstI CTGCAG 1 cut(s) 304
PsuI RGATCY 2 cut(s) 186, 842
PsyI GACNNNGTC 1 cut(s) 278
RsaI GTAC 2 cut(s) 211, 566
RsaNI GTAC 2 cut(s) 210, 565
SalI GTCGAC 1 cut(s) 26
SaqAI TTAA 1 cut(s) 743
SatI GCNGC 2 cut(s) 303, 704
Sau3AI GATC 2 cut(s) 186, 842
Sau96I GGNCC 1 cut(s) 767
ScrFI CCNGG 1 cut(s) 840
SduI GDGCHC 1 cut(s) 804
SetI ASST 9 cut(s) 25, 154, 289, 556, 566, 647, 759, 832, 922
SfaNI GCATC 2 cut(s) 247, 880
SfcI CTRYAG 1 cut(s) 300
SfuI TTCGAA 1 cut(s) 535
SmlI CTYRAG 1 cut(s) 594
SmoI CTYRAG 1 cut(s) 594
SpeI ACTAGT 1 cut(s) 100
Sse9I AATT 7 cut(s) 38, 134, 341, 386, 523, 771, 853
SsiI CCGC 3 cut(s) 32, 619, 687
SspI AATATT 2 cut(s) 356, 532
SspMI CTAG 3 cut(s) 92, 101, 122
StyD4I CCNGG 1 cut(s) 838
StyI CCWWGG 2 cut(s) 409, 695
TaaI ACNGT 5 cut(s) 209, 270, 280, 424, 788
TaiI ACGT 4 cut(s) 289, 556, 566, 832
TaqI TCGA 3 cut(s) 27, 45, 535
TasI AATT 7 cut(s) 38, 134, 341, 386, 523, 771, 853
TfiI GAWTC 3 cut(s) 118, 507, 558
Tru1I TTAA 1 cut(s) 743
Tru9I TTAA 1 cut(s) 743
TseFI GTSAC 2 cut(s) 289, 544
TseI GCWGC 2 cut(s) 302, 703
Tsp45I GTSAC 2 cut(s) 289, 544
TspDTI ATGAA 1 cut(s) 499
TspGWI ACGGA 1 cut(s) 638
Tth111I GACNNNGTC 1 cut(s) 278
XapI RAATTY 4 cut(s) 38, 134, 341, 523
XceI RCATGY 1 cut(s) 808
XmiI GTMKAC 1 cut(s) 27
XmnI GAANNNNTTC 1 cut(s) 644
XspI CTAG 3 cut(s) 92, 101, 122
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.