RchiOBHm_Chr7g0197111

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
7
OG0000258
Physical Location & Seq
Forward (+)
15043359 .. 15046070
2712 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ17633

Sequence Viewer

Length: 972 bp
ATGTTGAACATGGTTGATGGATTTGTCATGTTTGTAAATGTGGAATTGTTCTATTTTGTGGAGGAGTTTGGAGTGGAGATTGTGTTTTGGAAAAGAAAATCTAGAGAGGAGTTGAAATTTAGAGATGGAATTGACGTACTGAGCCCTCGAGCGAGGAGGACACAGACAGGCAGCAGGGTTAGCTGCGGGATTTACTTATTTCAGATTTGCCGAGATCGCGTCCAGGTTCTAGAGACTTTGGAATCAGCGCTTCCGTTTTTGTCCGGGAGGTTCTGCCGAATTTTCGGTAGGATTTCGCTTAAAGTGGGCCCCGCAGGCTCGTATCCAGGTTTCGGGGCGATTCCTGGGTCGGGTCCTGTCATTGATGCCTGGAAACATTGTGAGTTTCTCTGCAGGAACTATATTCTCAATGGTCTGGATGATACTTTGTATGATGTATATTGGTCATACACCACTGCAAAGGAACTCTGGAATTCTTTGGAGAAAAAATACAAAGTTGATGACGCAGGTTCAAAGAAGTTCATTATTGGAAAATTTTTGAACTATAAGATGGTGGATAGCAAGACTGTTGTTAGTCAAGTTGATGAACTCCAGGTGATTATTCATGAACTTCATGCTGAAGGTATGGTGATTAATGAAAGCTTTCAAGTTGGTTCTGTTATAGAAAAATTACCACCTTCTTGGAAGGATTTCAAAGTGCATTTGAAGCACAAGAAGAGCGAAATGACCATGGAGGATCTGGTTTTGAAACTACGAGTTCAAGAAGACCACCTGAAAAGTGAGAAGCAACCCGATGGATCTGTCATCGAAGCCAAAGCAAATATGGTTGAGGGAGAAACTTCCAAACCAAAATTCAAAGGTCAGAAATTCAAAGGCAATAAACATGATGTCAAATATGCAACAAAGACCAAGAATTTCAATAAAATTAAAGGTAGTTGCTGGGTGTGTGGAAAGCCTGGACACAAGGCATAA
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
Retrotran_gag_2 zf-CCHC

Protein Analysis

323

Amino Acids

36.94

Weight (kDa)

9.15

Isoelectric Point (pI)

29.77

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 121 - 261 2.5e-26 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 497
AccII CGCG 1 cut(s) 219
AciI CCGC 2 cut(s) 186, 312
AclWI GGATC 2 cut(s) 744, 805
AcsI RAATTY 7 cut(s) 116, 279, 472, 533, 851, 866, 913
AcuI CTGAAG 1 cut(s) 639
AfaI GTAC 1 cut(s) 138
AfeI AGCGCT 1 cut(s) 249
AfiI CCNNNNNNNGG 2 cut(s) 332, 350
AjnI CCWGG 6 cut(s) 222, 325, 343, 368, 591, 955
AjuI GAANNNNNNNTTGG 2 cut(s) 836, 868
AluBI AGCT 2 cut(s) 183, 642
AluI AGCT 2 cut(s) 183, 642
Alw26I GTCTC 1 cut(s) 227
AlwI GGATC 2 cut(s) 744, 805
Ama87I CYCGRG 1 cut(s) 147
Aor51HI AGCGCT 1 cut(s) 249
AoxI GGCC 1 cut(s) 307
ApaI GGGCCC 1 cut(s) 311
ApeKI GCWGC 2 cut(s) 171, 183
ApoI RAATTY 7 cut(s) 116, 279, 472, 533, 851, 866, 913
AseI ATTAAT 1 cut(s) 633
Asp700I GAANNNNTTC 2 cut(s) 642, 689
AspLEI GCGC 1 cut(s) 250
AspS9I GGNCC 3 cut(s) 307, 308, 353
AsuC2I CCSGG 1 cut(s) 265
AsuHPI GGTGA 2 cut(s) 607, 640
AvaI CYCGRG 1 cut(s) 147
AvaII GGWCC 1 cut(s) 353
BaeGI GKGCMC 1 cut(s) 311
BanII GRGCYC 2 cut(s) 146, 311
BbsI GAAGAC 1 cut(s) 771
BbvI GCAGC 2 cut(s) 170, 183
BccI CCATC 4 cut(s) 11, 119, 544, 788
BciT130I CCWGG 6 cut(s) 224, 327, 345, 370, 593, 957
BciVI GTATCC 1 cut(s) 333
BcnI CCSGG 1 cut(s) 265
BcoDI GTCTC 1 cut(s) 227
BfaI CTAG 2 cut(s) 102, 230
BfmI CTRYAG 1 cut(s) 391
BfoI RGCGCY 1 cut(s) 251
BfuAI ACCTGC 1 cut(s) 497
BfuI GTATCC 1 cut(s) 333
BglI GCCNNNNNGGC 1 cut(s) 315
BisI GCNGC 2 cut(s) 172, 184
BlsI GCNGC 2 cut(s) 173, 185
Bme1390I CCNGG 7 cut(s) 224, 265, 327, 345, 370, 593, 957
Bme18I GGWCC 1 cut(s) 353
BmeT110I CYCGRG 1 cut(s) 147
BmgT120I GGNCC 3 cut(s) 307, 308, 353
BmiI GGNNCC 3 cut(s) 309, 310, 354
BmrFI CCNGG 7 cut(s) 224, 265, 327, 345, 370, 593, 957
BmsI GCATC 1 cut(s) 355
BpiI GAAGAC 1 cut(s) 771
BpmI CTGGAG 1 cut(s) 575
BpuMI CCSGG 1 cut(s) 265
BsaJI CCNNGG 2 cut(s) 344, 729
BsaXI ACNNNNNCTCC 2 cut(s) 68, 98
Bsc4I CCNNNNNNNGG 2 cut(s) 332, 350
BseBI CCWGG 6 cut(s) 224, 327, 345, 370, 593, 957
BseDI CCNNGG 2 cut(s) 344, 729
BseGI GGATG 1 cut(s) 424
BseLI CCNNNNNNNGG 2 cut(s) 332, 350
BseMII CTCAG 1 cut(s) 131
BseRI GAGGAG 3 cut(s) 77, 122, 169
BseSI GKGCMC 1 cut(s) 311
BseXI GCAGC 2 cut(s) 170, 183
BseYI CCCAGC 1 cut(s) 939
Bsh1236I CGCG 1 cut(s) 219
BshFI GGCC 1 cut(s) 309
BsiHKCI CYCGRG 1 cut(s) 147
BsiSI CCGG 1 cut(s) 264
BslI CCNNNNNNNGG 2 cut(s) 332, 350
BsmAI GTCTC 1 cut(s) 227
BsnI GGCC 1 cut(s) 309
BsoBI CYCGRG 1 cut(s) 147
Bsp120I GGGCCC 1 cut(s) 307
Bsp1286I GDGCHC 2 cut(s) 146, 311
Bsp143I GATC 3 cut(s) 214, 736, 797
Bsp19I CCATGG 1 cut(s) 729
BspACI CCGC 2 cut(s) 186, 312
BspANI GGCC 1 cut(s) 309
BspCNI CTCAG 1 cut(s) 132
BspFNI CGCG 1 cut(s) 219
BspHI TCATGA 1 cut(s) 604
BspLI GGNNCC 3 cut(s) 309, 310, 354
BspMAI CTGCAG 1 cut(s) 395
BspMI ACCTGC 1 cut(s) 497
BspPI GGATC 2 cut(s) 744, 805
BspQI GCTCTTC 1 cut(s) 710
BssECI CCNNGG 2 cut(s) 344, 729
BssMI GATC 3 cut(s) 214, 736, 797
BssT1I CCWWGG 1 cut(s) 729
Bst2UI CCWGG 6 cut(s) 224, 327, 345, 370, 593, 957
Bst4CI ACNGT 1 cut(s) 568
Bst6I CTCTTC 1 cut(s) 710
BstC8I GCNNGC 1 cut(s) 316
BstDEI CTNAG 1 cut(s) 140
BstDSI CCRYGG 1 cut(s) 729
BstF5I GGATG 1 cut(s) 424
BstFNI CGCG 1 cut(s) 219
BstH2I RGCGCY 1 cut(s) 251
BstHHI GCGC 1 cut(s) 250
BstKTI GATC 3 cut(s) 217, 739, 800
BstMAI GTCTC 1 cut(s) 227
BstMBI GATC 3 cut(s) 214, 736, 797
BstMWI GCNNNNNNNGC 4 cut(s) 180, 216, 315, 706
BstNI CCWGG 6 cut(s) 224, 327, 345, 370, 593, 957
BstSCI CCNGG 7 cut(s) 222, 263, 325, 343, 368, 591, 955
BstSFI CTRYAG 1 cut(s) 391
BstSLI GKGCMC 1 cut(s) 311
BstUI CGCG 1 cut(s) 219
BstV1I GCAGC 2 cut(s) 170, 183
BstV2I GAAGAC 1 cut(s) 771
BstX2I RGATCY 2 cut(s) 736, 797
BstXI CCANNNNNNTGG 1 cut(s) 681
BstYI RGATCY 2 cut(s) 736, 797
BsuI GTATCC 1 cut(s) 333
BsuRI GGCC 1 cut(s) 309
BtgI CCRYGG 1 cut(s) 729
BtsCI GGATG 1 cut(s) 424
BtsI GCAGTG 1 cut(s) 453
BtsIMutI CAGTG 1 cut(s) 453
BveI ACCTGC 1 cut(s) 497
Cac8I GCNNGC 1 cut(s) 316
CciI TCATGA 1 cut(s) 604
CfoI GCGC 1 cut(s) 250
Cfr13I GGNCC 3 cut(s) 307, 308, 353
CseI GACGC 2 cut(s) 208, 512
Csp6I GTAC 1 cut(s) 137
CviAII CATG 6 cut(s) 10, 28, 605, 614, 730, 884
CviJI RGCY 7 cut(s) 144, 183, 309, 318, 642, 812, 955
CviKI_1 RGCY 7 cut(s) 144, 183, 309, 318, 642, 812, 955
CviQI GTAC 1 cut(s) 137
DdeI CTNAG 1 cut(s) 140
DpnI GATC 3 cut(s) 216, 738, 799
DpnII GATC 3 cut(s) 214, 736, 797
Eam1104I CTCTTC 1 cut(s) 710
EarI CTCTTC 1 cut(s) 710
Eco130I CCWWGG 1 cut(s) 729
Eco24I GRGCYC 2 cut(s) 146, 311
Eco47I GGWCC 1 cut(s) 353
Eco47III AGCGCT 1 cut(s) 249
Eco57I CTGAAG 1 cut(s) 639
Eco88I CYCGRG 1 cut(s) 147
EcoO109I RGGNCCY 2 cut(s) 308, 353
EcoRI GAATTC 1 cut(s) 472
EcoRII CCWGG 6 cut(s) 222, 325, 343, 368, 591, 955
EcoT14I CCWWGG 1 cut(s) 729
EcoT38I GRGCYC 2 cut(s) 146, 311
ErhI CCWWGG 1 cut(s) 729
FaeI CATG 6 cut(s) 13, 31, 608, 617, 733, 887
FatI CATG 6 cut(s) 9, 27, 604, 613, 729, 883
FauI CCCGC 2 cut(s) 179, 319
Fnu4HI GCNGC 2 cut(s) 172, 184
FokI GGATG 1 cut(s) 431
FriOI GRGCYC 2 cut(s) 146, 311
Fsp4HI GCNGC 2 cut(s) 172, 184
FspBI CTAG 2 cut(s) 102, 230
GlaI GCGC 1 cut(s) 249
GluI GCNGC 2 cut(s) 172, 184
GsaI CCCAGC 1 cut(s) 943
GsuI CTGGAG 1 cut(s) 575
HaeII RGCGCY 1 cut(s) 251
HaeIII GGCC 1 cut(s) 309
HapII CCGG 1 cut(s) 264
HgaI GACGC 2 cut(s) 208, 512
HhaI GCGC 1 cut(s) 250
Hin1II CATG 6 cut(s) 13, 31, 608, 617, 733, 887
Hin6I GCGC 1 cut(s) 248
HinP1I GCGC 1 cut(s) 248
HindIII AAGCTT 1 cut(s) 640
HinfI GANTC 2 cut(s) 242, 340
HpaII CCGG 1 cut(s) 264
HphI GGTGA 2 cut(s) 607, 640
Hpy188I TCNGA 2 cut(s) 204, 864
Hpy188III TCNNGA 6 cut(s) 102, 230, 416, 469, 605, 761
HpyAV CCTTC 3 cut(s) 614, 679, 687
HpyCH4III ACNGT 1 cut(s) 568
HpyCH4IV ACGT 1 cut(s) 135
HpyCH4V TGCA 4 cut(s) 393, 458, 700, 899
HpyF10VI GCNNNNNNNGC 4 cut(s) 180, 216, 315, 706
HpyF3I CTNAG 1 cut(s) 140
HpySE526I ACGT 1 cut(s) 135
Hsp92II CATG 6 cut(s) 13, 31, 608, 617, 733, 887
HspAI GCGC 1 cut(s) 248
Kzo9I GATC 3 cut(s) 214, 736, 797
LguI GCTCTTC 1 cut(s) 710
Lsp1109I GCAGC 2 cut(s) 170, 183
LweI GCATC 1 cut(s) 355
MaeI CTAG 2 cut(s) 102, 230
MaeII ACGT 1 cut(s) 135
MalI GATC 3 cut(s) 216, 738, 799
MboI GATC 3 cut(s) 214, 736, 797
MboII GAAGA 2 cut(s) 727, 776
MflI RGATCY 2 cut(s) 736, 797
MhlI GDGCHC 2 cut(s) 146, 311
MnlI CCTC 8 cut(s) 55, 100, 147, 150, 156, 261, 727, 823
MroXI GAANNNNTTC 2 cut(s) 642, 689
MseI TTAA 3 cut(s) 300, 633, 927
MspI CCGG 1 cut(s) 264
MspR9I CCNGG 7 cut(s) 224, 265, 327, 345, 370, 593, 957
MvaI CCWGG 6 cut(s) 224, 327, 345, 370, 593, 957
MvnI CGCG 1 cut(s) 219
MwoI GCNNNNNNNGC 4 cut(s) 180, 216, 315, 706
NciI CCSGG 1 cut(s) 265
NcoI CCATGG 1 cut(s) 729
NdeII GATC 3 cut(s) 214, 736, 797
NlaIII CATG 6 cut(s) 13, 31, 608, 617, 733, 887
NlaIV GGNNCC 3 cut(s) 309, 310, 354
NmeAIII GCCGAG 1 cut(s) 236
PaeR7I CTCGAG 1 cut(s) 147
PagI TCATGA 1 cut(s) 604
PciSI GCTCTTC 1 cut(s) 710
PdmI GAANNNNTTC 2 cut(s) 642, 689
PfeI GAWTC 2 cut(s) 242, 340
PfoI TCCNGGA 1 cut(s) 263
PkrI GCNGC 2 cut(s) 173, 185
PpuMI RGGWCCY 1 cut(s) 353
PshBI ATTAAT 1 cut(s) 633
Psp5II RGGWCCY 1 cut(s) 353
Psp6I CCWGG 6 cut(s) 222, 325, 343, 368, 591, 955
PspFI CCCAGC 1 cut(s) 939
PspGI CCWGG 6 cut(s) 222, 325, 343, 368, 591, 955
PspN4I GGNNCC 3 cut(s) 309, 310, 354
PspOMI GGGCCC 1 cut(s) 307
PspPI GGNCC 3 cut(s) 307, 308, 353
PspPPI RGGWCCY 1 cut(s) 353
PspXI VCTCGAGB 1 cut(s) 147
PstI CTGCAG 1 cut(s) 395
PsuI RGATCY 2 cut(s) 736, 797
RsaI GTAC 1 cut(s) 138
RsaNI GTAC 1 cut(s) 137
SapI GCTCTTC 1 cut(s) 710
SaqAI TTAA 3 cut(s) 300, 633, 927
SatI GCNGC 2 cut(s) 172, 184
Sau3AI GATC 3 cut(s) 214, 736, 797
Sau96I GGNCC 3 cut(s) 307, 308, 353
ScrFI CCNGG 7 cut(s) 224, 265, 327, 345, 370, 593, 957
SduI GDGCHC 2 cut(s) 146, 311
SfaNI GCATC 1 cut(s) 355
SfcI CTRYAG 1 cut(s) 391
Sfr274I CTCGAG 1 cut(s) 147
SinI GGWCC 1 cut(s) 353
SlaI CTCGAG 1 cut(s) 147
SmlI CTYRAG 1 cut(s) 147
SmoI CTYRAG 1 cut(s) 147
SsiI CCGC 2 cut(s) 186, 312
SspMI CTAG 2 cut(s) 102, 230
StyD4I CCNGG 7 cut(s) 222, 263, 325, 343, 368, 591, 955
StyI CCWWGG 1 cut(s) 729
TaaI ACNGT 1 cut(s) 568
TaiI ACGT 1 cut(s) 138
TaqI TCGA 2 cut(s) 148, 807
TfiI GAWTC 2 cut(s) 242, 340
Tru1I TTAA 3 cut(s) 300, 633, 927
Tru9I TTAA 3 cut(s) 300, 633, 927
TscAI CASTG 1 cut(s) 460
TseI GCWGC 2 cut(s) 171, 183
TspDTI ATGAA 6 cut(s) 511, 593, 600, 602, 621, 651
TspGWI ACGGA 1 cut(s) 243
TspRI CASTG 1 cut(s) 460
VpaK11BI GGWCC 1 cut(s) 353
VspI ATTAAT 1 cut(s) 633
XapI RAATTY 7 cut(s) 116, 279, 472, 533, 851, 866, 913
XbaI TCTAGA 2 cut(s) 101, 229
XcmI CCANNNNNNNNNTGG 2 cut(s) 736, 820
XhoI CTCGAG 1 cut(s) 147
XmnI GAANNNNTTC 2 cut(s) 642, 689
XspI CTAG 2 cut(s) 102, 230
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.