Rh5DG461100

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0000258
Physical Location & Seq
Forward (+)
73245617 .. 73256139
10523 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG461100.1

Sequence Viewer

Length: 930 bp
ATGGATGCTGCTTTGACCAACACCAAGATTCCTGATGTGTCCAAGATTGATGTGTTCAAGGGTTCCTTCTTCAAAAGGTGGCAAGAAAGGGTTTTCTCCGTCCTCGATGTCATGAATTTGGCTGATTACCTCACGAAGGCCAAGCCCAAGGAAGGTAGCGAGAATTATAACAAAGAGTTGGCTGAATGGGAGAAAGGCATTGAATTACCTGAAGCATTTCTATCTGGAAGTCTCATTGAAAAGTTGCCTGAATCATGGAAGGACTACAAAAACAACATGAAGCACAAAAAGAAACAAATGAGTCTTGAAGATGTGGTTGTGCATATCCGAATTGAAGAAACAAACCGTCTTCAAGACAAAGCCGACCAAGAGAAAGAGATGATATCTAAAGCCAACATTGTTGAACGTATGCCTTCCAAGTCAACTGGTAAGCGTAAAATTTTTATTGTCAAGCATGATTACAAATCTCAACACAAGCATGACAATAAGCCTTTCCCTAAGACTGAAAATAAGCTTAAGCCTTTCATTCCCAATATCAAAAAGAAAGGAAGTTGTTATGTTTGTGGAAAACTTGGGCACCATGCTTTCCAATGTCAAGACAGGAAACGCCAGAATCAGGCCCGTGCTAATGTGGTTGTTGAAGATGACATTATTGCAGAGAAGCCAGATGATGATGGCGGTGCCTGGTCGGATCCGGGTAGACTGGGTCAAGAGCTTTGGTCCTCTACTTATGACGGCTGTATTGATGCTGACGGCTGGGATACATTTTGTTTTGCGACTAAGCCTGGCAATATGTACGGCGATGGATGCGGTGGTGACCAAGTTGGCGGAGATGACGGCCGGGAAAAGGTTGGCCGAGATATGGCGCCGGGTTTGGTCCTCTACGGCGGCAACGGTGTTTGGCTCGAGGTGGAGGATGTCCAAGCTTAG
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
No domains found.

Protein Analysis

309

Amino Acids

34.96

Weight (kDa)

6.42

Isoelectric Point (pI)

38.98

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 66 - 120 8.3e-06 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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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)
AanI TTATAA 1 cut(s) 168
AccB1I GGYRCC 3 cut(s) 576, 680, 865
AccI GTMKAC 1 cut(s) 700
AciI CCGC 4 cut(s) 678, 810, 828, 888
AclWI GGATC 2 cut(s) 686, 699
AcoI YGGCCR 2 cut(s) 838, 853
AcsI RAATTY 2 cut(s) 115, 438
AcuI CTGAAG 1 cut(s) 231
AcyI GRCGYC 1 cut(s) 866
AfaI GTAC 1 cut(s) 797
AfiI CCNNNNNNNGG 5 cut(s) 136, 152, 616, 847, 862
AflII CTTAAG 1 cut(s) 515
AgsI TTSAA 9 cut(s) 58, 73, 203, 239, 308, 335, 353, 404, 641
AjnI CCWGG 2 cut(s) 683, 784
AluBI AGCT 3 cut(s) 514, 715, 926
AluI AGCT 3 cut(s) 514, 715, 926
Alw26I GTCTC 1 cut(s) 236
AlwI GGATC 2 cut(s) 686, 699
Ama87I CYCGRG 1 cut(s) 905
AoxI GGCC 4 cut(s) 138, 618, 838, 853
ApeKI GCWGC 1 cut(s) 8
ApoI RAATTY 2 cut(s) 115, 438
Asp700I GAANNNNTTC 1 cut(s) 216
AspLEI GCGC 1 cut(s) 868
AspS9I GGNCC 3 cut(s) 619, 720, 877
AsuC2I CCSGG 3 cut(s) 696, 842, 870
AsuHPI GGTGA 1 cut(s) 827
AvaI CYCGRG 1 cut(s) 905
AvaII GGWCC 2 cut(s) 720, 877
BaeGI GKGCMC 1 cut(s) 579
BamHI GGATCC 1 cut(s) 691
BanI GGYRCC 3 cut(s) 576, 680, 865
BbsI GAAGAC 1 cut(s) 341
BccI CCATC 2 cut(s) 668, 797
BceAI ACGGC 5 cut(s) 751, 769, 814, 853, 901
BciT130I CCWGG 2 cut(s) 685, 786
BciVI GTATCC 1 cut(s) 754
BcnI CCSGG 3 cut(s) 696, 842, 870
BcoDI GTCTC 1 cut(s) 236
BfoI RGCGCY 1 cut(s) 869
BfrI CTTAAG 1 cut(s) 515
BfuI GTATCC 1 cut(s) 754
BisI GCNGC 2 cut(s) 9, 889
BlsI GCNGC 2 cut(s) 10, 890
Bme1390I CCNGG 5 cut(s) 685, 696, 786, 842, 870
Bme18I GGWCC 2 cut(s) 720, 877
BmeT110I CYCGRG 1 cut(s) 905
BmgT120I GGNCC 3 cut(s) 619, 720, 877
BmiI GGNNCC 5 cut(s) 64, 578, 682, 693, 867
BmrFI CCNGG 5 cut(s) 685, 696, 786, 842, 870
BmrI ACTGGG 1 cut(s) 713
BmsI GCATC 2 cut(s) 736, 797
BmuI ACTGGG 1 cut(s) 713
BpiI GAAGAC 1 cut(s) 341
BpuMI CCSGG 3 cut(s) 696, 842, 870
BsaHI GRCGYC 1 cut(s) 866
BsaJI CCNNGG 1 cut(s) 147
Bsc4I CCNNNNNNNGG 5 cut(s) 136, 152, 616, 847, 862
Bse1I ACTGG 2 cut(s) 430, 708
BseBI CCWGG 2 cut(s) 685, 786
BseDI CCNNGG 1 cut(s) 147
BseGI GGATG 3 cut(s) 10, 812, 922
BseLI CCNNNNNNNGG 5 cut(s) 136, 152, 616, 847, 862
BseNI ACTGG 2 cut(s) 430, 708
BseSI GKGCMC 1 cut(s) 579
BseX3I CGGCCG 1 cut(s) 838
BseYI CCCAGC 1 cut(s) 756
Bsh1285I CGRYCG 1 cut(s) 841
BshFI GGCC 4 cut(s) 140, 620, 840, 855
BshNI GGYRCC 3 cut(s) 576, 680, 865
BsiEI CGRYCG 1 cut(s) 841
BsiHKCI CYCGRG 1 cut(s) 905
BsiSI CCGG 3 cut(s) 695, 841, 869
BslI CCNNNNNNNGG 5 cut(s) 136, 152, 616, 847, 862
BsmAI GTCTC 1 cut(s) 236
BsnI GGCC 4 cut(s) 140, 620, 840, 855
BsoBI CYCGRG 1 cut(s) 905
Bsp1286I GDGCHC 1 cut(s) 579
Bsp143I GATC 1 cut(s) 691
BspACI CCGC 4 cut(s) 678, 810, 828, 888
BspANI GGCC 4 cut(s) 140, 620, 840, 855
BspHI TCATGA 1 cut(s) 111
BspLI GGNNCC 5 cut(s) 64, 578, 682, 693, 867
BspPI GGATC 2 cut(s) 686, 699
BspT107I GGYRCC 3 cut(s) 576, 680, 865
BspTI CTTAAG 1 cut(s) 515
BsrI ACTGG 2 cut(s) 430, 708
BssECI CCNNGG 1 cut(s) 147
BssMI GATC 1 cut(s) 691
BssNI GRCGYC 1 cut(s) 866
BssT1I CCWWGG 1 cut(s) 147
Bst2UI CCWGG 2 cut(s) 685, 786
Bst4CI ACNGT 2 cut(s) 347, 896
BstACI GRCGYC 1 cut(s) 866
BstAFI CTTAAG 1 cut(s) 515
BstDEI CTNAG 3 cut(s) 498, 780, 927
BstEII GGTNACC 1 cut(s) 815
BstENI CCTNNNNNAGG 1 cut(s) 134
BstF5I GGATG 3 cut(s) 10, 812, 922
BstH2I RGCGCY 1 cut(s) 869
BstHHI GCGC 1 cut(s) 868
BstKTI GATC 1 cut(s) 694
BstMAI GTCTC 1 cut(s) 236
BstMBI GATC 1 cut(s) 691
BstMCI CGRYCG 1 cut(s) 841
BstMWI GCNNNNNNNGC 1 cut(s) 807
BstNI CCWGG 2 cut(s) 685, 786
BstPI GGTNACC 1 cut(s) 815
BstSCI CCNGG 5 cut(s) 683, 694, 784, 840, 868
BstSLI GKGCMC 1 cut(s) 579
BstV2I GAAGAC 1 cut(s) 341
BstX2I RGATCY 1 cut(s) 691
BstYI RGATCY 1 cut(s) 691
BstZI CGGCCG 1 cut(s) 838
BsuI GTATCC 1 cut(s) 754
BsuRI GGCC 4 cut(s) 140, 620, 840, 855
BtgZI GCGATG 1 cut(s) 816
BtsCI GGATG 3 cut(s) 10, 812, 922
CciI TCATGA 1 cut(s) 111
CfoI GCGC 1 cut(s) 868
Cfr13I GGNCC 3 cut(s) 619, 720, 877
Csp6I GTAC 1 cut(s) 796
CviAII CATG 6 cut(s) 112, 255, 277, 455, 479, 581
CviQI GTAC 1 cut(s) 796
DdeI CTNAG 3 cut(s) 498, 780, 927
DinI GGCGCC 1 cut(s) 867
DpnI GATC 1 cut(s) 693
DpnII GATC 1 cut(s) 691
EaeI YGGCCR 2 cut(s) 838, 853
EagI CGGCCG 1 cut(s) 838
EciI GGCGGA 1 cut(s) 843
EclXI CGGCCG 1 cut(s) 838
Eco130I CCWWGG 1 cut(s) 147
Eco32I GATATC 1 cut(s) 384
Eco47I GGWCC 2 cut(s) 720, 877
Eco52I CGGCCG 1 cut(s) 838
Eco57I CTGAAG 1 cut(s) 231
Eco88I CYCGRG 1 cut(s) 905
Eco91I GGTNACC 1 cut(s) 815
EcoNI CCTNNNNNAGG 1 cut(s) 134
EcoO65I GGTNACC 1 cut(s) 815
EcoRII CCWGG 2 cut(s) 683, 784
EcoRV GATATC 1 cut(s) 384
EcoT14I CCWWGG 1 cut(s) 147
EgeI GGCGCC 1 cut(s) 867
EheI GGCGCC 1 cut(s) 867
ErhI CCWWGG 1 cut(s) 147
FaeI CATG 6 cut(s) 115, 258, 280, 458, 482, 584
FalI AAGNNNNNCTT 2 cut(s) 50, 82
FatI CATG 6 cut(s) 111, 254, 276, 454, 478, 580
FblI GTMKAC 1 cut(s) 700
Fnu4HI GCNGC 2 cut(s) 9, 889
FokI GGATG 2 cut(s) 17, 819
Fsp4HI GCNGC 2 cut(s) 9, 889
GlaI GCGC 1 cut(s) 867
GluI GCNGC 2 cut(s) 9, 889
GsaI CCCAGC 1 cut(s) 760
HaeII RGCGCY 1 cut(s) 869
HaeIII GGCC 4 cut(s) 140, 620, 840, 855
HapII CCGG 3 cut(s) 695, 841, 869
HhaI GCGC 1 cut(s) 868
Hin1I GRCGYC 1 cut(s) 866
Hin1II CATG 6 cut(s) 115, 258, 280, 458, 482, 584
Hin6I GCGC 1 cut(s) 866
HinP1I GCGC 1 cut(s) 866
HincII GTYRAC 1 cut(s) 423
HindII GTYRAC 1 cut(s) 423
HindIII AAGCTT 2 cut(s) 512, 924
HinfI GANTC 4 cut(s) 28, 251, 301, 613
HpaII CCGG 3 cut(s) 695, 841, 869
HphI GGTGA 1 cut(s) 827
Hpy166II GTNNAC 2 cut(s) 423, 701
Hpy188I TCNGA 2 cut(s) 329, 691
Hpy188III TCNNGA 8 cut(s) 32, 112, 133, 225, 305, 353, 596, 710
Hpy8I GTNNAC 2 cut(s) 423, 701
HpyAV CCTTC 5 cut(s) 76, 130, 146, 253, 423
HpyCH4III ACNGT 2 cut(s) 347, 896
HpyCH4IV ACGT 1 cut(s) 406
HpyCH4V TGCA 2 cut(s) 322, 656
HpyF10VI GCNNNNNNNGC 1 cut(s) 807
HpyF3I CTNAG 3 cut(s) 498, 780, 927
HpySE526I ACGT 1 cut(s) 406
Hsp92I GRCGYC 1 cut(s) 866
Hsp92II CATG 6 cut(s) 115, 258, 280, 458, 482, 584
HspAI GCGC 1 cut(s) 866
KasI GGCGCC 1 cut(s) 865
Kzo9I GATC 1 cut(s) 691
LweI GCATC 2 cut(s) 736, 797
MaeII ACGT 1 cut(s) 406
MaeIII GTNAC 1 cut(s) 815
MalI GATC 1 cut(s) 693
MboI GATC 1 cut(s) 691
MboII GAAGA 5 cut(s) 61, 320, 341, 347, 653
MflI RGATCY 1 cut(s) 691
MhlI GDGCHC 1 cut(s) 579
MluCI AATT 5 cut(s) 115, 163, 203, 330, 438
Mly113I GGCGCC 1 cut(s) 866
MlyI GAGTC 1 cut(s) 310
MmeI TCCRAC 1 cut(s) 669
MnlI CCTC 6 cut(s) 113, 140, 733, 890, 901, 907
MroXI GAANNNNTTC 1 cut(s) 216
MseI TTAA 1 cut(s) 516
MslI CAYNNNNRTG 1 cut(s) 477
MspCI CTTAAG 1 cut(s) 515
MspI CCGG 3 cut(s) 695, 841, 869
MspR9I CCNGG 5 cut(s) 685, 696, 786, 842, 870
MvaI CCWGG 2 cut(s) 685, 786
MwoI GCNNNNNNNGC 1 cut(s) 807
NarI GGCGCC 1 cut(s) 866
NciI CCSGG 3 cut(s) 696, 842, 870
NdeII GATC 1 cut(s) 691
NlaIII CATG 6 cut(s) 115, 258, 280, 458, 482, 584
NlaIV GGNNCC 5 cut(s) 64, 578, 682, 693, 867
NmeAIII GCCGAG 1 cut(s) 881
NmuCI GTSAC 1 cut(s) 815
PaeR7I CTCGAG 1 cut(s) 905
PagI TCATGA 1 cut(s) 111
PdmI GAANNNNTTC 1 cut(s) 216
PfeI GAWTC 3 cut(s) 28, 251, 613
PflFI GACNNNGTC 1 cut(s) 705
PkrI GCNGC 2 cut(s) 10, 890
PleI GAGTC 1 cut(s) 309
PluTI GGCGCC 1 cut(s) 869
PpsI GAGTC 1 cut(s) 309
PsiI TTATAA 1 cut(s) 168
Psp6I CCWGG 2 cut(s) 683, 784
PspEI GGTNACC 1 cut(s) 815
PspFI CCCAGC 1 cut(s) 756
PspGI CCWGG 2 cut(s) 683, 784
PspN4I GGNNCC 5 cut(s) 64, 578, 682, 693, 867
PspPI GGNCC 3 cut(s) 619, 720, 877
PspXI VCTCGAGB 1 cut(s) 905
PsuI RGATCY 1 cut(s) 691
PsyI GACNNNGTC 1 cut(s) 705
RsaI GTAC 1 cut(s) 797
RsaNI GTAC 1 cut(s) 796
RseI CAYNNNNRTG 1 cut(s) 477
SaqAI TTAA 1 cut(s) 516
SatI GCNGC 2 cut(s) 9, 889
Sau3AI GATC 1 cut(s) 691
Sau96I GGNCC 3 cut(s) 619, 720, 877
SchI GAGTC 1 cut(s) 310
ScrFI CCNGG 5 cut(s) 685, 696, 786, 842, 870
SduI GDGCHC 1 cut(s) 579
SfaNI GCATC 2 cut(s) 736, 797
SfoI GGCGCC 1 cut(s) 867
Sfr274I CTCGAG 1 cut(s) 905
SinI GGWCC 2 cut(s) 720, 877
SlaI CTCGAG 1 cut(s) 905
SmiMI CAYNNNNRTG 1 cut(s) 477
SmlI CTYRAG 2 cut(s) 515, 905
SmoI CTYRAG 2 cut(s) 515, 905
Sse9I AATT 5 cut(s) 115, 163, 203, 330, 438
SsiI CCGC 4 cut(s) 678, 810, 828, 888
SspDI GGCGCC 1 cut(s) 865
StyD4I CCNGG 5 cut(s) 683, 694, 784, 840, 868
StyI CCWWGG 1 cut(s) 147
TaaI ACNGT 2 cut(s) 347, 896
TaiI ACGT 1 cut(s) 409
TaqI TCGA 2 cut(s) 105, 906
TasI AATT 5 cut(s) 115, 163, 203, 330, 438
TauI GCSGC 1 cut(s) 891
TfiI GAWTC 3 cut(s) 28, 251, 613
Tru1I TTAA 1 cut(s) 516
Tru9I TTAA 1 cut(s) 516
TseFI GTSAC 1 cut(s) 815
TseI GCWGC 1 cut(s) 8
Tsp45I GTSAC 1 cut(s) 815
TspDTI ATGAA 3 cut(s) 128, 293, 514
TspGWI ACGGA 1 cut(s) 88
Tth111I GACNNNGTC 1 cut(s) 705
Vha464I CTTAAG 1 cut(s) 515
VpaK11BI GGWCC 2 cut(s) 720, 877
XagI CCTNNNNNAGG 1 cut(s) 134
XapI RAATTY 2 cut(s) 115, 438
XhoI CTCGAG 1 cut(s) 905
XmiI GTMKAC 1 cut(s) 700
XmnI GAANNNNTTC 1 cut(s) 216
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.