Rw1G025510

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0000258
Physical Location & Seq
Forward (+)
52190702 .. 52192536
1835 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G025510.1

Sequence Viewer

Length: 972 bp
ATGATAGCATCCGCCTGCGGAATATATAAGGTTTTAACTCTGATGGAAGAGAAAAACGTTAGAGAGGACCTGGAGGACACGATGTCGATTGAAGACCATCTCAAGAATATAGTTGACAAAACAGACCAGTTGAACCTTCAAGAAGATGAAAAATTGCAGGCAAAACAAGAGCTCCTAAACAAGAGACACCGAAGTTTGTTGTCTCATTATTTCAAACCGACAGCTGAACAAGACAATGAAAAGCAAGTTCCTACCACTGAAGAACCAGAAGTTAGTTTGGGAACCAGAGAAAAGGAGAATGAGAACAAGAGTTCTGTATCAAAGTTAAGATCCCGACTAGCTCAGATTGAGCCTATTCGTTTTTATGGGAAGAACTACCATATCTGGGCGCAACAGATGAAACTTTACCTAAAGAAATTGAAGGTTGCATATGTACTCTGTGAGCCCTGCCCAACCATTATGCTTGGATTAGAAGCAAGTCCAGAGGAAATTGTTCAATCCATGGCTGCTAAACAGAAATGGATGAATGATGACACCAGGTGTGGTCGTACAATCTTGCATCATCTATCTGTTTGTCTATTTCATGCTTACTCACAGAAACAGGAGACTATGACTGCGAAAGATCTGTGGAAAGATCTAGAATTAAAATTTGGAACAGAAGAATCTATGATTACAACAGAGACATCTCTGGTTGAAAAGTACATCAAATTTCGGATCCTTAGGACAAAACCAATTGTGGAGCAAGTTAAAGAATTCAATAGTATCTTTGATTCTCTTTTCGCTTCTGGACTGGTGGTCGATGAGAAATTCCATGTCAATGTCCTCATCTCTAAGCTCAACCCTTCTTGGAAAAATGTTTTCAACCGGTTGATAGGCAAGGAATATCTGAGTAGTCTTGCAATGGTGATGGATATTTTGAGGGTTGAAGAAGGGCGGCGCTTCATGAGGAAGAATTTGAAGTTACATTCATGA
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
DEK_C PC4 Retrotran_gag_2

Protein Analysis

323

Amino Acids

37.7

Weight (kDa)

8.12

Isoelectric Point (pI)

53.97

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 161 - 315 1.5e-14 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)
AciI CCGC 3 cut(s) 12, 18, 934
AclI AACGTT 1 cut(s) 57
AclWI GGATC 3 cut(s) 324, 709, 722
AcsI RAATTY 5 cut(s) 647, 707, 752, 806, 952
AcuI CTGAAG 1 cut(s) 279
AdeI CACNNNGTG 1 cut(s) 540
AfaI GTAC 3 cut(s) 435, 550, 701
AfiI CCNNNNNNNGG 1 cut(s) 385
AgeI ACCGGT 1 cut(s) 864
AhdI GACNNNNNGTC 2 cut(s) 82, 794
AjnI CCWGG 2 cut(s) 69, 536
AjuI GAANNNNNNNTTGG 2 cut(s) 633, 665
AluBI AGCT 4 cut(s) 172, 224, 341, 835
AluI AGCT 4 cut(s) 172, 224, 341, 835
Alw21I GWGCWC 1 cut(s) 174
Alw26I GTCTC 4 cut(s) 178, 207, 599, 674
AlwI GGATC 3 cut(s) 324, 709, 722
ApeKI GCWGC 1 cut(s) 506
ApoI RAATTY 5 cut(s) 647, 707, 752, 806, 952
AsiGI ACCGGT 1 cut(s) 864
Asp700I GAANNNNTTC 1 cut(s) 492
AspLEI GCGC 2 cut(s) 391, 939
AspS9I GGNCC 1 cut(s) 67
AsuHPI GGTGA 1 cut(s) 916
AvaII GGWCC 1 cut(s) 67
AxyI CCTNAGG 1 cut(s) 719
BamHI GGATCC 1 cut(s) 714
BanII GRGCYC 2 cut(s) 174, 447
BbsI GAAGAC 1 cut(s) 99
Bbv12I GWGCWC 1 cut(s) 174
BbvI GCAGC 1 cut(s) 493
BccI CCATC 3 cut(s) 37, 105, 901
BciT130I CCWGG 2 cut(s) 71, 538
BcoDI GTCTC 4 cut(s) 178, 207, 599, 674
BfaI CTAG 2 cut(s) 338, 638
BfoI RGCGCY 1 cut(s) 940
BglII AGATCT 2 cut(s) 622, 634
BisI GCNGC 2 cut(s) 507, 935
BlsI GCNGC 2 cut(s) 508, 936
Bme1390I CCNGG 2 cut(s) 71, 538
Bme18I GGWCC 1 cut(s) 67
BmeRI GACNNNNNGTC 2 cut(s) 82, 794
BmgT120I GGNCC 1 cut(s) 67
BmiI GGNNCC 2 cut(s) 283, 716
BmrFI CCNGG 2 cut(s) 71, 538
BmsI GCATC 2 cut(s) 17, 568
BpiI GAAGAC 1 cut(s) 99
BpmI CTGGAG 1 cut(s) 92
BpuEI CTTGAG 1 cut(s) 86
BsaJI CCNNGG 1 cut(s) 501
BsaWI WCCGGW 1 cut(s) 864
BsaXI ACNNNNNCTCC 2 cut(s) 156, 186
Bsc4I CCNNNNNNNGG 1 cut(s) 385
Bse118I RCCGGY 1 cut(s) 864
Bse1I ACTGG 2 cut(s) 127, 795
Bse21I CCTNAGG 1 cut(s) 719
Bse3DI GCAATG 1 cut(s) 906
BseBI CCWGG 2 cut(s) 71, 538
BseDI CCNNGG 1 cut(s) 501
BseGI GGATG 2 cut(s) 8, 528
BseLI CCNNNNNNNGG 1 cut(s) 385
BseMI GCAATG 1 cut(s) 906
BseMII CTCAG 2 cut(s) 356, 878
BseNI ACTGG 2 cut(s) 127, 795
BseXI GCAGC 1 cut(s) 493
BshTI ACCGGT 1 cut(s) 864
BsiHKAI GWGCWC 1 cut(s) 174
BsiSI CCGG 1 cut(s) 865
BslI CCNNNNNNNGG 1 cut(s) 385
BsmAI GTCTC 4 cut(s) 178, 207, 599, 674
Bsp1286I GDGCHC 2 cut(s) 174, 447
Bsp143I GATC 4 cut(s) 329, 622, 634, 714
Bsp19I CCATGG 1 cut(s) 501
BspACI CCGC 3 cut(s) 12, 18, 934
BspCNI CTCAG 2 cut(s) 355, 879
BspHI TCATGA 2 cut(s) 942, 968
BspLI GGNNCC 2 cut(s) 283, 716
BspPI GGATC 3 cut(s) 324, 709, 722
BsrDI GCAATG 1 cut(s) 906
BsrFI RCCGGY 1 cut(s) 864
BsrI ACTGG 2 cut(s) 127, 795
BssAI RCCGGY 1 cut(s) 864
BssECI CCNNGG 1 cut(s) 501
BssMI GATC 4 cut(s) 329, 622, 634, 714
BssT1I CCWWGG 1 cut(s) 501
Bst2UI CCWGG 2 cut(s) 71, 538
Bst6I CTCTTC 1 cut(s) 42
BstC8I GCNNGC 2 cut(s) 16, 159
BstDEI CTNAG 4 cut(s) 342, 719, 831, 887
BstDSI CCRYGG 1 cut(s) 501
BstF5I GGATG 2 cut(s) 8, 528
BstH2I RGCGCY 1 cut(s) 940
BstHHI GCGC 2 cut(s) 391, 939
BstKTI GATC 4 cut(s) 332, 625, 637, 717
BstMAI GTCTC 4 cut(s) 178, 207, 599, 674
BstMBI GATC 4 cut(s) 329, 622, 634, 714
BstNI CCWGG 2 cut(s) 71, 538
BstSCI CCNGG 2 cut(s) 69, 536
BstV1I GCAGC 1 cut(s) 493
BstV2I GAAGAC 1 cut(s) 99
BstX2I RGATCY 4 cut(s) 329, 622, 634, 714
BstYI RGATCY 4 cut(s) 329, 622, 634, 714
Bsu36I CCTNAGG 1 cut(s) 719
BtgI CCRYGG 1 cut(s) 501
BtsCI GGATG 2 cut(s) 8, 528
BtsIMutI CAGTG 1 cut(s) 255
Cac8I GCNNGC 2 cut(s) 16, 159
CciI TCATGA 2 cut(s) 942, 968
CfoI GCGC 2 cut(s) 391, 939
Cfr10I RCCGGY 1 cut(s) 864
Cfr13I GGNCC 1 cut(s) 67
CsiI ACCWGGT 1 cut(s) 536
Csp6I GTAC 3 cut(s) 434, 549, 700
CspAI ACCGGT 1 cut(s) 864
CviAII CATG 5 cut(s) 502, 584, 812, 943, 969
CviJI RGCY 7 cut(s) 172, 224, 341, 352, 445, 506, 835
CviKI_1 RGCY 7 cut(s) 172, 224, 341, 352, 445, 506, 835
CviQI GTAC 3 cut(s) 434, 549, 700
DdeI CTNAG 4 cut(s) 342, 719, 831, 887
DpnI GATC 4 cut(s) 331, 624, 636, 716
DpnII GATC 4 cut(s) 329, 622, 634, 714
DraIII CACNNNGTG 1 cut(s) 540
DriI GACNNNNNGTC 2 cut(s) 82, 794
Eam1104I CTCTTC 1 cut(s) 42
Eam1105I GACNNNNNGTC 2 cut(s) 82, 794
EarI CTCTTC 1 cut(s) 42
Ecl136II GAGCTC 1 cut(s) 172
Eco130I CCWWGG 1 cut(s) 501
Eco24I GRGCYC 2 cut(s) 174, 447
Eco47I GGWCC 1 cut(s) 67
Eco53kI GAGCTC 1 cut(s) 172
Eco57I CTGAAG 1 cut(s) 279
Eco81I CCTNAGG 1 cut(s) 719
EcoICRI GAGCTC 1 cut(s) 172
EcoO109I RGGNCCY 1 cut(s) 67
EcoRI GAATTC 1 cut(s) 752
EcoRII CCWGG 2 cut(s) 69, 536
EcoT14I CCWWGG 1 cut(s) 501
EcoT38I GRGCYC 2 cut(s) 174, 447
ErhI CCWWGG 1 cut(s) 501
FaeI CATG 5 cut(s) 505, 587, 815, 946, 972
FatI CATG 5 cut(s) 501, 583, 811, 942, 968
FauNDI CATATG 1 cut(s) 430
Fnu4HI GCNGC 2 cut(s) 507, 935
FokI GGATG 1 cut(s) 535
FriOI GRGCYC 2 cut(s) 174, 447
Fsp4HI GCNGC 2 cut(s) 507, 935
FspBI CTAG 2 cut(s) 338, 638
GlaI GCGC 2 cut(s) 390, 938
GluI GCNGC 2 cut(s) 507, 935
GsuI CTGGAG 1 cut(s) 92
HaeII RGCGCY 1 cut(s) 940
HapII CCGG 1 cut(s) 865
HhaI GCGC 2 cut(s) 391, 939
Hin1II CATG 5 cut(s) 505, 587, 815, 946, 972
Hin6I GCGC 2 cut(s) 389, 937
HinP1I GCGC 2 cut(s) 389, 937
HincII GTYRAC 1 cut(s) 115
HindII GTYRAC 1 cut(s) 115
HinfI GANTC 2 cut(s) 662, 770
HpaII CCGG 1 cut(s) 865
HphI GGTGA 1 cut(s) 916
Hpy166II GTNNAC 1 cut(s) 115
Hpy188I TCNGA 4 cut(s) 42, 345, 714, 888
Hpy188III TCNNGA 8 cut(s) 103, 140, 333, 482, 638, 786, 943, 969
Hpy8I GTNNAC 1 cut(s) 115
HpyAV CCTTC 4 cut(s) 146, 415, 852, 923
HpyCH4IV ACGT 1 cut(s) 57
HpyCH4V TGCA 4 cut(s) 157, 428, 559, 899
HpyF3I CTNAG 4 cut(s) 342, 719, 831, 887
HpySE526I ACGT 1 cut(s) 57
Hsp92II CATG 5 cut(s) 505, 587, 815, 946, 972
HspAI GCGC 2 cut(s) 389, 937
Kzo9I GATC 4 cut(s) 329, 622, 634, 714
LmnI GCTCC 2 cut(s) 177, 739
Lsp1109I GCAGC 1 cut(s) 493
LweI GCATC 2 cut(s) 17, 568
MabI ACCWGGT 1 cut(s) 536
MaeI CTAG 2 cut(s) 338, 638
MaeII ACGT 1 cut(s) 57
MaeIII GTNAC 1 cut(s) 960
MalI GATC 4 cut(s) 331, 624, 636, 716
MboI GATC 4 cut(s) 329, 622, 634, 714
MboII GAAGA 8 cut(s) 59, 104, 155, 272, 382, 671, 938, 961
MfeI CAATTG 1 cut(s) 732
MflI RGATCY 4 cut(s) 329, 622, 634, 714
MhlI GDGCHC 2 cut(s) 174, 447
MnlI CCTC 6 cut(s) 58, 67, 478, 833, 912, 939
MroXI GAANNNNTTC 1 cut(s) 492
MseI TTAA 4 cut(s) 35, 326, 644, 747
MslI CAYNNNNRTG 1 cut(s) 816
MspA1I CMGCKG 1 cut(s) 224
MspI CCGG 1 cut(s) 865
MspR9I CCNGG 2 cut(s) 71, 538
MunI CAATTG 1 cut(s) 732
MvaI CCWGG 2 cut(s) 71, 538
NcoI CCATGG 1 cut(s) 501
NdeI CATATG 1 cut(s) 430
NdeII GATC 4 cut(s) 329, 622, 634, 714
NlaIII CATG 5 cut(s) 505, 587, 815, 946, 972
NlaIV GGNNCC 2 cut(s) 283, 716
PagI TCATGA 2 cut(s) 942, 968
PdmI GAANNNNTTC 1 cut(s) 492
PfeI GAWTC 2 cut(s) 662, 770
PinAI ACCGGT 1 cut(s) 864
PkrI GCNGC 2 cut(s) 508, 936
PpuMI RGGWCCY 1 cut(s) 67
Psp124BI GAGCTC 1 cut(s) 174
Psp1406I AACGTT 1 cut(s) 57
Psp5II RGGWCCY 1 cut(s) 67
Psp6I CCWGG 2 cut(s) 69, 536
PspGI CCWGG 2 cut(s) 69, 536
PspN4I GGNNCC 2 cut(s) 283, 716
PspPI GGNCC 1 cut(s) 67
PspPPI RGGWCCY 1 cut(s) 67
PsuI RGATCY 4 cut(s) 329, 622, 634, 714
PvuII CAGCTG 1 cut(s) 224
RsaI GTAC 3 cut(s) 435, 550, 701
RsaNI GTAC 3 cut(s) 434, 549, 700
RseI CAYNNNNRTG 1 cut(s) 816
SacI GAGCTC 1 cut(s) 174
SaqAI TTAA 4 cut(s) 35, 326, 644, 747
SatI GCNGC 2 cut(s) 507, 935
Sau3AI GATC 4 cut(s) 329, 622, 634, 714
Sau96I GGNCC 1 cut(s) 67
ScrFI CCNGG 2 cut(s) 71, 538
SduI GDGCHC 2 cut(s) 174, 447
SexAI ACCWGGT 1 cut(s) 536
SfaNI GCATC 2 cut(s) 17, 568
SinI GGWCC 1 cut(s) 67
SmiMI CAYNNNNRTG 1 cut(s) 816
SmlI CTYRAG 1 cut(s) 101
SmoI CTYRAG 1 cut(s) 101
SsiI CCGC 3 cut(s) 12, 18, 934
SspMI CTAG 2 cut(s) 338, 638
SstI GAGCTC 1 cut(s) 174
StyD4I CCNGG 2 cut(s) 69, 536
StyI CCWWGG 1 cut(s) 501
TaiI ACGT 1 cut(s) 60
TaqI TCGA 2 cut(s) 86, 798
TatI WGTACW 2 cut(s) 433, 699
TauI GCSGC 1 cut(s) 937
TfiI GAWTC 2 cut(s) 662, 770
Tru1I TTAA 4 cut(s) 35, 326, 644, 747
Tru9I TTAA 4 cut(s) 35, 326, 644, 747
TscAI CASTG 1 cut(s) 262
TseI GCWGC 1 cut(s) 506
TspDTI ATGAA 7 cut(s) 162, 252, 413, 539, 572, 931, 957
TspRI CASTG 1 cut(s) 262
VpaK11BI GGWCC 1 cut(s) 67
XapI RAATTY 5 cut(s) 647, 707, 752, 806, 952
XbaI TCTAGA 1 cut(s) 637
XmnI GAANNNNTTC 1 cut(s) 492
XspI CTAG 2 cut(s) 338, 638
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.