Rw5G043920

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000106
Physical Location & Seq
Reverse (-)
77099502 .. 77101027
1526 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G043920.1

Sequence Viewer

Length: 1167 bp
ATGACAAATACAAACGTACCAGAAAAACAGAAACCTTCAGGCAGCAGTATCATGGATGCATCAAATCCATATTACATTCATCCATCAGATCACCCCGGCCACGTACTTAGTAAATCTATACTTCATGCCCTCATAGCAAAGAATAAAGTTGGCTTCATCAACGGTTCTGTTAAGCCTCCTTCACAAACAGAACAACCAACTGAACACGCATTCTGGAATCAATGCAATAGTATGATTTTATCATGGCTTGCTAACTCAGTGGAACCAGATCTTGCCAAAGGCGTTATTCATGCAAAAACCGCACATCAGGTATGGGATGACTTCGAACATCAATTTTCACAACATAATGCACCAACAGTCTATCAGATTCAAAAAGCAATTGGCTCCCACTCACAAGGCACCATGACAGTCCAGACTTATTATACACAACTCAAAGGTCTCTGGGATGAATTAGAGACATATCGAGATCTTCCAGCTTGCAGTCAGATGGAAGCACATAATAAACAAAGAGAAGAAGATAGGCTGATGCAATTTCTTATAGGGCTTAGTGACACCTATAATGGTGTTCGTAGCAACATCCTCATGATGACACCATTGCCTAATGTTCGTCAAGCTTATTCAATTGTCAGTCAAGATGAGAAACAAAGACAGGTGACATCAAGATCAATAGAGAACTTCTCTATAGCTGCTGCAGTTCAGAATCGGGCAAGTAATTTTTCACCAAATTTCCTGAATAATTTCACAAACAAGCATTGTAGTCATTGCGACAAAGATGGCCATACCATTGAAACATGTCGAATTCTGAAATACTATTGCACATTTTGTGACAAGAGAGGTCATACCGATGATAGATGCAGAAATAAAAGAAATGGTGGAAATCAAGGCAGCAGACAAAACAATAAATCACAACAGCAACGTGGAGGCAACCCACATGGTTCCTTCCATGCCGCGAATGCAACAGATACAAGCCTTATCCTTCCTCGACAAGAATCCCAGGCGTCAACTTCAGCATCTTTGCGAAATCCTTTGCATAGCCTTTCGCCAGAGCAACTTCAGCAATTGGCTCAGACCATTTCTATGATGACCACACAAAATGCTTCTGGTAAGAACAACGCTTTTGCAAATGCTGCAAGACTTGGCTACGGGGAAGATGATTGGCTCAGGTGA
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_3 Retrotrans_gag

Protein Analysis

388

Amino Acids

43.55

Weight (kDa)

8.54

Isoelectric Point (pI)

43.1

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 44 - 220 1e-08 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 398
AccII CGCG 1 cut(s) 950
AciI CCGC 2 cut(s) 300, 948
AcoI YGGCCR 2 cut(s) 97, 775
AcsI RAATTY 2 cut(s) 724, 798
AcuI CTGAAG 3 cut(s) 21, 990, 1037
AcyI GRCGYC 1 cut(s) 998
AfaI GTAC 2 cut(s) 18, 105
AflIII ACRYGT 1 cut(s) 791
AgsI TTSAA 3 cut(s) 371, 621, 788
AjnI CCWGG 1 cut(s) 993
AluBI AGCT 3 cut(s) 476, 614, 686
AluI AGCT 3 cut(s) 476, 614, 686
Alw26I GTCTC 2 cut(s) 443, 449
AoxI GGCC 2 cut(s) 97, 775
ApeKI GCWGC 5 cut(s) 42, 686, 689, 885, 1127
ApoI RAATTY 2 cut(s) 724, 798
Asp700I GAANNNNTTC 1 cut(s) 737
AsuC2I CCSGG 1 cut(s) 96
AsuHPI GGTGA 3 cut(s) 83, 664, 711
AsuII TTCGAA 1 cut(s) 324
BaeI ACNNNNGTAYC 1 cut(s) 33
BalI TGGCCA 1 cut(s) 777
BanI GGYRCC 1 cut(s) 398
BbvI GCAGC 5 cut(s) 54, 673, 676, 897, 1114
BccI CCATC 3 cut(s) 91, 481, 767
BciT130I CCWGG 1 cut(s) 995
BcnI CCSGG 1 cut(s) 96
BcoDI GTCTC 2 cut(s) 443, 449
BfmI CTRYAG 2 cut(s) 681, 690
BglII AGATCT 2 cut(s) 268, 466
BisI GCNGC 6 cut(s) 43, 687, 690, 886, 948, 1128
BlsI GCNGC 6 cut(s) 44, 688, 691, 887, 949, 1129
Bme1390I CCNGG 2 cut(s) 96, 995
BmiI GGNNCC 4 cut(s) 264, 385, 400, 937
BmrFI CCNGG 2 cut(s) 96, 995
BmsI GCATC 5 cut(s) 46, 68, 516, 842, 1019
BplI GAGNNNNNCTC 2 cut(s) 662, 694
Bpu10I CCTNAGC 1 cut(s) 1160
Bpu14I TTCGAA 1 cut(s) 324
BpuMI CCSGG 1 cut(s) 96
BsaAI YACGTR 1 cut(s) 103
BsaHI GRCGYC 1 cut(s) 998
BsaI GGTCTC 1 cut(s) 443
BsaJI CCNNGG 2 cut(s) 94, 993
Bse3DI GCAATG 2 cut(s) 593, 760
BseBI CCWGG 1 cut(s) 995
BseDI CCNNGG 2 cut(s) 94, 993
BseGI GGATG 5 cut(s) 61, 79, 322, 451, 576
BseMI GCAATG 2 cut(s) 593, 760
BseMII CTCAG 2 cut(s) 270, 1079
BseXI GCAGC 5 cut(s) 54, 673, 676, 897, 1114
Bsh1236I CGCG 1 cut(s) 950
BshFI GGCC 2 cut(s) 99, 777
BshNI GGYRCC 1 cut(s) 398
BsiSI CCGG 1 cut(s) 96
BsmAI GTCTC 2 cut(s) 443, 449
BsmI GAATGC 2 cut(s) 209, 958
BsnI GGCC 2 cut(s) 99, 777
Bso31I GGTCTC 1 cut(s) 443
Bsp119I TTCGAA 1 cut(s) 324
Bsp143I GATC 4 cut(s) 88, 268, 466, 662
BspACI CCGC 2 cut(s) 300, 948
BspANI GGCC 2 cut(s) 99, 777
BspCNI CTCAG 2 cut(s) 269, 1078
BspFNI CGCG 1 cut(s) 950
BspHI TCATGA 1 cut(s) 582
BspLI GGNNCC 4 cut(s) 264, 385, 400, 937
BspMAI CTGCAG 1 cut(s) 694
BspT104I TTCGAA 1 cut(s) 324
BspT107I GGYRCC 1 cut(s) 398
BspTNI GGTCTC 1 cut(s) 443
BsrDI GCAATG 2 cut(s) 593, 760
BssECI CCNNGG 2 cut(s) 94, 993
BssMI GATC 4 cut(s) 88, 268, 466, 662
BssNI GRCGYC 1 cut(s) 998
Bst2UI CCWGG 1 cut(s) 995
Bst4CI ACNGT 3 cut(s) 164, 358, 409
BstACI GRCGYC 1 cut(s) 998
BstAPI GCANNNNNTGC 1 cut(s) 1127
BstBAI YACGTR 1 cut(s) 103
BstBI TTCGAA 1 cut(s) 324
BstC8I GCNNGC 2 cut(s) 249, 478
BstDEI CTNAG 5 cut(s) 107, 256, 545, 1065, 1160
BstF5I GGATG 5 cut(s) 61, 79, 322, 451, 576
BstFNI CGCG 1 cut(s) 950
BstKTI GATC 4 cut(s) 91, 271, 469, 665
BstMAI GTCTC 2 cut(s) 443, 449
BstMBI GATC 4 cut(s) 88, 268, 466, 662
BstMWI GCNNNNNNNGC 5 cut(s) 134, 299, 953, 1054, 1127
BstNI CCWGG 1 cut(s) 995
BstNSI RCATGY 1 cut(s) 795
BstSCI CCNGG 2 cut(s) 94, 993
BstSFI CTRYAG 2 cut(s) 681, 690
BstUI CGCG 1 cut(s) 950
BstV1I GCAGC 5 cut(s) 54, 673, 676, 897, 1114
BstX2I RGATCY 2 cut(s) 268, 466
BstYI RGATCY 2 cut(s) 268, 466
BsuRI GGCC 2 cut(s) 99, 777
BtsCI GGATG 5 cut(s) 61, 79, 322, 451, 576
BtsIMutI CAGTG 1 cut(s) 264
Cac8I GCNNGC 2 cut(s) 249, 478
CciI TCATGA 1 cut(s) 582
CseI GACGC 1 cut(s) 987
Csp6I GTAC 2 cut(s) 17, 104
CviAII CATG 9 cut(s) 52, 125, 243, 290, 403, 583, 792, 932, 944
CviQI GTAC 2 cut(s) 17, 104
DdeI CTNAG 5 cut(s) 107, 256, 545, 1065, 1160
DpnI GATC 4 cut(s) 90, 270, 468, 664
DpnII GATC 4 cut(s) 88, 268, 466, 662
EaeI YGGCCR 2 cut(s) 97, 775
Eco31I GGTCTC 1 cut(s) 443
Eco57I CTGAAG 3 cut(s) 21, 990, 1037
EcoRI GAATTC 1 cut(s) 798
EcoRII CCWGG 1 cut(s) 993
EcoT22I ATGCAT 1 cut(s) 61
FaeI CATG 9 cut(s) 55, 128, 246, 293, 406, 586, 795, 935, 947
FatI CATG 9 cut(s) 51, 124, 242, 289, 402, 582, 791, 931, 943
Fnu4HI GCNGC 6 cut(s) 43, 687, 690, 886, 948, 1128
FokI GGATG 5 cut(s) 66, 68, 329, 458, 563
Fsp4HI GCNGC 6 cut(s) 43, 687, 690, 886, 948, 1128
GluI GCNGC 6 cut(s) 43, 687, 690, 886, 948, 1128
HaeIII GGCC 2 cut(s) 99, 777
HapII CCGG 1 cut(s) 96
HgaI GACGC 1 cut(s) 987
Hin1I GRCGYC 1 cut(s) 998
Hin1II CATG 9 cut(s) 55, 128, 246, 293, 406, 586, 795, 935, 947
HincII GTYRAC 1 cut(s) 1002
HindII GTYRAC 1 cut(s) 1002
HindIII AAGCTT 1 cut(s) 612
HinfI GANTC 4 cut(s) 217, 367, 700, 989
HpaII CCGG 1 cut(s) 96
HphI GGTGA 3 cut(s) 83, 664, 711
Hpy166II GTNNAC 1 cut(s) 1002
Hpy188I TCNGA 6 cut(s) 88, 366, 486, 699, 804, 1068
Hpy188III TCNNGA 7 cut(s) 214, 412, 464, 583, 632, 660, 730
Hpy8I GTNNAC 1 cut(s) 1002
HpyAV CCTTC 4 cut(s) 45, 189, 949, 986
HpyCH4III ACNGT 3 cut(s) 164, 358, 409
HpyCH4IV ACGT 3 cut(s) 15, 102, 916
HpyF10VI GCNNNNNNNGC 5 cut(s) 134, 299, 953, 1054, 1127
HpyF3I CTNAG 5 cut(s) 107, 256, 545, 1065, 1160
HpySE526I ACGT 3 cut(s) 15, 102, 916
Hsp92I GRCGYC 1 cut(s) 998
Hsp92II CATG 9 cut(s) 55, 128, 246, 293, 406, 586, 795, 935, 947
Kzo9I GATC 4 cut(s) 88, 268, 466, 662
LmnI GCTCC 1 cut(s) 389
Lsp1109I GCAGC 5 cut(s) 54, 673, 676, 897, 1114
LweI GCATC 5 cut(s) 46, 68, 516, 842, 1019
MaeII ACGT 3 cut(s) 15, 102, 916
MaeIII GTNAC 3 cut(s) 548, 652, 824
MalI GATC 4 cut(s) 90, 270, 468, 664
MboI GATC 4 cut(s) 88, 268, 466, 662
MboII GAAGA 4 cut(s) 461, 524, 527, 1160
MfeI CAATTG 3 cut(s) 378, 621, 1058
MflI RGATCY 2 cut(s) 268, 466
MlsI TGGCCA 1 cut(s) 777
MluNI TGGCCA 1 cut(s) 777
MnlI CCTC 6 cut(s) 140, 186, 590, 827, 914, 990
Mox20I TGGCCA 1 cut(s) 777
Mph1103I ATGCAT 1 cut(s) 61
MroXI GAANNNNTTC 1 cut(s) 737
MscI TGGCCA 1 cut(s) 777
MseI TTAA 1 cut(s) 171
MslI CAYNNNNRTG 3 cut(s) 581, 843, 1076
Msp20I TGGCCA 1 cut(s) 777
MspI CCGG 1 cut(s) 96
MspR9I CCNGG 2 cut(s) 96, 995
MunI CAATTG 3 cut(s) 378, 621, 1058
Mva1269I GAATGC 2 cut(s) 209, 958
MvaI CCWGG 1 cut(s) 995
MvnI CGCG 1 cut(s) 950
MwoI GCNNNNNNNGC 5 cut(s) 134, 299, 953, 1054, 1127
NciI CCSGG 1 cut(s) 96
NdeII GATC 4 cut(s) 88, 268, 466, 662
NlaIII CATG 9 cut(s) 55, 128, 246, 293, 406, 586, 795, 935, 947
NlaIV GGNNCC 4 cut(s) 264, 385, 400, 937
NmuCI GTSAC 3 cut(s) 548, 652, 824
NsiI ATGCAT 1 cut(s) 61
NspI RCATGY 1 cut(s) 795
NspV TTCGAA 1 cut(s) 324
PagI TCATGA 1 cut(s) 582
PciI ACATGT 1 cut(s) 791
PctI GAATGC 2 cut(s) 209, 958
PdmI GAANNNNTTC 1 cut(s) 737
PfeI GAWTC 4 cut(s) 217, 367, 700, 989
PkrI GCNGC 6 cut(s) 44, 688, 691, 887, 949, 1129
Ppu21I YACGTR 1 cut(s) 103
PscI ACATGT 1 cut(s) 791
Psp6I CCWGG 1 cut(s) 993
PspGI CCWGG 1 cut(s) 993
PspN4I GGNNCC 4 cut(s) 264, 385, 400, 937
PstI CTGCAG 1 cut(s) 694
PsuI RGATCY 2 cut(s) 268, 466
RsaI GTAC 2 cut(s) 18, 105
RsaNI GTAC 2 cut(s) 17, 104
RseI CAYNNNNRTG 3 cut(s) 581, 843, 1076
SaqAI TTAA 1 cut(s) 171
SatI GCNGC 6 cut(s) 43, 687, 690, 886, 948, 1128
Sau3AI GATC 4 cut(s) 88, 268, 466, 662
ScrFI CCNGG 2 cut(s) 96, 995
SfaNI GCATC 5 cut(s) 46, 68, 516, 842, 1019
SfcI CTRYAG 2 cut(s) 681, 690
SfuI TTCGAA 1 cut(s) 324
SmiMI CAYNNNNRTG 3 cut(s) 581, 843, 1076
SsiI CCGC 2 cut(s) 300, 948
StyD4I CCNGG 2 cut(s) 94, 993
TaaI ACNGT 3 cut(s) 164, 358, 409
TaiI ACGT 3 cut(s) 18, 105, 919
TaqI TCGA 4 cut(s) 324, 463, 796, 982
TauI GCSGC 1 cut(s) 950
TfiI GAWTC 4 cut(s) 217, 367, 700, 989
Tru1I TTAA 1 cut(s) 171
Tru9I TTAA 1 cut(s) 171
TscAI CASTG 1 cut(s) 264
TseFI GTSAC 3 cut(s) 548, 652, 824
TseI GCWGC 5 cut(s) 42, 686, 689, 885, 1127
Tsp45I GTSAC 3 cut(s) 548, 652, 824
TspDTI ATGAA 5 cut(s) 68, 113, 145, 278, 462
TspRI CASTG 1 cut(s) 264
XapI RAATTY 2 cut(s) 724, 798
XceI RCATGY 1 cut(s) 795
XmnI GAANNNNTTC 1 cut(s) 737
Zsp2I ATGCAT 1 cut(s) 61
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.