Rw5G019500

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000258
Physical Location & Seq
Forward (+)
25436382 .. 25439159
2778 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G019500.1

Sequence Viewer

Length: 1299 bp
ATGGATCAATCGCTGAATGTTGTTAAGAACAACTCTCATGCTGAGAAACCAGAGCAATTCAAGGGAGTTGATTTCAAGCGCTGGCAACAGAAAATGTTGTTTTACCTCACAACATTGAACTTGGCCCATGTGATTTCTCAAGAGAAACCTGTGGCAGAAGAACTTCCAATCTCAAAGGAAACTTTGAATGCAATAGATGCTTGCACACATAGTGAGTTCCTATGCAGGAACTATATCCTCAATGGATTGGATAACACCCTCTATGACGTTTATGTGACTTGCAAGACTGCAAAGGAACTATGGGAGTCATTAGAGAAGAAGTATCTGTCACAAGCTGCAAGTGCAGGCAAGTTCATCGTCGGCAAGTTCATGAACTACAGGATGGTGGATCTCAAGTCAATTCTCAACCAAGTTGAAGAGTTGAAGATCATCATTCATGAATTGCACACCGAAGGCATGAACCTCGATGAAAAATTTCAAGTGGGTGCATTCATAGAGAAGCTTCCTCCATCCTGGAAATATTTTAAGCAAACCTTGAAGCACTTGACTGAAGAATTGTCTGTGGAAAAACTGGTTTTGAAGCTTCGGGTTGAAGAAGGAAATAGAATGAATGAGAAGAATGAAGTCTCATCTTTTGAAGCCAAAGCAAACATTGTGGAAGGAGACTCAACCAAGTCTAAGCCCACTTTGCAAAAGAAGAACAAAGGCAAAGCCCCAACAAAAGGTTTATCCTTTGCTCCGAAAGGGAAAAATTTCAAAACCAAAGGAGGCTGTTGGGTCTGTGGGAAACCAGGCCATAGAGCACAGGTTTGTCGTCATAGAAAGGACCAAAACACTAGTGGAAATCAAGGTAACAATAATCAAGCACATGTGGCTATTGATACTGATTTTGTTGCTGTGGTTTCTGAGGTTAATATGGTTGGAGACACCAAGGATTGGTGGGTGGACACCAGTGCAACAAGGCACATATGCTTTGACAGAAGTTTGTTCACTACCTATCAAGAAATTGAAGCTGAAAATCTGTTCATGGGAAATGCATCAACATCTGCTGTGAAAGGGAAGGGAAAGGTGATACTGAAACTCACTTCTGGCAAACAATTGGCTCTCCTTGATGTGTTGCACGTCCCTGACATAAGAAAGAATCTGGTTTCTGGTCCCATTTTAAGCAACAAGGGATTTAAGCTTGTATTTGAATCTGATAAGTTTGTACTCACCAAAGGTAGGATATTTGGAAAGGGCTATCTTGCAGATGGTCTCTTTAAACTCAATGACAATGCAAGCAAACATGATGCCATATGA
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

Protein Analysis

432

Amino Acids

48.65

Weight (kDa)

9.12

Isoelectric Point (pI)

25.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 205 2.2e-25 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 313 - 393 1.7e-23 Pol polyprotein, beta-barrel domain
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)
AccB7I CCANNNNNTGG 1 cut(s) 936
AclWI GGATC 2 cut(s) 12, 396
AcsI RAATTY 2 cut(s) 473, 751
AcuI CTGAAG 1 cut(s) 570
AdeI CACNNNGTG 1 cut(s) 212
AfaI GTAC 1 cut(s) 1209
AfeI AGCGCT 1 cut(s) 80
AfiI CCNNNNNNNGG 3 cut(s) 722, 936, 1221
AflIII ACRYGT 1 cut(s) 868
AhlI ACTAGT 1 cut(s) 836
AjiI CACGTC 1 cut(s) 1123
AjnI CCWGG 2 cut(s) 512, 790
AluBI AGCT 5 cut(s) 335, 502, 583, 1013, 1183
AluI AGCT 5 cut(s) 335, 502, 583, 1013, 1183
Alw21I GWGCWC 1 cut(s) 805
Alw26I GTCTC 4 cut(s) 631, 657, 918, 1259
AlwI GGATC 2 cut(s) 12, 396
Aor51HI AGCGCT 1 cut(s) 80
AoxI GGCC 2 cut(s) 123, 793
ApeKI GCWGC 1 cut(s) 335
ApoI RAATTY 2 cut(s) 473, 751
Asp700I GAANNNNTTC 3 cut(s) 162, 474, 752
AspLEI GCGC 1 cut(s) 81
AspS9I GGNCC 3 cut(s) 124, 826, 1154
AsuHPI GGTGA 2 cut(s) 1081, 1204
AvaII GGWCC 2 cut(s) 826, 1154
Bbv12I GWGCWC 1 cut(s) 805
BbvI GCAGC 1 cut(s) 322
BccI CCATC 3 cut(s) 376, 517, 1244
BcgI CGANNNNNNTGC 4 cut(s) 337, 371, 445, 479
BciT130I CCWGG 2 cut(s) 514, 792
BcoDI GTCTC 4 cut(s) 631, 657, 918, 1259
BcuI ACTAGT 1 cut(s) 836
BfaI CTAG 1 cut(s) 837
BfmI CTRYAG 1 cut(s) 376
BfoI RGCGCY 1 cut(s) 82
BisI GCNGC 1 cut(s) 336
BlsI GCNGC 1 cut(s) 337
Bme1390I CCNGG 2 cut(s) 514, 792
Bme18I GGWCC 2 cut(s) 826, 1154
BmgBI CACGTC 1 cut(s) 1123
BmgT120I GGNCC 3 cut(s) 124, 826, 1154
BmiI GGNNCC 1 cut(s) 1156
BmrFI CCNGG 2 cut(s) 514, 792
BmsI GCATC 3 cut(s) 187, 1046, 1279
BpuEI CTTGAG 2 cut(s) 123, 377
BsaI GGTCTC 1 cut(s) 1259
BsaJI CCNNGG 1 cut(s) 930
Bsc4I CCNNNNNNNGG 3 cut(s) 722, 936, 1221
Bse1I ACTGG 2 cut(s) 576, 951
BseBI CCWGG 2 cut(s) 514, 792
BseDI CCNNGG 1 cut(s) 930
BseGI GGATG 2 cut(s) 387, 509
BseLI CCNNNNNNNGG 3 cut(s) 722, 936, 1221
BseMII CTCAG 2 cut(s) 33, 897
BseNI ACTGG 2 cut(s) 576, 951
BseXI GCAGC 1 cut(s) 322
BsgI GTGCAG 1 cut(s) 363
BshFI GGCC 2 cut(s) 125, 795
BsiHKAI GWGCWC 1 cut(s) 805
BslFI GGGAC 2 cut(s) 1109, 1140
BslI CCNNNNNNNGG 3 cut(s) 722, 936, 1221
BsmAI GTCTC 4 cut(s) 631, 657, 918, 1259
BsmFI GGGAC 2 cut(s) 1109, 1140
BsmI GAATGC 2 cut(s) 193, 488
BsnI GGCC 2 cut(s) 125, 795
Bso31I GGTCTC 1 cut(s) 1259
Bsp1286I GDGCHC 1 cut(s) 805
Bsp143I GATC 3 cut(s) 4, 388, 426
BspANI GGCC 2 cut(s) 125, 795
BspCNI CTCAG 2 cut(s) 34, 898
BspHI TCATGA 2 cut(s) 369, 436
BspLI GGNNCC 1 cut(s) 1156
BspPI GGATC 2 cut(s) 12, 396
BspTNI GGTCTC 1 cut(s) 1259
BsrI ACTGG 2 cut(s) 576, 951
BssECI CCNNGG 1 cut(s) 930
BssMI GATC 3 cut(s) 4, 388, 426
BssT1I CCWWGG 1 cut(s) 930
Bst2UI CCWGG 2 cut(s) 514, 792
Bst6I CTCTTC 1 cut(s) 411
BstAPI GCANNNNNTGC 1 cut(s) 197
BstC8I GCNNGC 4 cut(s) 83, 202, 346, 1279
BstDEI CTNAG 3 cut(s) 42, 678, 906
BstF5I GGATG 2 cut(s) 387, 509
BstH2I RGCGCY 1 cut(s) 82
BstHHI GCGC 1 cut(s) 81
BstKTI GATC 3 cut(s) 7, 391, 429
BstMAI GTCTC 4 cut(s) 631, 657, 918, 1259
BstMBI GATC 3 cut(s) 4, 388, 426
BstMWI GCNNNNNNNGC 4 cut(s) 197, 341, 688, 872
BstNI CCWGG 2 cut(s) 514, 792
BstNSI RCATGY 1 cut(s) 872
BstSCI CCNGG 2 cut(s) 512, 790
BstSFI CTRYAG 1 cut(s) 376
BstV1I GCAGC 1 cut(s) 322
BstX2I RGATCY 1 cut(s) 388
BstYI RGATCY 1 cut(s) 388
BsuRI GGCC 2 cut(s) 125, 795
BtrI CACGTC 1 cut(s) 1123
BtsCI GGATG 2 cut(s) 387, 509
BtsIMutI CAGTG 1 cut(s) 958
Cac8I GCNNGC 4 cut(s) 83, 202, 346, 1279
CciI TCATGA 2 cut(s) 369, 436
CfoI GCGC 1 cut(s) 81
Cfr13I GGNCC 3 cut(s) 124, 826, 1154
Csp6I GTAC 1 cut(s) 1208
CspCI CAANNNNNGTGG 2 cut(s) 636, 671
CviAII CATG 8 cut(s) 38, 128, 370, 437, 457, 869, 1027, 1286
CviQI GTAC 1 cut(s) 1208
DdeI CTNAG 3 cut(s) 42, 678, 906
DpnI GATC 3 cut(s) 6, 390, 428
DpnII GATC 3 cut(s) 4, 388, 426
DraI TTTAAA 1 cut(s) 1261
DraIII CACNNNGTG 1 cut(s) 212
Eam1104I CTCTTC 1 cut(s) 411
EarI CTCTTC 1 cut(s) 411
Eco130I CCWWGG 1 cut(s) 930
Eco31I GGTCTC 1 cut(s) 1259
Eco47I GGWCC 2 cut(s) 826, 1154
Eco47III AGCGCT 1 cut(s) 80
Eco57I CTGAAG 1 cut(s) 570
EcoRII CCWGG 2 cut(s) 512, 790
EcoT14I CCWWGG 1 cut(s) 930
EcoT22I ATGCAT 1 cut(s) 1039
ErhI CCWWGG 1 cut(s) 930
FaeI CATG 8 cut(s) 41, 131, 373, 440, 460, 872, 1030, 1289
FalI AAGNNNNNCTT 2 cut(s) 518, 550
FaqI GGGAC 2 cut(s) 1109, 1140
FatI CATG 8 cut(s) 37, 127, 369, 436, 456, 868, 1026, 1285
FauNDI CATATG 2 cut(s) 968, 1295
Fnu4HI GCNGC 1 cut(s) 336
FokI GGATG 2 cut(s) 394, 496
Fsp4HI GCNGC 1 cut(s) 336
FspBI CTAG 1 cut(s) 837
GlaI GCGC 1 cut(s) 80
GluI GCNGC 1 cut(s) 336
HaeII RGCGCY 1 cut(s) 82
HaeIII GGCC 2 cut(s) 125, 795
HhaI GCGC 1 cut(s) 81
Hin1II CATG 8 cut(s) 41, 131, 373, 440, 460, 872, 1030, 1289
Hin6I GCGC 1 cut(s) 79
HinP1I GCGC 1 cut(s) 79
HindIII AAGCTT 3 cut(s) 500, 581, 1181
HinfI GANTC 4 cut(s) 305, 665, 1141, 1193
HphI GGTGA 2 cut(s) 1081, 1204
Hpy166II GTNNAC 2 cut(s) 946, 990
Hpy188I TCNGA 3 cut(s) 741, 907, 1198
Hpy188III TCNNGA 4 cut(s) 140, 370, 437, 1001
Hpy8I GTNNAC 2 cut(s) 946, 990
Hpy99I CGWCG 1 cut(s) 362
HpyAV CCTTC 4 cut(s) 446, 590, 653, 1054
HpyCH4IV ACGT 2 cut(s) 267, 1122
HpyF10VI GCNNNNNNNGC 4 cut(s) 197, 341, 688, 872
HpyF3I CTNAG 3 cut(s) 42, 678, 906
HpySE526I ACGT 2 cut(s) 267, 1122
Hsp92II CATG 8 cut(s) 41, 131, 373, 440, 460, 872, 1030, 1289
HspAI GCGC 1 cut(s) 79
Kzo9I GATC 3 cut(s) 4, 388, 426
LmnI GCTCC 1 cut(s) 742
Lsp1109I GCAGC 1 cut(s) 322
LweI GCATC 3 cut(s) 187, 1046, 1279
MaeI CTAG 1 cut(s) 837
MaeII ACGT 2 cut(s) 267, 1122
MaeIII GTNAC 3 cut(s) 274, 327, 851
MalI GATC 3 cut(s) 6, 390, 428
MboI GATC 3 cut(s) 4, 388, 426
MboII GAAGA 8 cut(s) 170, 328, 428, 436, 563, 605, 628, 709
MfeI CAATTG 1 cut(s) 1097
MflI RGATCY 1 cut(s) 388
MhlI GDGCHC 1 cut(s) 805
MluCI AATT 8 cut(s) 56, 399, 440, 473, 554, 751, 1005, 1097
MlyI GAGTC 2 cut(s) 314, 659
MmeI TCCRAC 1 cut(s) 901
MnlI CCTC 7 cut(s) 116, 248, 269, 473, 516, 761, 901
Mph1103I ATGCAT 1 cut(s) 1039
MroXI GAANNNNTTC 3 cut(s) 162, 474, 752
MseI TTAA 6 cut(s) 24, 525, 912, 1163, 1179, 1260
MspR9I CCNGG 2 cut(s) 514, 792
MunI CAATTG 1 cut(s) 1097
Mva1269I GAATGC 2 cut(s) 193, 488
MvaI CCWGG 2 cut(s) 514, 792
MwoI GCNNNNNNNGC 4 cut(s) 197, 341, 688, 872
NdeI CATATG 2 cut(s) 968, 1295
NdeII GATC 3 cut(s) 4, 388, 426
NlaIII CATG 8 cut(s) 41, 131, 373, 440, 460, 872, 1030, 1289
NlaIV GGNNCC 1 cut(s) 1156
NmuCI GTSAC 2 cut(s) 274, 327
NsiI ATGCAT 1 cut(s) 1039
NspI RCATGY 1 cut(s) 872
PagI TCATGA 2 cut(s) 369, 436
PciI ACATGT 1 cut(s) 868
PctI GAATGC 2 cut(s) 193, 488
PdmI GAANNNNTTC 3 cut(s) 162, 474, 752
PfeI GAWTC 2 cut(s) 1141, 1193
PflMI CCANNNNNTGG 1 cut(s) 936
PfoI TCCNGGA 1 cut(s) 512
PkrI GCNGC 1 cut(s) 337
PleI GAGTC 2 cut(s) 313, 659
PpsI GAGTC 2 cut(s) 313, 659
PscI ACATGT 1 cut(s) 868
Psp6I CCWGG 2 cut(s) 512, 790
PspGI CCWGG 2 cut(s) 512, 790
PspN4I GGNNCC 1 cut(s) 1156
PspPI GGNCC 3 cut(s) 124, 826, 1154
PsuI RGATCY 1 cut(s) 388
RsaI GTAC 1 cut(s) 1209
RsaNI GTAC 1 cut(s) 1208
SaqAI TTAA 6 cut(s) 24, 525, 912, 1163, 1179, 1260
SatI GCNGC 1 cut(s) 336
Sau3AI GATC 3 cut(s) 4, 388, 426
Sau96I GGNCC 3 cut(s) 124, 826, 1154
SchI GAGTC 2 cut(s) 314, 659
ScrFI CCNGG 2 cut(s) 514, 792
SduI GDGCHC 1 cut(s) 805
SfaNI GCATC 3 cut(s) 187, 1046, 1279
SfcI CTRYAG 1 cut(s) 376
SinI GGWCC 2 cut(s) 826, 1154
SmlI CTYRAG 2 cut(s) 138, 392
SmoI CTYRAG 2 cut(s) 138, 392
SpeI ACTAGT 1 cut(s) 836
Sse9I AATT 8 cut(s) 56, 399, 440, 473, 554, 751, 1005, 1097
SspI AATATT 1 cut(s) 521
SspMI CTAG 1 cut(s) 837
StyD4I CCNGG 2 cut(s) 512, 790
StyI CCWWGG 1 cut(s) 930
TaiI ACGT 2 cut(s) 270, 1125
TaqI TCGA 1 cut(s) 465
TasI AATT 8 cut(s) 56, 399, 440, 473, 554, 751, 1005, 1097
TatI WGTACW 1 cut(s) 1207
TfiI GAWTC 2 cut(s) 1141, 1193
Tru1I TTAA 6 cut(s) 24, 525, 912, 1163, 1179, 1260
Tru9I TTAA 6 cut(s) 24, 525, 912, 1163, 1179, 1260
TscAI CASTG 1 cut(s) 958
TseFI GTSAC 2 cut(s) 274, 327
TseI GCWGC 1 cut(s) 335
Tsp45I GTSAC 2 cut(s) 274, 327
TspRI CASTG 1 cut(s) 958
Van91I CCANNNNNTGG 1 cut(s) 936
VpaK11BI GGWCC 2 cut(s) 826, 1154
XapI RAATTY 2 cut(s) 473, 751
XceI RCATGY 1 cut(s) 872
XcmI CCANNNNNNNNNTGG 1 cut(s) 836
XmnI GAANNNNTTC 3 cut(s) 162, 474, 752
XspI CTAG 1 cut(s) 837
Zsp2I ATGCAT 1 cut(s) 1039
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.