Rw2G036510

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000258
Physical Location & Seq
Reverse (-)
60089947 .. 60093185
3239 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G036510.1

Sequence Viewer

Length: 1296 bp
ATGGATCCTGCTGGTGTTAAGTCCCACATTGAGAAGCCTGAGAAATTCAAAGGTGTGGATTTCAAACGATGGCAGCAAAAGATGTTGTTCTACTTAACAACGTTGAACCTGGCGCAAGGAGAAATCCCTGTTGCAACTCGTAAGGCTGTTGAAGCATGGAATCAAAGCGAGTTCCTGTGTAAAAACTACATTCTGAATGCCTTAGACGATTCATTATATGATGTCTATTCGTCATTCAAAACTGCTAAGGAGTTGTGGGAATCCCTCGAGAAGAAGTACAAATCCGAGGTTGCAAGTGCCAAAAAGTTTGTCATTAGAAGGTTCCTGAACTTCAAGATGAACGACATCAACTCTGTTGTGAAACAAGTGGAGGAACTCCAGATTATTGTTCACGAGTTAGATGATGAAGGTATGGGACTAAACGAGACTTTTCTTGTTGGTTCAATCATTGAAAAATTACCCCCTTCTTGGAAAGATTTCAAAATCTATCTCAAACACCTAACTGAAGATATGACCCTTGATGAACTAATTCTCAAACTTCGTGTGGAAGAGGATCATCGAAAGAATGAGAAATCTGATGTGACTTCTATGGAGGCAAAAGCCAACATAATTGAAGGCAGCACATTGAAGCCTAAGTTTTCCCTCAATCAAAAGAAGAAAGGAAAAGTTGCTGTCAAGAAAGCATTCACTGCCCCAAAGGCTAATACTTTCAAGAAGAAAATTCAAGGTGGCTGCTGGGTGTGTGGGAAGCCTGGTCATAGAGCCAAGGACTGTCGCCACAAGAAGGAAGGGAATTCTGGAACTTCTAACCAAGCAAATATGGCAGAAGATCAGTTTGTTGCTGTTGTATCTGAGGTTAACCTAATGACTAATGCCAATGAATGGTGGGTTGACACAGGTGCGACTAGACATGTGTGTGCTGAGAAGGACATGTTTGCTGCATATGAACAAGTATCTGGTGGAGAAAATCTGTACATGGGGAATGCTAGTACTGCTGCTGTTGAAGGAAAGGGAAAAGTGGTTCTCAAACTCACTTCCGGAAAAGAACTCACGCTCACTAATGTGCTGCATGTTTCTGAGATCCGAAAGAATCTGATTTCTGGTTCCCTTCTTAGCAACAAAGGCTTCAAGTTAGTAATTGAATCTGATAAGTTTGTACTCACCAAGGGTGGGATGTATGTAGGGAAGGGCTACGTTATGGAAGGGCTCTTCAAGCTTAATGTACTACCTATTATTAATAATAATAATGCAGGCAATAGCGCTGCTTCTATCTACTTACAAAATGCTAAACTCTAG
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

431

Amino Acids

48.32

Weight (kDa)

9.15

Isoelectric Point (pI)

29.27

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 28 - 191 1.1e-28 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 295 - 376 4.6e-25 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) 882
AccIII TCCGGA 1 cut(s) 1037
AclI AACGTT 1 cut(s) 101
AclWI GGATC 3 cut(s) 12, 561, 1075
AcsI RAATTY 3 cut(s) 44, 720, 793
AcuI CTGAAG 1 cut(s) 525
AfaI GTAC 5 cut(s) 278, 974, 991, 1158, 1224
AfeI AGCGCT 1 cut(s) 1261
AfiI CCNNNNNNNGG 4 cut(s) 468, 784, 882, 1170
AflIII ACRYGT 2 cut(s) 910, 930
AjnI CCWGG 2 cut(s) 108, 751
AleI CACNNNNGTG 1 cut(s) 1061
AloI GAACNNNNNNTCC 2 cut(s) 1005, 1037
AluBI AGCT 1 cut(s) 1216
AluI AGCT 1 cut(s) 1216
Alw26I GTCTC 1 cut(s) 419
AlwI GGATC 3 cut(s) 12, 561, 1075
Ama87I CYCGRG 1 cut(s) 266
Aor13HI TCCGGA 1 cut(s) 1037
Aor51HI AGCGCT 1 cut(s) 1261
ApeKI GCWGC 7 cut(s) 73, 618, 732, 938, 995, 1066, 1262
ApoI RAATTY 3 cut(s) 44, 720, 793
ArsI GACNNNNNNTTYG 2 cut(s) 294, 326
AseI ATTAAT 1 cut(s) 1236
Asp700I GAANNNNTTC 3 cut(s) 476, 528, 683
AspLEI GCGC 2 cut(s) 115, 1262
AsuHPI GGTGA 1 cut(s) 1153
AvaI CYCGRG 1 cut(s) 266
BamHI GGATCC 1 cut(s) 4
BanII GRGCYC 1 cut(s) 1209
BauI CACGAG 1 cut(s) 392
BbvI GCAGC 7 cut(s) 85, 630, 719, 925, 982, 1053, 1249
BccI CCATC 1 cut(s) 63
BciT130I CCWGG 2 cut(s) 110, 753
BcoDI GTCTC 1 cut(s) 419
BfaI CTAG 3 cut(s) 906, 987, 1294
BfoI RGCGCY 1 cut(s) 1263
BglI GCCNNNNNGGC 1 cut(s) 698
BisI GCNGC 7 cut(s) 74, 619, 733, 939, 996, 1067, 1263
BlsI GCNGC 7 cut(s) 75, 620, 734, 940, 997, 1068, 1264
BmcAI AGTACT 1 cut(s) 991
Bme1390I CCNGG 2 cut(s) 110, 753
BmeT110I CYCGRG 1 cut(s) 266
BmiI GGNNCC 3 cut(s) 6, 323, 1105
BmrFI CCNGG 2 cut(s) 110, 753
BpmI CTGGAG 1 cut(s) 362
Bpu10I CCTNAGC 1 cut(s) 246
BsaJI CCNNGG 3 cut(s) 285, 765, 1164
BsaWI WCCGGW 1 cut(s) 1037
Bsc4I CCNNNNNNNGG 4 cut(s) 468, 784, 882, 1170
BseAI TCCGGA 1 cut(s) 1037
BseBI CCWGG 2 cut(s) 110, 753
BseDI CCNNGG 3 cut(s) 285, 765, 1164
BseGI GGATG 1 cut(s) 1179
BseLI CCNNNNNNNGG 4 cut(s) 468, 784, 882, 1170
BseMII CTCAG 4 cut(s) 30, 843, 912, 1068
BseXI GCAGC 7 cut(s) 85, 630, 719, 925, 982, 1053, 1249
BseYI CCCAGC 1 cut(s) 735
BsiHKCI CYCGRG 1 cut(s) 266
BsiSI CCGG 1 cut(s) 1038
BslFI GGGAC 2 cut(s) 7, 429
BslI CCNNNNNNNGG 4 cut(s) 468, 784, 882, 1170
BsmAI GTCTC 1 cut(s) 419
BsmFI GGGAC 2 cut(s) 7, 429
BsmI GAATGC 3 cut(s) 202, 683, 988
BsoBI CYCGRG 1 cut(s) 266
Bsp1286I GDGCHC 1 cut(s) 1209
Bsp13I TCCGGA 1 cut(s) 1037
Bsp1407I TGTACA 1 cut(s) 972
Bsp143I GATC 4 cut(s) 4, 553, 829, 1080
BspCNI CTCAG 4 cut(s) 31, 844, 913, 1069
BspEI TCCGGA 1 cut(s) 1037
BspLI GGNNCC 3 cut(s) 6, 323, 1105
BspPI GGATC 3 cut(s) 12, 561, 1075
BspQI GCTCTTC 1 cut(s) 1214
BsrGI TGTACA 1 cut(s) 972
BssECI CCNNGG 3 cut(s) 285, 765, 1164
BssMI GATC 4 cut(s) 4, 553, 829, 1080
BssSI CACGAG 1 cut(s) 392
BssT1I CCWWGG 2 cut(s) 765, 1164
Bst2BI CACGAG 1 cut(s) 392
Bst2UI CCWGG 2 cut(s) 110, 753
Bst4CI ACNGT 1 cut(s) 773
Bst6I CTCTTC 2 cut(s) 543, 1214
BstAPI GCANNNNNTGC 1 cut(s) 689
BstAUI TGTACA 1 cut(s) 972
BstC8I GCNNGC 1 cut(s) 1252
BstDEI CTNAG 8 cut(s) 39, 202, 246, 633, 852, 921, 1077, 1112
BstF5I GGATG 1 cut(s) 1179
BstH2I RGCGCY 1 cut(s) 1263
BstHHI GCGC 2 cut(s) 115, 1262
BstKTI GATC 4 cut(s) 7, 556, 832, 1083
BstMAI GTCTC 1 cut(s) 419
BstMBI GATC 4 cut(s) 4, 553, 829, 1080
BstMWI GCNNNNNNNGC 7 cut(s) 152, 689, 698, 821, 992, 1122, 1213
BstNI CCWGG 2 cut(s) 110, 753
BstNSI RCATGY 3 cut(s) 914, 934, 1073
BstSCI CCNGG 2 cut(s) 108, 751
BstV1I GCAGC 7 cut(s) 85, 630, 719, 925, 982, 1053, 1249
BstX2I RGATCY 2 cut(s) 4, 1080
BstYI RGATCY 2 cut(s) 4, 1080
BtsCI GGATG 1 cut(s) 1179
BtsI GCAGTG 1 cut(s) 687
BtsIMutI CAGTG 1 cut(s) 687
Cac8I GCNNGC 1 cut(s) 1252
CfoI GCGC 2 cut(s) 115, 1262
Csp6I GTAC 5 cut(s) 277, 973, 990, 1157, 1223
CviAII CATG 5 cut(s) 156, 911, 931, 976, 1070
CviQI GTAC 5 cut(s) 277, 973, 990, 1157, 1223
DdeI CTNAG 8 cut(s) 39, 202, 246, 633, 852, 921, 1077, 1112
DpnI GATC 4 cut(s) 6, 555, 831, 1082
DpnII GATC 4 cut(s) 4, 553, 829, 1080
Eam1104I CTCTTC 2 cut(s) 543, 1214
EarI CTCTTC 2 cut(s) 543, 1214
Eco130I CCWWGG 2 cut(s) 765, 1164
Eco24I GRGCYC 1 cut(s) 1209
Eco47III AGCGCT 1 cut(s) 1261
Eco57I CTGAAG 1 cut(s) 525
Eco88I CYCGRG 1 cut(s) 266
EcoRI GAATTC 1 cut(s) 793
EcoRII CCWGG 2 cut(s) 108, 751
EcoT14I CCWWGG 2 cut(s) 765, 1164
EcoT38I GRGCYC 1 cut(s) 1209
ErhI CCWWGG 2 cut(s) 765, 1164
FaeI CATG 5 cut(s) 159, 914, 934, 979, 1073
FaqI GGGAC 2 cut(s) 7, 429
FatI CATG 5 cut(s) 155, 910, 930, 975, 1069
FauNDI CATATG 1 cut(s) 943
Fnu4HI GCNGC 7 cut(s) 74, 619, 733, 939, 996, 1067, 1263
FokI GGATG 1 cut(s) 1186
FriOI GRGCYC 1 cut(s) 1209
Fsp4HI GCNGC 7 cut(s) 74, 619, 733, 939, 996, 1067, 1263
FspBI CTAG 3 cut(s) 906, 987, 1294
GlaI GCGC 2 cut(s) 114, 1261
GluI GCNGC 7 cut(s) 74, 619, 733, 939, 996, 1067, 1263
GsaI CCCAGC 1 cut(s) 739
GsuI CTGGAG 1 cut(s) 362
HaeII RGCGCY 1 cut(s) 1263
HapII CCGG 1 cut(s) 1038
HhaI GCGC 2 cut(s) 115, 1262
Hin1II CATG 5 cut(s) 159, 914, 934, 979, 1073
Hin6I GCGC 2 cut(s) 113, 1260
HinP1I GCGC 2 cut(s) 113, 1260
HincII GTYRAC 2 cut(s) 859, 892
HindII GTYRAC 2 cut(s) 859, 892
HindIII AAGCTT 1 cut(s) 1214
HinfI GANTC 5 cut(s) 160, 209, 260, 1090, 1142
HpaI GTTAAC 1 cut(s) 859
HpaII CCGG 1 cut(s) 1038
HphI GGTGA 1 cut(s) 1153
Hpy166II GTNNAC 3 cut(s) 391, 859, 892
Hpy188I TCNGA 8 cut(s) 195, 286, 577, 853, 1078, 1085, 1095, 1147
Hpy188III TCNNGA 9 cut(s) 268, 325, 334, 379, 392, 676, 712, 798, 1038
Hpy8I GTNNAC 3 cut(s) 391, 859, 892
HpyCH4III ACNGT 1 cut(s) 773
HpyCH4IV ACGT 2 cut(s) 101, 1194
HpyCH4V TGCA 5 cut(s) 134, 293, 941, 1069, 1250
HpyF10VI GCNNNNNNNGC 7 cut(s) 152, 689, 698, 821, 992, 1122, 1213
HpyF3I CTNAG 8 cut(s) 39, 202, 246, 633, 852, 921, 1077, 1112
HpySE526I ACGT 2 cut(s) 101, 1194
Hsp92II CATG 5 cut(s) 159, 914, 934, 979, 1073
HspAI GCGC 2 cut(s) 113, 1260
Kpn2I TCCGGA 1 cut(s) 1037
KspAI GTTAAC 1 cut(s) 859
Kzo9I GATC 4 cut(s) 4, 553, 829, 1080
LguI GCTCTTC 1 cut(s) 1214
Lsp1109I GCAGC 7 cut(s) 85, 630, 719, 925, 982, 1053, 1249
MaeI CTAG 3 cut(s) 906, 987, 1294
MaeII ACGT 2 cut(s) 101, 1194
MaeIII GTNAC 1 cut(s) 580
MalI GATC 4 cut(s) 6, 555, 831, 1082
MboI GATC 4 cut(s) 4, 553, 829, 1080
MboII GAAGA 7 cut(s) 283, 518, 560, 667, 727, 839, 1201
MflI RGATCY 2 cut(s) 4, 1080
MhlI GDGCHC 1 cut(s) 1209
MluCI AATT 7 cut(s) 44, 455, 528, 609, 720, 793, 1137
MnlI CCTC 7 cut(s) 275, 280, 364, 544, 586, 653, 847
MroI TCCGGA 1 cut(s) 1037
MroXI GAANNNNTTC 3 cut(s) 476, 528, 683
MseI TTAA 5 cut(s) 18, 95, 858, 1218, 1236
MslI CAYNNNNRTG 2 cut(s) 915, 1061
MspI CCGG 1 cut(s) 1038
MspR9I CCNGG 2 cut(s) 110, 753
Mva1269I GAATGC 3 cut(s) 202, 683, 988
MvaI CCWGG 2 cut(s) 110, 753
MwoI GCNNNNNNNGC 7 cut(s) 152, 689, 698, 821, 992, 1122, 1213
NdeI CATATG 1 cut(s) 943
NdeII GATC 4 cut(s) 4, 553, 829, 1080
NlaIII CATG 5 cut(s) 159, 914, 934, 979, 1073
NlaIV GGNNCC 3 cut(s) 6, 323, 1105
NmuCI GTSAC 1 cut(s) 580
NspI RCATGY 3 cut(s) 914, 934, 1073
OliI CACNNNNGTG 1 cut(s) 1061
PaeR7I CTCGAG 1 cut(s) 266
PciI ACATGT 2 cut(s) 910, 930
PciSI GCTCTTC 1 cut(s) 1214
PctI GAATGC 3 cut(s) 202, 683, 988
PdmI GAANNNNTTC 3 cut(s) 476, 528, 683
PfeI GAWTC 5 cut(s) 160, 209, 260, 1090, 1142
PflMI CCANNNNNTGG 1 cut(s) 882
PkrI GCNGC 7 cut(s) 75, 620, 734, 940, 997, 1068, 1264
PscI ACATGT 2 cut(s) 910, 930
PshBI ATTAAT 1 cut(s) 1236
Psp1406I AACGTT 1 cut(s) 101
Psp6I CCWGG 2 cut(s) 108, 751
PspFI CCCAGC 1 cut(s) 735
PspGI CCWGG 2 cut(s) 108, 751
PspN4I GGNNCC 3 cut(s) 6, 323, 1105
PsuI RGATCY 2 cut(s) 4, 1080
RsaI GTAC 5 cut(s) 278, 974, 991, 1158, 1224
RsaNI GTAC 5 cut(s) 277, 973, 990, 1157, 1223
RseI CAYNNNNRTG 2 cut(s) 915, 1061
SapI GCTCTTC 1 cut(s) 1214
SaqAI TTAA 5 cut(s) 18, 95, 858, 1218, 1236
SatI GCNGC 7 cut(s) 74, 619, 733, 939, 996, 1067, 1263
Sau3AI GATC 4 cut(s) 4, 553, 829, 1080
ScaI AGTACT 1 cut(s) 991
ScrFI CCNGG 2 cut(s) 110, 753
SduI GDGCHC 1 cut(s) 1209
Sfr274I CTCGAG 1 cut(s) 266
SlaI CTCGAG 1 cut(s) 266
SmiMI CAYNNNNRTG 2 cut(s) 915, 1061
SmlI CTYRAG 1 cut(s) 266
SmoI CTYRAG 1 cut(s) 266
Sse9I AATT 7 cut(s) 44, 455, 528, 609, 720, 793, 1137
SspMI CTAG 3 cut(s) 906, 987, 1294
StyD4I CCNGG 2 cut(s) 108, 751
StyI CCWWGG 2 cut(s) 765, 1164
TaaI ACNGT 1 cut(s) 773
TaiI ACGT 2 cut(s) 104, 1197
TaqI TCGA 2 cut(s) 267, 559
TasI AATT 7 cut(s) 44, 455, 528, 609, 720, 793, 1137
TatI WGTACW 5 cut(s) 276, 972, 989, 1156, 1222
TfiI GAWTC 5 cut(s) 160, 209, 260, 1090, 1142
Tru1I TTAA 5 cut(s) 18, 95, 858, 1218, 1236
Tru9I TTAA 5 cut(s) 18, 95, 858, 1218, 1236
TscAI CASTG 1 cut(s) 694
TseFI GTSAC 1 cut(s) 580
TseI GCWGC 7 cut(s) 73, 618, 732, 938, 995, 1066, 1262
Tsp45I GTSAC 1 cut(s) 580
TspDTI ATGAA 6 cut(s) 201, 353, 420, 537, 894, 960
TspRI CASTG 1 cut(s) 694
Van91I CCANNNNNTGG 1 cut(s) 882
VspI ATTAAT 1 cut(s) 1236
XapI RAATTY 3 cut(s) 44, 720, 793
XceI RCATGY 3 cut(s) 914, 934, 1073
XhoI CTCGAG 1 cut(s) 266
XmnI GAANNNNTTC 3 cut(s) 476, 528, 683
XspI CTAG 3 cut(s) 906, 987, 1294
ZrmI AGTACT 1 cut(s) 991
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.