Rw1G008490

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0000258
Physical Location & Seq
Reverse (-)
18334936 .. 18336329
1394 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G008490.1

Sequence Viewer

Length: 1290 bp
ATGAACGGTGACAATTCAAATGTTACTAGGGATGATATGGGACAAAGCGAGGCAAATCCTATATCTGTGGTGATATCAGGCTTCTCTAAACATGGAGAGAAACCTGAGAAGTTCAATGGAACAGACTTCAAAAGGTGGCAACAAAAGATGCTCTTCTACCTGACAACATTAAGTTTGACAAAATTTCTGAAGGAAGATGTCCCTGCCAGTGGCTCATCTGTGGAGGCTGCTGCGGCTGCAGATGCTTGGCATCATTCTGATTTTCTGTGCAAAAATTACATCCTCAATGGATTGGACAATGCATTATACAATGTCTATAGTCCAATGAAAATTGCTAAGGCCTTATGGGAGTCTCTTGACAAGAAATATAAGACCAAGGACGCTGGAAAGAAGAAATATATCATTGGGCGTTTTCTTGATTACAAGATGATAGACTCCAAATCAGTCATGAGTCAACTCCAAGAATTCCAATTAATTCTTCATGAAATGCAGGCTGAAAAAATGGATATGACTGAAGCTTTACAATCTAAGAATTATCTCAAGCATAAGCGCAAGGAAATGGACCTTGAAGGTTTGACTGTGAGGCTAAGGGTTGAGGAAGACAACCGTATTGCTGACAAGAAAAATGGAATTAATTCCATGGTAGCAAATGCTCATGTTGTTGAAGATGGACAAGAGAATAAAAAGAGAAAATATTCTGGAGAAGGCAAAGAGCAAGAGAATACAAAGAAGCATCGTAATTTCAAAGGAAAATGTTTCAATTGTAACAAGCCTGGGCATAGAGCTTCTGATTGTCGTAGCCGTAAAGGAAAGACAAACAACTACAAAAAATATAAAGGGAAGGCCAAGGAGGTTCATATAGCCGAAGAGGACAAACTCTCATGTGGAATATCTGATATCAATTTATCAGCTGTGATCTCTGAAGTAAACATGATGACCAGCAGTGATGATTGGTGGGTGGACACTGGGGCTACACGCTACATTTGTTTTGACAAGAAGATGTTTATTACATATGAAGCAGTGGAACAAGGAGAGCAGCTTTTTATGGGAAATTCCTCTACTTCAGGGGTTGAAGGAAATGTGACACTCAAGTTGACATCTGGAAAGGTACTCACTCTAACAGAAGTACTTCATGTTCCTGATATTAGAAAAAACTTGGTTTCTAGATCGCTGCTCAGTAAGAATGGTTTCAAGTTGGTTTTTGAGGCTGACAAGTTTATGTTAACTAAGAACGGGATGTATGTGGGGAAAGGTTATTTTAGTCATGGCCTCTTCAAGATCCAAGGATGA
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

429

Amino Acids

48.67

Weight (kDa)

9.19

Isoelectric Point (pI)

29.35

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 50 - 176 2.5e-15 gag-polypeptide of LTR copia-type
zf-CCHC PF00098 250 - 266 3.5e-06 Zinc knuckle
Pol_BBD PF22936 318 - 397 5e-19 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)
AciI CCGC 1 cut(s) 233
AclWI GGATC 1 cut(s) 1273
AcsI RAATTY 3 cut(s) 182, 464, 1051
AcuI CTGAAG 4 cut(s) 209, 534, 942, 1047
AfaI GTAC 2 cut(s) 1110, 1128
AfiI CCNNNNNNNGG 1 cut(s) 209
AjnI CCWGG 1 cut(s) 772
AjuI GAANNNNNNNTTGG 2 cut(s) 462, 494
AluBI AGCT 4 cut(s) 518, 785, 911, 1039
AluI AGCT 4 cut(s) 518, 785, 911, 1039
Alw26I GTCTC 1 cut(s) 357
AlwI GGATC 1 cut(s) 1273
AoxI GGCC 3 cut(s) 339, 843, 1267
ApeKI GCWGC 5 cut(s) 227, 230, 236, 1036, 1171
ApoI RAATTY 3 cut(s) 182, 464, 1051
AseI ATTAAT 2 cut(s) 473, 633
Asp700I GAANNNNTTC 4 cut(s) 634, 694, 1128, 1187
AspLEI GCGC 1 cut(s) 552
AspS9I GGNCC 1 cut(s) 562
AsuHPI GGTGA 2 cut(s) 20, 82
AvaII GGWCC 1 cut(s) 562
BbsI GAAGAC 1 cut(s) 606
BbvI GCAGC 5 cut(s) 214, 217, 223, 1048, 1158
BccI CCATC 1 cut(s) 662
BceAI ACGGC 1 cut(s) 786
BciT130I CCWGG 1 cut(s) 774
BcoDI GTCTC 1 cut(s) 357
BfaI CTAG 2 cut(s) 27, 1164
BfmI CTRYAG 2 cut(s) 237, 316
BisI GCNGC 6 cut(s) 228, 231, 234, 237, 1037, 1172
BlsI GCNGC 6 cut(s) 229, 232, 235, 238, 1038, 1173
BmcAI AGTACT 1 cut(s) 1128
Bme1390I CCNGG 1 cut(s) 774
Bme18I GGWCC 1 cut(s) 562
BmgT120I GGNCC 1 cut(s) 562
BmrFI CCNGG 1 cut(s) 774
BmrI ACTGGG 1 cut(s) 975
BmsI GCATC 4 cut(s) 138, 232, 259, 742
BmuI ACTGGG 1 cut(s) 975
BpiI GAAGAC 1 cut(s) 606
BpmI CTGGAG 1 cut(s) 720
Bpu10I CCTNAGC 2 cut(s) 336, 587
BpuEI CTTGAG 2 cut(s) 524, 1073
BsaJI CCNNGG 5 cut(s) 375, 639, 773, 846, 1282
Bsc4I CCNNNNNNNGG 1 cut(s) 209
Bse1I ACTGG 2 cut(s) 207, 970
BseBI CCWGG 1 cut(s) 774
BseDI CCNNGG 5 cut(s) 375, 639, 773, 846, 1282
BseGI GGATG 3 cut(s) 37, 279, 1242
BseLI CCNNNNNNNGG 1 cut(s) 209
BseMII CTCAG 2 cut(s) 96, 1189
BseNI ACTGG 2 cut(s) 207, 970
BseXI GCAGC 5 cut(s) 214, 217, 223, 1048, 1158
BshFI GGCC 3 cut(s) 341, 845, 1269
BslFI GGGAC 2 cut(s) 54, 185
BslI CCNNNNNNNGG 1 cut(s) 209
BsmAI GTCTC 1 cut(s) 357
BsmFI GGGAC 2 cut(s) 54, 185
BsnI GGCC 3 cut(s) 341, 845, 1269
Bsp143I GATC 3 cut(s) 915, 1166, 1278
Bsp19I CCATGG 1 cut(s) 639
BspACI CCGC 1 cut(s) 233
BspANI GGCC 3 cut(s) 341, 845, 1269
BspCNI CTCAG 2 cut(s) 97, 1188
BspHI TCATGA 2 cut(s) 447, 481
BspMAI CTGCAG 1 cut(s) 241
BspPI GGATC 1 cut(s) 1273
BspQI GCTCTTC 1 cut(s) 158
BsrI ACTGG 2 cut(s) 207, 970
BssECI CCNNGG 5 cut(s) 375, 639, 773, 846, 1282
BssMI GATC 3 cut(s) 915, 1166, 1278
BssT1I CCWWGG 4 cut(s) 375, 639, 846, 1282
Bst2UI CCWGG 1 cut(s) 774
Bst4CI ACNGT 3 cut(s) 8, 580, 608
Bst6I CTCTTC 3 cut(s) 158, 861, 1277
BstC8I GCNNGC 1 cut(s) 492
BstDEI CTNAG 6 cut(s) 105, 336, 528, 587, 1175, 1227
BstDSI CCRYGG 1 cut(s) 639
BstF5I GGATG 3 cut(s) 37, 279, 1242
BstHHI GCGC 1 cut(s) 552
BstKTI GATC 3 cut(s) 918, 1169, 1281
BstMAI GTCTC 1 cut(s) 357
BstMBI GATC 3 cut(s) 915, 1166, 1278
BstMWI GCNNNNNNNGC 3 cut(s) 233, 236, 242
BstNI CCWGG 1 cut(s) 774
BstSCI CCNGG 1 cut(s) 772
BstSFI CTRYAG 2 cut(s) 237, 316
BstV1I GCAGC 5 cut(s) 214, 217, 223, 1048, 1158
BstV2I GAAGAC 1 cut(s) 606
BstX2I RGATCY 1 cut(s) 1278
BstYI RGATCY 1 cut(s) 1278
BsuRI GGCC 3 cut(s) 341, 845, 1269
BtgI CCRYGG 1 cut(s) 639
BtsCI GGATG 3 cut(s) 37, 279, 1242
BtsI GCAGTG 2 cut(s) 949, 1026
BtsIMutI CAGTG 4 cut(s) 214, 949, 963, 1026
Cac8I GCNNGC 1 cut(s) 492
CciI TCATGA 2 cut(s) 447, 481
CfoI GCGC 1 cut(s) 552
Cfr13I GGNCC 1 cut(s) 562
CseI GACGC 1 cut(s) 389
Csp6I GTAC 2 cut(s) 1109, 1127
CviAII CATG 9 cut(s) 92, 448, 482, 640, 656, 882, 931, 1133, 1265
CviQI GTAC 2 cut(s) 1109, 1127
DdeI CTNAG 6 cut(s) 105, 336, 528, 587, 1175, 1227
DpnI GATC 3 cut(s) 917, 1168, 1280
DpnII GATC 3 cut(s) 915, 1166, 1278
Eam1104I CTCTTC 3 cut(s) 158, 861, 1277
EarI CTCTTC 3 cut(s) 158, 861, 1277
Eco130I CCWWGG 4 cut(s) 375, 639, 846, 1282
Eco147I AGGCCT 1 cut(s) 341
Eco32I GATATC 2 cut(s) 75, 898
Eco47I GGWCC 1 cut(s) 562
Eco57I CTGAAG 4 cut(s) 209, 534, 942, 1047
EcoRI GAATTC 1 cut(s) 464
EcoRII CCWGG 1 cut(s) 772
EcoRV GATATC 2 cut(s) 75, 898
EcoT14I CCWWGG 4 cut(s) 375, 639, 846, 1282
EcoT22I ATGCAT 1 cut(s) 304
ErhI CCWWGG 4 cut(s) 375, 639, 846, 1282
FaeI CATG 9 cut(s) 95, 451, 485, 643, 659, 885, 934, 1136, 1268
FalI AAGNNNNNCTT 2 cut(s) 137, 169
FaqI GGGAC 2 cut(s) 54, 185
FatI CATG 9 cut(s) 91, 447, 481, 639, 655, 881, 930, 1132, 1264
FauNDI CATATG 1 cut(s) 1012
Fnu4HI GCNGC 6 cut(s) 228, 231, 234, 237, 1037, 1172
FokI GGATG 3 cut(s) 44, 266, 1249
Fsp4HI GCNGC 6 cut(s) 228, 231, 234, 237, 1037, 1172
FspBI CTAG 2 cut(s) 27, 1164
GlaI GCGC 1 cut(s) 551
GluI GCNGC 6 cut(s) 228, 231, 234, 237, 1037, 1172
GsuI CTGGAG 1 cut(s) 720
HaeIII GGCC 3 cut(s) 341, 845, 1269
HgaI GACGC 1 cut(s) 389
HhaI GCGC 1 cut(s) 552
Hin1II CATG 9 cut(s) 95, 451, 485, 643, 659, 885, 934, 1136, 1268
Hin6I GCGC 1 cut(s) 550
HinP1I GCGC 1 cut(s) 550
HincII GTYRAC 3 cut(s) 455, 1095, 1224
HindII GTYRAC 3 cut(s) 455, 1095, 1224
HindIII AAGCTT 1 cut(s) 516
HinfI GANTC 3 cut(s) 350, 434, 451
HpaI GTTAAC 1 cut(s) 1224
HphI GGTGA 2 cut(s) 20, 82
Hpy166II GTNNAC 5 cut(s) 455, 928, 961, 1095, 1224
Hpy188I TCNGA 5 cut(s) 189, 259, 790, 895, 922
Hpy188III TCNNGA 9 cut(s) 356, 416, 448, 482, 699, 1101, 1139, 1164, 1276
Hpy8I GTNNAC 5 cut(s) 455, 928, 961, 1095, 1224
HpyAV CCTTC 5 cut(s) 184, 563, 698, 835, 1067
HpyCH4III ACNGT 3 cut(s) 8, 580, 608
HpyCH4V TGCA 4 cut(s) 239, 270, 302, 490
HpyF10VI GCNNNNNNNGC 3 cut(s) 233, 236, 242
HpyF3I CTNAG 6 cut(s) 105, 336, 528, 587, 1175, 1227
Hsp92II CATG 9 cut(s) 95, 451, 485, 643, 659, 885, 934, 1136, 1268
HspAI GCGC 1 cut(s) 550
KspAI GTTAAC 1 cut(s) 1224
Kzo9I GATC 3 cut(s) 915, 1166, 1278
LguI GCTCTTC 1 cut(s) 158
Lsp1109I GCAGC 5 cut(s) 214, 217, 223, 1048, 1158
LweI GCATC 4 cut(s) 138, 232, 259, 742
MaeI CTAG 2 cut(s) 27, 1164
MaeIII GTNAC 4 cut(s) 8, 22, 764, 1081
MalI GATC 3 cut(s) 917, 1168, 1280
MboI GATC 3 cut(s) 915, 1166, 1278
MboII GAAGA 9 cut(s) 145, 206, 403, 470, 611, 677, 878, 1009, 1264
MfeI CAATTG 1 cut(s) 760
MflI RGATCY 1 cut(s) 1278
MlyI GAGTC 3 cut(s) 359, 428, 460
Mph1103I ATGCAT 1 cut(s) 304
MroXI GAANNNNTTC 4 cut(s) 634, 694, 1128, 1187
MseI TTAA 4 cut(s) 170, 473, 633, 1223
MspA1I CMGCKG 1 cut(s) 911
MspR9I CCNGG 1 cut(s) 774
MunI CAATTG 1 cut(s) 760
MvaI CCWGG 1 cut(s) 774
MwoI GCNNNNNNNGC 3 cut(s) 233, 236, 242
NcoI CCATGG 1 cut(s) 639
NdeI CATATG 1 cut(s) 1012
NdeII GATC 3 cut(s) 915, 1166, 1278
NlaIII CATG 9 cut(s) 95, 451, 485, 643, 659, 885, 934, 1136, 1268
NmuCI GTSAC 2 cut(s) 8, 1081
NsiI ATGCAT 1 cut(s) 304
PagI TCATGA 2 cut(s) 447, 481
PceI AGGCCT 1 cut(s) 341
PciSI GCTCTTC 1 cut(s) 158
PdmI GAANNNNTTC 4 cut(s) 634, 694, 1128, 1187
PkrI GCNGC 6 cut(s) 229, 232, 235, 238, 1038, 1173
PleI GAGTC 3 cut(s) 358, 428, 459
PpsI GAGTC 3 cut(s) 358, 428, 459
PshBI ATTAAT 2 cut(s) 473, 633
Psp6I CCWGG 1 cut(s) 772
PspGI CCWGG 1 cut(s) 772
PspPI GGNCC 1 cut(s) 562
PsrI GAACNNNNNNTAC 2 cut(s) 1119, 1151
PstI CTGCAG 1 cut(s) 241
PsuI RGATCY 1 cut(s) 1278
PvuII CAGCTG 1 cut(s) 911
RsaI GTAC 2 cut(s) 1110, 1128
RsaNI GTAC 2 cut(s) 1109, 1127
SapI GCTCTTC 1 cut(s) 158
SaqAI TTAA 4 cut(s) 170, 473, 633, 1223
SatI GCNGC 6 cut(s) 228, 231, 234, 237, 1037, 1172
Sau3AI GATC 3 cut(s) 915, 1166, 1278
Sau96I GGNCC 1 cut(s) 562
ScaI AGTACT 1 cut(s) 1128
SchI GAGTC 3 cut(s) 359, 428, 460
ScrFI CCNGG 1 cut(s) 774
SfaNI GCATC 4 cut(s) 138, 232, 259, 742
SfcI CTRYAG 2 cut(s) 237, 316
SinI GGWCC 1 cut(s) 562
SmlI CTYRAG 2 cut(s) 539, 1088
SmoI CTYRAG 2 cut(s) 539, 1088
SseBI AGGCCT 1 cut(s) 341
SsiI CCGC 1 cut(s) 233
SspI AATATT 1 cut(s) 695
SspMI CTAG 2 cut(s) 27, 1164
StuI AGGCCT 1 cut(s) 341
StyD4I CCNGG 1 cut(s) 772
StyI CCWWGG 4 cut(s) 375, 639, 846, 1282
TaaI ACNGT 3 cut(s) 8, 580, 608
TatI WGTACW 1 cut(s) 1126
TauI GCSGC 1 cut(s) 236
Tru1I TTAA 4 cut(s) 170, 473, 633, 1223
Tru9I TTAA 4 cut(s) 170, 473, 633, 1223
TscAI CASTG 4 cut(s) 214, 949, 970, 1026
TseFI GTSAC 2 cut(s) 8, 1081
TseI GCWGC 5 cut(s) 227, 230, 236, 1036, 1171
Tsp45I GTSAC 2 cut(s) 8, 1081
TspDTI ATGAA 7 cut(s) 17, 341, 470, 498, 845, 1029, 1121
TspRI CASTG 4 cut(s) 214, 949, 970, 1026
VpaK11BI GGWCC 1 cut(s) 562
VspI ATTAAT 2 cut(s) 473, 633
XapI RAATTY 3 cut(s) 182, 464, 1051
XbaI TCTAGA 1 cut(s) 1163
XmnI GAANNNNTTC 4 cut(s) 634, 694, 1128, 1187
XspI CTAG 2 cut(s) 27, 1164
ZrmI AGTACT 1 cut(s) 1128
Zsp2I ATGCAT 1 cut(s) 304
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.