Rw1G002590

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0000258
Physical Location & Seq
Forward (+)
4699968 .. 4713064
13097 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G002590.1

Sequence Viewer

Length: 1299 bp
ATGGATGGTGACGATGCTAACATTATTGGAAATGATAAGGGAAAAGGAATGGCTATTGCTGCACCTGTGTTGGTTCCTTCTTCTTCCACTCATGGGGAGAAACCCGAGAAATTTAGTGGGACAAACTTCAAATGCTGGCAGCAAAAGATGTTGTTCTGCCTCACTACTCTGAACTTGGCCAAATTTTTGAAAGAAAGTGCTCCTGCATCAGGAAGCACTGTAGAAGAGGCTGCTGCTGTAGACGCATGGCATCATTCAGATTTTCTATGCAAGAATTACATTCTTAATGGATTGGACATTGTACTTTACAAAGTGTACAGTCCAATAAAGAATGCTAAAAGCTTGTGGGAGTCTTTAGAAAAGAAATACAAGACCGAAGATTCTGGAGCAAAGAAATATATAATCGGTCGTTTCCTTGACTACAAGATGGTAGATACTAAAACTGTACTTAGTCAAGTTGAGGAGTTTCAATTGATTCTACATGAGATGGCTGCAGAAAATCGGTCAATTAATGAAACTTTGCAAGTGGTATGTATTATTGAGAAACTTCCTCCATCTTGGAAGGATTTCAGGAATTATCTCAAGCATAAGCGCAAGGAGATGGATCTTGAGGGTCTAATTGTGAGGCTACGGGTTGAGGAAGGCAATCGCATATCTGACAAGAGAAGTGATGCTAGTTCTATGATGGCCAAGGTACTTTTCTCTGGGAAAAATTATAAGCCAGGAAACTCAAAGAAGTTCAAAGGCAAGTGTTTCAATTGTAATAAGACAGGTCATCGTGCTATGGAATGTCATAGAAAGAAAAACAAAGGCTACAAGAAAGCCACTGAAGCAAACATGACTGAGGGAGATAGATTGTCTGTTGACATTGTTGATATGAACCTTTCAGCCATGGTGACTGAAGTCAATATGATAACAAGCGCCGAAGAATGGTGGATAGACACAGGGGCTACTTGCCATATATGTTTTGATAAGAAGATGTTCTCTACCTATGCGGAAGTAAATCAAGGAGAGCAATTATTCATGGGCAATGCTTCCACATCAATGGTTCAAGGCACTGGTAATATTGTTTTAAAGTTGATATCTGGGAAAGAAATTACTTTAAACAATGTACTTCATGTGCCTGATATTCGAAAGAATTTAATCTCTGGTTCGATGTTGATCAAAAATGGATTTCGTGTGATCTTTGAAGTTGATAAAGTCATACTTACCAAGAACGGGATATATGTAGGAAAAGGTTATCTCAGTAATGGCCTTTTCAAGATATGCTCCCAAGAAGTCCAAGGAAAGAGTATCTAA
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

48.47

Weight (kDa)

9.03

Isoelectric Point (pI)

29.42

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 52 - 220 7.1e-25 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 311 - 392 3.1e-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)
AanI TTATAA 1 cut(s) 717
AccI GTMKAC 1 cut(s) 240
AciI CCGC 1 cut(s) 995
AclWI GGATC 1 cut(s) 612
AcoI YGGCCR 2 cut(s) 177, 687
AcsI RAATTY 3 cut(s) 110, 182, 1138
AcuI CTGAAG 2 cut(s) 849, 921
AfaI GTAC 5 cut(s) 303, 317, 447, 696, 1113
AfiI CCNNNNNNNGG 4 cut(s) 93, 209, 930, 1218
AgsI TTSAA 8 cut(s) 130, 190, 470, 742, 757, 1052, 1190, 1261
AjnI CCWGG 1 cut(s) 721
AjuI GAANNNNNNNTTGG 2 cut(s) 683, 715
AluBI AGCT 1 cut(s) 342
AluI AGCT 1 cut(s) 342
Alw21I GWGCWC 1 cut(s) 202
AlwI GGATC 1 cut(s) 612
Ama87I CYCGRG 1 cut(s) 104
AoxI GGCC 3 cut(s) 177, 687, 1252
ApeKI GCWGC 5 cut(s) 59, 139, 230, 233, 491
ApoI RAATTY 3 cut(s) 110, 182, 1138
AseI ATTAAT 1 cut(s) 510
Asp700I GAANNNNTTC 2 cut(s) 566, 980
AspLEI GCGC 2 cut(s) 594, 923
AsuHPI GGTGA 2 cut(s) 20, 907
AsuII TTCGAA 1 cut(s) 1132
AvaI CYCGRG 1 cut(s) 104
BalI TGGCCA 2 cut(s) 179, 689
Bbv12I GWGCWC 1 cut(s) 202
BbvI GCAGC 5 cut(s) 46, 151, 217, 220, 478
BccI CCATC 5 cut(s) 421, 481, 562, 595, 679
BciT130I CCWGG 1 cut(s) 723
BclI TGATCA 1 cut(s) 1161
BfaI CTAG 1 cut(s) 675
BfmI CTRYAG 3 cut(s) 219, 237, 492
BfoI RGCGCY 1 cut(s) 924
BisI GCNGC 5 cut(s) 60, 140, 231, 234, 492
BlsI GCNGC 5 cut(s) 61, 141, 232, 235, 493
Bme1390I CCNGG 1 cut(s) 723
BmeT110I CYCGRG 1 cut(s) 104
BmiI GGNNCC 1 cut(s) 75
BmrFI CCNGG 1 cut(s) 723
BmsI GCATC 4 cut(s) 4, 215, 259, 661
BoxI GACNNNNGTC 1 cut(s) 902
BpmI CTGGAG 1 cut(s) 405
Bpu14I TTCGAA 1 cut(s) 1132
BpuEI CTTGAG 2 cut(s) 566, 629
BsaBI GATNNNNATC 1 cut(s) 1160
BsaJI CCNNGG 3 cut(s) 690, 891, 1282
Bsc4I CCNNNNNNNGG 4 cut(s) 93, 209, 930, 1218
Bse1I ACTGG 1 cut(s) 1063
Bse3DI GCAATG 1 cut(s) 1036
Bse8I GATNNNNATC 1 cut(s) 1160
BseBI CCWGG 1 cut(s) 723
BseDI CCNNGG 3 cut(s) 690, 891, 1282
BseGI GGATG 1 cut(s) 10
BseJI GATNNNNATC 1 cut(s) 1160
BseLI CCNNNNNNNGG 4 cut(s) 93, 209, 930, 1218
BseMI GCAATG 1 cut(s) 1036
BseMII CTCAG 2 cut(s) 834, 1258
BseNI ACTGG 1 cut(s) 1063
BseRI GAGGAG 1 cut(s) 476
BseXI GCAGC 5 cut(s) 46, 151, 217, 220, 478
BsgI GTGCAG 1 cut(s) 45
Bsh1285I CGRYCG 1 cut(s) 409
BshFI GGCC 3 cut(s) 179, 689, 1254
BsiEI CGRYCG 1 cut(s) 409
BsiHKAI GWGCWC 1 cut(s) 202
BsiHKCI CYCGRG 1 cut(s) 104
BslFI GGGAC 1 cut(s) 133
BslI CCNNNNNNNGG 4 cut(s) 93, 209, 930, 1218
BsmFI GGGAC 1 cut(s) 133
BsmI GAATGC 1 cut(s) 337
BsnI GGCC 3 cut(s) 179, 689, 1254
BsoBI CYCGRG 1 cut(s) 104
Bsp119I TTCGAA 1 cut(s) 1132
Bsp1286I GDGCHC 1 cut(s) 202
Bsp1407I TGTACA 1 cut(s) 315
Bsp143I GATC 3 cut(s) 604, 1161, 1182
Bsp19I CCATGG 1 cut(s) 891
BspACI CCGC 1 cut(s) 995
BspANI GGCC 3 cut(s) 179, 689, 1254
BspCNI CTCAG 2 cut(s) 835, 1257
BspLI GGNNCC 1 cut(s) 75
BspMAI CTGCAG 1 cut(s) 496
BspPI GGATC 1 cut(s) 612
BspT104I TTCGAA 1 cut(s) 1132
BsrDI GCAATG 1 cut(s) 1036
BsrGI TGTACA 1 cut(s) 315
BsrI ACTGG 1 cut(s) 1063
BssECI CCNNGG 3 cut(s) 690, 891, 1282
BssMI GATC 3 cut(s) 604, 1161, 1182
BssT1I CCWWGG 3 cut(s) 690, 891, 1282
Bst2UI CCWGG 1 cut(s) 723
Bst4CI ACNGT 3 cut(s) 220, 320, 445
Bst6I CTCTTC 1 cut(s) 219
BstAUI TGTACA 1 cut(s) 315
BstBI TTCGAA 1 cut(s) 1132
BstC8I GCNNGC 1 cut(s) 137
BstDEI CTNAG 3 cut(s) 449, 843, 1244
BstDSI CCRYGG 1 cut(s) 891
BstENI CCTNNNNNAGG 1 cut(s) 207
BstF5I GGATG 1 cut(s) 10
BstH2I RGCGCY 1 cut(s) 924
BstHHI GCGC 2 cut(s) 594, 923
BstKTI GATC 3 cut(s) 607, 1164, 1185
BstMBI GATC 3 cut(s) 604, 1161, 1182
BstMCI CGRYCG 1 cut(s) 409
BstMWI GCNNNNNNNGC 3 cut(s) 59, 242, 830
BstNI CCWGG 1 cut(s) 723
BstPAI GACNNNNGTC 1 cut(s) 902
BstSCI CCNGG 1 cut(s) 721
BstSFI CTRYAG 3 cut(s) 219, 237, 492
BstV1I GCAGC 5 cut(s) 46, 151, 217, 220, 478
BstX2I RGATCY 1 cut(s) 604
BstXI CCANNNNNNTGG 1 cut(s) 1045
BstYI RGATCY 1 cut(s) 604
BsuRI GGCC 3 cut(s) 179, 689, 1254
BtgI CCRYGG 1 cut(s) 891
BtsCI GGATG 1 cut(s) 10
BtsIMutI CAGTG 3 cut(s) 216, 825, 1056
Cac8I GCNNGC 1 cut(s) 137
CfoI GCGC 2 cut(s) 594, 923
CseI GACGC 1 cut(s) 251
Csp6I GTAC 5 cut(s) 302, 316, 446, 695, 1112
CviAII CATG 7 cut(s) 92, 246, 482, 838, 892, 1024, 1118
CviQI GTAC 5 cut(s) 302, 316, 446, 695, 1112
DdeI CTNAG 3 cut(s) 449, 843, 1244
DpnI GATC 3 cut(s) 606, 1163, 1184
DpnII GATC 3 cut(s) 604, 1161, 1182
DraI TTTAAA 2 cut(s) 1074, 1104
EaeI YGGCCR 2 cut(s) 177, 687
Eam1104I CTCTTC 1 cut(s) 219
EarI CTCTTC 1 cut(s) 219
Eco130I CCWWGG 3 cut(s) 690, 891, 1282
Eco32I GATATC 1 cut(s) 1083
Eco57I CTGAAG 2 cut(s) 849, 921
Eco88I CYCGRG 1 cut(s) 104
EcoNI CCTNNNNNAGG 1 cut(s) 207
EcoRII CCWGG 1 cut(s) 721
EcoRV GATATC 1 cut(s) 1083
EcoT14I CCWWGG 3 cut(s) 690, 891, 1282
ErhI CCWWGG 3 cut(s) 690, 891, 1282
FaeI CATG 7 cut(s) 95, 249, 485, 841, 895, 1027, 1121
FalI AAGNNNNNCTT 2 cut(s) 1191, 1223
FaqI GGGAC 1 cut(s) 133
FatI CATG 7 cut(s) 91, 245, 481, 837, 891, 1023, 1117
FbaI TGATCA 1 cut(s) 1161
FblI GTMKAC 1 cut(s) 240
Fnu4HI GCNGC 5 cut(s) 60, 140, 231, 234, 492
FokI GGATG 1 cut(s) 17
Fsp4HI GCNGC 5 cut(s) 60, 140, 231, 234, 492
FspBI CTAG 1 cut(s) 675
GlaI GCGC 2 cut(s) 593, 922
GluI GCNGC 5 cut(s) 60, 140, 231, 234, 492
GsuI CTGGAG 1 cut(s) 405
HaeII RGCGCY 1 cut(s) 924
HaeIII GGCC 3 cut(s) 179, 689, 1254
HgaI GACGC 1 cut(s) 251
HhaI GCGC 2 cut(s) 594, 923
Hin1II CATG 7 cut(s) 95, 249, 485, 841, 895, 1027, 1121
Hin6I GCGC 2 cut(s) 592, 921
HinP1I GCGC 2 cut(s) 592, 921
HincII GTYRAC 1 cut(s) 865
HindII GTYRAC 1 cut(s) 865
HindIII AAGCTT 1 cut(s) 340
HinfI GANTC 3 cut(s) 350, 380, 475
HphI GGTGA 2 cut(s) 20, 907
Hpy166II GTNNAC 3 cut(s) 241, 316, 865
Hpy188I TCNGA 3 cut(s) 171, 259, 658
Hpy188III TCNNGA 5 cut(s) 210, 384, 571, 608, 1261
Hpy8I GTNNAC 3 cut(s) 241, 316, 865
HpyAV CCTTC 3 cut(s) 87, 556, 635
HpyCH4III ACNGT 3 cut(s) 220, 320, 445
HpyCH4V TGCA 5 cut(s) 62, 206, 270, 494, 523
HpyF10VI GCNNNNNNNGC 3 cut(s) 59, 242, 830
HpyF3I CTNAG 3 cut(s) 449, 843, 1244
Hsp92II CATG 7 cut(s) 95, 249, 485, 841, 895, 1027, 1121
HspAI GCGC 2 cut(s) 592, 921
Ksp22I TGATCA 1 cut(s) 1161
Kzo9I GATC 3 cut(s) 604, 1161, 1182
LmnI GCTCC 3 cut(s) 205, 386, 1274
Lsp1109I GCAGC 5 cut(s) 46, 151, 217, 220, 478
LweI GCATC 4 cut(s) 4, 215, 259, 661
MaeI CTAG 1 cut(s) 675
MaeIII GTNAC 2 cut(s) 8, 895
MalI GATC 3 cut(s) 606, 1163, 1184
MboI GATC 3 cut(s) 604, 1161, 1182
MboII GAAGA 6 cut(s) 72, 75, 236, 389, 938, 988
MfeI CAATTG 2 cut(s) 470, 757
MflI RGATCY 1 cut(s) 604
MhlI GDGCHC 1 cut(s) 202
MlsI TGGCCA 2 cut(s) 179, 689
MluNI TGGCCA 2 cut(s) 179, 689
MlyI GAGTC 1 cut(s) 359
MnlI CCTC 8 cut(s) 170, 220, 454, 561, 604, 618, 631, 838
Mox20I TGGCCA 2 cut(s) 179, 689
MroXI GAANNNNTTC 2 cut(s) 566, 980
MscI TGGCCA 2 cut(s) 179, 689
MseI TTAA 5 cut(s) 285, 510, 1073, 1103, 1142
MslI CAYNNNNRTG 1 cut(s) 1043
Msp20I TGGCCA 2 cut(s) 179, 689
MspR9I CCNGG 1 cut(s) 723
MunI CAATTG 2 cut(s) 470, 757
Mva1269I GAATGC 1 cut(s) 337
MvaI CCWGG 1 cut(s) 723
MwoI GCNNNNNNNGC 3 cut(s) 59, 242, 830
NcoI CCATGG 1 cut(s) 891
NdeII GATC 3 cut(s) 604, 1161, 1182
NlaIII CATG 7 cut(s) 95, 249, 485, 841, 895, 1027, 1121
NlaIV GGNNCC 1 cut(s) 75
NmuCI GTSAC 2 cut(s) 8, 895
NspV TTCGAA 1 cut(s) 1132
PctI GAATGC 1 cut(s) 337
PdmI GAANNNNTTC 2 cut(s) 566, 980
PfeI GAWTC 2 cut(s) 380, 475
PkrI GCNGC 5 cut(s) 61, 141, 232, 235, 493
PleI GAGTC 1 cut(s) 358
PpsI GAGTC 1 cut(s) 358
PshAI GACNNNNGTC 1 cut(s) 902
PshBI ATTAAT 1 cut(s) 510
PsiI TTATAA 1 cut(s) 717
Psp6I CCWGG 1 cut(s) 721
PspGI CCWGG 1 cut(s) 721
PspN4I GGNNCC 1 cut(s) 75
PstI CTGCAG 1 cut(s) 496
PsuI RGATCY 1 cut(s) 604
RsaI GTAC 5 cut(s) 303, 317, 447, 696, 1113
RsaNI GTAC 5 cut(s) 302, 316, 446, 695, 1112
RseI CAYNNNNRTG 1 cut(s) 1043
SaqAI TTAA 5 cut(s) 285, 510, 1073, 1103, 1142
SatI GCNGC 5 cut(s) 60, 140, 231, 234, 492
Sau3AI GATC 3 cut(s) 604, 1161, 1182
SchI GAGTC 1 cut(s) 359
ScrFI CCNGG 1 cut(s) 723
SduI GDGCHC 1 cut(s) 202
SetI ASST 7 cut(s) 67, 344, 696, 775, 885, 992, 1240
SfaNI GCATC 4 cut(s) 4, 215, 259, 661
SfcI CTRYAG 3 cut(s) 219, 237, 492
SfuI TTCGAA 1 cut(s) 1132
SmiMI CAYNNNNRTG 1 cut(s) 1043
SmlI CTYRAG 2 cut(s) 581, 608
SmoI CTYRAG 2 cut(s) 581, 608
SsiI CCGC 1 cut(s) 995
SspI AATATT 1 cut(s) 1066
SspMI CTAG 1 cut(s) 675
StyD4I CCNGG 1 cut(s) 721
StyI CCWWGG 3 cut(s) 690, 891, 1282
TaaI ACNGT 3 cut(s) 220, 320, 445
TaqI TCGA 2 cut(s) 1132, 1154
TaqII GACCGA 3 cut(s) 389, 395, 492
TatI WGTACW 4 cut(s) 301, 315, 445, 1111
TfiI GAWTC 2 cut(s) 380, 475
Tru1I TTAA 5 cut(s) 285, 510, 1073, 1103, 1142
Tru9I TTAA 5 cut(s) 285, 510, 1073, 1103, 1142
TscAI CASTG 3 cut(s) 223, 832, 1063
TseFI GTSAC 2 cut(s) 8, 895
TseI GCWGC 5 cut(s) 59, 139, 230, 233, 491
Tsp45I GTSAC 2 cut(s) 8, 895
TspDTI ATGAA 4 cut(s) 528, 893, 1012, 1106
TspRI CASTG 3 cut(s) 223, 832, 1063
VspI ATTAAT 1 cut(s) 510
XagI CCTNNNNNAGG 1 cut(s) 207
XapI RAATTY 3 cut(s) 110, 182, 1138
XmiI GTMKAC 1 cut(s) 240
XmnI GAANNNNTTC 2 cut(s) 566, 980
XspI CTAG 1 cut(s) 675
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.