Rw6G015670

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000258
Physical Location & Seq
Reverse (-)
30277264 .. 30278612
1349 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G015670.1

Sequence Viewer

Length: 1251 bp
ATGGCTGGTGACGATGCTGACGTTACTGGAAATGATAAGGGAAAAGGAATGGCTATTGCTGCACCTGTGTTGATTCCTCCTTCCTCCACTCATGGGGAGAAACCCGAGAAATTTAGTGGGACAAACTTCAAATGCTGGTATGCTCCTGCATCAGGAAGCACTGCAGAAGAGGCTGCTGCTGTAGACGCATGGCATCATTCAGATTTTCTATGCAAGAATTACATTCTTAATGGATTGGACATTGTACTTTACAAAGTGTACAGTCCAATAAAGAATGCTAAAAGCTTGTGGGAGTCTTTAGAAAAGAAATACAAGACCGAAGATGTTGGAGCAAAGAAATATATAATCGGTCGTTTCCTTGACTACAAGATGGTAGATACTAAAACTGTACTCAGTCAAGTTGAGGAGTTTCAATTGATTCTACATGAGATGGCTGCAGAAAATCTGTCAATTAATGAAACTTTGCAAGTGGGATGTATTATTGAGAAACTTCCTCCATCTTGGAAGGATTTCAAGAATTATCTCAAGCATAAGCGCAAGGAAATGGATCTTGAGGGTCTAATTGTGAGGCTACGGGTTGAGGAAGGCAATCGCATATCTGACAAGAGAAGTGATGCTAATGAACCACAAAACAAAAATAAGAAGAGAAAGTTCTCTGGGAAAAATTATAAGCCAGGAAACTCAAAGAAGTTCAAAGGCAAGTGTTTCAATTGTAATAAGACAGGTCATCGTGTTATGGAATGTCATAGCAAGAAAAACAAAGGCTACAAGAAAGCCACTGAAGCAAACATGACTGAGGGAGATAGATTGTCTGTTGACATTGCTGATATGAACCTTTCAGCCATGGTGACTGAAGTCAATATGATAACAAGCGCCGAAGAATGGTGGATAGACACAGGGGCTACTTGCCATATATGTTTTGATAAGAAGATGTTCTCTACCTATGCGGAAGTAAATCAAGGAGAGCAATTATTCATGGGCAATGCTTCCACATCAATGGTTCAAGGCACTGGTAATATTGTTTTAAAGTTGATATCTGGGAAAGAAATTACTTTAAACAATGTACTTCATGTGCCTGATATTCGAAAGAATTTAATCTCTGGTTCGATGTTGATCAAAAATGGATTTCGTGTGATCTTTGAAGTTGATAAAGTCATACTTACCAAGAACGGGATATATGTAGGAAAAGGTTATCTCAGTAATGGCCTTTTCAAGATATGCTCCCAAGAAGTCCAAGGAAAGAGTATCTAA
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

416

Amino Acids

46.57

Weight (kDa)

8.99

Isoelectric Point (pI)

27.0

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 55 - 201 4.8e-24 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 295 - 376 2.9e-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) 669
AccI GTMKAC 1 cut(s) 183
AciI CCGC 1 cut(s) 947
AclWI GGATC 1 cut(s) 555
AcsI RAATTY 2 cut(s) 110, 1090
AcuI CTGAAG 2 cut(s) 801, 873
AfaI GTAC 4 cut(s) 246, 260, 390, 1065
AfiI CCNNNNNNNGG 4 cut(s) 93, 152, 882, 1170
AgsI TTSAA 8 cut(s) 130, 413, 514, 694, 709, 1004, 1142, 1213
AjnI CCWGG 1 cut(s) 673
AluBI AGCT 1 cut(s) 285
AluI AGCT 1 cut(s) 285
AlwI GGATC 1 cut(s) 555
Ama87I CYCGRG 1 cut(s) 104
AoxI GGCC 1 cut(s) 1204
ApeKI GCWGC 4 cut(s) 59, 173, 176, 434
ApoI RAATTY 2 cut(s) 110, 1090
AseI ATTAAT 1 cut(s) 453
Asp700I GAANNNNTTC 2 cut(s) 509, 932
AspLEI GCGC 2 cut(s) 537, 875
AsuHPI GGTGA 2 cut(s) 20, 859
AsuII TTCGAA 1 cut(s) 1084
AvaI CYCGRG 1 cut(s) 104
BbvI GCAGC 4 cut(s) 46, 160, 163, 421
BccI CCATC 3 cut(s) 364, 424, 505
BciT130I CCWGG 1 cut(s) 675
BclI TGATCA 1 cut(s) 1113
BfmI CTRYAG 3 cut(s) 162, 180, 435
BfoI RGCGCY 1 cut(s) 876
BisI GCNGC 4 cut(s) 60, 174, 177, 435
BlsI GCNGC 4 cut(s) 61, 175, 178, 436
Bme1390I CCNGG 1 cut(s) 675
BmeT110I CYCGRG 1 cut(s) 104
BmrFI CCNGG 1 cut(s) 675
BmsI GCATC 4 cut(s) 4, 158, 202, 604
BoxI GACNNNNGTC 1 cut(s) 854
Bpu14I TTCGAA 1 cut(s) 1084
BpuEI CTTGAG 2 cut(s) 509, 572
BsaBI GATNNNNATC 1 cut(s) 1112
BsaJI CCNNGG 2 cut(s) 843, 1234
Bsc4I CCNNNNNNNGG 4 cut(s) 93, 152, 882, 1170
Bse1I ACTGG 2 cut(s) 31, 1015
Bse3DI GCAATG 2 cut(s) 819, 988
Bse8I GATNNNNATC 1 cut(s) 1112
BseBI CCWGG 1 cut(s) 675
BseDI CCNNGG 2 cut(s) 843, 1234
BseGI GGATG 1 cut(s) 479
BseJI GATNNNNATC 1 cut(s) 1112
BseLI CCNNNNNNNGG 4 cut(s) 93, 152, 882, 1170
BseMI GCAATG 2 cut(s) 819, 988
BseMII CTCAG 3 cut(s) 406, 786, 1210
BseNI ACTGG 2 cut(s) 31, 1015
BseRI GAGGAG 1 cut(s) 419
BseXI GCAGC 4 cut(s) 46, 160, 163, 421
BsgI GTGCAG 1 cut(s) 45
Bsh1285I CGRYCG 1 cut(s) 352
BshFI GGCC 1 cut(s) 1206
BsiEI CGRYCG 1 cut(s) 352
BsiHKCI CYCGRG 1 cut(s) 104
BslFI GGGAC 1 cut(s) 133
BslI CCNNNNNNNGG 4 cut(s) 93, 152, 882, 1170
BsmFI GGGAC 1 cut(s) 133
BsmI GAATGC 1 cut(s) 280
BsnI GGCC 1 cut(s) 1206
BsoBI CYCGRG 1 cut(s) 104
Bsp119I TTCGAA 1 cut(s) 1084
Bsp1407I TGTACA 1 cut(s) 258
Bsp143I GATC 3 cut(s) 547, 1113, 1134
Bsp19I CCATGG 1 cut(s) 843
BspACI CCGC 1 cut(s) 947
BspANI GGCC 1 cut(s) 1206
BspCNI CTCAG 3 cut(s) 405, 787, 1209
BspMAI CTGCAG 2 cut(s) 166, 439
BspPI GGATC 1 cut(s) 555
BspT104I TTCGAA 1 cut(s) 1084
BsrDI GCAATG 2 cut(s) 819, 988
BsrGI TGTACA 1 cut(s) 258
BsrI ACTGG 2 cut(s) 31, 1015
BssECI CCNNGG 2 cut(s) 843, 1234
BssMI GATC 3 cut(s) 547, 1113, 1134
BssT1I CCWWGG 2 cut(s) 843, 1234
Bst2UI CCWGG 1 cut(s) 675
Bst4CI ACNGT 2 cut(s) 263, 388
Bst6I CTCTTC 2 cut(s) 162, 638
BstAUI TGTACA 1 cut(s) 258
BstBI TTCGAA 1 cut(s) 1084
BstDEI CTNAG 3 cut(s) 392, 795, 1196
BstDSI CCRYGG 1 cut(s) 843
BstENI CCTNNNNNAGG 1 cut(s) 150
BstF5I GGATG 1 cut(s) 479
BstH2I RGCGCY 1 cut(s) 876
BstHHI GCGC 2 cut(s) 537, 875
BstKTI GATC 3 cut(s) 550, 1116, 1137
BstMBI GATC 3 cut(s) 547, 1113, 1134
BstMCI CGRYCG 1 cut(s) 352
BstMWI GCNNNNNNNGC 4 cut(s) 59, 170, 185, 782
BstNI CCWGG 1 cut(s) 675
BstPAI GACNNNNGTC 1 cut(s) 854
BstSCI CCNGG 1 cut(s) 673
BstSFI CTRYAG 3 cut(s) 162, 180, 435
BstV1I GCAGC 4 cut(s) 46, 160, 163, 421
BstX2I RGATCY 1 cut(s) 547
BstXI CCANNNNNNTGG 1 cut(s) 997
BstYI RGATCY 1 cut(s) 547
BsuRI GGCC 1 cut(s) 1206
BtgI CCRYGG 1 cut(s) 843
BtsCI GGATG 1 cut(s) 479
BtsI GCAGTG 1 cut(s) 159
BtsIMutI CAGTG 3 cut(s) 159, 777, 1008
CfoI GCGC 2 cut(s) 537, 875
CseI GACGC 1 cut(s) 194
Csp6I GTAC 4 cut(s) 245, 259, 389, 1064
CviAII CATG 7 cut(s) 92, 189, 425, 790, 844, 976, 1070
CviQI GTAC 4 cut(s) 245, 259, 389, 1064
DdeI CTNAG 3 cut(s) 392, 795, 1196
DpnI GATC 3 cut(s) 549, 1115, 1136
DpnII GATC 3 cut(s) 547, 1113, 1134
DraI TTTAAA 2 cut(s) 1026, 1056
Eam1104I CTCTTC 2 cut(s) 162, 638
EarI CTCTTC 2 cut(s) 162, 638
Eco130I CCWWGG 2 cut(s) 843, 1234
Eco32I GATATC 1 cut(s) 1035
Eco57I CTGAAG 2 cut(s) 801, 873
Eco88I CYCGRG 1 cut(s) 104
EcoNI CCTNNNNNAGG 1 cut(s) 150
EcoRII CCWGG 1 cut(s) 673
EcoRV GATATC 1 cut(s) 1035
EcoT14I CCWWGG 2 cut(s) 843, 1234
ErhI CCWWGG 2 cut(s) 843, 1234
FaeI CATG 7 cut(s) 95, 192, 428, 793, 847, 979, 1073
FalI AAGNNNNNCTT 2 cut(s) 1143, 1175
FaqI GGGAC 1 cut(s) 133
FatI CATG 7 cut(s) 91, 188, 424, 789, 843, 975, 1069
FbaI TGATCA 1 cut(s) 1113
FblI GTMKAC 1 cut(s) 183
Fnu4HI GCNGC 4 cut(s) 60, 174, 177, 435
FokI GGATG 1 cut(s) 486
Fsp4HI GCNGC 4 cut(s) 60, 174, 177, 435
GlaI GCGC 2 cut(s) 536, 874
GluI GCNGC 4 cut(s) 60, 174, 177, 435
HaeII RGCGCY 1 cut(s) 876
HaeIII GGCC 1 cut(s) 1206
HgaI GACGC 1 cut(s) 194
HhaI GCGC 2 cut(s) 537, 875
Hin1II CATG 7 cut(s) 95, 192, 428, 793, 847, 979, 1073
Hin6I GCGC 2 cut(s) 535, 873
HinP1I GCGC 2 cut(s) 535, 873
HincII GTYRAC 1 cut(s) 817
HindII GTYRAC 1 cut(s) 817
HindIII AAGCTT 1 cut(s) 283
HinfI GANTC 3 cut(s) 73, 293, 418
HphI GGTGA 2 cut(s) 20, 859
Hpy166II GTNNAC 3 cut(s) 184, 259, 817
Hpy188I TCNGA 2 cut(s) 202, 601
Hpy188III TCNNGA 4 cut(s) 153, 514, 551, 1213
Hpy8I GTNNAC 3 cut(s) 184, 259, 817
HpyAV CCTTC 3 cut(s) 90, 499, 578
HpyCH4III ACNGT 2 cut(s) 263, 388
HpyCH4IV ACGT 1 cut(s) 21
HpyCH4V TGCA 6 cut(s) 62, 149, 164, 213, 437, 466
HpyF10VI GCNNNNNNNGC 4 cut(s) 59, 170, 185, 782
HpyF3I CTNAG 3 cut(s) 392, 795, 1196
HpySE526I ACGT 1 cut(s) 21
Hsp92II CATG 7 cut(s) 95, 192, 428, 793, 847, 979, 1073
HspAI GCGC 2 cut(s) 535, 873
Ksp22I TGATCA 1 cut(s) 1113
Kzo9I GATC 3 cut(s) 547, 1113, 1134
LmnI GCTCC 3 cut(s) 148, 329, 1226
Lsp1109I GCAGC 4 cut(s) 46, 160, 163, 421
LweI GCATC 4 cut(s) 4, 158, 202, 604
MaeII ACGT 1 cut(s) 21
MaeIII GTNAC 3 cut(s) 8, 22, 847
MalI GATC 3 cut(s) 549, 1115, 1136
MboI GATC 3 cut(s) 547, 1113, 1134
MboII GAAGA 5 cut(s) 179, 332, 655, 890, 940
MfeI CAATTG 2 cut(s) 413, 709
MflI RGATCY 1 cut(s) 547
MlyI GAGTC 1 cut(s) 302
MmeI TCCRAC 1 cut(s) 307
MnlI CCTC 9 cut(s) 87, 94, 163, 397, 504, 547, 561, 574, 790
MroXI GAANNNNTTC 2 cut(s) 509, 932
MseI TTAA 5 cut(s) 228, 453, 1025, 1055, 1094
MslI CAYNNNNRTG 1 cut(s) 995
MspR9I CCNGG 1 cut(s) 675
MunI CAATTG 2 cut(s) 413, 709
Mva1269I GAATGC 1 cut(s) 280
MvaI CCWGG 1 cut(s) 675
MwoI GCNNNNNNNGC 4 cut(s) 59, 170, 185, 782
NcoI CCATGG 1 cut(s) 843
NdeII GATC 3 cut(s) 547, 1113, 1134
NlaIII CATG 7 cut(s) 95, 192, 428, 793, 847, 979, 1073
NmuCI GTSAC 2 cut(s) 8, 847
NspV TTCGAA 1 cut(s) 1084
PcsI WCGNNNNNNNCGW 1 cut(s) 18
PctI GAATGC 1 cut(s) 280
PdmI GAANNNNTTC 2 cut(s) 509, 932
PfeI GAWTC 2 cut(s) 73, 418
PkrI GCNGC 4 cut(s) 61, 175, 178, 436
PleI GAGTC 1 cut(s) 301
PpsI GAGTC 1 cut(s) 301
PshAI GACNNNNGTC 1 cut(s) 854
PshBI ATTAAT 1 cut(s) 453
PsiI TTATAA 1 cut(s) 669
Psp6I CCWGG 1 cut(s) 673
PspGI CCWGG 1 cut(s) 673
PstI CTGCAG 2 cut(s) 166, 439
PsuI RGATCY 1 cut(s) 547
RsaI GTAC 4 cut(s) 246, 260, 390, 1065
RsaNI GTAC 4 cut(s) 245, 259, 389, 1064
RseI CAYNNNNRTG 1 cut(s) 995
SaqAI TTAA 5 cut(s) 228, 453, 1025, 1055, 1094
SatI GCNGC 4 cut(s) 60, 174, 177, 435
Sau3AI GATC 3 cut(s) 547, 1113, 1134
SchI GAGTC 1 cut(s) 302
ScrFI CCNGG 1 cut(s) 675
SetI ASST 7 cut(s) 24, 67, 287, 727, 837, 944, 1192
SfaNI GCATC 4 cut(s) 4, 158, 202, 604
SfcI CTRYAG 3 cut(s) 162, 180, 435
SfuI TTCGAA 1 cut(s) 1084
SmiMI CAYNNNNRTG 1 cut(s) 995
SmlI CTYRAG 2 cut(s) 524, 551
SmoI CTYRAG 2 cut(s) 524, 551
SsiI CCGC 1 cut(s) 947
SspI AATATT 1 cut(s) 1018
StyD4I CCNGG 1 cut(s) 673
StyI CCWWGG 2 cut(s) 843, 1234
TaaI ACNGT 2 cut(s) 263, 388
TaiI ACGT 1 cut(s) 24
TaqI TCGA 2 cut(s) 1084, 1106
TaqII GACCGA 2 cut(s) 332, 338
TatI WGTACW 4 cut(s) 244, 258, 388, 1063
TfiI GAWTC 2 cut(s) 73, 418
Tru1I TTAA 5 cut(s) 228, 453, 1025, 1055, 1094
Tru9I TTAA 5 cut(s) 228, 453, 1025, 1055, 1094
TscAI CASTG 3 cut(s) 166, 784, 1015
TseFI GTSAC 2 cut(s) 8, 847
TseI GCWGC 4 cut(s) 59, 173, 176, 434
Tsp45I GTSAC 2 cut(s) 8, 847
TspDTI ATGAA 5 cut(s) 471, 636, 845, 964, 1058
TspRI CASTG 3 cut(s) 166, 784, 1015
VspI ATTAAT 1 cut(s) 453
XagI CCTNNNNNAGG 1 cut(s) 150
XapI RAATTY 2 cut(s) 110, 1090
XmiI GTMKAC 1 cut(s) 183
XmnI GAANNNNTTC 2 cut(s) 509, 932
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.