Rw5G025890

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000258
Physical Location & Seq
Forward (+)
37083607 .. 37084944
1338 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G025890.1

Sequence Viewer

Length: 1338 bp
ATGAACGGTGACAATTCAAATGTTACTAGGGATGATATGGGACAAAGCGAGGCAAATCCTATATCTGTGGTGATATCAGACTCCTCTAAACATGGAGAGAAACCTGAGAAGTTCAATGGAACAGACTTCAAAAGGTGGCAACAAAAGATGCTCTTCTACCTGACAACCTTGAGTTTGACAAAATTTCTGAAGGAAGATGCCCCTGCCAGTGGCTCATCTGTGGAGGCTGCTGCGGCTGCAGATGCTTGGCATCATTCTGATTTTCTGTGCAAAAATTACATCCTCAATGGATTGGACAATGCATTATACAATGTCTATAGTCCAATGAAATCTGCTAAGGCCTTATGGGAGTCTCTTGACAAGAAATATAAGACCGAGGACGCTGGAAAGAAGAAATATATCATTGGGCGTTTTCTTGATTACAAGATGATAGACTCCAAATCAGTCATGAGTCAACTCCAAGAATTCCAATTAATTCTTCATGAAATGCAGGCTGAAAAAATGGATATGACTGAAGCTTTACAAGTTGGTTGTGTGATTGAAAAATTACCTCCATCTTGGAAAGAGTTTAAGAATTATCTCAAGCATAAGCGCAAGGAAATGGACCTTGAAGGTTTGACTGTGAGGCTAAGGGTTGAGGAAGACAACCGTATTGCTGACAAGAAAAATGGAATTAATTCCATGGCAGCAAATGCTCATGTTGTTGAAGATGGACAAGAGAATAAAAAGAGAAAATATTCTGGTGAAGGCAAAGAGCAAGAGAATACAAAGAAGCATCGTAATTTCAAAGGAAAATGTTTCAATTGTAACAAGCCTGGGCATAGAGCTTCTGATTGTCGTAGCCGTAAAGGAAAGACAAACAACTACAAAAAATATAAAGGCAAGGCCAAGGAGGTTCATATAGCCGAAGAGGACAAACTCTCATGTGGAATATCTGATATCAATTTATCAGCTGTGATCTCTGAAGTAAACATGATGACCAGTAGTGATGATTGGTGGGTGGACACTGGGGCTACACGCCACATTTGTTTTGACAAGAAGATGTTTACTACATATGAAGCAGTGGAACAAGGAGAGCAGCTCTTTATGGGAAATTCCTCTACTTCAGGGGTTGAAGGACAAGGAAATGTGACACTCAAGTTGACATCTGGAAAGGTACTCACTCTAACAGAAGTACTTCATGTTCCTGATATTAGAAAAAACTTGGTTTCTGGATCGCTGCTCAGTAAGAATGGTTTCAAGTTGGTTTTTGAGGCTGACAAGTTTATGTTAACTAAGAACGGGATGTATGTGGGGAAAGGTTATCTTAGTCATGGCCTCTTCAAGATCCAAGGATGA
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

445

Amino Acids

50.22

Weight (kDa)

8.95

Isoelectric Point (pI)

31.26

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 50 - 220 3e-25 gag-polypeptide of LTR copia-type
zf-CCHC PF00098 264 - 280 3.7e-06 Zinc knuckle
Pol_BBD PF22936 332 - 413 9.4e-25 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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 2 cut(s) 1222, 1321
AcsI RAATTY 3 cut(s) 182, 464, 1093
AcuI CTGAAG 4 cut(s) 209, 534, 984, 1089
AfaI GTAC 2 cut(s) 1158, 1176
AfiI CCNNNNNNNGG 1 cut(s) 209
AjnI CCWGG 1 cut(s) 814
AjuI GAANNNNNNNTTGG 2 cut(s) 462, 494
AluBI AGCT 4 cut(s) 518, 827, 953, 1081
AluI AGCT 4 cut(s) 518, 827, 953, 1081
Alw26I GTCTC 1 cut(s) 357
AlwI GGATC 2 cut(s) 1222, 1321
AoxI GGCC 3 cut(s) 339, 885, 1315
ApeKI GCWGC 6 cut(s) 227, 230, 236, 686, 1078, 1219
ApoI RAATTY 3 cut(s) 182, 464, 1093
AseI ATTAAT 2 cut(s) 473, 675
Asp700I GAANNNNTTC 4 cut(s) 676, 736, 1176, 1235
AspLEI GCGC 1 cut(s) 594
AspS9I GGNCC 1 cut(s) 604
AsuHPI GGTGA 3 cut(s) 20, 82, 755
AvaII GGWCC 1 cut(s) 604
BbsI GAAGAC 1 cut(s) 648
BbvI GCAGC 6 cut(s) 214, 217, 223, 698, 1090, 1206
BccI CCATC 2 cut(s) 562, 704
BceAI ACGGC 1 cut(s) 828
BciT130I CCWGG 1 cut(s) 816
BcoDI GTCTC 1 cut(s) 357
BfaI CTAG 1 cut(s) 27
BfmI CTRYAG 2 cut(s) 237, 316
BisI GCNGC 7 cut(s) 228, 231, 234, 237, 687, 1079, 1220
BlsI GCNGC 7 cut(s) 229, 232, 235, 238, 688, 1080, 1221
BmcAI AGTACT 1 cut(s) 1176
Bme1390I CCNGG 1 cut(s) 816
Bme18I GGWCC 1 cut(s) 604
BmgT120I GGNCC 1 cut(s) 604
BmrFI CCNGG 1 cut(s) 816
BmrI ACTGGG 1 cut(s) 1017
BmsI GCATC 5 cut(s) 138, 187, 232, 259, 784
BmuI ACTGGG 1 cut(s) 1017
BpiI GAAGAC 1 cut(s) 648
BplI GAGNNNNNCTC 2 cut(s) 1065, 1097
Bpu10I CCTNAGC 2 cut(s) 336, 629
BpuEI CTTGAG 3 cut(s) 190, 566, 1121
BsaJI CCNNGG 5 cut(s) 375, 681, 815, 888, 1330
Bsc4I CCNNNNNNNGG 1 cut(s) 209
Bse1I ACTGG 3 cut(s) 207, 981, 1012
BseBI CCWGG 1 cut(s) 816
BseDI CCNNGG 5 cut(s) 375, 681, 815, 888, 1330
BseGI GGATG 3 cut(s) 37, 279, 1290
BseLI CCNNNNNNNGG 1 cut(s) 209
BseMII CTCAG 2 cut(s) 96, 1237
BseNI ACTGG 3 cut(s) 207, 981, 1012
BseRI GAGGAG 1 cut(s) 73
BseXI GCAGC 6 cut(s) 214, 217, 223, 698, 1090, 1206
BshFI GGCC 3 cut(s) 341, 887, 1317
BslFI GGGAC 1 cut(s) 54
BslI CCNNNNNNNGG 1 cut(s) 209
BsmAI GTCTC 1 cut(s) 357
BsmFI GGGAC 1 cut(s) 54
BsnI GGCC 3 cut(s) 341, 887, 1317
Bsp143I GATC 3 cut(s) 957, 1214, 1326
Bsp19I CCATGG 1 cut(s) 681
BspACI CCGC 1 cut(s) 233
BspANI GGCC 3 cut(s) 341, 887, 1317
BspCNI CTCAG 2 cut(s) 97, 1236
BspHI TCATGA 2 cut(s) 447, 481
BspMAI CTGCAG 1 cut(s) 241
BspPI GGATC 2 cut(s) 1222, 1321
BspQI GCTCTTC 1 cut(s) 158
BsrI ACTGG 3 cut(s) 207, 981, 1012
BssECI CCNNGG 5 cut(s) 375, 681, 815, 888, 1330
BssMI GATC 3 cut(s) 957, 1214, 1326
BssT1I CCWWGG 3 cut(s) 681, 888, 1330
Bst2UI CCWGG 1 cut(s) 816
Bst4CI ACNGT 3 cut(s) 8, 622, 650
Bst6I CTCTTC 3 cut(s) 158, 903, 1325
BstAPI GCANNNNNTGC 1 cut(s) 692
BstC8I GCNNGC 1 cut(s) 492
BstDEI CTNAG 6 cut(s) 105, 336, 629, 1223, 1275, 1307
BstDSI CCRYGG 1 cut(s) 681
BstF5I GGATG 3 cut(s) 37, 279, 1290
BstHHI GCGC 1 cut(s) 594
BstKTI GATC 3 cut(s) 960, 1217, 1329
BstMAI GTCTC 1 cut(s) 357
BstMBI GATC 3 cut(s) 957, 1214, 1326
BstMWI GCNNNNNNNGC 4 cut(s) 233, 236, 242, 692
BstNI CCWGG 1 cut(s) 816
BstSCI CCNGG 1 cut(s) 814
BstSFI CTRYAG 2 cut(s) 237, 316
BstV1I GCAGC 6 cut(s) 214, 217, 223, 698, 1090, 1206
BstV2I GAAGAC 1 cut(s) 648
BstX2I RGATCY 1 cut(s) 1326
BstYI RGATCY 1 cut(s) 1326
BsuRI GGCC 3 cut(s) 341, 887, 1317
BtgI CCRYGG 1 cut(s) 681
BtsCI GGATG 3 cut(s) 37, 279, 1290
BtsI GCAGTG 1 cut(s) 1068
BtsIMutI CAGTG 3 cut(s) 214, 1005, 1068
Cac8I GCNNGC 1 cut(s) 492
CciI TCATGA 2 cut(s) 447, 481
CfoI GCGC 1 cut(s) 594
Cfr13I GGNCC 1 cut(s) 604
CseI GACGC 1 cut(s) 389
Csp6I GTAC 2 cut(s) 1157, 1175
CviAII CATG 9 cut(s) 92, 448, 482, 682, 698, 924, 973, 1181, 1313
CviQI GTAC 2 cut(s) 1157, 1175
DdeI CTNAG 6 cut(s) 105, 336, 629, 1223, 1275, 1307
DpnI GATC 3 cut(s) 959, 1216, 1328
DpnII GATC 3 cut(s) 957, 1214, 1326
Eam1104I CTCTTC 3 cut(s) 158, 903, 1325
EarI CTCTTC 3 cut(s) 158, 903, 1325
Eco130I CCWWGG 3 cut(s) 681, 888, 1330
Eco147I AGGCCT 1 cut(s) 341
Eco32I GATATC 2 cut(s) 75, 940
Eco47I GGWCC 1 cut(s) 604
Eco57I CTGAAG 4 cut(s) 209, 534, 984, 1089
EcoRI GAATTC 1 cut(s) 464
EcoRII CCWGG 1 cut(s) 814
EcoRV GATATC 2 cut(s) 75, 940
EcoT14I CCWWGG 3 cut(s) 681, 888, 1330
EcoT22I ATGCAT 1 cut(s) 304
ErhI CCWWGG 3 cut(s) 681, 888, 1330
FaeI CATG 9 cut(s) 95, 451, 485, 685, 701, 927, 976, 1184, 1316
FalI AAGNNNNNCTT 4 cut(s) 137, 169, 1290, 1322
FaqI GGGAC 1 cut(s) 54
FatI CATG 9 cut(s) 91, 447, 481, 681, 697, 923, 972, 1180, 1312
FauNDI CATATG 1 cut(s) 1054
Fnu4HI GCNGC 7 cut(s) 228, 231, 234, 237, 687, 1079, 1220
FokI GGATG 3 cut(s) 44, 266, 1297
Fsp4HI GCNGC 7 cut(s) 228, 231, 234, 237, 687, 1079, 1220
FspBI CTAG 1 cut(s) 27
GlaI GCGC 1 cut(s) 593
GluI GCNGC 7 cut(s) 228, 231, 234, 237, 687, 1079, 1220
HaeIII GGCC 3 cut(s) 341, 887, 1317
HgaI GACGC 1 cut(s) 389
HhaI GCGC 1 cut(s) 594
Hin1II CATG 9 cut(s) 95, 451, 485, 685, 701, 927, 976, 1184, 1316
Hin6I GCGC 1 cut(s) 592
HinP1I GCGC 1 cut(s) 592
HincII GTYRAC 3 cut(s) 455, 1143, 1272
HindII GTYRAC 3 cut(s) 455, 1143, 1272
HindIII AAGCTT 1 cut(s) 516
HinfI GANTC 4 cut(s) 80, 350, 434, 451
HpaI GTTAAC 1 cut(s) 1272
HphI GGTGA 3 cut(s) 20, 82, 755
Hpy166II GTNNAC 6 cut(s) 455, 970, 1003, 1047, 1143, 1272
Hpy188I TCNGA 6 cut(s) 79, 189, 259, 832, 937, 964
Hpy188III TCNNGA 8 cut(s) 356, 416, 448, 482, 1149, 1187, 1212, 1324
Hpy8I GTNNAC 6 cut(s) 455, 970, 1003, 1047, 1143, 1272
HpyAV CCTTC 4 cut(s) 184, 605, 740, 1109
HpyCH4III ACNGT 3 cut(s) 8, 622, 650
HpyCH4V TGCA 4 cut(s) 239, 270, 302, 490
HpyF10VI GCNNNNNNNGC 4 cut(s) 233, 236, 242, 692
HpyF3I CTNAG 6 cut(s) 105, 336, 629, 1223, 1275, 1307
Hsp92II CATG 9 cut(s) 95, 451, 485, 685, 701, 927, 976, 1184, 1316
HspAI GCGC 1 cut(s) 592
KspAI GTTAAC 1 cut(s) 1272
Kzo9I GATC 3 cut(s) 957, 1214, 1326
LguI GCTCTTC 1 cut(s) 158
Lsp1109I GCAGC 6 cut(s) 214, 217, 223, 698, 1090, 1206
LweI GCATC 5 cut(s) 138, 187, 232, 259, 784
MaeI CTAG 1 cut(s) 27
MaeIII GTNAC 4 cut(s) 8, 22, 806, 1129
MalI GATC 3 cut(s) 959, 1216, 1328
MboI GATC 3 cut(s) 957, 1214, 1326
MboII GAAGA 9 cut(s) 145, 206, 403, 470, 653, 719, 920, 1051, 1312
MfeI CAATTG 1 cut(s) 802
MflI RGATCY 1 cut(s) 1326
MlyI GAGTC 4 cut(s) 74, 359, 428, 460
Mph1103I ATGCAT 1 cut(s) 304
MroXI GAANNNNTTC 4 cut(s) 676, 736, 1176, 1235
MseI TTAA 4 cut(s) 473, 570, 675, 1271
MspA1I CMGCKG 1 cut(s) 953
MspR9I CCNGG 1 cut(s) 816
MunI CAATTG 1 cut(s) 802
MvaI CCWGG 1 cut(s) 816
MwoI GCNNNNNNNGC 4 cut(s) 233, 236, 242, 692
NcoI CCATGG 1 cut(s) 681
NdeI CATATG 1 cut(s) 1054
NdeII GATC 3 cut(s) 957, 1214, 1326
NlaIII CATG 9 cut(s) 95, 451, 485, 685, 701, 927, 976, 1184, 1316
NmuCI GTSAC 2 cut(s) 8, 1129
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) 676, 736, 1176, 1235
PkrI GCNGC 7 cut(s) 229, 232, 235, 238, 688, 1080, 1221
PleI GAGTC 4 cut(s) 74, 358, 428, 459
PpsI GAGTC 4 cut(s) 74, 358, 428, 459
PshBI ATTAAT 2 cut(s) 473, 675
Psp6I CCWGG 1 cut(s) 814
PspGI CCWGG 1 cut(s) 814
PspPI GGNCC 1 cut(s) 604
PsrI GAACNNNNNNTAC 2 cut(s) 1167, 1199
PstI CTGCAG 1 cut(s) 241
PsuI RGATCY 1 cut(s) 1326
PvuII CAGCTG 1 cut(s) 953
RsaI GTAC 2 cut(s) 1158, 1176
RsaNI GTAC 2 cut(s) 1157, 1175
SapI GCTCTTC 1 cut(s) 158
SaqAI TTAA 4 cut(s) 473, 570, 675, 1271
SatI GCNGC 7 cut(s) 228, 231, 234, 237, 687, 1079, 1220
Sau3AI GATC 3 cut(s) 957, 1214, 1326
Sau96I GGNCC 1 cut(s) 604
ScaI AGTACT 1 cut(s) 1176
SchI GAGTC 4 cut(s) 74, 359, 428, 460
ScrFI CCNGG 1 cut(s) 816
SfaNI GCATC 5 cut(s) 138, 187, 232, 259, 784
SfcI CTRYAG 2 cut(s) 237, 316
SinI GGWCC 1 cut(s) 604
SmlI CTYRAG 3 cut(s) 169, 581, 1136
SmoI CTYRAG 3 cut(s) 169, 581, 1136
SseBI AGGCCT 1 cut(s) 341
SsiI CCGC 1 cut(s) 233
SspI AATATT 1 cut(s) 737
SspMI CTAG 1 cut(s) 27
StuI AGGCCT 1 cut(s) 341
StyD4I CCNGG 1 cut(s) 814
StyI CCWWGG 3 cut(s) 681, 888, 1330
TaaI ACNGT 3 cut(s) 8, 622, 650
TaqII GACCGA 1 cut(s) 389
TatI WGTACW 1 cut(s) 1174
TauI GCSGC 1 cut(s) 236
Tru1I TTAA 4 cut(s) 473, 570, 675, 1271
Tru9I TTAA 4 cut(s) 473, 570, 675, 1271
TscAI CASTG 3 cut(s) 214, 1012, 1068
TseFI GTSAC 2 cut(s) 8, 1129
TseI GCWGC 6 cut(s) 227, 230, 236, 686, 1078, 1219
Tsp45I GTSAC 2 cut(s) 8, 1129
TspDTI ATGAA 7 cut(s) 17, 341, 470, 498, 887, 1071, 1169
TspRI CASTG 3 cut(s) 214, 1012, 1068
VpaK11BI GGWCC 1 cut(s) 604
VspI ATTAAT 2 cut(s) 473, 675
XapI RAATTY 3 cut(s) 182, 464, 1093
XmnI GAANNNNTTC 4 cut(s) 676, 736, 1176, 1235
XspI CTAG 1 cut(s) 27
ZrmI AGTACT 1 cut(s) 1176
Zsp2I ATGCAT 1 cut(s) 304
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.