Rmu_sc0001035.1_g000023

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0001035.1
OG0000106
Physical Location & Seq
Reverse (-)
111334 .. 111714
381 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0001035.1_g000023.1.cds

Sequence Viewer

Length: 381 bp
atgcagttcttgatgggattaaatgagacttacagtgcaacccgtagtcaaatcctcttgatgaacccccttccaagtgtcaaacaagcatatgctgccgttgcacaagaagaaaagcaacgtttcattgcagcagcggaatccagttcaagtgccgctgccatggtagttagaagtggcggccggccgaaccagaattgcagcagaggcggtcgtggtgaccgatcgaattttcagaccggtccaagtcttgaagcaaataaccttctgcaccagtcacgccctctccttctgctaaccaggttagtgcgacaggcatcgtcgaagaggagaatagatcagcaattactttatctgaggcccaattcaagcagtttttag
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_3

Protein Analysis

126

Amino Acids

13.91

Weight (kDa)

11.1

Isoelectric Point (pI)

66.99

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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

Orthologous Genes (Group: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 4 cut(s) 137, 156, 180, 210
AclI AACGTT 1 cut(s) 121
AcoI YGGCCR 2 cut(s) 181, 185
AcsI RAATTY 1 cut(s) 229
AgeI ACCGGT 1 cut(s) 239
AgsI TTSAA 3 cut(s) 150, 254, 369
AjnI CCWGG 1 cut(s) 299
Alw26I GTCTC 1 cut(s) 20
AoxI GGCC 3 cut(s) 181, 185, 359
ApeKI GCWGC 5 cut(s) 95, 131, 134, 158, 201
ApoI RAATTY 1 cut(s) 229
AsiGI ACCGGT 1 cut(s) 239
AspS9I GGNCC 2 cut(s) 242, 360
AsuHPI GGTGA 1 cut(s) 230
AvaII GGWCC 1 cut(s) 242
BbvI GCAGC 5 cut(s) 82, 143, 145, 146, 213
BccI CCATC 1 cut(s) 7
BceAI ACGGC 1 cut(s) 83
BciT130I CCWGG 1 cut(s) 301
BcoDI GTCTC 1 cut(s) 20
BisI GCNGC 7 cut(s) 96, 132, 135, 156, 159, 181, 202
BlsI GCNGC 7 cut(s) 97, 133, 136, 157, 160, 182, 203
Bme1390I CCNGG 1 cut(s) 301
Bme18I GGWCC 1 cut(s) 242
BmgT120I GGNCC 2 cut(s) 242, 360
BmrFI CCNGG 1 cut(s) 301
BmsI GCATC 1 cut(s) 326
BsaJI CCNNGG 1 cut(s) 162
BsaWI WCCGGW 1 cut(s) 239
BsaXI ACNNNNNCTCC 2 cut(s) 270, 300
Bse118I RCCGGY 2 cut(s) 183, 239
Bse1I ACTGG 2 cut(s) 144, 274
Bse3DI GCAATG 1 cut(s) 126
BseBI CCWGG 1 cut(s) 301
BseDI CCNNGG 1 cut(s) 162
BseMI GCAATG 1 cut(s) 126
BseMII CTCAG 1 cut(s) 347
BseNI ACTGG 2 cut(s) 144, 274
BseRI GAGGAG 1 cut(s) 343
BseX3I CGGCCG 2 cut(s) 181, 185
BseXI GCAGC 5 cut(s) 82, 143, 145, 146, 213
BsgI GTGCAG 1 cut(s) 254
Bsh1285I CGRYCG 4 cut(s) 184, 188, 214, 227
BshFI GGCC 3 cut(s) 183, 187, 361
BshTI ACCGGT 1 cut(s) 239
BsiEI CGRYCG 4 cut(s) 184, 188, 214, 227
BsiSI CCGG 2 cut(s) 184, 240
BsmAI GTCTC 1 cut(s) 20
BsnI GGCC 3 cut(s) 183, 187, 361
Bsp143I GATC 2 cut(s) 224, 337
Bsp19I CCATGG 1 cut(s) 162
BspACI CCGC 4 cut(s) 137, 156, 180, 210
BspANI GGCC 3 cut(s) 183, 187, 361
BspCNI CTCAG 1 cut(s) 348
BsrDI GCAATG 1 cut(s) 126
BsrFI RCCGGY 2 cut(s) 183, 239
BsrI ACTGG 2 cut(s) 144, 274
BssAI RCCGGY 2 cut(s) 183, 239
BssECI CCNNGG 1 cut(s) 162
BssMI GATC 2 cut(s) 224, 337
BssT1I CCWWGG 1 cut(s) 162
Bst2UI CCWGG 1 cut(s) 301
Bst4CI ACNGT 1 cut(s) 35
Bst6I CTCTTC 1 cut(s) 320
BstAPI GCANNNNNTGC 1 cut(s) 95
BstC8I GCNNGC 1 cut(s) 185
BstDEI CTNAG 1 cut(s) 356
BstDSI CCRYGG 1 cut(s) 162
BstEII GGTNACC 1 cut(s) 218
BstKTI GATC 2 cut(s) 227, 340
BstMAI GTCTC 1 cut(s) 20
BstMBI GATC 2 cut(s) 224, 337
BstMCI CGRYCG 4 cut(s) 184, 188, 214, 227
BstMWI GCNNNNNNNGC 3 cut(s) 95, 101, 207
BstNI CCWGG 1 cut(s) 301
BstPI GGTNACC 1 cut(s) 218
BstSCI CCNGG 1 cut(s) 299
BstV1I GCAGC 5 cut(s) 82, 143, 145, 146, 213
BstZI CGGCCG 2 cut(s) 181, 185
BsuRI GGCC 3 cut(s) 183, 187, 361
BtgI CCRYGG 1 cut(s) 162
BtsIMutI CAGTG 1 cut(s) 40
Cac8I GCNNGC 1 cut(s) 185
Cfr10I RCCGGY 2 cut(s) 183, 239
Cfr13I GGNCC 2 cut(s) 242, 360
CsiI ACCWGGT 1 cut(s) 299
CspAI ACCGGT 1 cut(s) 239
CviAII CATG 1 cut(s) 163
CviJI RGCY 3 cut(s) 183, 187, 361
CviKI_1 RGCY 3 cut(s) 183, 187, 361
DdeI CTNAG 1 cut(s) 356
DpnI GATC 2 cut(s) 226, 339
DpnII GATC 2 cut(s) 224, 337
EaeI YGGCCR 2 cut(s) 181, 185
EagI CGGCCG 2 cut(s) 181, 185
Eam1104I CTCTTC 1 cut(s) 320
EarI CTCTTC 1 cut(s) 320
EclXI CGGCCG 2 cut(s) 181, 185
Eco130I CCWWGG 1 cut(s) 162
Eco47I GGWCC 1 cut(s) 242
Eco52I CGGCCG 2 cut(s) 181, 185
Eco91I GGTNACC 1 cut(s) 218
EcoO65I GGTNACC 1 cut(s) 218
EcoRII CCWGG 1 cut(s) 299
EcoT14I CCWWGG 1 cut(s) 162
ErhI CCWWGG 1 cut(s) 162
FaeI CATG 1 cut(s) 166
FaiI YATR 3 cut(s) 91, 93, 164
FatI CATG 1 cut(s) 162
FauNDI CATATG 1 cut(s) 91
Fnu4HI GCNGC 7 cut(s) 96, 132, 135, 156, 159, 181, 202
FseI GGCCGGCC 1 cut(s) 187
Fsp4HI GCNGC 7 cut(s) 96, 132, 135, 156, 159, 181, 202
GluI GCNGC 7 cut(s) 96, 132, 135, 156, 159, 181, 202
HaeIII GGCC 3 cut(s) 183, 187, 361
HapII CCGG 2 cut(s) 184, 240
Hin1II CATG 1 cut(s) 166
HinfI GANTC 1 cut(s) 140
HpaII CCGG 2 cut(s) 184, 240
HphI GGTGA 1 cut(s) 230
Hpy188I TCNGA 2 cut(s) 237, 357
Hpy188III TCNNGA 3 cut(s) 10, 58, 251
Hpy99I CGWCG 1 cut(s) 325
HpyAV CCTTC 3 cut(s) 80, 275, 299
HpyCH4III ACNGT 1 cut(s) 35
HpyCH4IV ACGT 1 cut(s) 121
HpyCH4V TGCA 6 cut(s) 4, 38, 104, 131, 201, 271
HpyF10VI GCNNNNNNNGC 3 cut(s) 95, 101, 207
HpyF3I CTNAG 1 cut(s) 356
HpySE526I ACGT 1 cut(s) 121
Hsp92II CATG 1 cut(s) 166
KroI GCCGGC 1 cut(s) 183
KroNI GCCGGC 1 cut(s) 185
Kzo9I GATC 2 cut(s) 224, 337
LpnPI CCDG 8 cut(s) 157, 197, 206, 253, 286, 287, 299, 313
Lsp1109I GCAGC 5 cut(s) 82, 143, 145, 146, 213
LweI GCATC 1 cut(s) 326
MabI ACCWGGT 1 cut(s) 299
MaeII ACGT 1 cut(s) 121
MaeIII GTNAC 2 cut(s) 218, 276
MalI GATC 2 cut(s) 226, 339
MboI GATC 2 cut(s) 224, 337
MboII GAAGA 2 cut(s) 122, 337
MluCI AATT 4 cut(s) 196, 229, 344, 364
MnlI CCTC 5 cut(s) 65, 200, 294, 321, 351
MroNI GCCGGC 1 cut(s) 183
MseI TTAA 1 cut(s) 20
MspA1I CMGCKG 2 cut(s) 137, 158
MspI CCGG 2 cut(s) 184, 240
MspR9I CCNGG 1 cut(s) 301
MvaI CCWGG 1 cut(s) 301
MwoI GCNNNNNNNGC 3 cut(s) 95, 101, 207
NaeI GCCGGC 1 cut(s) 185
NcoI CCATGG 1 cut(s) 162
NdeI CATATG 1 cut(s) 91
NdeII GATC 2 cut(s) 224, 337
NgoMIV GCCGGC 1 cut(s) 183
NlaIII CATG 1 cut(s) 166
NmuCI GTSAC 2 cut(s) 218, 276
PcsI WCGNNNNNNNCGW 1 cut(s) 220
PdiI GCCGGC 1 cut(s) 185
PfeI GAWTC 1 cut(s) 140
PinAI ACCGGT 1 cut(s) 239
PkrI GCNGC 7 cut(s) 97, 133, 136, 157, 160, 182, 203
Ple19I CGATCG 1 cut(s) 227
Psp1406I AACGTT 1 cut(s) 121
Psp6I CCWGG 1 cut(s) 299
PspEI GGTNACC 1 cut(s) 218
PspGI CCWGG 1 cut(s) 299
PspPI GGNCC 2 cut(s) 242, 360
PvuI CGATCG 1 cut(s) 227
RigI GGCCGGCC 1 cut(s) 187
SaqAI TTAA 1 cut(s) 20
SatI GCNGC 7 cut(s) 96, 132, 135, 156, 159, 181, 202
Sau3AI GATC 2 cut(s) 224, 337
Sau96I GGNCC 2 cut(s) 242, 360
ScrFI CCNGG 1 cut(s) 301
SetI ASST 3 cut(s) 124, 267, 305
SexAI ACCWGGT 1 cut(s) 299
SfaNI GCATC 1 cut(s) 326
SinI GGWCC 1 cut(s) 242
Sse9I AATT 4 cut(s) 196, 229, 344, 364
SsiI CCGC 4 cut(s) 137, 156, 180, 210
StyD4I CCNGG 1 cut(s) 299
StyI CCWWGG 1 cut(s) 162
TaaI ACNGT 1 cut(s) 35
TaiI ACGT 1 cut(s) 124
TaqI TCGA 2 cut(s) 227, 323
TaqII GACCGA 1 cut(s) 237
TasI AATT 4 cut(s) 196, 229, 344, 364
TauI GCSGC 2 cut(s) 158, 183
TfiI GAWTC 1 cut(s) 140
Tru1I TTAA 1 cut(s) 20
Tru9I TTAA 1 cut(s) 20
TscAI CASTG 1 cut(s) 40
TseFI GTSAC 2 cut(s) 218, 276
TseI GCWGC 5 cut(s) 95, 131, 134, 158, 201
Tsp45I GTSAC 2 cut(s) 218, 276
TspDTI ATGAA 2 cut(s) 77, 115
TspRI CASTG 1 cut(s) 40
VpaK11BI GGWCC 1 cut(s) 242
XapI RAATTY 1 cut(s) 229
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.