Rmu_sc0001616.1_g000046

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0001616.1
OG0000258
Physical Location & Seq
Forward (+)
224943 .. 225305
363 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0001616.1_g000046.1.cds

Sequence Viewer

Length: 363 bp
atggatgctgctatgaccaacaccaagatcccagatgtttctaagatcgatgttttcaatggctcattcttcaaaagatggcaagaaagagtcttctctgctcttgatgtcatgaacctggcagattatctcacgaaggccaagcccaaggaaggtagcgagaattataacaaagagttggctgaatgggagaaaggtaacaaaatttgtaggcatactattctaagcacactttcaaatgagctttttgatatatattgtgcctacaggcctgctgctgaaatttgggagattctcataaaaaagtacgtgactgaagatgctggaacccagcaattgggaattttcttaaatttcaaatga
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

120

Amino Acids

13.88

Weight (kDa)

5.85

Isoelectric Point (pI)

21.94

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: 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) 168
AccB7I CCANNNNNTGG 1 cut(s) 337
AclWI GGATC 1 cut(s) 22
AcsI RAATTY 4 cut(s) 204, 282, 342, 352
AcuI CTGAAG 1 cut(s) 336
AfaI GTAC 1 cut(s) 308
AfiI CCNNNNNNNGG 2 cut(s) 152, 337
AgsI TTSAA 4 cut(s) 58, 73, 237, 358
AjnI CCWGG 1 cut(s) 117
AluBI AGCT 1 cut(s) 244
AluI AGCT 1 cut(s) 244
AlwI GGATC 1 cut(s) 22
AoxI GGCC 2 cut(s) 138, 269
ApeKI GCWGC 2 cut(s) 8, 275
ApoI RAATTY 4 cut(s) 204, 282, 342, 352
BbsI GAAGAC 1 cut(s) 85
BbvI GCAGC 1 cut(s) 262
BccI CCATC 1 cut(s) 72
BciT130I CCWGG 1 cut(s) 119
BfmI CTRYAG 1 cut(s) 265
BisI GCNGC 2 cut(s) 9, 276
BlsI GCNGC 2 cut(s) 10, 277
Bme1390I CCNGG 1 cut(s) 119
BmiI GGNNCC 1 cut(s) 328
BmrFI CCNGG 1 cut(s) 119
BmsI GCATC 1 cut(s) 310
BpiI GAAGAC 1 cut(s) 85
Bsa29I ATCGAT 1 cut(s) 48
BsaAI YACGTR 1 cut(s) 310
BsaJI CCNNGG 1 cut(s) 147
Bsc4I CCNNNNNNNGG 2 cut(s) 152, 337
BseBI CCWGG 1 cut(s) 119
BseCI ATCGAT 1 cut(s) 48
BseDI CCNNGG 1 cut(s) 147
BseGI GGATG 1 cut(s) 10
BseLI CCNNNNNNNGG 2 cut(s) 152, 337
BseXI GCAGC 1 cut(s) 262
BseYI CCCAGC 1 cut(s) 330
BshFI GGCC 2 cut(s) 140, 271
BshVI ATCGAT 1 cut(s) 48
BslI CCNNNNNNNGG 2 cut(s) 152, 337
BsnI GGCC 2 cut(s) 140, 271
Bsp143I GATC 2 cut(s) 27, 45
BspANI GGCC 2 cut(s) 140, 271
BspDI ATCGAT 1 cut(s) 48
BspHI TCATGA 1 cut(s) 111
BspLI GGNNCC 1 cut(s) 328
BspPI GGATC 1 cut(s) 22
BssECI CCNNGG 1 cut(s) 147
BssMI GATC 2 cut(s) 27, 45
BssT1I CCWWGG 1 cut(s) 147
Bst2UI CCWGG 1 cut(s) 119
BstBAI YACGTR 1 cut(s) 310
BstC8I GCNNGC 1 cut(s) 273
BstDEI CTNAG 2 cut(s) 42, 224
BstF5I GGATG 1 cut(s) 10
BstKTI GATC 2 cut(s) 30, 48
BstMBI GATC 2 cut(s) 27, 45
BstNI CCWGG 1 cut(s) 119
BstSCI CCNGG 1 cut(s) 117
BstSFI CTRYAG 1 cut(s) 265
BstV1I GCAGC 1 cut(s) 262
BstV2I GAAGAC 1 cut(s) 85
BstX2I RGATCY 1 cut(s) 27
BstYI RGATCY 1 cut(s) 27
Bsu15I ATCGAT 1 cut(s) 48
BsuRI GGCC 2 cut(s) 140, 271
BsuTUI ATCGAT 1 cut(s) 48
BtsCI GGATG 1 cut(s) 10
Cac8I GCNNGC 1 cut(s) 273
CciI TCATGA 1 cut(s) 111
ClaI ATCGAT 1 cut(s) 48
Csp6I GTAC 1 cut(s) 307
CviAII CATG 1 cut(s) 112
CviJI RGCY 6 cut(s) 63, 140, 145, 182, 244, 271
CviKI_1 RGCY 6 cut(s) 63, 140, 145, 182, 244, 271
CviQI GTAC 1 cut(s) 307
DdeI CTNAG 2 cut(s) 42, 224
DpnI GATC 2 cut(s) 29, 47
DpnII GATC 2 cut(s) 27, 45
Eco130I CCWWGG 1 cut(s) 147
Eco147I AGGCCT 1 cut(s) 271
Eco57I CTGAAG 1 cut(s) 336
EcoRII CCWGG 1 cut(s) 117
EcoT14I CCWWGG 1 cut(s) 147
ErhI CCWWGG 1 cut(s) 147
FaeI CATG 1 cut(s) 115
FaiI YATR 7 cut(s) 14, 113, 168, 216, 254, 256, 299
FatI CATG 1 cut(s) 111
Fnu4HI GCNGC 2 cut(s) 9, 276
FokI GGATG 1 cut(s) 17
Fsp4HI GCNGC 2 cut(s) 9, 276
GluI GCNGC 2 cut(s) 9, 276
GsaI CCCAGC 1 cut(s) 334
HaeIII GGCC 2 cut(s) 140, 271
Hin1II CATG 1 cut(s) 115
HinfI GANTC 2 cut(s) 90, 292
Hpy188III TCNNGA 3 cut(s) 104, 112, 133
HpyAV CCTTC 2 cut(s) 130, 146
HpyCH4IV ACGT 1 cut(s) 309
HpyF3I CTNAG 2 cut(s) 42, 224
HpySE526I ACGT 1 cut(s) 309
Hsp92II CATG 1 cut(s) 115
Kzo9I GATC 2 cut(s) 27, 45
LpnPI CCDG 7 cut(s) 45, 104, 131, 253, 285, 309, 344
Lsp1109I GCAGC 1 cut(s) 262
LweI GCATC 1 cut(s) 310
MaeII ACGT 1 cut(s) 309
MaeIII GTNAC 2 cut(s) 197, 310
MalI GATC 2 cut(s) 29, 47
MboI GATC 2 cut(s) 27, 45
MboII GAAGA 3 cut(s) 61, 85, 329
MfeI CAATTG 1 cut(s) 335
MflI RGATCY 1 cut(s) 27
MluCI AATT 6 cut(s) 163, 204, 282, 335, 342, 352
MlyI GAGTC 1 cut(s) 99
MseI TTAA 1 cut(s) 350
MspR9I CCNGG 1 cut(s) 119
MunI CAATTG 1 cut(s) 335
MvaI CCWGG 1 cut(s) 119
NdeII GATC 2 cut(s) 27, 45
NlaIII CATG 1 cut(s) 115
NlaIV GGNNCC 1 cut(s) 328
NmuCI GTSAC 1 cut(s) 310
PagI TCATGA 1 cut(s) 111
PceI AGGCCT 1 cut(s) 271
PfeI GAWTC 1 cut(s) 292
PflMI CCANNNNNTGG 1 cut(s) 337
PkrI GCNGC 2 cut(s) 10, 277
PleI GAGTC 1 cut(s) 98
PpsI GAGTC 1 cut(s) 98
Ppu21I YACGTR 1 cut(s) 310
PsiI TTATAA 1 cut(s) 168
Psp6I CCWGG 1 cut(s) 117
PspFI CCCAGC 1 cut(s) 330
PspGI CCWGG 1 cut(s) 117
PspN4I GGNNCC 1 cut(s) 328
PsuI RGATCY 1 cut(s) 27
RsaI GTAC 1 cut(s) 308
RsaNI GTAC 1 cut(s) 307
SaqAI TTAA 1 cut(s) 350
SatI GCNGC 2 cut(s) 9, 276
Sau3AI GATC 2 cut(s) 27, 45
SchI GAGTC 1 cut(s) 99
ScrFI CCNGG 1 cut(s) 119
SetI ASST 5 cut(s) 120, 157, 199, 246, 312
SfaNI GCATC 1 cut(s) 310
SfcI CTRYAG 1 cut(s) 265
Sse9I AATT 6 cut(s) 163, 204, 282, 335, 342, 352
SseBI AGGCCT 1 cut(s) 271
StuI AGGCCT 1 cut(s) 271
StyD4I CCNGG 1 cut(s) 117
StyI CCWWGG 1 cut(s) 147
TaiI ACGT 1 cut(s) 312
TaqI TCGA 1 cut(s) 48
TasI AATT 6 cut(s) 163, 204, 282, 335, 342, 352
TfiI GAWTC 1 cut(s) 292
Tru1I TTAA 1 cut(s) 350
Tru9I TTAA 1 cut(s) 350
TseFI GTSAC 1 cut(s) 310
TseI GCWGC 2 cut(s) 8, 275
Tsp45I GTSAC 1 cut(s) 310
TspDTI ATGAA 1 cut(s) 128
Van91I CCANNNNNTGG 1 cut(s) 337
XapI RAATTY 4 cut(s) 204, 282, 342, 352
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.