Rmu_sc0000381.1_g000031

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0000381.1
OG0000258
Physical Location & Seq
Reverse (-)
146383 .. 146955
573 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0000381.1_g000031.1.cds

Sequence Viewer

Length: 573 bp
atggatgctgctatgaccaacaccaagatcccagatatttccaagatcgatgttttcaatggctcgttcttcaaaagatggcaagaaagagtcttctctgctcttgatgtcatgaacctagcagattatctcactaaggccaagcccaaggaaggcagcgagaattataacaaagagttggctgaatgggagaaaggtaacaaaatttgtaggcatactattctgagcacactttcaagtgagctttttgatatatattgtgcctacaagactgctgctgaaatttgggagattctcataaaaaagtacgtgactgaagatgctggaacccaaaaatatgcaattgggaattttcttaaatttcaaatgacggaggacaaggatgtttcacttcaaattcatgagtttcacaaggtcgtcaatgatttgaagattgaaggcattgaattacctgaagcatttctgtctggaagtttcattgaaaagctacatgaatcatggaaggactacaaaaacaacatgaaacacaaaaagaaacaaatgagtaatgaagatgtggttttccatatctga
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

190

Amino Acids

22.16

Weight (kDa)

6.09

Isoelectric Point (pI)

39.82

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
AclWI GGATC 1 cut(s) 22
AcsI RAATTY 5 cut(s) 204, 282, 349, 359, 396
AcuI CTGAAG 2 cut(s) 336, 474
AfaI GTAC 1 cut(s) 308
AfiI CCNNNNNNNGG 1 cut(s) 152
AgsI TTSAA 9 cut(s) 58, 73, 237, 365, 395, 430, 437, 446, 482
AluBI AGCT 2 cut(s) 244, 487
AluI AGCT 2 cut(s) 244, 487
Alw21I GWGCWC 1 cut(s) 230
AlwI GGATC 1 cut(s) 22
AoxI GGCC 1 cut(s) 138
ApeKI GCWGC 3 cut(s) 8, 156, 275
ApoI RAATTY 5 cut(s) 204, 282, 349, 359, 396
Asp700I GAANNNNTTC 1 cut(s) 459
BbsI GAAGAC 1 cut(s) 85
Bbv12I GWGCWC 1 cut(s) 230
BbvI GCAGC 2 cut(s) 168, 262
BccI CCATC 1 cut(s) 72
BfaI CTAG 1 cut(s) 119
BisI GCNGC 3 cut(s) 9, 157, 276
BlsI GCNGC 3 cut(s) 10, 158, 277
BmiI GGNNCC 1 cut(s) 328
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 1 cut(s) 152
BseCI ATCGAT 1 cut(s) 48
BseDI CCNNGG 1 cut(s) 147
BseGI GGATG 2 cut(s) 10, 388
BseLI CCNNNNNNNGG 1 cut(s) 152
BseMII CTCAG 1 cut(s) 215
BseXI GCAGC 2 cut(s) 168, 262
BshFI GGCC 1 cut(s) 140
BshVI ATCGAT 1 cut(s) 48
BsiHKAI GWGCWC 1 cut(s) 230
BslI CCNNNNNNNGG 1 cut(s) 152
BsnI GGCC 1 cut(s) 140
Bsp1286I GDGCHC 1 cut(s) 230
Bsp143I GATC 2 cut(s) 27, 45
BspANI GGCC 1 cut(s) 140
BspCNI CTCAG 1 cut(s) 216
BspDI ATCGAT 1 cut(s) 48
BspHI TCATGA 2 cut(s) 111, 400
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
BstBAI YACGTR 1 cut(s) 310
BstDEI CTNAG 2 cut(s) 135, 224
BstF5I GGATG 2 cut(s) 10, 388
BstKTI GATC 2 cut(s) 30, 48
BstMBI GATC 2 cut(s) 27, 45
BstV1I GCAGC 2 cut(s) 168, 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 1 cut(s) 140
BsuTUI ATCGAT 1 cut(s) 48
BtsCI GGATG 2 cut(s) 10, 388
CciI TCATGA 2 cut(s) 111, 400
ClaI ATCGAT 1 cut(s) 48
Csp6I GTAC 1 cut(s) 307
CviAII CATG 5 cut(s) 112, 401, 491, 498, 520
CviJI RGCY 6 cut(s) 63, 140, 145, 182, 244, 487
CviKI_1 RGCY 6 cut(s) 63, 140, 145, 182, 244, 487
CviQI GTAC 1 cut(s) 307
DdeI CTNAG 2 cut(s) 135, 224
DpnI GATC 2 cut(s) 29, 47
DpnII GATC 2 cut(s) 27, 45
Eco130I CCWWGG 1 cut(s) 147
Eco57I CTGAAG 2 cut(s) 336, 474
EcoT14I CCWWGG 1 cut(s) 147
ErhI CCWWGG 1 cut(s) 147
FaeI CATG 5 cut(s) 115, 404, 494, 501, 523
FatI CATG 5 cut(s) 111, 400, 490, 497, 519
Fnu4HI GCNGC 3 cut(s) 9, 157, 276
FokI GGATG 2 cut(s) 17, 395
Fsp4HI GCNGC 3 cut(s) 9, 157, 276
FspBI CTAG 1 cut(s) 119
GluI GCNGC 3 cut(s) 9, 157, 276
HaeIII GGCC 1 cut(s) 140
Hin1II CATG 5 cut(s) 115, 404, 494, 501, 523
HinfI GANTC 3 cut(s) 90, 292, 494
Hpy188I TCNGA 2 cut(s) 225, 572
Hpy188III TCNNGA 4 cut(s) 104, 112, 401, 468
HpyAV CCTTC 3 cut(s) 146, 431, 496
HpyCH4IV ACGT 1 cut(s) 309
HpyCH4V TGCA 1 cut(s) 341
HpyF3I CTNAG 2 cut(s) 135, 224
HpySE526I ACGT 1 cut(s) 309
Hsp92II CATG 5 cut(s) 115, 404, 494, 501, 523
Kzo9I GATC 2 cut(s) 27, 45
LpnPI CCDG 4 cut(s) 45, 309, 453, 465
Lsp1109I GCAGC 2 cut(s) 168, 262
LweI GCATC 1 cut(s) 310
MaeI CTAG 1 cut(s) 119
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 5 cut(s) 61, 85, 329, 442, 563
MfeI CAATTG 1 cut(s) 342
MflI RGATCY 1 cut(s) 27
MhlI GDGCHC 1 cut(s) 230
MluCI AATT 8 cut(s) 163, 204, 282, 342, 349, 359, 396, 446
MlyI GAGTC 1 cut(s) 99
MnlI CCTC 1 cut(s) 367
MroXI GAANNNNTTC 1 cut(s) 459
MseI TTAA 1 cut(s) 357
MunI CAATTG 1 cut(s) 342
NdeII GATC 2 cut(s) 27, 45
NlaIII CATG 5 cut(s) 115, 404, 494, 501, 523
NlaIV GGNNCC 1 cut(s) 328
NmuCI GTSAC 1 cut(s) 310
PagI TCATGA 2 cut(s) 111, 400
PdmI GAANNNNTTC 1 cut(s) 459
PfeI GAWTC 2 cut(s) 292, 494
PkrI GCNGC 3 cut(s) 10, 158, 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
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) 357
SatI GCNGC 3 cut(s) 9, 157, 276
Sau3AI GATC 2 cut(s) 27, 45
SchI GAGTC 1 cut(s) 99
SduI GDGCHC 1 cut(s) 230
SetI ASST 7 cut(s) 120, 199, 246, 312, 417, 454, 489
SfaNI GCATC 1 cut(s) 310
Sse9I AATT 8 cut(s) 163, 204, 282, 342, 349, 359, 396, 446
SspMI CTAG 1 cut(s) 119
StyI CCWWGG 1 cut(s) 147
TaiI ACGT 1 cut(s) 312
TaqI TCGA 1 cut(s) 48
TasI AATT 8 cut(s) 163, 204, 282, 342, 349, 359, 396, 446
TfiI GAWTC 2 cut(s) 292, 494
Tru1I TTAA 1 cut(s) 357
Tru9I TTAA 1 cut(s) 357
TseFI GTSAC 1 cut(s) 310
TseI GCWGC 3 cut(s) 8, 156, 275
Tsp45I GTSAC 1 cut(s) 310
TspDTI ATGAA 6 cut(s) 128, 389, 466, 507, 536, 564
TspGWI ACGGA 1 cut(s) 386
XapI RAATTY 5 cut(s) 204, 282, 349, 359, 396
XmnI GAANNNNTTC 1 cut(s) 459
XspI CTAG 1 cut(s) 119
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.