Rmu_sc0009799.1_g000011

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0009799.1
OG0000258
Physical Location & Seq
Forward (+)
30972 .. 31262
291 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0009799.1_g000011.1.cds

Sequence Viewer

Length: 291 bp
atggcatctttgaaggagtttactgcaaactttgttaaacttgatcgttttgatggagcaaatttcagacgatggcaaaagaaattgcatttcctactttcaagcctgaaggtggtctatgtgcttactactccaaaacctcaagaaatagaagatgaaacccttgctgcacagcgtgaacgagttaagtgggaacaagatgattatatttgcaagggccatatttgcaactccatgtctgatgcattatttgatatttaccatgagatgactactgcaaaagaaatatag
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

96

Amino Acids

11.33

Weight (kDa)

6.28

Isoelectric Point (pI)

43.09

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
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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)
AcsI RAATTY 1 cut(s) 61
AcuI CTGAAG 1 cut(s) 128
AdeI CACNNNGTG 1 cut(s) 176
AfiI CCNNNNNNNGG 1 cut(s) 112
AgsI TTSAA 2 cut(s) 13, 102
AoxI GGCC 1 cut(s) 217
ApeKI GCWGC 1 cut(s) 167
ApoI RAATTY 1 cut(s) 61
AspS9I GGNCC 1 cut(s) 217
BbvI GCAGC 1 cut(s) 154
BccI CCATC 2 cut(s) 47, 66
BisI GCNGC 1 cut(s) 168
BlsI GCNGC 1 cut(s) 169
BmgT120I GGNCC 1 cut(s) 217
BmsI GCATC 2 cut(s) 14, 232
BpuEI CTTGAG 1 cut(s) 126
Bsc4I CCNNNNNNNGG 1 cut(s) 112
BseLI CCNNNNNNNGG 1 cut(s) 112
BseXI GCAGC 1 cut(s) 154
BsgI GTGCAG 1 cut(s) 153
BshFI GGCC 1 cut(s) 219
BslI CCNNNNNNNGG 1 cut(s) 112
BsnI GGCC 1 cut(s) 219
Bsp143I GATC 1 cut(s) 43
BspANI GGCC 1 cut(s) 219
BssMI GATC 1 cut(s) 43
BstKTI GATC 1 cut(s) 46
BstMBI GATC 1 cut(s) 43
BstMWI GCNNNNNNNGC 1 cut(s) 225
BstV1I GCAGC 1 cut(s) 154
BsuRI GGCC 1 cut(s) 219
Cfr13I GGNCC 1 cut(s) 217
CviAII CATG 2 cut(s) 235, 263
CviJI RGCY 2 cut(s) 105, 219
CviKI_1 RGCY 2 cut(s) 105, 219
DpnI GATC 1 cut(s) 45
DpnII GATC 1 cut(s) 43
DraIII CACNNNGTG 1 cut(s) 176
Eco57I CTGAAG 1 cut(s) 128
EcoT22I ATGCAT 1 cut(s) 247
FaeI CATG 2 cut(s) 238, 266
FaiI YATR 6 cut(s) 120, 207, 222, 236, 264, 289
FatI CATG 2 cut(s) 234, 262
Fnu4HI GCNGC 1 cut(s) 168
Fsp4HI GCNGC 1 cut(s) 168
GluI GCNGC 1 cut(s) 168
HaeIII GGCC 1 cut(s) 219
Hin1II CATG 2 cut(s) 238, 266
Hpy166II GTNNAC 2 cut(s) 21, 179
Hpy188I TCNGA 2 cut(s) 68, 241
Hpy188III TCNNGA 1 cut(s) 143
Hpy8I GTNNAC 2 cut(s) 21, 179
HpyAV CCTTC 2 cut(s) 7, 103
HpyCH4V TGCA 7 cut(s) 26, 88, 170, 213, 228, 245, 278
HpyF10VI GCNNNNNNNGC 1 cut(s) 225
Hsp92II CATG 2 cut(s) 238, 266
Kzo9I GATC 1 cut(s) 43
LmnI GCTCC 1 cut(s) 56
LpnPI CCDG 1 cut(s) 119
Lsp1109I GCAGC 1 cut(s) 154
LweI GCATC 2 cut(s) 14, 232
MalI GATC 1 cut(s) 45
MboI GATC 1 cut(s) 43
MboII GAAGA 1 cut(s) 164
MluCI AATT 2 cut(s) 61, 83
MnlI CCTC 1 cut(s) 150
Mph1103I ATGCAT 1 cut(s) 247
MseI TTAA 2 cut(s) 36, 186
MwoI GCNNNNNNNGC 1 cut(s) 225
NdeII GATC 1 cut(s) 43
NlaIII CATG 2 cut(s) 238, 266
NsiI ATGCAT 1 cut(s) 247
PkrI GCNGC 1 cut(s) 169
PspPI GGNCC 1 cut(s) 217
SaqAI TTAA 2 cut(s) 36, 186
SatI GCNGC 1 cut(s) 168
Sau3AI GATC 1 cut(s) 43
Sau96I GGNCC 1 cut(s) 217
SetI ASST 2 cut(s) 114, 142
SfaNI GCATC 2 cut(s) 14, 232
SmlI CTYRAG 1 cut(s) 141
SmoI CTYRAG 1 cut(s) 141
Sse9I AATT 2 cut(s) 61, 83
TasI AATT 2 cut(s) 61, 83
Tru1I TTAA 2 cut(s) 36, 186
Tru9I TTAA 2 cut(s) 36, 186
TseI GCWGC 1 cut(s) 167
TspDTI ATGAA 1 cut(s) 171
XapI RAATTY 1 cut(s) 61
Zsp2I ATGCAT 1 cut(s) 247
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.