Rmu_sc0008949.1_g000003

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0008949.1
OG0000258
Physical Location & Seq
Reverse (-)
8763 .. 9032
270 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0008949.1_g000003.1.cds

Sequence Viewer

Length: 270 bp
atggatcaatcaggatctgctgtgaaaaatcatgtggagaaacctgagaaattcaagggttcagatttcaaacgttggcaacagaagatgttgttctatttgacaactcttcatatggcagatgttctcacaactgaggctccaaaggctcttcccgaaggacatggaaagaatgctccaactgatgctcaaaaggctgaaaatcagaaggccattgttgtgatacggctaaagcaagcgcataatttaaccctgaaatgtcatcgttag
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
No domains found.

Protein Analysis

89

Amino Acids

10.08

Weight (kDa)

9.67

Isoelectric Point (pI)

43.26

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
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)
AclI AACGTT 1 cut(s) 73
AclWI GGATC 2 cut(s) 12, 22
AcsI RAATTY 1 cut(s) 50
AgsI TTSAA 2 cut(s) 55, 70
AlwI GGATC 2 cut(s) 12, 22
AlwNI CAGNNNCTG 1 cut(s) 17
AoxI GGCC 1 cut(s) 210
ApoI RAATTY 1 cut(s) 50
AspLEI GCGC 1 cut(s) 241
BceAI ACGGC 1 cut(s) 242
BmiI GGNNCC 1 cut(s) 141
BmsI GCATC 1 cut(s) 175
BsaXI ACNNNNNCTCC 2 cut(s) 124, 154
BseMII CTCAG 2 cut(s) 36, 126
BshFI GGCC 1 cut(s) 212
BsmI GAATGC 1 cut(s) 178
BsnI GGCC 1 cut(s) 212
Bsp143I GATC 2 cut(s) 4, 14
BspANI GGCC 1 cut(s) 212
BspCNI CTCAG 2 cut(s) 37, 127
BspLI GGNNCC 1 cut(s) 141
BspPI GGATC 2 cut(s) 12, 22
BspQI GCTCTTC 1 cut(s) 156
BssMI GATC 2 cut(s) 4, 14
Bst6I CTCTTC 2 cut(s) 114, 156
BstC8I GCNNGC 1 cut(s) 237
BstDEI CTNAG 2 cut(s) 45, 135
BstHHI GCGC 1 cut(s) 241
BstKTI GATC 2 cut(s) 7, 17
BstMBI GATC 2 cut(s) 4, 14
BstMWI GCNNNNNNNGC 2 cut(s) 146, 194
BstX2I RGATCY 1 cut(s) 14
BstYI RGATCY 1 cut(s) 14
BsuRI GGCC 1 cut(s) 212
Cac8I GCNNGC 1 cut(s) 237
CaiI CAGNNNCTG 1 cut(s) 17
CfoI GCGC 1 cut(s) 241
CviAII CATG 2 cut(s) 32, 164
CviJI RGCY 5 cut(s) 140, 149, 197, 212, 229
CviKI_1 RGCY 5 cut(s) 140, 149, 197, 212, 229
DdeI CTNAG 2 cut(s) 45, 135
DpnI GATC 2 cut(s) 6, 16
DpnII GATC 2 cut(s) 4, 14
Eam1104I CTCTTC 2 cut(s) 114, 156
EarI CTCTTC 2 cut(s) 114, 156
FaeI CATG 2 cut(s) 35, 167
FaiI YATR 5 cut(s) 33, 114, 116, 165, 243
FatI CATG 2 cut(s) 31, 163
FauNDI CATATG 1 cut(s) 114
GlaI GCGC 1 cut(s) 240
HaeIII GGCC 1 cut(s) 212
HhaI GCGC 1 cut(s) 241
Hin1II CATG 2 cut(s) 35, 167
Hin6I GCGC 1 cut(s) 239
HinP1I GCGC 1 cut(s) 239
Hpy188I TCNGA 2 cut(s) 64, 207
Hpy188III TCNNGA 2 cut(s) 12, 155
HpyAV CCTTC 2 cut(s) 152, 202
HpyCH4IV ACGT 1 cut(s) 73
HpyF10VI GCNNNNNNNGC 2 cut(s) 146, 194
HpyF3I CTNAG 2 cut(s) 45, 135
HpySE526I ACGT 1 cut(s) 73
Hsp92II CATG 2 cut(s) 35, 167
HspAI GCGC 1 cut(s) 239
Kzo9I GATC 2 cut(s) 4, 14
LguI GCTCTTC 1 cut(s) 156
LmnI GCTCC 2 cut(s) 145, 181
LpnPI CCDG 2 cut(s) 57, 266
LweI GCATC 1 cut(s) 175
MaeII ACGT 1 cut(s) 73
MalI GATC 2 cut(s) 6, 16
MboI GATC 2 cut(s) 4, 14
MboII GAAGA 3 cut(s) 97, 101, 143
MflI RGATCY 1 cut(s) 14
MluCI AATT 2 cut(s) 50, 244
MmeI TCCRAC 1 cut(s) 203
MnlI CCTC 1 cut(s) 130
MseI TTAA 1 cut(s) 248
MslI CAYNNNNRTG 1 cut(s) 218
Mva1269I GAATGC 1 cut(s) 178
MwoI GCNNNNNNNGC 2 cut(s) 146, 194
NdeI CATATG 1 cut(s) 114
NdeII GATC 2 cut(s) 4, 14
NlaIII CATG 2 cut(s) 35, 167
NlaIV GGNNCC 1 cut(s) 141
PciSI GCTCTTC 1 cut(s) 156
PctI GAATGC 1 cut(s) 178
Psp1406I AACGTT 1 cut(s) 73
PspN4I GGNNCC 1 cut(s) 141
PstNI CAGNNNCTG 1 cut(s) 17
PsuI RGATCY 1 cut(s) 14
RseI CAYNNNNRTG 1 cut(s) 218
SapI GCTCTTC 1 cut(s) 156
SaqAI TTAA 1 cut(s) 248
Sau3AI GATC 2 cut(s) 4, 14
SetI ASST 2 cut(s) 46, 76
SfaNI GCATC 1 cut(s) 175
SgeI CNNG 8 cut(s) 24, 44, 56, 67, 167, 176, 248, 265
SmiMI CAYNNNNRTG 1 cut(s) 218
Sse9I AATT 2 cut(s) 50, 244
TaiI ACGT 1 cut(s) 76
TasI AATT 2 cut(s) 50, 244
Tru1I TTAA 1 cut(s) 248
Tru9I TTAA 1 cut(s) 248
TspDTI ATGAA 1 cut(s) 101
XapI RAATTY 1 cut(s) 50
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.