Rmu_sc0011699.1_g000009

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0011699.1
OG0000258
Physical Location & Seq
Reverse (-)
26304 .. 26780
477 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0011699.1_g000009.1.cds

Sequence Viewer

Length: 477 bp
atgaggtattggctaaccgtcttagggctagtagaagccttagaagatacaactagtgagactccttctaagaaaaccacacttacaatttccactcccactagtgaaacacaaaactcaaaatccaccactcctaagatgacaaaagatgaaatagaatatcattgtcacaataggattcttagtgccctttctaatgatctctacgatgtctatcgtgataccactagtacaaagagcctttgggaagagttagaagctgagtatgggttagatgatgcaggcatagattgttttactgtgtcaacctttaacagctacaaaatggttgaggagaaaaccgtgagtgtgcaaatccatgagtttaaagacctcttcagaaaagtagagtcaaagggaaccaagtttacagaagaattcaaagtgtcttgcctcataaactaccccctagttggtcaaactttgccaaaagtctga
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

158

Amino Acids

18.06

Weight (kDa)

5.02

Isoelectric Point (pI)

35.83

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)
AcsI RAATTY 1 cut(s) 416
AcuI CTGAAG 1 cut(s) 361
AfaI GTAC 1 cut(s) 232
AfiI CCNNNNNNNGG 2 cut(s) 24, 452
AgsI TTSAA 1 cut(s) 421
AhlI ACTAGT 3 cut(s) 53, 101, 227
AluBI AGCT 2 cut(s) 260, 318
AluI AGCT 2 cut(s) 260, 318
Alw26I GTCTC 1 cut(s) 53
ApoI RAATTY 1 cut(s) 416
BaeGI GKGCMC 1 cut(s) 190
BcoDI GTCTC 1 cut(s) 53
BcuI ACTAGT 3 cut(s) 53, 101, 227
BfaI CTAG 5 cut(s) 29, 54, 102, 228, 449
BmiI GGNNCC 1 cut(s) 400
BmsI GCATC 1 cut(s) 268
BsaBI GATNNNNATC 1 cut(s) 213
Bsc4I CCNNNNNNNGG 2 cut(s) 24, 452
Bse8I GATNNNNATC 1 cut(s) 213
BseJI GATNNNNATC 1 cut(s) 213
BseLI CCNNNNNNNGG 2 cut(s) 24, 452
BseMII CTCAG 1 cut(s) 252
BseRI GAGGAG 1 cut(s) 347
BseSI GKGCMC 1 cut(s) 190
BslI CCNNNNNNNGG 2 cut(s) 24, 452
BsmAI GTCTC 1 cut(s) 53
Bsp1286I GDGCHC 1 cut(s) 190
Bsp143I GATC 1 cut(s) 199
BspCNI CTCAG 1 cut(s) 253
BspLI GGNNCC 1 cut(s) 400
BssMI GATC 1 cut(s) 199
Bst4CI ACNGT 3 cut(s) 19, 301, 343
Bst6I CTCTTC 2 cut(s) 243, 380
BstC8I GCNNGC 1 cut(s) 283
BstDEI CTNAG 6 cut(s) 22, 40, 69, 135, 182, 261
BstKTI GATC 1 cut(s) 202
BstMAI GTCTC 1 cut(s) 53
BstMBI GATC 1 cut(s) 199
BstSLI GKGCMC 1 cut(s) 190
Cac8I GCNNGC 1 cut(s) 283
Csp6I GTAC 1 cut(s) 231
CviAII CATG 1 cut(s) 359
CviJI RGCY 6 cut(s) 13, 28, 38, 240, 260, 318
CviKI_1 RGCY 6 cut(s) 13, 28, 38, 240, 260, 318
CviQI GTAC 1 cut(s) 231
DdeI CTNAG 6 cut(s) 22, 40, 69, 135, 182, 261
DpnI GATC 1 cut(s) 201
DpnII GATC 1 cut(s) 199
DraI TTTAAA 1 cut(s) 367
Eam1104I CTCTTC 2 cut(s) 243, 380
EarI CTCTTC 2 cut(s) 243, 380
Eco57I CTGAAG 1 cut(s) 361
EcoRI GAATTC 1 cut(s) 416
FaeI CATG 1 cut(s) 362
FaiI YATR 4 cut(s) 267, 287, 360, 437
FatI CATG 1 cut(s) 358
FspBI CTAG 5 cut(s) 29, 54, 102, 228, 449
Hin1II CATG 1 cut(s) 362
HincII GTYRAC 1 cut(s) 306
HindII GTYRAC 1 cut(s) 306
HinfI GANTC 3 cut(s) 61, 178, 389
Hpy166II GTNNAC 2 cut(s) 306, 408
Hpy188I TCNGA 2 cut(s) 380, 476
Hpy188III TCNNGA 1 cut(s) 218
Hpy8I GTNNAC 2 cut(s) 306, 408
HpyAV CCTTC 1 cut(s) 75
HpyCH4III ACNGT 3 cut(s) 19, 301, 343
HpyCH4V TGCA 2 cut(s) 281, 352
HpyF3I CTNAG 6 cut(s) 22, 40, 69, 135, 182, 261
Hsp92II CATG 1 cut(s) 362
Kzo9I GATC 1 cut(s) 199
LpnPI CCDG 1 cut(s) 267
LweI GCATC 1 cut(s) 268
MaeI CTAG 5 cut(s) 29, 54, 102, 228, 449
MaeIII GTNAC 1 cut(s) 167
MalI GATC 1 cut(s) 201
MboI GATC 1 cut(s) 199
MboII GAAGA 4 cut(s) 56, 260, 367, 425
MhlI GDGCHC 1 cut(s) 190
MluCI AATT 2 cut(s) 87, 416
MlyI GAGTC 2 cut(s) 55, 398
MnlI CCTC 3 cut(s) 325, 383, 443
MseI TTAA 2 cut(s) 312, 366
NdeII GATC 1 cut(s) 199
NlaIII CATG 1 cut(s) 362
NlaIV GGNNCC 1 cut(s) 400
NmuCI GTSAC 1 cut(s) 167
PfeI GAWTC 1 cut(s) 178
PleI GAGTC 2 cut(s) 55, 397
PpsI GAGTC 2 cut(s) 55, 397
PspN4I GGNNCC 1 cut(s) 400
PsrI GAACNNNNNNTAC 2 cut(s) 391, 423
RsaI GTAC 1 cut(s) 232
RsaNI GTAC 1 cut(s) 231
SaqAI TTAA 2 cut(s) 312, 366
Sau3AI GATC 1 cut(s) 199
SchI GAGTC 2 cut(s) 55, 398
SduI GDGCHC 1 cut(s) 190
SetI ASST 5 cut(s) 8, 262, 311, 320, 375
SfaNI GCATC 1 cut(s) 268
SpeI ACTAGT 3 cut(s) 53, 101, 227
Sse9I AATT 2 cut(s) 87, 416
SspMI CTAG 5 cut(s) 29, 54, 102, 228, 449
TaaI ACNGT 3 cut(s) 19, 301, 343
TasI AATT 2 cut(s) 87, 416
TatI WGTACW 1 cut(s) 230
TfiI GAWTC 1 cut(s) 178
Tru1I TTAA 2 cut(s) 312, 366
Tru9I TTAA 2 cut(s) 312, 366
TseFI GTSAC 1 cut(s) 167
Tsp45I GTSAC 1 cut(s) 167
TspDTI ATGAA 1 cut(s) 165
XapI RAATTY 1 cut(s) 416
XspI CTAG 5 cut(s) 29, 54, 102, 228, 449
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.