Rmu_sc0002536.1_g000017

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0002536.1
OG0018449
Physical Location & Seq
Reverse (-)
65264 .. 70376
5113 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0002536.1_g000017.1.cds

Sequence Viewer

Length: 747 bp
atgcatgagaatatagactattgctttactgaggataagcctatagagttgaatgaaaagagcaccaagaaagaaactgacctttacaagaagtggcatagatccaatagaatggctaagaatctcattcgtacctctatgtccaagactgtcaggggaagtatagaagaacctgagctagcatcagattttctggaactcataggtgctaagtttaaagaaagtgaaaaggcagaagcagctagactaaccaaggagtttcatgatttgaaggatctggaacaagcaccctcacccgctcgacttcaagtccactttgtctacattacccagcaccaaatcttcttcagctcatggtctacccggagcatatactccctcccatcatcaccggaagaagactgcccaaccctgatccaccattatgaggaccccatgatgaaactgtgtggtgaattcgatctgcaagtgctactgagtacggatgacgaactgggtgcaaaattttcaccgtttctttcgcaatttgaaatcacgcaaggcagcgaggagcacaccagaatattgggtgaggtcaagcgtgtgggcagggaatttggcccggagaggaagaatcaagggttatttgccttgctagtttcgattttaagagtatacacgacatatcgttgcgagagtaatcctaagcgggatgtagaggcggaagagatgtcagattgggacgttatagagggggaagagatgtag
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

248

Amino Acids

28.82

Weight (kDa)

5.11

Isoelectric Point (pI)

58.59

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: OG0018449)

Species Orthologous Gene IDs
fragaria_vesca FvH4_5g35350 FvH4_5g35361
rosa_chinensis RchiOBHm_Chr7g0236701
rosa_laevigata RLG00000001067
rosa_multiflora Rmu_sc0002536.1_g000017
rosa_roxburghii Rroxscaffold_3G00224950
rosa_rugosa Rorug07G0298300
rosa_samantha Rh7AG453700 Rh7CG472200 Rh7DG441100

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 299
AccI GTMKAC 3 cut(s) 321, 359, 654
AciI CCGC 3 cut(s) 297, 688, 701
AclWI GGATC 3 cut(s) 96, 282, 409
AcsI RAATTY 3 cut(s) 455, 503, 593
AcuI CTGAAG 1 cut(s) 331
AfaI GTAC 2 cut(s) 133, 481
AfiI CCNNNNNNNGG 1 cut(s) 427
AgsI TTSAA 4 cut(s) 52, 271, 308, 530
AhdI GACNNNNNGTC 1 cut(s) 308
AluBI AGCT 3 cut(s) 178, 242, 351
AluI AGCT 3 cut(s) 178, 242, 351
Alw21I GWGCWC 2 cut(s) 65, 555
AlwI GGATC 3 cut(s) 96, 282, 409
AoxI GGCC 1 cut(s) 598
ApeKI GCWGC 2 cut(s) 239, 543
ApoI RAATTY 3 cut(s) 455, 503, 593
AspS9I GGNCC 2 cut(s) 430, 599
AsuC2I CCSGG 2 cut(s) 364, 602
AsuHPI GGTGA 5 cut(s) 285, 381, 464, 501, 581
AsuNHI GCTAGC 1 cut(s) 178
AvaII GGWCC 1 cut(s) 430
BbsI GAAGAC 1 cut(s) 405
Bbv12I GWGCWC 2 cut(s) 65, 555
BbvI GCAGC 2 cut(s) 251, 555
BccI CCATC 1 cut(s) 391
BcgI CGANNNNNNTGC 2 cut(s) 479, 513
BcnI CCSGG 2 cut(s) 364, 602
BfaI CTAG 3 cut(s) 179, 243, 635
BfmI CTRYAG 1 cut(s) 42
BisI GCNGC 2 cut(s) 240, 544
BlsI GCNGC 2 cut(s) 241, 545
Bme1390I CCNGG 2 cut(s) 364, 602
Bme18I GGWCC 1 cut(s) 430
BmeRI GACNNNNNGTC 1 cut(s) 308
BmgT120I GGNCC 2 cut(s) 430, 599
BmiI GGNNCC 1 cut(s) 432
BmrFI CCNGG 2 cut(s) 364, 602
BmrI ACTGGG 1 cut(s) 503
BmsI GCATC 1 cut(s) 191
BmtI GCTAGC 1 cut(s) 182
BmuI ACTGGG 1 cut(s) 503
BpiI GAAGAC 1 cut(s) 405
Bpu10I CCTNAGC 2 cut(s) 174, 684
BpuMI CCSGG 2 cut(s) 364, 602
BsaJI CCNNGG 1 cut(s) 252
BsaWI WCCGGW 1 cut(s) 391
Bsc4I CCNNNNNNNGG 1 cut(s) 427
Bse1I ACTGG 1 cut(s) 498
BseDI CCNNGG 1 cut(s) 252
BseGI GGATG 2 cut(s) 490, 697
BseLI CCNNNNNNNGG 1 cut(s) 427
BseMII CTCAG 3 cut(s) 21, 165, 467
BseNI ACTGG 1 cut(s) 498
BseRI GAGGAG 1 cut(s) 563
BseXI GCAGC 2 cut(s) 251, 555
BseYI CCCAGC 1 cut(s) 330
BshFI GGCC 1 cut(s) 600
BsiHKAI GWGCWC 2 cut(s) 65, 555
BsiSI CCGG 3 cut(s) 364, 392, 602
BslFI GGGAC 1 cut(s) 734
BslI CCNNNNNNNGG 1 cut(s) 427
BsmFI GGGAC 1 cut(s) 734
BsnI GGCC 1 cut(s) 600
Bsp1286I GDGCHC 2 cut(s) 65, 555
Bsp143I GATC 4 cut(s) 101, 274, 414, 460
BspACI CCGC 3 cut(s) 297, 688, 701
BspANI GGCC 1 cut(s) 600
BspCNI CTCAG 3 cut(s) 22, 166, 468
BspHI TCATGA 1 cut(s) 262
BspLI GGNNCC 1 cut(s) 432
BspOI GCTAGC 1 cut(s) 182
BspPI GGATC 3 cut(s) 96, 282, 409
BsrBI CCGCTC 1 cut(s) 299
BsrI ACTGG 1 cut(s) 498
BssECI CCNNGG 1 cut(s) 252
BssMI GATC 4 cut(s) 101, 274, 414, 460
BssNAI GTATAC 1 cut(s) 655
BssT1I CCWWGG 1 cut(s) 252
Bst1107I GTATAC 1 cut(s) 655
Bst4CI ACNGT 3 cut(s) 151, 447, 513
Bst6I CTCTTC 2 cut(s) 699, 732
BstC8I GCNNGC 1 cut(s) 180
BstDEI CTNAG 6 cut(s) 30, 117, 174, 210, 476, 684
BstF5I GGATG 2 cut(s) 490, 697
BstKTI GATC 4 cut(s) 104, 277, 417, 463
BstMBI GATC 4 cut(s) 101, 274, 414, 460
BstMWI GCNNNNNNNGC 1 cut(s) 239
BstSCI CCNGG 2 cut(s) 362, 600
BstSFI CTRYAG 1 cut(s) 42
BstV1I GCAGC 2 cut(s) 251, 555
BstV2I GAAGAC 1 cut(s) 405
BstX2I RGATCY 2 cut(s) 101, 274
BstXI CCANNNNNNTGG 2 cut(s) 112, 565
BstYI RGATCY 2 cut(s) 101, 274
BstZ17I GTATAC 1 cut(s) 655
BsuRI GGCC 1 cut(s) 600
BtsCI GGATG 2 cut(s) 490, 697
Cac8I GCNNGC 1 cut(s) 180
CciI TCATGA 1 cut(s) 262
Cfr13I GGNCC 2 cut(s) 430, 599
Csp6I GTAC 2 cut(s) 132, 480
CviAII CATG 4 cut(s) 5, 263, 354, 436
CviJI RGCY 6 cut(s) 40, 116, 178, 242, 351, 600
CviKI_1 RGCY 6 cut(s) 40, 116, 178, 242, 351, 600
CviQI GTAC 2 cut(s) 132, 480
DdeI CTNAG 6 cut(s) 30, 117, 174, 210, 476, 684
DpnI GATC 4 cut(s) 103, 276, 416, 462
DpnII GATC 4 cut(s) 101, 274, 414, 460
DraI TTTAAA 1 cut(s) 217
DriI GACNNNNNGTC 1 cut(s) 308
Eam1104I CTCTTC 2 cut(s) 699, 732
Eam1105I GACNNNNNGTC 1 cut(s) 308
EarI CTCTTC 2 cut(s) 699, 732
EciI GGCGGA 1 cut(s) 716
Eco130I CCWWGG 1 cut(s) 252
Eco47I GGWCC 1 cut(s) 430
Eco57I CTGAAG 1 cut(s) 331
EcoO109I RGGNCCY 1 cut(s) 430
EcoRI GAATTC 1 cut(s) 455
EcoT14I CCWWGG 1 cut(s) 252
EcoT22I ATGCAT 1 cut(s) 6
ErhI CCWWGG 1 cut(s) 252
FaeI CATG 4 cut(s) 8, 266, 357, 439
FaqI GGGAC 1 cut(s) 734
FatI CATG 4 cut(s) 4, 262, 353, 435
FauI CCCGC 2 cut(s) 304, 681
FblI GTMKAC 3 cut(s) 321, 359, 654
Fnu4HI GCNGC 2 cut(s) 240, 544
FokI GGATG 2 cut(s) 497, 704
Fsp4HI GCNGC 2 cut(s) 240, 544
FspBI CTAG 3 cut(s) 179, 243, 635
GluI GCNGC 2 cut(s) 240, 544
GsaI CCCAGC 1 cut(s) 334
HaeIII GGCC 1 cut(s) 600
HapII CCGG 3 cut(s) 364, 392, 602
Hin1II CATG 4 cut(s) 8, 266, 357, 439
HinfI GANTC 2 cut(s) 121, 613
HpaII CCGG 3 cut(s) 364, 392, 602
HphI GGTGA 5 cut(s) 285, 381, 464, 501, 581
Hpy166II GTNNAC 4 cut(s) 313, 322, 360, 655
Hpy188I TCNGA 2 cut(s) 187, 715
Hpy188III TCNNGA 3 cut(s) 194, 263, 278
Hpy8I GTNNAC 4 cut(s) 313, 322, 360, 655
HpyAV CCTTC 1 cut(s) 265
HpyCH4III ACNGT 3 cut(s) 151, 447, 513
HpyCH4IV ACGT 1 cut(s) 723
HpyCH4V TGCA 3 cut(s) 4, 466, 500
HpyF10VI GCNNNNNNNGC 1 cut(s) 239
HpyF3I CTNAG 6 cut(s) 30, 117, 174, 210, 476, 684
HpySE526I ACGT 1 cut(s) 723
Hsp92II CATG 4 cut(s) 8, 266, 357, 439
Kzo9I GATC 4 cut(s) 101, 274, 414, 460
LmnI GCTCC 2 cut(s) 366, 550
Lsp1109I GCAGC 2 cut(s) 251, 555
LweI GCATC 1 cut(s) 191
MaeI CTAG 3 cut(s) 179, 243, 635
MaeII ACGT 1 cut(s) 723
MalI GATC 4 cut(s) 103, 276, 416, 462
MbiI CCGCTC 1 cut(s) 299
MboI GATC 4 cut(s) 101, 274, 414, 460
MboII GAAGA 7 cut(s) 179, 334, 337, 407, 410, 622, 716
MflI RGATCY 2 cut(s) 101, 274
MhlI GDGCHC 2 cut(s) 65, 555
MluCI AATT 4 cut(s) 455, 503, 524, 593
Mph1103I ATGCAT 1 cut(s) 6
MseI TTAA 2 cut(s) 216, 647
MslI CAYNNNNRTG 1 cut(s) 423
MspI CCGG 3 cut(s) 364, 392, 602
MspR9I CCNGG 2 cut(s) 364, 602
MwoI GCNNNNNNNGC 1 cut(s) 239
NciI CCSGG 2 cut(s) 364, 602
NdeII GATC 4 cut(s) 101, 274, 414, 460
NheI GCTAGC 1 cut(s) 178
NlaIII CATG 4 cut(s) 8, 266, 357, 439
NlaIV GGNNCC 1 cut(s) 432
NsiI ATGCAT 1 cut(s) 6
PagI TCATGA 1 cut(s) 262
PfeI GAWTC 2 cut(s) 121, 613
PkrI GCNGC 2 cut(s) 241, 545
PpuMI RGGWCCY 1 cut(s) 430
Psp5II RGGWCCY 1 cut(s) 430
PspFI CCCAGC 1 cut(s) 330
PspN4I GGNNCC 1 cut(s) 432
PspPI GGNCC 2 cut(s) 430, 599
PspPPI RGGWCCY 1 cut(s) 430
PsuI RGATCY 2 cut(s) 101, 274
RsaI GTAC 2 cut(s) 133, 481
RsaNI GTAC 2 cut(s) 132, 480
RseI CAYNNNNRTG 1 cut(s) 423
SaqAI TTAA 2 cut(s) 216, 647
SatI GCNGC 2 cut(s) 240, 544
Sau3AI GATC 4 cut(s) 101, 274, 414, 460
Sau96I GGNCC 2 cut(s) 430, 599
ScrFI CCNGG 2 cut(s) 364, 602
SduI GDGCHC 2 cut(s) 65, 555
SetI ASST 9 cut(s) 84, 137, 175, 180, 208, 244, 353, 576, 726
SfaNI GCATC 1 cut(s) 191
SfcI CTRYAG 1 cut(s) 42
SinI GGWCC 1 cut(s) 430
SmiMI CAYNNNNRTG 1 cut(s) 423
Sse9I AATT 4 cut(s) 455, 503, 524, 593
SsiI CCGC 3 cut(s) 297, 688, 701
SspI AATATT 1 cut(s) 564
SspMI CTAG 3 cut(s) 179, 243, 635
StyD4I CCNGG 2 cut(s) 362, 600
StyI CCWWGG 1 cut(s) 252
TaaI ACNGT 3 cut(s) 151, 447, 513
TaiI ACGT 1 cut(s) 726
TaqI TCGA 3 cut(s) 301, 459, 641
TasI AATT 4 cut(s) 455, 503, 524, 593
TfiI GAWTC 2 cut(s) 121, 613
Tru1I TTAA 2 cut(s) 216, 647
Tru9I TTAA 2 cut(s) 216, 647
TseI GCWGC 2 cut(s) 239, 543
TspDTI ATGAA 3 cut(s) 69, 251, 455
TspGWI ACGGA 1 cut(s) 497
VpaK11BI GGWCC 1 cut(s) 430
XapI RAATTY 3 cut(s) 455, 503, 593
XmiI GTMKAC 3 cut(s) 321, 359, 654
XspI CTAG 3 cut(s) 179, 243, 635
Zsp2I ATGCAT 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.