Rh7DG228300

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr7D
OG0000370
Physical Location & Seq
Reverse (-)
22502816 .. 22503394
579 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh7DG228300.1

Sequence Viewer

Length: 579 bp
ATGGAAGTCATAGCTGCTATTCAAGATATGGCAAGTGCAATAAGGGAAAATCGCAATGATAATCATCAAGAAGGTAATGGAGAACGAGTTATGAGAATACAAGGTGAATTTCGTAAGGCCCGACCTCCTATATTCAAGGGTACCTTAGATCCCATGATAGCTGAAGAATGGTTGAGACAAATGAAGAGGACTCTGAATAATCAAAAAGTGCCGGAAGATTTGAAAGTAATTATCTCATGTACGTACTTGGAAGGTGCAGCTTATCACTGGTGGGAATCAGTTCTTGCTACTCCAAACACTGAAATTACAACCTGGGATGCATTTGAAGTTATTTTTCTTGAGAAATATTTCCCAGACACAGTAAAGCAAGCCAAGGCAAAAGAGTTTATGTTTCTATCTAAAGGGGAAATGACAATAGCTGAATACCAAGGTAGATTTGAGGAACTTATGCGGTTTGCTCCAGGTATTATTCCCAATGAGGTTACTAAAGCAAAGAAATTTGAGGAAGGACTTAATCCTGAGATTAGGGAGAAAGTATCGATTCTAAAGTTATTGAAATATTCTGAAGTGGTGGACTGA
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
RVP_2 Retrotrans_gag

Protein Analysis

192

Amino Acids

22.32

Weight (kDa)

5.46

Isoelectric Point (pI)

26.58

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 39 - 183 6.3e-10 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 81 - 173 9e-17 Retrotransposon gag 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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 140
AccB1I GGYRCC 1 cut(s) 140
AciI CCGC 1 cut(s) 451
AclWI GGATC 1 cut(s) 143
AcsI RAATTY 2 cut(s) 107, 497
AcuI CTGAAG 1 cut(s) 183
AfaI GTAC 3 cut(s) 142, 241, 245
AgsI TTSAA 5 cut(s) 23, 136, 223, 326, 556
AjnI CCWGG 2 cut(s) 311, 460
AluBI AGCT 4 cut(s) 14, 161, 260, 419
AluI AGCT 4 cut(s) 14, 161, 260, 419
Alw26I GTCTC 1 cut(s) 169
AlwI GGATC 1 cut(s) 143
AoxI GGCC 1 cut(s) 117
ApeKI GCWGC 2 cut(s) 14, 257
ApoI RAATTY 2 cut(s) 107, 497
Asp700I GAANNNNTTC 2 cut(s) 279, 347
Asp718I GGTACC 1 cut(s) 140
AspS9I GGNCC 1 cut(s) 118
AsuHPI GGTGA 1 cut(s) 116
BanI GGYRCC 1 cut(s) 140
BbvI GCAGC 1 cut(s) 269
BciT130I CCWGG 2 cut(s) 313, 462
BcoDI GTCTC 1 cut(s) 169
BisI GCNGC 2 cut(s) 15, 258
BlsI GCNGC 2 cut(s) 16, 259
Bme1390I CCNGG 2 cut(s) 313, 462
BmgT120I GGNCC 1 cut(s) 118
BmiI GGNNCC 1 cut(s) 142
BmrFI CCNGG 2 cut(s) 313, 462
BmsI GCATC 1 cut(s) 307
BpmI CTGGAG 1 cut(s) 444
BpuEI CTTGAG 1 cut(s) 359
Bsa29I ATCGAT 1 cut(s) 539
BsaAI YACGTR 1 cut(s) 243
BsaBI GATNNNNATC 1 cut(s) 63
BsaJI CCNNGG 3 cut(s) 312, 372, 427
BsaXI ACNNNNNCTCC 2 cut(s) 72, 102
Bse1I ACTGG 1 cut(s) 272
Bse3DI GCAATG 1 cut(s) 61
Bse8I GATNNNNATC 1 cut(s) 63
BseBI CCWGG 2 cut(s) 313, 462
BseCI ATCGAT 1 cut(s) 539
BseDI CCNNGG 3 cut(s) 312, 372, 427
BseGI GGATG 1 cut(s) 322
BseJI GATNNNNATC 1 cut(s) 63
BseMI GCAATG 1 cut(s) 61
BseMII CTCAG 1 cut(s) 510
BseNI ACTGG 1 cut(s) 272
BseXI GCAGC 1 cut(s) 269
BsgI GTGCAG 1 cut(s) 276
BshFI GGCC 1 cut(s) 119
BshNI GGYRCC 1 cut(s) 140
BshVI ATCGAT 1 cut(s) 539
BsiSI CCGG 1 cut(s) 212
BsmAI GTCTC 1 cut(s) 169
BsnI GGCC 1 cut(s) 119
Bsp143I GATC 1 cut(s) 148
BspACI CCGC 1 cut(s) 451
BspANI GGCC 1 cut(s) 119
BspCNI CTCAG 1 cut(s) 511
BspDI ATCGAT 1 cut(s) 539
BspLI GGNNCC 1 cut(s) 142
BspPI GGATC 1 cut(s) 143
BspT107I GGYRCC 1 cut(s) 140
BsrDI GCAATG 1 cut(s) 61
BsrI ACTGG 1 cut(s) 272
BssECI CCNNGG 3 cut(s) 312, 372, 427
BssMI GATC 1 cut(s) 148
BssT1I CCWWGG 2 cut(s) 372, 427
Bst2UI CCWGG 2 cut(s) 313, 462
Bst4CI ACNGT 1 cut(s) 361
Bst6I CTCTTC 1 cut(s) 179
BstBAI YACGTR 1 cut(s) 243
BstC8I GCNNGC 1 cut(s) 369
BstDEI CTNAG 2 cut(s) 145, 519
BstF5I GGATG 1 cut(s) 322
BstKTI GATC 1 cut(s) 151
BstMAI GTCTC 1 cut(s) 169
BstMBI GATC 1 cut(s) 148
BstNI CCWGG 2 cut(s) 313, 462
BstSCI CCNGG 2 cut(s) 311, 460
BstSNI TACGTA 1 cut(s) 243
BstV1I GCAGC 1 cut(s) 269
BstX2I RGATCY 1 cut(s) 148
BstYI RGATCY 1 cut(s) 148
Bsu15I ATCGAT 1 cut(s) 539
BsuRI GGCC 1 cut(s) 119
BsuTUI ATCGAT 1 cut(s) 539
BtsCI GGATG 1 cut(s) 322
BtsIMutI CAGTG 2 cut(s) 265, 297
Cac8I GCNNGC 1 cut(s) 369
Cfr13I GGNCC 1 cut(s) 118
ClaI ATCGAT 1 cut(s) 539
Csp6I GTAC 3 cut(s) 141, 240, 244
CviAII CATG 2 cut(s) 154, 237
CviJI RGCY 6 cut(s) 14, 119, 161, 260, 371, 419
CviKI_1 RGCY 6 cut(s) 14, 119, 161, 260, 371, 419
CviQI GTAC 3 cut(s) 141, 240, 244
DdeI CTNAG 2 cut(s) 145, 519
DpnI GATC 1 cut(s) 150
DpnII GATC 1 cut(s) 148
Eam1104I CTCTTC 1 cut(s) 179
EarI CTCTTC 1 cut(s) 179
Eco105I TACGTA 1 cut(s) 243
Eco130I CCWWGG 2 cut(s) 372, 427
Eco57I CTGAAG 1 cut(s) 183
EcoRII CCWGG 2 cut(s) 311, 460
EcoT14I CCWWGG 2 cut(s) 372, 427
EcoT22I ATGCAT 1 cut(s) 322
ErhI CCWWGG 2 cut(s) 372, 427
FaeI CATG 2 cut(s) 157, 240
FaiI YATR 8 cut(s) 11, 29, 92, 131, 155, 238, 389, 449
FalI AAGNNNNNCTT 2 cut(s) 128, 160
FatI CATG 2 cut(s) 153, 236
Fnu4HI GCNGC 2 cut(s) 15, 258
FokI GGATG 1 cut(s) 329
Fsp4HI GCNGC 2 cut(s) 15, 258
GluI GCNGC 2 cut(s) 15, 258
GsuI CTGGAG 1 cut(s) 444
HaeIII GGCC 1 cut(s) 119
HapII CCGG 1 cut(s) 212
Hin1II CATG 2 cut(s) 157, 240
HinfI GANTC 3 cut(s) 190, 275, 541
HpaII CCGG 1 cut(s) 212
HphI GGTGA 1 cut(s) 116
Hpy166II GTNNAC 1 cut(s) 574
Hpy188I TCNGA 2 cut(s) 195, 565
Hpy188III TCNNGA 4 cut(s) 23, 68, 338, 518
Hpy8I GTNNAC 1 cut(s) 574
HpyAV CCTTC 3 cut(s) 65, 245, 500
HpyCH4III ACNGT 1 cut(s) 361
HpyCH4IV ACGT 1 cut(s) 242
HpyCH4V TGCA 3 cut(s) 38, 257, 320
HpyF3I CTNAG 2 cut(s) 145, 519
HpySE526I ACGT 1 cut(s) 242
Hsp92II CATG 2 cut(s) 157, 240
KpnI GGTACC 1 cut(s) 144
Kzo9I GATC 1 cut(s) 148
LmnI GCTCC 1 cut(s) 463
LpnPI CCDG 8 cut(s) 225, 253, 298, 325, 366, 447, 474, 531
Lsp1109I GCAGC 1 cut(s) 269
LweI GCATC 1 cut(s) 307
MaeII ACGT 1 cut(s) 242
MaeIII GTNAC 1 cut(s) 481
MalI GATC 1 cut(s) 150
MboI GATC 1 cut(s) 148
MboII GAAGA 3 cut(s) 176, 196, 227
MflI RGATCY 1 cut(s) 148
MluCI AATT 4 cut(s) 107, 228, 303, 497
MlyI GAGTC 1 cut(s) 184
MnlI CCTC 5 cut(s) 135, 180, 433, 472, 496
Mph1103I ATGCAT 1 cut(s) 322
MroXI GAANNNNTTC 2 cut(s) 279, 347
MseI TTAA 1 cut(s) 513
MspI CCGG 1 cut(s) 212
MspR9I CCNGG 2 cut(s) 313, 462
MvaI CCWGG 2 cut(s) 313, 462
NdeII GATC 1 cut(s) 148
NlaIII CATG 2 cut(s) 157, 240
NlaIV GGNNCC 1 cut(s) 142
NsiI ATGCAT 1 cut(s) 322
PcsI WCGNNNNNNNCGW 1 cut(s) 118
PdmI GAANNNNTTC 2 cut(s) 279, 347
PfeI GAWTC 2 cut(s) 275, 541
PkrI GCNGC 2 cut(s) 16, 259
PleI GAGTC 1 cut(s) 184
PpsI GAGTC 1 cut(s) 184
Ppu21I YACGTR 1 cut(s) 243
Psp6I CCWGG 2 cut(s) 311, 460
PspGI CCWGG 2 cut(s) 311, 460
PspN4I GGNNCC 1 cut(s) 142
PspPI GGNCC 1 cut(s) 118
PsuI RGATCY 1 cut(s) 148
RsaI GTAC 3 cut(s) 142, 241, 245
RsaNI GTAC 3 cut(s) 141, 240, 244
SaqAI TTAA 1 cut(s) 513
SatI GCNGC 2 cut(s) 15, 258
Sau3AI GATC 1 cut(s) 148
Sau96I GGNCC 1 cut(s) 118
SchI GAGTC 1 cut(s) 184
ScrFI CCNGG 2 cut(s) 313, 462
SfaNI GCATC 1 cut(s) 307
SmlI CTYRAG 1 cut(s) 338
SmoI CTYRAG 1 cut(s) 338
SnaBI TACGTA 1 cut(s) 243
Sse9I AATT 4 cut(s) 107, 228, 303, 497
SsiI CCGC 1 cut(s) 451
SspI AATATT 2 cut(s) 347, 560
StyD4I CCNGG 2 cut(s) 311, 460
StyI CCWWGG 2 cut(s) 372, 427
TaaI ACNGT 1 cut(s) 361
TaiI ACGT 1 cut(s) 245
TaqI TCGA 1 cut(s) 539
TasI AATT 4 cut(s) 107, 228, 303, 497
TfiI GAWTC 2 cut(s) 275, 541
Tru1I TTAA 1 cut(s) 513
Tru9I TTAA 1 cut(s) 513
TscAI CASTG 2 cut(s) 272, 304
TseI GCWGC 2 cut(s) 14, 257
TspDTI ATGAA 1 cut(s) 197
TspRI CASTG 2 cut(s) 272, 304
XapI RAATTY 2 cut(s) 107, 497
XmnI GAANNNNTTC 2 cut(s) 279, 347
Zsp2I ATGCAT 1 cut(s) 322
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.