Rh2AG175800

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2A
OG0000370
Physical Location & Seq
Forward (+)
16771150 .. 16771557
408 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2AG175800.1

Sequence Viewer

Length: 408 bp
ATGGCAGAAGAACAACATAAGGGTGAGGTTAGTAGCAACATGGAAGTCATAGCTGCTATTCAAGATATGGCAAGTGCAATAAGGGAAAATCGCAATGGTAATCACCAAGAAGGTAATGAAGAACGAGTTATGAGAATACAAGGTGAATTTCGTAAGGCCCAACCTCCTATATTCAAGGGTACCTTAGATCCCATGATAGCTAAAGAATGGTTGAGGAAAATGAAGAGAACCCTGAATAATCAAAAAGTGCCCGAAGATTTGAAAGTAATTATTTCATGTACTTACTTGGAAGGTGCAGCTTATCACTGGTGGGAATCAGTTCTTGCTACTCCAGACACTGAAATTACAACCTGGGATGCATTTGAAGTTATTTTTCTTGAGAAATATTTCCCAGACACAGTAAAGTAA
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

135

Amino Acids

15.66

Weight (kDa)

5.26

Isoelectric Point (pI)

33.9

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 94 - 133 9.1e-06 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) 179
AccB1I GGYRCC 1 cut(s) 179
AclWI GGATC 1 cut(s) 182
AcsI RAATTY 1 cut(s) 146
AfaI GTAC 2 cut(s) 181, 280
AgsI TTSAA 4 cut(s) 62, 175, 262, 365
AjnI CCWGG 1 cut(s) 350
AluBI AGCT 3 cut(s) 53, 200, 299
AluI AGCT 3 cut(s) 53, 200, 299
AlwI GGATC 1 cut(s) 182
AlwNI CAGNNNCTG 1 cut(s) 338
AoxI GGCC 1 cut(s) 156
ApeKI GCWGC 2 cut(s) 53, 296
ApoI RAATTY 1 cut(s) 146
Asp700I GAANNNNTTC 2 cut(s) 318, 386
Asp718I GGTACC 1 cut(s) 179
AspS9I GGNCC 1 cut(s) 157
AsuHPI GGTGA 3 cut(s) 35, 95, 155
BaeGI GKGCMC 1 cut(s) 252
BanI GGYRCC 1 cut(s) 179
BbvI GCAGC 2 cut(s) 40, 308
BciT130I CCWGG 1 cut(s) 352
BisI GCNGC 2 cut(s) 54, 297
BlsI GCNGC 2 cut(s) 55, 298
Bme1390I CCNGG 1 cut(s) 352
BmgT120I GGNCC 1 cut(s) 157
BmiI GGNNCC 1 cut(s) 181
BmrFI CCNGG 1 cut(s) 352
BmsI GCATC 1 cut(s) 346
BpmI CTGGAG 1 cut(s) 315
BpuEI CTTGAG 1 cut(s) 398
BsaJI CCNNGG 1 cut(s) 351
Bse1I ACTGG 1 cut(s) 311
Bse3DI GCAATG 1 cut(s) 100
BseBI CCWGG 1 cut(s) 352
BseDI CCNNGG 1 cut(s) 351
BseGI GGATG 1 cut(s) 361
BseMI GCAATG 1 cut(s) 100
BseNI ACTGG 1 cut(s) 311
BseSI GKGCMC 1 cut(s) 252
BseXI GCAGC 2 cut(s) 40, 308
BsgI GTGCAG 1 cut(s) 315
BshFI GGCC 1 cut(s) 158
BshNI GGYRCC 1 cut(s) 179
BsnI GGCC 1 cut(s) 158
Bsp1286I GDGCHC 1 cut(s) 252
Bsp143I GATC 1 cut(s) 187
BspANI GGCC 1 cut(s) 158
BspLI GGNNCC 1 cut(s) 181
BspPI GGATC 1 cut(s) 182
BspT107I GGYRCC 1 cut(s) 179
BsrDI GCAATG 1 cut(s) 100
BsrI ACTGG 1 cut(s) 311
BssECI CCNNGG 1 cut(s) 351
BssMI GATC 1 cut(s) 187
Bst2UI CCWGG 1 cut(s) 352
Bst4CI ACNGT 1 cut(s) 400
Bst6I CTCTTC 1 cut(s) 218
BstDEI CTNAG 1 cut(s) 184
BstF5I GGATG 1 cut(s) 361
BstKTI GATC 1 cut(s) 190
BstMBI GATC 1 cut(s) 187
BstNI CCWGG 1 cut(s) 352
BstSCI CCNGG 1 cut(s) 350
BstSLI GKGCMC 1 cut(s) 252
BstV1I GCAGC 2 cut(s) 40, 308
BstX2I RGATCY 1 cut(s) 187
BstYI RGATCY 1 cut(s) 187
BsuRI GGCC 1 cut(s) 158
BtsCI GGATG 1 cut(s) 361
BtsIMutI CAGTG 2 cut(s) 304, 336
CaiI CAGNNNCTG 1 cut(s) 338
Cfr13I GGNCC 1 cut(s) 157
Csp6I GTAC 2 cut(s) 180, 279
CviAII CATG 3 cut(s) 40, 193, 276
CviJI RGCY 4 cut(s) 53, 158, 200, 299
CviKI_1 RGCY 4 cut(s) 53, 158, 200, 299
CviQI GTAC 2 cut(s) 180, 279
DdeI CTNAG 1 cut(s) 184
DpnI GATC 1 cut(s) 189
DpnII GATC 1 cut(s) 187
Eam1104I CTCTTC 1 cut(s) 218
EarI CTCTTC 1 cut(s) 218
EcoRII CCWGG 1 cut(s) 350
EcoT22I ATGCAT 1 cut(s) 361
FaeI CATG 3 cut(s) 43, 196, 279
FaiI YATR 8 cut(s) 18, 41, 50, 68, 131, 170, 194, 277
FalI AAGNNNNNCTT 2 cut(s) 167, 199
FatI CATG 3 cut(s) 39, 192, 275
Fnu4HI GCNGC 2 cut(s) 54, 297
FokI GGATG 1 cut(s) 368
Fsp4HI GCNGC 2 cut(s) 54, 297
GluI GCNGC 2 cut(s) 54, 297
GsuI CTGGAG 1 cut(s) 315
HaeIII GGCC 1 cut(s) 158
Hin1II CATG 3 cut(s) 43, 196, 279
HinfI GANTC 1 cut(s) 314
HphI GGTGA 3 cut(s) 35, 95, 155
Hpy188III TCNNGA 3 cut(s) 62, 332, 377
HpyAV CCTTC 2 cut(s) 104, 284
HpyCH4III ACNGT 1 cut(s) 400
HpyCH4V TGCA 3 cut(s) 77, 296, 359
HpyF3I CTNAG 1 cut(s) 184
Hsp92II CATG 3 cut(s) 43, 196, 279
KpnI GGTACC 1 cut(s) 183
Kzo9I GATC 1 cut(s) 187
LpnPI CCDG 5 cut(s) 245, 292, 337, 345, 364
Lsp1109I GCAGC 2 cut(s) 40, 308
LweI GCATC 1 cut(s) 346
MalI GATC 1 cut(s) 189
MboI GATC 1 cut(s) 187
MboII GAAGA 4 cut(s) 20, 131, 235, 266
MflI RGATCY 1 cut(s) 187
MhlI GDGCHC 1 cut(s) 252
MluCI AATT 3 cut(s) 146, 267, 342
MnlI CCTC 3 cut(s) 19, 174, 207
Mph1103I ATGCAT 1 cut(s) 361
MroXI GAANNNNTTC 2 cut(s) 318, 386
MslI CAYNNNNRTG 1 cut(s) 21
MspR9I CCNGG 1 cut(s) 352
MvaI CCWGG 1 cut(s) 352
NdeII GATC 1 cut(s) 187
NlaIII CATG 3 cut(s) 43, 196, 279
NlaIV GGNNCC 1 cut(s) 181
NsiI ATGCAT 1 cut(s) 361
PdmI GAANNNNTTC 2 cut(s) 318, 386
PfeI GAWTC 1 cut(s) 314
PkrI GCNGC 2 cut(s) 55, 298
Psp6I CCWGG 1 cut(s) 350
PspGI CCWGG 1 cut(s) 350
PspN4I GGNNCC 1 cut(s) 181
PspPI GGNCC 1 cut(s) 157
PstNI CAGNNNCTG 1 cut(s) 338
PsuI RGATCY 1 cut(s) 187
RsaI GTAC 2 cut(s) 181, 280
RsaNI GTAC 2 cut(s) 180, 279
RseI CAYNNNNRTG 1 cut(s) 21
SatI GCNGC 2 cut(s) 54, 297
Sau3AI GATC 1 cut(s) 187
Sau96I GGNCC 1 cut(s) 157
ScrFI CCNGG 1 cut(s) 352
SduI GDGCHC 1 cut(s) 252
SfaNI GCATC 1 cut(s) 346
SmiMI CAYNNNNRTG 1 cut(s) 21
SmlI CTYRAG 1 cut(s) 377
SmoI CTYRAG 1 cut(s) 377
Sse9I AATT 3 cut(s) 146, 267, 342
SspI AATATT 1 cut(s) 386
StyD4I CCNGG 1 cut(s) 350
TaaI ACNGT 1 cut(s) 400
TasI AATT 3 cut(s) 146, 267, 342
TatI WGTACW 1 cut(s) 278
TfiI GAWTC 1 cut(s) 314
TscAI CASTG 2 cut(s) 311, 343
TseI GCWGC 2 cut(s) 53, 296
TspDTI ATGAA 3 cut(s) 132, 236, 264
TspRI CASTG 2 cut(s) 311, 343
XapI RAATTY 1 cut(s) 146
XmnI GAANNNNTTC 2 cut(s) 318, 386
Zsp2I ATGCAT 1 cut(s) 361
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.