Rroxscaffold_157G00438380

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000157
OG0000118
Physical Location & Seq
Reverse (-)
74801 .. 75872
1072 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_157G00438380.1

Sequence Viewer

Length: 600 bp
ATGTCAGTATCTGAGTATATGCAAAAGTTTGACGAGTTAAAGACAAGGAGTCAAATTGTAGAAGACTCTAGACAAACTCTTGCAAGGTTCAAGGATGGTTTGAGACCTGACATAAAGATGGAGATGATTCGACAACCAGTGTACAGCGTAGAACATGCTTTCCAAGTTGCTTTGGACTTGGAAGAATATTTGGGTTACACCACAGTGAGGAAATCTGGGAGTCAGGGTAATGACACAGCTCAAAGAAAATATTTTGAGGCTGCCGGTAAGACAAGGACAGGAAACCCATCATTCAATCGAGCACTAGATTCTAAACCCTCTTCTTCAAAGGCCATTGAATCAAGGGTTTGCTTCAAGTGTGGGCAACCAGGTCACATGGGATATCAATGTCCAAAGAAGAATCTGCATATTGGAATAGAGCAAGAGGAAGAACCAGAGCATCAAGCGGGAAACGATGACTTTGACTATGGGGAATATGATGCAGATGATCTTGAGGAAGAAGACCATGACACTTCCCTTTCCTCTGTCATGAGACGTGTGCTAGCAGCTCCTAAAACGGGGGAGAAAACTGGAGTCGAACAGCAATTTTTCAAATGTTAG
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
RVT_1 Retrotrans_gag zf-CCHC

Protein Analysis

199

Amino Acids

22.62

Weight (kDa)

5.23

Isoelectric Point (pI)

51.6

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-CCHC PF00098 115 - 132 2.3e-06 Zinc knuckle
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: OG0000118)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g01361 FvH4_1g07161 FvH4_1g07431 FvH4_1g07821 FvH4_1g08223 FvH4_1g10041 FvH4_1g12132 FvH4_1g15053 FvH4_1g18161 FvH4_1g18400 FvH4_1g18931 FvH4_1g19242 FvH4_1g19461 FvH4_1g20550 FvH4_1g21381 FvH4_1g21542 FvH4_1g22102 FvH4_1g23991 FvH4_1g24542 FvH4_1g24951 FvH4_1g24960 FvH4_1g25272 FvH4_1g25552 FvH4_1g25771 FvH4_1g28771 FvH4_1g29201 FvH4_1g29611 FvH4_2g01181 FvH4_2g02491 FvH4_2g04621 FvH4_2g04631 FvH4_2g07460 FvH4_2g08540 FvH4_2g08550 FvH4_2g09292 FvH4_2g10501 FvH4_2g12101 FvH4_2g12220 FvH4_2g12551 FvH4_2g14071 FvH4_2g14241 FvH4_2g15041 FvH4_2g15311 FvH4_2g18971 FvH4_2g19220 FvH4_2g19260 FvH4_2g19611 FvH4_2g19652 FvH4_2g20211 FvH4_2g20231 FvH4_2g21541 FvH4_2g22380 FvH4_2g27712 FvH4_2g28171 FvH4_2g29879 FvH4_2g32391 FvH4_3g02171 FvH4_3g05531 FvH4_3g09750 FvH4_3g10310 FvH4_3g10460 FvH4_3g13172 FvH4_3g15232 FvH4_3g18481 FvH4_3g18621 FvH4_3g20504 FvH4_3g20812 FvH4_3g22320 FvH4_3g22930 FvH4_3g22940 FvH4_3g23752 FvH4_3g24791 FvH4_3g26411 FvH4_3g26432 FvH4_3g27201 FvH4_3g27862 FvH4_3g28871 FvH4_3g28954 FvH4_3g29131 FvH4_3g29832 FvH4_3g29922 FvH4_3g30190 FvH4_3g32231 FvH4_3g32250 FvH4_3g33460 FvH4_3g34670 FvH4_3g36982 FvH4_3g37001 FvH4_3g38252 FvH4_3g38772 FvH4_3g40141 FvH4_3g40181 FvH4_3g42521 FvH4_4g00090 FvH4_4g00290 FvH4_4g00301 FvH4_4g00530 FvH4_4g00823 FvH4_4g02300 FvH4_4g02450 FvH4_4g03360 FvH4_4g04481 FvH4_4g04761 FvH4_4g06301 FvH4_4g06630 FvH4_4g08312 FvH4_4g08552 FvH4_4g10053 FvH4_4g11971 FvH4_4g13211 FvH4_4g13511 FvH4_4g15351 FvH4_4g16360 FvH4_4g16601 FvH4_4g18462 FvH4_4g22911 FvH4_4g23221 FvH4_4g24301 FvH4_4g24721 FvH4_4g27905 FvH4_4g28971 FvH4_4g29540 FvH4_4g30720 FvH4_4g31521 FvH4_4g33371 FvH4_4g34111 FvH4_4g35740 FvH4_5g00131 FvH4_5g02530 FvH4_5g02550 FvH4_5g02560 FvH4_5g02580 FvH4_5g03783 FvH4_5g05681 FvH4_5g05681 FvH4_5g09371 FvH4_5g09381 FvH4_5g14611 FvH4_5g15341 FvH4_5g19801 FvH4_5g20110 FvH4_5g20911 FvH4_5g22230 FvH4_5g25751 FvH4_5g26070 FvH4_5g26471 FvH4_5g27072 FvH4_5g27471 FvH4_5g27471 FvH4_5g27998 FvH4_5g28291 FvH4_5g30951 FvH4_5g31082 FvH4_5g31890 FvH4_5g32251 FvH4_5g34112 FvH4_5g37184 FvH4_5g37993 FvH4_5g38271 FvH4_6g00153 FvH4_6g00640 FvH4_6g05921 FvH4_6g08591 FvH4_6g09511 FvH4_6g10331 FvH4_6g10401 FvH4_6g14161 FvH4_6g14171 FvH4_6g18481 FvH4_6g19721 FvH4_6g19980 FvH4_6g20104 FvH4_6g20112 FvH4_6g21261 FvH4_6g21651 FvH4_6g22051 FvH4_6g23141 FvH4_6g24822 FvH4_6g25082 FvH4_6g25391 FvH4_6g25560 FvH4_6g26350 FvH4_6g27031 FvH4_6g27810 FvH4_6g27971 FvH4_6g28331 FvH4_6g29391 FvH4_6g30781 FvH4_6g32221 FvH4_6g34680 FvH4_6g36181 FvH4_6g36551 FvH4_6g37491 FvH4_6g37663 FvH4_6g39590 FvH4_6g40582 FvH4_6g43843 FvH4_6g50551 FvH4_7g00240 FvH4_7g00731 FvH4_7g01031 FvH4_7g03301 FvH4_7g08180 FvH4_7g08180 FvH4_7g10631 FvH4_7g19710 FvH4_7g23892 FvH4_7g25280 FvH4_7g25551 FvH4_7g30121 FvH4_7g31931 FvH4_7g32672 FvH4_c21g00040 FvH4_c2g00053
prunus_persica Prupe.1G448800_v2.0.a1
rosa_chinensis RchiOBHm_Chr1g0322451 RchiOBHm_Chr5g0015171
rosa_laevigata RLG00000003077 RLG00000018186 RLG00000030343
rosa_multiflora Rmu_co8096726.1_g000001
rosa_roxburghii Rroxscaffold_157G00438380 Rroxscaffold_1G00001730 Rroxscaffold_3G00236310
rosa_rugosa Rorug02G0236500
rosa_samantha Rh4BG247300 Rh6BG286200 Rh6CG287300 Rh7DG257500

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 446
AfaI GTAC 1 cut(s) 143
AfiI CCNNNNNNNGG 2 cut(s) 207, 557
AflIII ACRYGT 1 cut(s) 535
AgsI TTSAA 6 cut(s) 91, 295, 327, 338, 355, 592
AhdI GACNNNNNGTC 1 cut(s) 48
AjiI CACGTC 1 cut(s) 536
AjnI CCWGG 1 cut(s) 367
AleI CACNNNNGTG 1 cut(s) 203
AloI GAACNNNNNNTCC 2 cut(s) 144, 176
AluBI AGCT 2 cut(s) 239, 548
AluI AGCT 2 cut(s) 239, 548
Alw21I GWGCWC 1 cut(s) 304
Alw26I GTCTC 2 cut(s) 97, 526
AlwNI CAGNNNCTG 1 cut(s) 11
AoxI GGCC 1 cut(s) 330
ApeKI GCWGC 2 cut(s) 260, 545
AsuNHI GCTAGC 1 cut(s) 541
BbsI GAAGAC 2 cut(s) 69, 507
Bbv12I GWGCWC 1 cut(s) 304
BbvI GCAGC 2 cut(s) 247, 557
BccI CCATC 3 cut(s) 89, 112, 295
BciT130I CCWGG 1 cut(s) 369
BcoDI GTCTC 2 cut(s) 97, 526
BfaI CTAG 3 cut(s) 69, 305, 542
BisI GCNGC 2 cut(s) 261, 546
BlsI GCNGC 2 cut(s) 262, 547
Bme1390I CCNGG 1 cut(s) 369
BmeRI GACNNNNNGTC 1 cut(s) 48
BmgBI CACGTC 1 cut(s) 536
BmrFI CCNGG 1 cut(s) 369
BmsI GCATC 2 cut(s) 448, 469
BmtI GCTAGC 1 cut(s) 545
BpiI GAAGAC 2 cut(s) 69, 507
BpmI CTGGAG 1 cut(s) 591
BpuEI CTTGAG 1 cut(s) 512
BsaI GGTCTC 1 cut(s) 97
BsaXI ACNNNNNCTCC 2 cut(s) 211, 241
Bsc4I CCNNNNNNNGG 2 cut(s) 207, 557
Bse118I RCCGGY 1 cut(s) 263
Bse1I ACTGG 2 cut(s) 137, 574
BseBI CCWGG 1 cut(s) 369
BseGI GGATG 1 cut(s) 100
BseLI CCNNNNNNNGG 2 cut(s) 207, 557
BseNI ACTGG 2 cut(s) 137, 574
BseXI GCAGC 2 cut(s) 247, 557
BshFI GGCC 1 cut(s) 332
BsiHKAI GWGCWC 1 cut(s) 304
BsiSI CCGG 1 cut(s) 264
BslI CCNNNNNNNGG 2 cut(s) 207, 557
BsmAI GTCTC 2 cut(s) 97, 526
BsmBI CGTCTC 1 cut(s) 526
BsnI GGCC 1 cut(s) 332
Bso31I GGTCTC 1 cut(s) 97
Bsp1286I GDGCHC 1 cut(s) 304
Bsp1407I TGTACA 1 cut(s) 141
Bsp143I GATC 1 cut(s) 487
BspACI CCGC 1 cut(s) 446
BspANI GGCC 1 cut(s) 332
BspCNI CTCAG 1 cut(s) 4
BspHI TCATGA 1 cut(s) 528
BspOI GCTAGC 1 cut(s) 545
BspTNI GGTCTC 1 cut(s) 97
BsrFI RCCGGY 1 cut(s) 263
BsrGI TGTACA 1 cut(s) 141
BsrI ACTGG 2 cut(s) 137, 574
BssAI RCCGGY 1 cut(s) 263
BssMI GATC 1 cut(s) 487
Bst2UI CCWGG 1 cut(s) 369
Bst4CI ACNGT 1 cut(s) 205
Bst6I CTCTTC 1 cut(s) 325
BstAUI TGTACA 1 cut(s) 141
BstC8I GCNNGC 1 cut(s) 543
BstDEI CTNAG 1 cut(s) 12
BstF5I GGATG 1 cut(s) 100
BstKTI GATC 1 cut(s) 490
BstMAI GTCTC 2 cut(s) 97, 526
BstMBI GATC 1 cut(s) 487
BstNI CCWGG 1 cut(s) 369
BstNSI RCATGY 1 cut(s) 158
BstSCI CCNGG 1 cut(s) 367
BstV1I GCAGC 2 cut(s) 247, 557
BstV2I GAAGAC 2 cut(s) 69, 507
BsuRI GGCC 1 cut(s) 332
BtrI CACGTC 1 cut(s) 536
BtsCI GGATG 1 cut(s) 100
BtsIMutI CAGTG 2 cut(s) 144, 210
Cac8I GCNNGC 1 cut(s) 543
CaiI CAGNNNCTG 1 cut(s) 11
CciI TCATGA 1 cut(s) 528
Cfr10I RCCGGY 1 cut(s) 263
CsiI ACCWGGT 1 cut(s) 367
Csp6I GTAC 1 cut(s) 142
CviAII CATG 4 cut(s) 155, 376, 506, 529
CviJI RGCY 4 cut(s) 239, 260, 332, 548
CviKI_1 RGCY 4 cut(s) 239, 260, 332, 548
CviQI GTAC 1 cut(s) 142
DdeI CTNAG 1 cut(s) 12
DpnI GATC 1 cut(s) 489
DpnII GATC 1 cut(s) 487
DriI GACNNNNNGTC 1 cut(s) 48
Eam1104I CTCTTC 1 cut(s) 325
Eam1105I GACNNNNNGTC 1 cut(s) 48
EarI CTCTTC 1 cut(s) 325
Eco31I GGTCTC 1 cut(s) 97
Eco32I GATATC 1 cut(s) 383
EcoRII CCWGG 1 cut(s) 367
EcoRV GATATC 1 cut(s) 383
Esp3I CGTCTC 1 cut(s) 526
FaeI CATG 4 cut(s) 158, 379, 509, 532
FatI CATG 4 cut(s) 154, 375, 505, 528
FauI CCCGC 1 cut(s) 439
Fnu4HI GCNGC 2 cut(s) 261, 546
FokI GGATG 1 cut(s) 107
Fsp4HI GCNGC 2 cut(s) 261, 546
FspBI CTAG 3 cut(s) 69, 305, 542
GluI GCNGC 2 cut(s) 261, 546
GsuI CTGGAG 1 cut(s) 591
HaeIII GGCC 1 cut(s) 332
HapII CCGG 1 cut(s) 264
Hin1II CATG 4 cut(s) 158, 379, 509, 532
HinfI GANTC 8 cut(s) 49, 65, 127, 220, 308, 338, 400, 573
HpaII CCGG 1 cut(s) 264
Hpy166II GTNNAC 1 cut(s) 142
Hpy188I TCNGA 1 cut(s) 13
Hpy188III TCNNGA 3 cut(s) 69, 491, 529
Hpy8I GTNNAC 1 cut(s) 142
HpyCH4III ACNGT 1 cut(s) 205
HpyCH4IV ACGT 1 cut(s) 535
HpyCH4V TGCA 4 cut(s) 22, 83, 406, 482
HpyF3I CTNAG 1 cut(s) 12
HpySE526I ACGT 1 cut(s) 535
Hsp92II CATG 4 cut(s) 158, 379, 509, 532
Kzo9I GATC 1 cut(s) 487
LmnI GCTCC 1 cut(s) 553
Lsp1109I GCAGC 2 cut(s) 247, 557
LweI GCATC 2 cut(s) 448, 469
MabI ACCWGGT 1 cut(s) 367
MaeI CTAG 3 cut(s) 69, 305, 542
MaeII ACGT 1 cut(s) 535
MaeIII GTNAC 2 cut(s) 194, 371
MalI GATC 1 cut(s) 489
MboI GATC 1 cut(s) 487
MboII GAAGA 8 cut(s) 74, 194, 312, 315, 409, 440, 509, 512
MhlI GDGCHC 1 cut(s) 304
MluCI AATT 2 cut(s) 54, 584
MlyI GAGTC 4 cut(s) 58, 59, 229, 582
MnlI CCTC 6 cut(s) 201, 250, 328, 418, 487, 532
MseI TTAA 1 cut(s) 38
MslI CAYNNNNRTG 2 cut(s) 116, 203
MspI CCGG 1 cut(s) 264
MspR9I CCNGG 1 cut(s) 369
MvaI CCWGG 1 cut(s) 369
NdeII GATC 1 cut(s) 487
NheI GCTAGC 1 cut(s) 541
NlaIII CATG 4 cut(s) 158, 379, 509, 532
NmuCI GTSAC 1 cut(s) 371
NspI RCATGY 1 cut(s) 158
OliI CACNNNNGTG 1 cut(s) 203
PagI TCATGA 1 cut(s) 528
PfeI GAWTC 4 cut(s) 127, 308, 338, 400
PkrI GCNGC 2 cut(s) 262, 547
PleI GAGTC 4 cut(s) 57, 59, 228, 581
PpsI GAGTC 4 cut(s) 57, 59, 228, 581
Psp6I CCWGG 1 cut(s) 367
PspGI CCWGG 1 cut(s) 367
PstNI CAGNNNCTG 1 cut(s) 11
RsaI GTAC 1 cut(s) 143
RsaNI GTAC 1 cut(s) 142
RseI CAYNNNNRTG 2 cut(s) 116, 203
SaqAI TTAA 1 cut(s) 38
SatI GCNGC 2 cut(s) 261, 546
Sau3AI GATC 1 cut(s) 487
SchI GAGTC 4 cut(s) 58, 59, 229, 582
ScrFI CCNGG 1 cut(s) 369
SduI GDGCHC 1 cut(s) 304
SetI ASST 6 cut(s) 89, 109, 241, 373, 538, 550
SexAI ACCWGGT 1 cut(s) 367
SfaNI GCATC 2 cut(s) 448, 469
SmiMI CAYNNNNRTG 2 cut(s) 116, 203
SmlI CTYRAG 1 cut(s) 491
SmoI CTYRAG 1 cut(s) 491
Sse9I AATT 2 cut(s) 54, 584
SsiI CCGC 1 cut(s) 446
SspI AATATT 2 cut(s) 188, 251
SspMI CTAG 3 cut(s) 69, 305, 542
StyD4I CCNGG 1 cut(s) 367
TaaI ACNGT 1 cut(s) 205
TaiI ACGT 1 cut(s) 538
TaqI TCGA 3 cut(s) 130, 298, 576
TasI AATT 2 cut(s) 54, 584
TatI WGTACW 1 cut(s) 141
TfiI GAWTC 4 cut(s) 127, 308, 338, 400
Tru1I TTAA 1 cut(s) 38
Tru9I TTAA 1 cut(s) 38
TscAI CASTG 2 cut(s) 144, 210
TseFI GTSAC 1 cut(s) 371
TseI GCWGC 2 cut(s) 260, 545
Tsp45I GTSAC 1 cut(s) 371
TspRI CASTG 2 cut(s) 144, 210
XbaI TCTAGA 1 cut(s) 68
XceI RCATGY 1 cut(s) 158
XspI CTAG 3 cut(s) 69, 305, 542
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.