FvH4_3g28463

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000370
Physical Location & Seq
Reverse (-)
21453349 .. 21454067
719 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g28463.t1

Sequence Viewer

Length: 498 bp
ATGATGGAAGCTGGGAGCCGAAGTAATGTGGAGTTTGGTAACAACTCTGGAGTAATTGCGGCCATTCAAGAGATGGCTATGTTCAAAGGGAGCACAGACCCAATGATTGCAGAAGAATGGGTACGGCAGATGAAAAGGAGTTTGACGAATAAGAGGATTCCTGACGATTTGCAACGTCGTCTGAAAGCTAAGGAGTTCTCCACTCTTCTACAAATGAAAATGCACGTGGGAGATTATCAAGCTAAGTTTGAGGAGTTAATGCGTTTTGTACCTGAGCTTGTGCCAGATGACTATGCTAAAGCAAGGCGTTTTGAGGAGGGTCTGAGACTTTCACTTAAAGAGAAAGTAGTAATGCTCAAGCTTGATAGGTACATTGATGTAGTCGAACGCGCTCTTATGGCTGAACAGATGGTACAAGAATCGAAAGAAAATTGGGAAGTTACTAGTGGAGGTGGATCCAGACCAAGTAATAAACATCAACGACCTAATCCTCCTTGA
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

166

Amino Acids

19.06

Weight (kDa)

8.83

Isoelectric Point (pI)

54.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 42 - 109 7.5e-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
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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)
AccII CGCG 1 cut(s) 390
AciI CCGC 1 cut(s) 59
AclWI GGATC 2 cut(s) 450, 463
AcoI YGGCCR 1 cut(s) 60
AcvI CACGTG 1 cut(s) 226
AfaI GTAC 4 cut(s) 123, 270, 371, 414
AgsI TTSAA 2 cut(s) 68, 85
AhlI ACTAGT 1 cut(s) 443
AluBI AGCT 5 cut(s) 11, 188, 242, 277, 361
AluI AGCT 5 cut(s) 11, 188, 242, 277, 361
Alw21I GWGCWC 1 cut(s) 95
Alw26I GTCTC 1 cut(s) 319
AlwI GGATC 2 cut(s) 450, 463
AoxI GGCC 1 cut(s) 60
AspLEI GCGC 1 cut(s) 392
BamHI GGATCC 1 cut(s) 455
BarI GAAGNNNNNNTAC 2 cut(s) 105, 137
BbrPI CACGTG 1 cut(s) 226
Bbv12I GWGCWC 1 cut(s) 95
BccI CCATC 2 cut(s) 67, 403
BceAI ACGGC 1 cut(s) 140
BcoDI GTCTC 1 cut(s) 319
BcuI ACTAGT 1 cut(s) 443
BfaI CTAG 1 cut(s) 444
BisI GCNGC 1 cut(s) 60
BlsI GCNGC 1 cut(s) 61
BmiI GGNNCC 2 cut(s) 17, 457
BpmI CTGGAG 1 cut(s) 69
Bpu10I CCTNAGC 2 cut(s) 189, 273
BpuEI CTTGAG 1 cut(s) 341
BsaAI YACGTR 1 cut(s) 226
BsaXI ACNNNNNCTCC 2 cut(s) 7, 37
BseMII CTCAG 2 cut(s) 264, 314
BseRI GAGGAG 2 cut(s) 266, 329
BseYI CCCAGC 1 cut(s) 11
Bsh1236I CGCG 1 cut(s) 390
BshFI GGCC 1 cut(s) 62
BsiHKAI GWGCWC 1 cut(s) 95
BsmAI GTCTC 1 cut(s) 319
BsnI GGCC 1 cut(s) 62
Bsp1286I GDGCHC 1 cut(s) 95
Bsp143I GATC 1 cut(s) 455
BspACI CCGC 1 cut(s) 59
BspANI GGCC 1 cut(s) 62
BspCNI CTCAG 2 cut(s) 265, 315
BspFNI CGCG 1 cut(s) 390
BspLI GGNNCC 2 cut(s) 17, 457
BspPI GGATC 2 cut(s) 450, 463
BssMI GATC 1 cut(s) 455
Bst6I CTCTTC 1 cut(s) 210
BstBAI YACGTR 1 cut(s) 226
BstDEI CTNAG 4 cut(s) 189, 243, 273, 323
BstFNI CGCG 1 cut(s) 390
BstHHI GCGC 1 cut(s) 392
BstKTI GATC 1 cut(s) 458
BstMAI GTCTC 1 cut(s) 319
BstMBI GATC 1 cut(s) 455
BstMWI GCNNNNNNNGC 1 cut(s) 398
BstUI CGCG 1 cut(s) 390
BstX2I RGATCY 1 cut(s) 455
BstYI RGATCY 1 cut(s) 455
BsuRI GGCC 1 cut(s) 62
CfoI GCGC 1 cut(s) 392
Csp6I GTAC 4 cut(s) 122, 269, 370, 413
CviJI RGCY 9 cut(s) 11, 18, 62, 77, 188, 242, 277, 361, 401
CviKI_1 RGCY 9 cut(s) 11, 18, 62, 77, 188, 242, 277, 361, 401
CviQI GTAC 4 cut(s) 122, 269, 370, 413
DdeI CTNAG 4 cut(s) 189, 243, 273, 323
DpnI GATC 1 cut(s) 457
DpnII GATC 1 cut(s) 455
EaeI YGGCCR 1 cut(s) 60
Eam1104I CTCTTC 1 cut(s) 210
EarI CTCTTC 1 cut(s) 210
Eco72I CACGTG 1 cut(s) 226
FaiI YATR 3 cut(s) 80, 294, 398
Fnu4HI GCNGC 1 cut(s) 60
Fsp4HI GCNGC 1 cut(s) 60
FspBI CTAG 1 cut(s) 444
GlaI GCGC 1 cut(s) 391
GluI GCNGC 1 cut(s) 60
GsaI CCCAGC 1 cut(s) 15
GsuI CTGGAG 1 cut(s) 69
HaeIII GGCC 1 cut(s) 62
HhaI GCGC 1 cut(s) 392
Hin6I GCGC 1 cut(s) 390
HinP1I GCGC 1 cut(s) 390
HindIII AAGCTT 1 cut(s) 359
HinfI GANTC 2 cut(s) 157, 419
Hpy188I TCNGA 2 cut(s) 183, 324
Hpy188III TCNNGA 4 cut(s) 48, 68, 161, 459
Hpy99I CGWCG 1 cut(s) 180
HpyCH4IV ACGT 2 cut(s) 175, 225
HpyCH4V TGCA 3 cut(s) 110, 172, 223
HpyF10VI GCNNNNNNNGC 1 cut(s) 398
HpyF3I CTNAG 4 cut(s) 189, 243, 273, 323
HpySE526I ACGT 2 cut(s) 175, 225
HspAI GCGC 1 cut(s) 390
Kzo9I GATC 1 cut(s) 455
LmnI GCTCC 2 cut(s) 15, 90
LpnPI CCDG 5 cut(s) 33, 174, 285, 297, 472
MaeI CTAG 1 cut(s) 444
MaeII ACGT 2 cut(s) 175, 225
MaeIII GTNAC 2 cut(s) 38, 439
MalI GATC 1 cut(s) 457
MboI GATC 1 cut(s) 455
MboII GAAGA 2 cut(s) 125, 197
MflI RGATCY 1 cut(s) 455
MhlI GDGCHC 1 cut(s) 95
MluCI AATT 2 cut(s) 54, 430
MnlI CCTC 5 cut(s) 147, 244, 307, 310, 443
MseI TTAA 2 cut(s) 257, 336
MvnI CGCG 1 cut(s) 390
MwoI GCNNNNNNNGC 1 cut(s) 398
NdeII GATC 1 cut(s) 455
NlaIV GGNNCC 2 cut(s) 17, 457
PfeI GAWTC 2 cut(s) 157, 419
PkrI GCNGC 1 cut(s) 61
PmaCI CACGTG 1 cut(s) 226
PmlI CACGTG 1 cut(s) 226
Ppu21I YACGTR 1 cut(s) 226
PspCI CACGTG 1 cut(s) 226
PspFI CCCAGC 1 cut(s) 11
PspN4I GGNNCC 2 cut(s) 17, 457
PsrI GAACNNNNNNTAC 2 cut(s) 396, 428
PsuI RGATCY 1 cut(s) 455
RsaI GTAC 4 cut(s) 123, 270, 371, 414
RsaNI GTAC 4 cut(s) 122, 269, 370, 413
SaqAI TTAA 2 cut(s) 257, 336
SatI GCNGC 1 cut(s) 60
Sau3AI GATC 1 cut(s) 455
SduI GDGCHC 1 cut(s) 95
SmlI CTYRAG 1 cut(s) 356
SmoI CTYRAG 1 cut(s) 356
SpeI ACTAGT 1 cut(s) 443
Sse9I AATT 2 cut(s) 54, 430
SsiI CCGC 1 cut(s) 59
SspMI CTAG 1 cut(s) 444
TaiI ACGT 2 cut(s) 178, 228
TaqI TCGA 2 cut(s) 384, 422
TasI AATT 2 cut(s) 54, 430
TauI GCSGC 1 cut(s) 62
TfiI GAWTC 2 cut(s) 157, 419
Tru1I TTAA 2 cut(s) 257, 336
Tru9I TTAA 2 cut(s) 257, 336
TspDTI ATGAA 2 cut(s) 146, 230
XcmI CCANNNNNNNNNTGG 1 cut(s) 70
XspI CTAG 1 cut(s) 444
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.