FvH4_3g31691

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000370
Physical Location & Seq
Forward (+)
26198240 .. 26198849
610 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g31691.t1

Sequence Viewer

Length: 504 bp
ATGGCTGAAGAACAACATAAGGGAGAGGTCAGTAGCAGTATAGATGTTGTAGATGCTATTCAGGATATGGCAAGTGTGATAAGAGAAAATCGCAATGGTAATCATCTAGAGGATAGTGAAGAGCGGGTTATGAGGATACAAGGAGAATTTCGCAAAGCCCGACCTCCCATGTTTAAGGGTGCCTTAGACCCCATGATAGCTGAAGAATGGCTAAGACAAATGAAGAGAACTTTGAATAATCAAAAGGTGCCAGAGGACTTGAAAGTTATTGTTGCTTGCACATATCTGGAAAGTGCAGTTTATCACTGGTGGGAATCAGTTCTTGCTACTCCAGATACTGATATTACTACCTGGAGTGCATTTGAAGCGATCTTTCTTGAGAAATATTTTCCAGACACAGTTAAGCAAGCCAAAGCTAAAGAGTTTATGTTTTTATCTAAAGGGGAAATGACAGTGGCTGAATATCAAGGCAGATTTGAAGAGCTGATAAATATTCTGAAGTAG
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

168

Amino Acids

19.38

Weight (kDa)

5.0

Isoelectric Point (pI)

37.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 92 - 164 2.9e-12 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)
AccB1I GGYRCC 2 cut(s) 179, 247
AccBSI CCGCTC 1 cut(s) 124
AciI CCGC 1 cut(s) 124
AcsI RAATTY 1 cut(s) 146
AcuI CTGAAG 2 cut(s) 27, 222
AgsI TTSAA 4 cut(s) 235, 262, 365, 479
AjnI CCWGG 1 cut(s) 350
AluBI AGCT 3 cut(s) 200, 416, 484
AluI AGCT 3 cut(s) 200, 416, 484
AlwNI CAGNNNCTG 2 cut(s) 338, 458
ApoI RAATTY 1 cut(s) 146
Asp700I GAANNNNTTC 1 cut(s) 318
BanI GGYRCC 2 cut(s) 179, 247
BciT130I CCWGG 1 cut(s) 352
BciVI GTATCC 1 cut(s) 129
BfaI CTAG 1 cut(s) 107
BfuI GTATCC 1 cut(s) 129
Bme1390I CCNGG 1 cut(s) 352
BmiI GGNNCC 2 cut(s) 181, 249
BmrFI CCNGG 1 cut(s) 352
BmsI GCATC 1 cut(s) 43
BpmI CTGGAG 2 cut(s) 315, 373
BpuEI CTTGAG 1 cut(s) 398
Bse1I ACTGG 1 cut(s) 311
Bse3DI GCAATG 1 cut(s) 100
BseBI CCWGG 1 cut(s) 352
BseMI GCAATG 1 cut(s) 100
BseNI ACTGG 1 cut(s) 311
BsgI GTGCAG 1 cut(s) 315
BshNI GGYRCC 2 cut(s) 179, 247
Bsp143I GATC 1 cut(s) 369
BspACI CCGC 1 cut(s) 124
BspLI GGNNCC 2 cut(s) 181, 249
BspQI GCTCTTC 2 cut(s) 114, 474
BspT107I GGYRCC 2 cut(s) 179, 247
BsrBI CCGCTC 1 cut(s) 124
BsrDI GCAATG 1 cut(s) 100
BsrI ACTGG 1 cut(s) 311
BssMI GATC 1 cut(s) 369
Bst2UI CCWGG 1 cut(s) 352
Bst4CI ACNGT 2 cut(s) 400, 454
Bst6I CTCTTC 3 cut(s) 114, 218, 474
BstC8I GCNNGC 2 cut(s) 277, 408
BstDEI CTNAG 2 cut(s) 184, 212
BstKTI GATC 1 cut(s) 372
BstMBI GATC 1 cut(s) 369
BstMWI GCNNNNNNNGC 1 cut(s) 365
BstNI CCWGG 1 cut(s) 352
BstSCI CCNGG 1 cut(s) 350
BsuI GTATCC 1 cut(s) 129
BtsIMutI CAGTG 2 cut(s) 304, 459
Cac8I GCNNGC 2 cut(s) 277, 408
CaiI CAGNNNCTG 2 cut(s) 338, 458
CviAII CATG 2 cut(s) 169, 193
CviJI RGCY 8 cut(s) 5, 158, 200, 211, 410, 416, 458, 484
CviKI_1 RGCY 8 cut(s) 5, 158, 200, 211, 410, 416, 458, 484
DdeI CTNAG 2 cut(s) 184, 212
DpnI GATC 1 cut(s) 371
DpnII GATC 1 cut(s) 369
Eam1104I CTCTTC 3 cut(s) 114, 218, 474
EarI CTCTTC 3 cut(s) 114, 218, 474
Eco57I CTGAAG 2 cut(s) 27, 222
EcoRII CCWGG 1 cut(s) 350
FaeI CATG 2 cut(s) 172, 196
FaiI YATR 8 cut(s) 18, 41, 68, 131, 170, 194, 283, 428
FalI AAGNNNNNCTT 2 cut(s) 167, 199
FatI CATG 2 cut(s) 168, 192
FauI CCCGC 1 cut(s) 117
FspBI CTAG 1 cut(s) 107
GsuI CTGGAG 2 cut(s) 315, 373
Hin1II CATG 2 cut(s) 172, 196
HinfI GANTC 1 cut(s) 314
Hpy188I TCNGA 1 cut(s) 498
Hpy188III TCNNGA 6 cut(s) 62, 107, 287, 332, 377, 392
HpyCH4III ACNGT 2 cut(s) 400, 454
HpyCH4V TGCA 3 cut(s) 279, 296, 359
HpyF10VI GCNNNNNNNGC 1 cut(s) 365
HpyF3I CTNAG 2 cut(s) 184, 212
Hsp92II CATG 2 cut(s) 172, 196
Kzo9I GATC 1 cut(s) 369
LguI GCTCTTC 2 cut(s) 114, 474
LpnPI CCDG 8 cut(s) 47, 264, 272, 292, 337, 345, 364, 405
LweI GCATC 1 cut(s) 43
MaeI CTAG 1 cut(s) 107
MalI GATC 1 cut(s) 371
MbiI CCGCTC 1 cut(s) 124
MboI GATC 1 cut(s) 369
MboII GAAGA 5 cut(s) 20, 131, 215, 235, 491
MluCI AATT 1 cut(s) 146
MnlI CCTC 5 cut(s) 19, 103, 126, 174, 247
MroXI GAANNNNTTC 1 cut(s) 318
MseI TTAA 2 cut(s) 174, 402
MspR9I CCNGG 1 cut(s) 352
MvaI CCWGG 1 cut(s) 352
MwoI GCNNNNNNNGC 1 cut(s) 365
NdeII GATC 1 cut(s) 369
NlaIII CATG 2 cut(s) 172, 196
NlaIV GGNNCC 2 cut(s) 181, 249
PciSI GCTCTTC 2 cut(s) 114, 474
PcsI WCGNNNNNNNCGW 1 cut(s) 157
PdmI GAANNNNTTC 1 cut(s) 318
PfeI GAWTC 1 cut(s) 314
Psp6I CCWGG 1 cut(s) 350
PspGI CCWGG 1 cut(s) 350
PspN4I GGNNCC 2 cut(s) 181, 249
PstNI CAGNNNCTG 2 cut(s) 338, 458
SapI GCTCTTC 2 cut(s) 114, 474
SaqAI TTAA 2 cut(s) 174, 402
Sau3AI GATC 1 cut(s) 369
ScrFI CCNGG 1 cut(s) 352
SetI ASST 7 cut(s) 30, 166, 202, 249, 353, 418, 486
SfaNI GCATC 1 cut(s) 43
SmlI CTYRAG 1 cut(s) 377
SmoI CTYRAG 1 cut(s) 377
Sse9I AATT 1 cut(s) 146
SsiI CCGC 1 cut(s) 124
SspI AATATT 2 cut(s) 386, 493
SspMI CTAG 1 cut(s) 107
StyD4I CCNGG 1 cut(s) 350
TaaI ACNGT 2 cut(s) 400, 454
TasI AATT 1 cut(s) 146
TfiI GAWTC 1 cut(s) 314
Tru1I TTAA 2 cut(s) 174, 402
Tru9I TTAA 2 cut(s) 174, 402
TscAI CASTG 2 cut(s) 311, 459
TspDTI ATGAA 1 cut(s) 236
TspRI CASTG 2 cut(s) 311, 459
XapI RAATTY 1 cut(s) 146
XbaI TCTAGA 1 cut(s) 106
XmnI GAANNNNTTC 1 cut(s) 318
XspI CTAG 1 cut(s) 107
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.