FvH4_5g22952

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0017469
Physical Location & Seq
Forward (+)
14274328 .. 14275110
783 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g22952.t1

Sequence Viewer

Length: 438 bp
ATGAGTGATGGCTTCATGGAGTCAATGAGCAAACTCTTTACTCTCTCATTCTCTGTGGCCCAAGTTTCAAATTCAGTCGAATTCTCATCTGATGCGACTTTGGCTCTAGTGAGAGCTGTAGAAGCTCGCGCTGCTCCTATGGCGAATAAAAACAACTCCAACTCTAATATGATATCACTCATTCCTCGTTTCAATGGTGAGAAGTATGATTATTGGAGCAAGAATGTCAAGGTATTGTTGAAGTCCCTGGAGATATGGAACGTTGTCGAAGAAGGATACGTCGAACCGGAGAATGAAGGTGCTTTAACACAACAACAGAGGAATGCTTTGAAGGAGAATCGAAAGAAGGATAGCAAGGCACTCTTCTATATCTACCAGACAATTCAAGAGTCTGTGTATGAAAGAATTGCTCAAGCTGAGACGTCCAAGGAAGCCTAG
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
DUF4219 Retrotran_gag_2 zf-CCHC

Protein Analysis

146

Amino Acids

16.43

Weight (kDa)

5.32

Isoelectric Point (pI)

31.49

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 77 - 145 1.4e-06 gag-polypeptide of LTR copia-type
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: OG0017469)

Species Orthologous Gene IDs
fragaria_vesca FvH4_5g22952
malus_domestica MD03G1249400.v1.1 MD12G1162500.v1.1
prunus_persica Prupe.3G159700_v2.0.a1 Prupe.8G004800_v2.0.a1
pyrus_communis pycom01g01870 pycom01g13710 pycom15g18800 pycom420g01040
rosa_roxburghii Rroxscaffold_4G00320150 Rroxscaffold_7G00185690
rosa_wichuraiana Rw5G007100

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 425
AccII CGCG 1 cut(s) 129
AclI AACGTT 1 cut(s) 261
AcsI RAATTY 2 cut(s) 70, 80
AcyI GRCGYC 1 cut(s) 422
AgsI TTSAA 5 cut(s) 69, 193, 241, 331, 386
AjnI CCWGG 1 cut(s) 246
AluBI AGCT 3 cut(s) 116, 125, 416
AluI AGCT 3 cut(s) 116, 125, 416
Alw26I GTCTC 1 cut(s) 413
AoxI GGCC 1 cut(s) 57
ApeKI GCWGC 1 cut(s) 131
ApoI RAATTY 2 cut(s) 70, 80
AspLEI GCGC 1 cut(s) 131
AspS9I GGNCC 1 cut(s) 58
AsuHPI GGTGA 1 cut(s) 209
BbvI GCAGC 1 cut(s) 118
BccI CCATC 1 cut(s) 2
BciT130I CCWGG 1 cut(s) 248
BciVI GTATCC 1 cut(s) 269
BcoDI GTCTC 1 cut(s) 413
BfaI CTAG 2 cut(s) 107, 436
BfmI CTRYAG 1 cut(s) 117
BfuI GTATCC 1 cut(s) 269
BisI GCNGC 1 cut(s) 132
BlsI GCNGC 1 cut(s) 133
Bme1390I CCNGG 1 cut(s) 248
BmgT120I GGNCC 1 cut(s) 58
BmrFI CCNGG 1 cut(s) 248
BmsI GCATC 1 cut(s) 82
BpmI CTGGAG 1 cut(s) 269
BpuEI CTTGAG 1 cut(s) 396
BsaHI GRCGYC 1 cut(s) 422
BsaJI CCNNGG 2 cut(s) 246, 426
BsaWI WCCGGW 1 cut(s) 286
BseBI CCWGG 1 cut(s) 248
BseDI CCNNGG 2 cut(s) 246, 426
BseMII CTCAG 1 cut(s) 408
BseXI GCAGC 1 cut(s) 118
Bsh1236I CGCG 1 cut(s) 129
BshFI GGCC 1 cut(s) 59
BsiSI CCGG 1 cut(s) 287
BslFI GGGAC 1 cut(s) 229
BsmAI GTCTC 1 cut(s) 413
BsmBI CGTCTC 1 cut(s) 413
BsmFI GGGAC 1 cut(s) 229
BsmI GAATGC 1 cut(s) 328
BsnI GGCC 1 cut(s) 59
BspANI GGCC 1 cut(s) 59
BspCNI CTCAG 1 cut(s) 409
BspFNI CGCG 1 cut(s) 129
BssECI CCNNGG 2 cut(s) 246, 426
BssNI GRCGYC 1 cut(s) 422
BssT1I CCWWGG 1 cut(s) 426
Bst2UI CCWGG 1 cut(s) 248
Bst6I CTCTTC 1 cut(s) 368
BstACI GRCGYC 1 cut(s) 422
BstC8I GCNNGC 1 cut(s) 127
BstDEI CTNAG 1 cut(s) 417
BstFNI CGCG 1 cut(s) 129
BstHHI GCGC 1 cut(s) 131
BstMAI GTCTC 1 cut(s) 413
BstMWI GCNNNNNNNGC 4 cut(s) 101, 122, 131, 140
BstNI CCWGG 1 cut(s) 248
BstSCI CCNGG 1 cut(s) 246
BstSFI CTRYAG 1 cut(s) 117
BstUI CGCG 1 cut(s) 129
BstV1I GCAGC 1 cut(s) 118
BsuI GTATCC 1 cut(s) 269
BsuRI GGCC 1 cut(s) 59
Cac8I GCNNGC 1 cut(s) 127
CfoI GCGC 1 cut(s) 131
Cfr13I GGNCC 1 cut(s) 58
CviAII CATG 1 cut(s) 16
CviJI RGCY 7 cut(s) 12, 59, 104, 116, 125, 416, 434
CviKI_1 RGCY 7 cut(s) 12, 59, 104, 116, 125, 416, 434
DdeI CTNAG 1 cut(s) 417
Eam1104I CTCTTC 1 cut(s) 368
EarI CTCTTC 1 cut(s) 368
Eco130I CCWWGG 1 cut(s) 426
Eco32I GATATC 1 cut(s) 174
EcoRI GAATTC 1 cut(s) 80
EcoRII CCWGG 1 cut(s) 246
EcoRV GATATC 1 cut(s) 174
EcoT14I CCWWGG 1 cut(s) 426
ErhI CCWWGG 1 cut(s) 426
Esp3I CGTCTC 1 cut(s) 413
FaeI CATG 1 cut(s) 19
FaiI YATR 7 cut(s) 17, 140, 170, 207, 256, 369, 399
FalI AAGNNNNNCTT 2 cut(s) 347, 379
FaqI GGGAC 1 cut(s) 229
FatI CATG 1 cut(s) 15
Fnu4HI GCNGC 1 cut(s) 132
Fsp4HI GCNGC 1 cut(s) 132
FspBI CTAG 2 cut(s) 107, 436
GlaI GCGC 1 cut(s) 130
GluI GCNGC 1 cut(s) 132
GsuI CTGGAG 1 cut(s) 269
HaeIII GGCC 1 cut(s) 59
HapII CCGG 1 cut(s) 287
HhaI GCGC 1 cut(s) 131
Hin1I GRCGYC 1 cut(s) 422
Hin1II CATG 1 cut(s) 19
Hin6I GCGC 1 cut(s) 129
HinP1I GCGC 1 cut(s) 129
HinfI GANTC 3 cut(s) 20, 337, 389
HpaII CCGG 1 cut(s) 287
HphI GGTGA 1 cut(s) 209
Hpy188I TCNGA 1 cut(s) 91
Hpy188III TCNNGA 1 cut(s) 386
Hpy99I CGWCG 1 cut(s) 284
HpyAV CCTTC 4 cut(s) 266, 290, 325, 340
HpyCH4IV ACGT 3 cut(s) 261, 279, 422
HpyF10VI GCNNNNNNNGC 4 cut(s) 101, 122, 131, 140
HpyF3I CTNAG 1 cut(s) 417
HpySE526I ACGT 3 cut(s) 261, 279, 422
Hsp92I GRCGYC 1 cut(s) 422
Hsp92II CATG 1 cut(s) 19
HspAI GCGC 1 cut(s) 129
LmnI GCTCC 2 cut(s) 139, 216
LpnPI CCDG 4 cut(s) 233, 260, 300, 389
Lsp1109I GCAGC 1 cut(s) 118
LweI GCATC 1 cut(s) 82
MaeI CTAG 2 cut(s) 107, 436
MaeII ACGT 3 cut(s) 261, 279, 422
MboII GAAGA 2 cut(s) 281, 355
MluCI AATT 4 cut(s) 70, 80, 381, 405
MlyI GAGTC 2 cut(s) 29, 398
MmeI TCCRAC 1 cut(s) 183
MnlI CCTC 2 cut(s) 195, 312
MseI TTAA 1 cut(s) 305
MspI CCGG 1 cut(s) 287
MspR9I CCNGG 1 cut(s) 248
Mva1269I GAATGC 1 cut(s) 328
MvaI CCWGG 1 cut(s) 248
MvnI CGCG 1 cut(s) 129
MwoI GCNNNNNNNGC 4 cut(s) 101, 122, 131, 140
NlaIII CATG 1 cut(s) 19
PctI GAATGC 1 cut(s) 328
PfeI GAWTC 1 cut(s) 337
PkrI GCNGC 1 cut(s) 133
PleI GAGTC 2 cut(s) 28, 397
PpsI GAGTC 2 cut(s) 28, 397
Psp1406I AACGTT 1 cut(s) 261
Psp6I CCWGG 1 cut(s) 246
PspGI CCWGG 1 cut(s) 246
PspPI GGNCC 1 cut(s) 58
SaqAI TTAA 1 cut(s) 305
SatI GCNGC 1 cut(s) 132
Sau96I GGNCC 1 cut(s) 58
SchI GAGTC 2 cut(s) 29, 398
ScrFI CCNGG 1 cut(s) 248
SetI ASST 8 cut(s) 118, 127, 234, 264, 282, 301, 418, 425
SfaNI GCATC 1 cut(s) 82
SfcI CTRYAG 1 cut(s) 117
SmlI CTYRAG 1 cut(s) 411
SmoI CTYRAG 1 cut(s) 411
Sse9I AATT 4 cut(s) 70, 80, 381, 405
SspMI CTAG 2 cut(s) 107, 436
StyD4I CCNGG 1 cut(s) 246
StyI CCWWGG 1 cut(s) 426
TaiI ACGT 3 cut(s) 264, 282, 425
TaqI TCGA 4 cut(s) 78, 267, 282, 340
TasI AATT 4 cut(s) 70, 80, 381, 405
TfiI GAWTC 1 cut(s) 337
Tru1I TTAA 1 cut(s) 305
Tru9I TTAA 1 cut(s) 305
TseI GCWGC 1 cut(s) 131
TspDTI ATGAA 3 cut(s) 4, 309, 414
XapI RAATTY 2 cut(s) 70, 80
XspI CTAG 2 cut(s) 107, 436
ZraI GACGTC 1 cut(s) 423
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.