FvH4_6g29471

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000278
Physical Location & Seq
Reverse (-)
22768683 .. 22769075
393 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g29471.t1

Sequence Viewer

Length: 393 bp
ATGAAGTGCAGGGATGGTCTAAGTGTTTCGGAACACTTGAGTGACTTCCAAGGCATGGTGCTTGATGATGAGTTGCAAGCACTATTGTTACTAAGCTCGTTGTCATACAGCTGGGACACGTTGGTGGTGTCATTGAGTAACTCAGCTCCTCAAGGCGTTCTCACACTGAGCACTATAAAAGACAACATGTTCCACGAAGAAGCAAGGAGGAAGGAGCAAGGAATATTGACCGAGTTAGAAGCCCTTGTCATCAACAACAGTGGAAGCAGCAAACAGTTCCACAACCGAGGCAAAACGGAAGACCGGTCAAGAGGCAAGTTTAGCCTGAAGGACATCGAATGTTTTCATTGTGATGAAAAGAACCACATGAAGAGGGATTGTAAAGTGCTCTAG
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
Retrotran_gag_2 zf-CCHC

Protein Analysis

131

Amino Acids

14.73

Weight (kDa)

5.93

Isoelectric Point (pI)

44.71

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 2 - 73 3.9e-07 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: OG0000278)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G29785
fragaria_vesca FvH4_1g10046 FvH4_1g17351 FvH4_1g18441 FvH4_1g24222 FvH4_2g00141 FvH4_2g05931 FvH4_2g06671 FvH4_2g14030 FvH4_2g15291 FvH4_2g22611 FvH4_2g22612 FvH4_2g26380 FvH4_2g39202 FvH4_2g39202 FvH4_3g06691 FvH4_3g08580 FvH4_3g20502 FvH4_3g20503 FvH4_3g22421 FvH4_3g42580 FvH4_4g02061 FvH4_4g06794 FvH4_4g08661 FvH4_4g11771 FvH4_4g14601 FvH4_4g14721 FvH4_4g20921 FvH4_4g33601 FvH4_4g33602 FvH4_5g07492 FvH4_5g20321 FvH4_5g21591 FvH4_5g30343 FvH4_5g37875 FvH4_6g04372 FvH4_6g04373 FvH4_6g04373 FvH4_6g21377 FvH4_6g23760 FvH4_6g29471 FvH4_6g43142 FvH4_7g14351 FvH4_7g14352 FvH4_7g22582 FvH4_7g22583 FvH4_7g22584
malus_domestica MD00G1179400.v1.1 MD01G1170500.v1.1 MD03G1286700.v1.1 MD04G1054600.v1.1 MD04G1071700.v1.1 MD04G1193900.v1.1 MD08G1054300.v1.1 MD08G1217500.v1.1 MD09G1034600.v1.1 MD09G1098100.v1.1 MD10G1018300.v1.1 MD10G1220000.v1.1 MD10G1250300.v1.1 MD12G1014400.v1.1 MD15G1021000.v1.1 MD16G1112200.v1.1
prunus_persica Prupe.1G188900_v2.0.a1 Prupe.1G258000_v2.0.a1 Prupe.4G233400_v2.0.a1
pyrus_communis pycom01g10100 pycom02g01340 pycom03g19700 pycom05g01320 pycom07g16000 pycom07g16520 pycom11g26500 pycom13g09380 pycom13g13960 pycom14g08180 pycom14g16810 pycom16g09590
rosa_chinensis RchiOBHm_Chr1g0319891 RchiOBHm_Chr1g0333711 RchiOBHm_Chr2g0115331 RchiOBHm_Chr2g0143411 RchiOBHm_Chr2g0167631 RchiOBHm_Chr3g0448581 RchiOBHm_Chr3g0494991 RchiOBHm_Chr4g0442471 RchiOBHm_Chr6g0262311 RchiOBHm_Chr6g0301831 RchiOBHm_Chr6g0301841 RchiOBHm_Chr7g0183451
rosa_roxburghii Rroxscaffold_1G00039280 Rroxscaffold_1G00047670 Rroxscaffold_1G00066330 Rroxscaffold_2G00107510 Rroxscaffold_3G00255410 Rroxscaffold_4G00301460 Rroxscaffold_5G00352730 Rroxscaffold_7G00166350 Rroxscaffold_7G00166360 Rroxscaffold_7G00203820
rosa_rugosa Rorug03G0240500 Rorug05G0191700 Rorug06G0310200
rosa_samantha Rh2BG287000 Rh4CG073500 Rh4CG176200 Rh4CG191400 Rh5BG356100 Rh5BG434100 Rh6AG110600 Rh6AG421900 Rh6AG422000 Rh6AG422100 Rh6BG428600 Rh6BG428700 Rh6BG428800 Rh6CG435200 Rh6CG435300 Rh6CG435400 Rh6DG422000 Rh6DG422100 Rh6DG422200 Rh7BG190500 Rh7CG172800 Rh7CG225200
rosa_wichuraiana Rw2G044060 Rw6G036540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 55
AcuI CTGAAG 1 cut(s) 347
AfiI CCNNNNNNNGG 1 cut(s) 55
AflIII ACRYGT 2 cut(s) 117, 186
AgeI ACCGGT 1 cut(s) 303
AleI CACNNNNGTG 2 cut(s) 39, 122
AluBI AGCT 3 cut(s) 96, 111, 146
AluI AGCT 3 cut(s) 96, 111, 146
Alw21I GWGCWC 2 cut(s) 173, 390
ApeKI GCWGC 1 cut(s) 267
AsiGI ACCGGT 1 cut(s) 303
Asp700I GAANNNNTTC 1 cut(s) 342
BbsI GAAGAC 1 cut(s) 306
Bbv12I GWGCWC 2 cut(s) 173, 390
BbvI GCAGC 1 cut(s) 279
BccI CCATC 1 cut(s) 8
BfaI CTAG 1 cut(s) 391
BisI GCNGC 1 cut(s) 268
BlsI GCNGC 1 cut(s) 269
BpiI GAAGAC 1 cut(s) 306
BpuEI CTTGAG 2 cut(s) 58, 135
BsaJI CCNNGG 2 cut(s) 49, 286
BsaWI WCCGGW 1 cut(s) 303
Bsc4I CCNNNNNNNGG 1 cut(s) 55
Bse118I RCCGGY 1 cut(s) 303
BseDI CCNNGG 2 cut(s) 49, 286
BseGI GGATG 1 cut(s) 19
BseLI CCNNNNNNNGG 1 cut(s) 55
BseMII CTCAG 2 cut(s) 156, 158
BseRI GAGGAG 1 cut(s) 138
BseXI GCAGC 1 cut(s) 279
BseYI CCCAGC 1 cut(s) 111
BsgI GTGCAG 1 cut(s) 28
BshTI ACCGGT 1 cut(s) 303
BsiHKAI GWGCWC 2 cut(s) 173, 390
BsiSI CCGG 1 cut(s) 304
BslFI GGGAC 1 cut(s) 128
BslI CCNNNNNNNGG 1 cut(s) 55
BsmFI GGGAC 1 cut(s) 128
Bsp1286I GDGCHC 2 cut(s) 173, 390
BspCNI CTCAG 2 cut(s) 155, 159
BsrFI RCCGGY 1 cut(s) 303
BssAI RCCGGY 1 cut(s) 303
BssECI CCNNGG 2 cut(s) 49, 286
BssT1I CCWWGG 1 cut(s) 49
Bst4CI ACNGT 2 cut(s) 260, 276
Bst6I CTCTTC 1 cut(s) 365
BstC8I GCNNGC 1 cut(s) 78
BstDEI CTNAG 4 cut(s) 20, 92, 142, 167
BstF5I GGATG 1 cut(s) 19
BstMWI GCNNNNNNNGC 1 cut(s) 321
BstNSI RCATGY 1 cut(s) 190
BstV1I GCAGC 1 cut(s) 279
BstV2I GAAGAC 1 cut(s) 306
BtsCI GGATG 1 cut(s) 19
BtsIMutI CAGTG 2 cut(s) 164, 265
Cac8I GCNNGC 1 cut(s) 78
Cfr10I RCCGGY 1 cut(s) 303
CspAI ACCGGT 1 cut(s) 303
CspCI CAANNNNNGTGG 2 cut(s) 241, 276
CviAII CATG 3 cut(s) 55, 187, 367
CviJI RGCY 5 cut(s) 96, 111, 146, 242, 324
CviKI_1 RGCY 5 cut(s) 96, 111, 146, 242, 324
DdeI CTNAG 4 cut(s) 20, 92, 142, 167
Eam1104I CTCTTC 1 cut(s) 365
EarI CTCTTC 1 cut(s) 365
Eco130I CCWWGG 1 cut(s) 49
Eco57I CTGAAG 1 cut(s) 347
EcoT14I CCWWGG 1 cut(s) 49
ErhI CCWWGG 1 cut(s) 49
FaeI CATG 3 cut(s) 58, 190, 370
FaiI YATR 5 cut(s) 56, 106, 176, 188, 368
FaqI GGGAC 1 cut(s) 128
FatI CATG 3 cut(s) 54, 186, 366
Fnu4HI GCNGC 1 cut(s) 268
FokI GGATG 1 cut(s) 26
Fsp4HI GCNGC 1 cut(s) 268
FspBI CTAG 1 cut(s) 391
GluI GCNGC 1 cut(s) 268
GsaI CCCAGC 1 cut(s) 115
HapII CCGG 1 cut(s) 304
Hin1II CATG 3 cut(s) 58, 190, 370
HpaII CCGG 1 cut(s) 304
Hpy188I TCNGA 1 cut(s) 31
Hpy188III TCNNGA 1 cut(s) 309
HpyAV CCTTC 2 cut(s) 205, 322
HpyCH4III ACNGT 2 cut(s) 260, 276
HpyCH4IV ACGT 1 cut(s) 119
HpyCH4V TGCA 2 cut(s) 9, 76
HpyF10VI GCNNNNNNNGC 1 cut(s) 321
HpyF3I CTNAG 4 cut(s) 20, 92, 142, 167
HpySE526I ACGT 1 cut(s) 119
Hsp92II CATG 3 cut(s) 58, 190, 370
LmnI GCTCC 2 cut(s) 151, 214
LpnPI CCDG 3 cut(s) 97, 317, 338
Lsp1109I GCAGC 1 cut(s) 279
MaeI CTAG 1 cut(s) 391
MaeII ACGT 1 cut(s) 119
MaeIII GTNAC 3 cut(s) 41, 87, 137
MboII GAAGA 3 cut(s) 209, 311, 382
MhlI GDGCHC 2 cut(s) 173, 390
MnlI CCTC 5 cut(s) 159, 201, 281, 305, 366
MroXI GAANNNNTTC 1 cut(s) 342
MslI CAYNNNNRTG 3 cut(s) 39, 122, 351
MspA1I CMGCKG 1 cut(s) 111
MspI CCGG 1 cut(s) 304
MwoI GCNNNNNNNGC 1 cut(s) 321
NlaIII CATG 3 cut(s) 58, 190, 370
NmuCI GTSAC 1 cut(s) 41
NspI RCATGY 1 cut(s) 190
OliI CACNNNNGTG 2 cut(s) 39, 122
PciI ACATGT 1 cut(s) 186
PdmI GAANNNNTTC 1 cut(s) 342
PflMI CCANNNNNTGG 1 cut(s) 55
PinAI ACCGGT 1 cut(s) 303
PkrI GCNGC 1 cut(s) 269
PscI ACATGT 1 cut(s) 186
PspFI CCCAGC 1 cut(s) 111
PvuII CAGCTG 1 cut(s) 111
RseI CAYNNNNRTG 3 cut(s) 39, 122, 351
SatI GCNGC 1 cut(s) 268
SduI GDGCHC 2 cut(s) 173, 390
SetI ASST 4 cut(s) 98, 113, 122, 148
SmiMI CAYNNNNRTG 3 cut(s) 39, 122, 351
SmlI CTYRAG 2 cut(s) 37, 150
SmoI CTYRAG 2 cut(s) 37, 150
SspI AATATT 1 cut(s) 225
SspMI CTAG 1 cut(s) 391
StyI CCWWGG 1 cut(s) 49
TaaI ACNGT 2 cut(s) 260, 276
TaiI ACGT 1 cut(s) 122
TaqI TCGA 1 cut(s) 336
TaqII GACCGA 1 cut(s) 245
TscAI CASTG 2 cut(s) 171, 265
TseFI GTSAC 1 cut(s) 41
TseI GCWGC 1 cut(s) 267
Tsp45I GTSAC 1 cut(s) 41
TspDTI ATGAA 4 cut(s) 17, 335, 369, 383
TspGWI ACGGA 1 cut(s) 311
TspRI CASTG 2 cut(s) 171, 265
Van91I CCANNNNNTGG 1 cut(s) 55
XceI RCATGY 1 cut(s) 190
XmnI GAANNNNTTC 1 cut(s) 342
XspI CTAG 1 cut(s) 391
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.