FvH4_4g06794

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000278
Physical Location & Seq
Forward (+)
6127982 .. 6128894
913 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g06794.t1

Sequence Viewer

Length: 783 bp
ATGTCTGGTTTGAATGTGAAGATTGATAAATTCACAGGGAGGAACAGTTTCAGTTTATGGCAGATCAAGATGCGAGCCTTGTTAAAACAACAAGGTATGTGGGCGCCGCTGGTTAAGAAGTCAAGGGATCAAGAAATCGCTGAGATGGCCAGTCTGGAGGAGAAGGCACACTCGACAATTCTGTTGTGTCTTGCAGATGATATAATCACCGAGGTCGCAGAGGAGGAAACTGCGGCTGGTCTGTGGTTGAAGCTTGAGAGTCTATACATGACGAAGTCTTTAACCAACAAGTTGCTTCTAAAGCGACGTCTGTTCGGTCTGCGTATGGAAGAAGGTACATCCCTAAGAGATCACCTAGATCAGTTAAACACTGTTCTATTAGAGTTGCGTAATATCGATGTTAAAGTTGATGATGAGGATGCTGCTCTAATTCTGTTGGTATCTCTACCTTCGTCGTATGAGAATTTTGTGGATTCTTTTATTGGTGGGAGAGATACTCTGACTCTGGAGGATGTTAGATCATCTTTACATACTAGAGATATGCGTCATAAGGCGACCGTTACTAGTTCAGACAGTCAGGCTACAGGGTTGGTAGCCAGTGGAAGTTTGGGACAGAAAGGCTCGGGGAAGAAGAAATTCAAGAATCCAGTTTCAAAGGGTTCCAAATCCAATGATGTCTGTAACTACTGTAAAGAGAAGGGACATTGGAAAAACGAATGTCCAAAGAAGAAGAAGCAGTCTGAGAAAGCATCAGAGAGTGGTTTTCAACCTATGAGCAGATAG
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

261

Amino Acids

29.11

Weight (kDa)

9.02

Isoelectric Point (pI)

49.62

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 24 - 185 1.7e-36 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)
AatII GACGTC 1 cut(s) 310
AccB1I GGYRCC 1 cut(s) 103
AciI CCGC 2 cut(s) 107, 233
AclWI GGATC 1 cut(s) 135
AcoI YGGCCR 1 cut(s) 147
AcsI RAATTY 3 cut(s) 29, 463, 635
AcyI GRCGYC 2 cut(s) 104, 307
AfaI GTAC 1 cut(s) 337
AgsI TTSAA 5 cut(s) 13, 250, 640, 654, 767
AhlI ACTAGT 1 cut(s) 563
AluBI AGCT 1 cut(s) 253
AluI AGCT 1 cut(s) 253
AlwI GGATC 1 cut(s) 135
Ama87I CYCGRG 1 cut(s) 622
AoxI GGCC 1 cut(s) 147
ApeKI GCWGC 1 cut(s) 422
ApoI RAATTY 3 cut(s) 29, 463, 635
Asp700I GAANNNNTTC 2 cut(s) 47, 635
AspLEI GCGC 1 cut(s) 106
AsuHPI GGTGA 2 cut(s) 199, 344
AvaI CYCGRG 1 cut(s) 622
BalI TGGCCA 1 cut(s) 149
BanI GGYRCC 1 cut(s) 103
BbvI GCAGC 1 cut(s) 409
BccI CCATC 1 cut(s) 139
BcuI ACTAGT 1 cut(s) 563
BfaI CTAG 3 cut(s) 356, 534, 564
BfmI CTRYAG 1 cut(s) 582
BfoI RGCGCY 1 cut(s) 107
BisI GCNGC 3 cut(s) 107, 234, 423
BlsI GCNGC 3 cut(s) 108, 235, 424
BmeT110I CYCGRG 1 cut(s) 622
BmiI GGNNCC 2 cut(s) 105, 661
BmsI GCATC 3 cut(s) 60, 409, 758
BplI GAGNNNNNCTC 2 cut(s) 481, 513
BpmI CTGGAG 2 cut(s) 176, 527
BpuEI CTTGAG 1 cut(s) 275
Bsa29I ATCGAT 1 cut(s) 396
BsaHI GRCGYC 2 cut(s) 104, 307
BsaJI CCNNGG 1 cut(s) 210
BsaXI ACNNNNNCTCC 2 cut(s) 31, 61
Bse1I ACTGG 3 cut(s) 150, 597, 647
BseCI ATCGAT 1 cut(s) 396
BseDI CCNNGG 1 cut(s) 210
BseGI GGATG 3 cut(s) 338, 424, 517
BseMII CTCAG 2 cut(s) 132, 732
BseNI ACTGG 3 cut(s) 150, 597, 647
BseRI GAGGAG 2 cut(s) 173, 236
BseXI GCAGC 1 cut(s) 409
Bsh1285I CGRYCG 1 cut(s) 558
BshFI GGCC 1 cut(s) 149
BshNI GGYRCC 1 cut(s) 103
BshVI ATCGAT 1 cut(s) 396
BsiEI CGRYCG 1 cut(s) 558
BsiHKCI CYCGRG 1 cut(s) 622
BslFI GGGAC 2 cut(s) 624, 714
BsmFI GGGAC 2 cut(s) 624, 714
BsnI GGCC 1 cut(s) 149
BsoBI CYCGRG 1 cut(s) 622
Bsp143I GATC 5 cut(s) 63, 127, 349, 358, 518
BspACI CCGC 2 cut(s) 107, 233
BspANI GGCC 1 cut(s) 149
BspCNI CTCAG 2 cut(s) 133, 733
BspDI ATCGAT 1 cut(s) 396
BspLI GGNNCC 2 cut(s) 105, 661
BspPI GGATC 1 cut(s) 135
BspT107I GGYRCC 1 cut(s) 103
BsrI ACTGG 3 cut(s) 150, 597, 647
BssECI CCNNGG 1 cut(s) 210
BssMI GATC 5 cut(s) 63, 127, 349, 358, 518
BssNI GRCGYC 2 cut(s) 104, 307
Bst4CI ACNGT 5 cut(s) 47, 373, 559, 575, 689
BstACI GRCGYC 2 cut(s) 104, 307
BstC8I GCNNGC 1 cut(s) 75
BstDEI CTNAG 3 cut(s) 141, 344, 741
BstF5I GGATG 3 cut(s) 338, 424, 517
BstH2I RGCGCY 1 cut(s) 107
BstHHI GCGC 1 cut(s) 106
BstKTI GATC 5 cut(s) 66, 130, 352, 361, 521
BstMBI GATC 5 cut(s) 63, 127, 349, 358, 518
BstMCI CGRYCG 1 cut(s) 558
BstMWI GCNNNNNNNGC 2 cut(s) 146, 301
BstSFI CTRYAG 1 cut(s) 582
BstV1I GCAGC 1 cut(s) 409
Bsu15I ATCGAT 1 cut(s) 396
BsuRI GGCC 1 cut(s) 149
BsuTUI ATCGAT 1 cut(s) 396
BtsCI GGATG 3 cut(s) 338, 424, 517
BtsIMutI CAGTG 2 cut(s) 369, 604
Cac8I GCNNGC 1 cut(s) 75
CfoI GCGC 1 cut(s) 106
ClaI ATCGAT 1 cut(s) 396
CseI GACGC 1 cut(s) 533
Csp6I GTAC 1 cut(s) 336
CspCI CAANNNNNGTGG 2 cut(s) 80, 115
CviAII CATG 1 cut(s) 268
CviJI RGCY 7 cut(s) 77, 149, 236, 253, 581, 596, 621
CviKI_1 RGCY 7 cut(s) 77, 149, 236, 253, 581, 596, 621
CviQI GTAC 1 cut(s) 336
DdeI CTNAG 3 cut(s) 141, 344, 741
DinI GGCGCC 1 cut(s) 105
DpnI GATC 5 cut(s) 65, 129, 351, 360, 520
DpnII GATC 5 cut(s) 63, 127, 349, 358, 518
EaeI YGGCCR 1 cut(s) 147
Eco88I CYCGRG 1 cut(s) 622
EgeI GGCGCC 1 cut(s) 105
EheI GGCGCC 1 cut(s) 105
FaeI CATG 1 cut(s) 271
FaqI GGGAC 2 cut(s) 624, 714
FatI CATG 1 cut(s) 267
Fnu4HI GCNGC 3 cut(s) 107, 234, 423
FokI GGATG 3 cut(s) 325, 431, 524
Fsp4HI GCNGC 3 cut(s) 107, 234, 423
FspBI CTAG 3 cut(s) 356, 534, 564
GlaI GCGC 1 cut(s) 105
GluI GCNGC 3 cut(s) 107, 234, 423
GsuI CTGGAG 2 cut(s) 176, 527
HaeII RGCGCY 1 cut(s) 107
HaeIII GGCC 1 cut(s) 149
HgaI GACGC 1 cut(s) 533
HhaI GCGC 1 cut(s) 106
Hin1I GRCGYC 2 cut(s) 104, 307
Hin1II CATG 1 cut(s) 271
Hin6I GCGC 1 cut(s) 104
HinP1I GCGC 1 cut(s) 104
HindIII AAGCTT 1 cut(s) 251
HinfI GANTC 4 cut(s) 259, 473, 502, 643
HphI GGTGA 2 cut(s) 199, 344
Hpy188I TCNGA 4 cut(s) 501, 571, 742, 754
Hpy188III TCNNGA 5 cut(s) 67, 131, 155, 506, 640
Hpy99I CGWCG 2 cut(s) 309, 457
HpyAV CCTTC 4 cut(s) 157, 326, 459, 691
HpyCH4III ACNGT 5 cut(s) 47, 373, 559, 575, 689
HpyCH4IV ACGT 1 cut(s) 307
HpyCH4V TGCA 1 cut(s) 194
HpyF10VI GCNNNNNNNGC 2 cut(s) 146, 301
HpyF3I CTNAG 3 cut(s) 141, 344, 741
HpySE526I ACGT 1 cut(s) 307
Hsp92I GRCGYC 2 cut(s) 104, 307
Hsp92II CATG 1 cut(s) 271
HspAI GCGC 1 cut(s) 104
KasI GGCGCC 1 cut(s) 103
Kzo9I GATC 5 cut(s) 63, 127, 349, 358, 518
Lsp1109I GCAGC 1 cut(s) 409
LweI GCATC 3 cut(s) 60, 409, 758
MaeI CTAG 3 cut(s) 356, 534, 564
MaeII ACGT 1 cut(s) 307
MaeIII GTNAC 2 cut(s) 559, 680
MalI GATC 5 cut(s) 65, 129, 351, 360, 520
MboI GATC 5 cut(s) 63, 127, 349, 358, 518
MboII GAAGA 6 cut(s) 31, 341, 640, 643, 739, 742
MlsI TGGCCA 1 cut(s) 149
MluCI AATT 5 cut(s) 29, 177, 429, 463, 635
MluNI TGGCCA 1 cut(s) 149
Mly113I GGCGCC 1 cut(s) 104
MlyI GAGTC 2 cut(s) 268, 496
MnlI CCTC 7 cut(s) 33, 151, 205, 214, 217, 409, 502
Mox20I TGGCCA 1 cut(s) 149
MroXI GAANNNNTTC 2 cut(s) 47, 635
MscI TGGCCA 1 cut(s) 149
MseI TTAA 5 cut(s) 83, 114, 281, 365, 402
Msp20I TGGCCA 1 cut(s) 149
MspA1I CMGCKG 1 cut(s) 109
MwoI GCNNNNNNNGC 2 cut(s) 146, 301
NarI GGCGCC 1 cut(s) 104
NdeII GATC 5 cut(s) 63, 127, 349, 358, 518
NlaIII CATG 1 cut(s) 271
NlaIV GGNNCC 2 cut(s) 105, 661
PdmI GAANNNNTTC 2 cut(s) 47, 635
PfeI GAWTC 2 cut(s) 473, 643
PflFI GACNNNGTC 1 cut(s) 274
PkrI GCNGC 3 cut(s) 108, 235, 424
PleI GAGTC 2 cut(s) 267, 496
PluTI GGCGCC 1 cut(s) 107
PpsI GAGTC 2 cut(s) 267, 496
PspN4I GGNNCC 2 cut(s) 105, 661
PsyI GACNNNGTC 1 cut(s) 274
RsaI GTAC 1 cut(s) 337
RsaNI GTAC 1 cut(s) 336
SaqAI TTAA 5 cut(s) 83, 114, 281, 365, 402
SatI GCNGC 3 cut(s) 107, 234, 423
Sau3AI GATC 5 cut(s) 63, 127, 349, 358, 518
SchI GAGTC 2 cut(s) 268, 496
SetI ASST 8 cut(s) 97, 216, 255, 310, 337, 357, 451, 772
SfaNI GCATC 3 cut(s) 60, 409, 758
SfcI CTRYAG 1 cut(s) 582
SfoI GGCGCC 1 cut(s) 105
SmlI CTYRAG 1 cut(s) 254
SmoI CTYRAG 1 cut(s) 254
SpeI ACTAGT 1 cut(s) 563
Sse9I AATT 5 cut(s) 29, 177, 429, 463, 635
SsiI CCGC 2 cut(s) 107, 233
SspDI GGCGCC 1 cut(s) 103
SspMI CTAG 3 cut(s) 356, 534, 564
TaaI ACNGT 5 cut(s) 47, 373, 559, 575, 689
TaiI ACGT 1 cut(s) 310
TaqI TCGA 2 cut(s) 173, 396
TaqII GACCGA 1 cut(s) 305
TasI AATT 5 cut(s) 29, 177, 429, 463, 635
TauI GCSGC 2 cut(s) 109, 236
TfiI GAWTC 2 cut(s) 473, 643
Tru1I TTAA 5 cut(s) 83, 114, 281, 365, 402
Tru9I TTAA 5 cut(s) 83, 114, 281, 365, 402
TscAI CASTG 2 cut(s) 376, 604
TseI GCWGC 1 cut(s) 422
TspRI CASTG 2 cut(s) 376, 604
Tth111I GACNNNGTC 1 cut(s) 274
XapI RAATTY 3 cut(s) 29, 463, 635
XcmI CCANNNNNNNNNTGG 1 cut(s) 604
XmnI GAANNNNTTC 2 cut(s) 47, 635
XspI CTAG 3 cut(s) 356, 534, 564
ZraI GACGTC 1 cut(s) 308
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.