FvH4_3g06691

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000278
Physical Location & Seq
Reverse (-)
3852720 .. 3855018
2299 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g06691.t1

Sequence Viewer

Length: 786 bp
ATGGGTGATGAACATGGAGATGCAGATAGATTTGCAAGAACAACGGTTCAGAATGCAAAGTTTGAGGTGGAGAAATTAGTTGGTACAAACAACTTTGGGATGTGGCAGTGCGAAGTGAAAGATGTGTTAGCTCAACAAGATTTGGATATGGCTTTAGAAGATAGGCCCGAGGAGTTGTGGCAAAAGTTAGAAGACAAATACATGATGAAAAGTGCTGAGAATCGTTTGCATTTGAAGAGGAGGCTGTTCAATTTCAAGTACAAAGAAGGTACGAAGATGATTCACCATCTTGATGCTTTTAATAAATTGGTTGCCGATTTGTTGAATTTAGATGAAGAAATTAAAGATGAAGATAAAGCTATACTTTTAGTGAATTCTCTGCCATATTCATATGAACATTTGAGTACTGCATCTACCTCAGATTGTTTGGTTGTTAGAGCAGGACAGTTGAAAGGAAAAATCACGGCAGTAGAAAAAAGTTTCATTCTCATCCAAGAGGAAACTCCAAAAACAGAAGAAGTTTGGGGAGATGAATGTGCATTTTGTCATGAGCAAGGGCATTGGAAGAATGATTGCCAGAAGTTGAAAAACAAGAACAAAGGCACTCATGCCAATGTGGCATTTAGTGAGGACGAGTCTGAATTTGTTCTCAATCAAAAGGCTACTGGTGGATCACCGCGGAAGAATGGTAGAGATGTTCACATGTGGAGTTTGACAAAGTTCAACCTTCCAAGTCTCAACAACCGACTCAAGAGACTCAAAGTGAAGAAGAACATGAAGGAGTGA
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

262

Amino Acids

30.17

Weight (kDa)

6.53

Isoelectric Point (pI)

33.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 57 - 159 4.7e-21 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)
AccII CGCG 1 cut(s) 679
AciI CCGC 2 cut(s) 677, 679
AclWI GGATC 1 cut(s) 679
AcsI RAATTY 3 cut(s) 325, 373, 641
AfaI GTAC 4 cut(s) 85, 260, 271, 406
AflIII ACRYGT 1 cut(s) 702
AgsI TTSAA 7 cut(s) 235, 250, 256, 325, 451, 586, 724
AluBI AGCT 2 cut(s) 131, 359
AluI AGCT 2 cut(s) 131, 359
Alw26I GTCTC 2 cut(s) 740, 748
AlwI GGATC 1 cut(s) 679
Ama87I CYCGRG 1 cut(s) 167
AoxI GGCC 1 cut(s) 164
ApoI RAATTY 3 cut(s) 325, 373, 641
Asp700I GAANNNNTTC 1 cut(s) 645
AspS9I GGNCC 1 cut(s) 165
AsuHPI GGTGA 3 cut(s) 17, 275, 666
AvaI CYCGRG 1 cut(s) 167
BbsI GAAGAC 1 cut(s) 198
BccI CCATC 1 cut(s) 294
BceAI ACGGC 1 cut(s) 480
BcoDI GTCTC 2 cut(s) 740, 748
BglI GCCNNNNNGGC 1 cut(s) 617
BmcAI AGTACT 1 cut(s) 406
BmeT110I CYCGRG 1 cut(s) 167
BmgT120I GGNCC 1 cut(s) 165
BmsI GCATC 3 cut(s) 10, 283, 419
BpiI GAAGAC 1 cut(s) 198
BpuEI CTTGAG 1 cut(s) 734
BsaJI CCNNGG 2 cut(s) 168, 677
Bse1I ACTGG 1 cut(s) 670
BseDI CCNNGG 2 cut(s) 168, 677
BseGI GGATG 2 cut(s) 105, 489
BseMII CTCAG 2 cut(s) 207, 432
BseNI ACTGG 1 cut(s) 670
BseRI GAGGAG 2 cut(s) 185, 253
Bsh1236I CGCG 1 cut(s) 679
BshFI GGCC 1 cut(s) 166
BsiHKCI CYCGRG 1 cut(s) 167
BsmAI GTCTC 2 cut(s) 740, 748
BsmI GAATGC 1 cut(s) 58
BsnI GGCC 1 cut(s) 166
BsoBI CYCGRG 1 cut(s) 167
Bsp143I GATC 1 cut(s) 671
BspACI CCGC 2 cut(s) 677, 679
BspANI GGCC 1 cut(s) 166
BspCNI CTCAG 2 cut(s) 208, 431
BspFNI CGCG 1 cut(s) 679
BspHI TCATGA 1 cut(s) 547
BspPI GGATC 1 cut(s) 679
BsrI ACTGG 1 cut(s) 670
BssECI CCNNGG 2 cut(s) 168, 677
BssMI GATC 1 cut(s) 671
Bst4CI ACNGT 2 cut(s) 46, 447
Bst6I CTCTTC 1 cut(s) 230
BstDEI CTNAG 2 cut(s) 216, 418
BstDSI CCRYGG 1 cut(s) 677
BstF5I GGATG 2 cut(s) 105, 489
BstFNI CGCG 1 cut(s) 679
BstKTI GATC 1 cut(s) 674
BstMAI GTCTC 2 cut(s) 740, 748
BstMBI GATC 1 cut(s) 671
BstMWI GCNNNNNNNGC 1 cut(s) 617
BstNSI RCATGY 1 cut(s) 706
BstUI CGCG 1 cut(s) 679
BstV2I GAAGAC 1 cut(s) 198
BsuRI GGCC 1 cut(s) 166
BtgI CCRYGG 1 cut(s) 677
BtsCI GGATG 2 cut(s) 105, 489
BtsI GCAGTG 1 cut(s) 113
BtsIMutI CAGTG 1 cut(s) 113
CciI TCATGA 1 cut(s) 547
Cfr13I GGNCC 1 cut(s) 165
Cfr42I CCGCGG 1 cut(s) 680
Csp6I GTAC 4 cut(s) 84, 259, 270, 405
CviAII CATG 6 cut(s) 14, 202, 548, 608, 703, 775
CviJI RGCY 6 cut(s) 131, 152, 166, 244, 359, 662
CviKI_1 RGCY 6 cut(s) 131, 152, 166, 244, 359, 662
CviQI GTAC 4 cut(s) 84, 259, 270, 405
DdeI CTNAG 2 cut(s) 216, 418
DpnI GATC 1 cut(s) 673
DpnII GATC 1 cut(s) 671
Eam1104I CTCTTC 1 cut(s) 230
EarI CTCTTC 1 cut(s) 230
Eco88I CYCGRG 1 cut(s) 167
EcoRI GAATTC 1 cut(s) 373
FaeI CATG 6 cut(s) 17, 205, 551, 611, 706, 778
FalI AAGNNNNNCTT 2 cut(s) 348, 380
FatI CATG 6 cut(s) 13, 201, 547, 607, 702, 774
FauNDI CATATG 1 cut(s) 391
FokI GGATG 2 cut(s) 112, 476
HaeIII GGCC 1 cut(s) 166
Hin1II CATG 6 cut(s) 17, 205, 551, 611, 706, 778
HinfI GANTC 5 cut(s) 220, 280, 635, 747, 756
HphI GGTGA 3 cut(s) 17, 275, 666
Hpy166II GTNNAC 1 cut(s) 700
Hpy188I TCNGA 3 cut(s) 51, 421, 640
Hpy188III TCNNGA 3 cut(s) 290, 548, 751
Hpy8I GTNNAC 1 cut(s) 700
HpyAV CCTTC 3 cut(s) 260, 737, 772
HpyCH4III ACNGT 2 cut(s) 46, 447
HpyCH4V TGCA 6 cut(s) 23, 35, 56, 229, 410, 539
HpyF10VI GCNNNNNNNGC 1 cut(s) 617
HpyF3I CTNAG 2 cut(s) 216, 418
Hsp92II CATG 6 cut(s) 17, 205, 551, 611, 706, 778
KspI CCGCGG 1 cut(s) 680
Kzo9I GATC 1 cut(s) 671
LpnPI CCDG 3 cut(s) 426, 590, 651
LweI GCATC 3 cut(s) 10, 283, 419
MalI GATC 1 cut(s) 673
MboI GATC 1 cut(s) 671
MluCI AATT 7 cut(s) 74, 250, 305, 325, 339, 373, 641
MlyI GAGTC 3 cut(s) 644, 741, 750
MnlI CCTC 7 cut(s) 58, 163, 231, 234, 427, 490, 622
MroXI GAANNNNTTC 1 cut(s) 645
MseI TTAA 2 cut(s) 300, 342
MslI CAYNNNNRTG 3 cut(s) 18, 291, 612
MspA1I CMGCKG 1 cut(s) 679
Mva1269I GAATGC 1 cut(s) 58
MvnI CGCG 1 cut(s) 679
MwoI GCNNNNNNNGC 1 cut(s) 617
NdeI CATATG 1 cut(s) 391
NdeII GATC 1 cut(s) 671
NlaIII CATG 6 cut(s) 17, 205, 551, 611, 706, 778
NspI RCATGY 1 cut(s) 706
PagI TCATGA 1 cut(s) 547
PciI ACATGT 1 cut(s) 702
PctI GAATGC 1 cut(s) 58
PdmI GAANNNNTTC 1 cut(s) 645
PfeI GAWTC 2 cut(s) 220, 280
PleI GAGTC 3 cut(s) 643, 741, 750
PpsI GAGTC 3 cut(s) 643, 741, 750
PscI ACATGT 1 cut(s) 702
PspPI GGNCC 1 cut(s) 165
RsaI GTAC 4 cut(s) 85, 260, 271, 406
RsaNI GTAC 4 cut(s) 84, 259, 270, 405
RseI CAYNNNNRTG 3 cut(s) 18, 291, 612
SacII CCGCGG 1 cut(s) 680
SaqAI TTAA 2 cut(s) 300, 342
Sau3AI GATC 1 cut(s) 671
Sau96I GGNCC 1 cut(s) 165
ScaI AGTACT 1 cut(s) 406
SchI GAGTC 3 cut(s) 644, 741, 750
SetI ASST 6 cut(s) 69, 133, 271, 361, 419, 729
SfaNI GCATC 3 cut(s) 10, 283, 419
Sfr303I CCGCGG 1 cut(s) 680
SgrBI CCGCGG 1 cut(s) 680
SmiMI CAYNNNNRTG 3 cut(s) 18, 291, 612
SmlI CTYRAG 1 cut(s) 749
SmoI CTYRAG 1 cut(s) 749
Sse9I AATT 7 cut(s) 74, 250, 305, 325, 339, 373, 641
SsiI CCGC 2 cut(s) 677, 679
TaaI ACNGT 2 cut(s) 46, 447
TasI AATT 7 cut(s) 74, 250, 305, 325, 339, 373, 641
TatI WGTACW 2 cut(s) 258, 404
TfiI GAWTC 2 cut(s) 220, 280
Tru1I TTAA 2 cut(s) 300, 342
Tru9I TTAA 2 cut(s) 300, 342
TscAI CASTG 1 cut(s) 113
TspDTI ATGAA 8 cut(s) 24, 221, 348, 363, 378, 408, 472, 546
TspRI CASTG 1 cut(s) 113
XapI RAATTY 3 cut(s) 325, 373, 641
XceI RCATGY 1 cut(s) 706
XmnI GAANNNNTTC 1 cut(s) 645
ZrmI AGTACT 1 cut(s) 406
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.