FvH4_6g43142

DNA integration

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000278
Physical Location & Seq
Forward (+)
33443471 .. 33447622
4152 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g43142.t1

Sequence Viewer

Length: 1056 bp
ATGGGTGATGAAAAAGGAGATGCAGATAGATTTGCAAGAAAAACGGTTCAGAATGCAAAGTTCGAGGTGGAGAAATTTGATAGTACAAACAACTTTGGGATGTGGCAGTGCGAAGTGCAAGATGTGTTAACTCAACAAGATTTGGATATGGCTTTGGAAGATAGGCCCGAGGATATGTCAGATAAAGATTGGCAAAAGATAAATAAGATGGCTTGTTCTACGATTCGCTTATGTTTGGCGAAGCAGCAAAAGTTTGATGTGATGCGGGAGACGGCAGTAAAGGAGCTCTGGCAGAAGTTAGAAGACAAATACATGACGAAAAGTGCTGAGAATTGTCTGCATTTGAAGAGGAGGCTGTTCAATTTCAAGTACAAAGAAGGTACGAAGATGATTCACCATCTTGATGCTTTTAATAAATTGGTTGCTGATTTGTTGAATCTAGATGAAGAAATTAAAGATGAAGATAAAGCTATGCTGTTAGTGAATTCTCTGCCGGATTCGTATGAACATTTGATTGTTTGGTTGTTAGAGGCAGGGCAGTTGAAAGGAAAAATTACGGCGGGACATTGGAAGAAGGATTGCCCGAAGTTGAAAAACAAGAACAAAGGCACTCATGCCAATGTGGCATTTAGTGAGGACGAGTCTGATTTTGTTCTCAATCAGAAAAAGGCTAATGTTGGATCACCGCGAGAGAATGGGAGAGATGTTCAACAGGTGGAGCTTGACAAAGTAGTTTCTCAAGCTTCCAAGTCTCAACAACCGACTCAAGGGCCTCAAATTGAAGAAGAACATGAAGAAGTGAATGGTGAACAGCTGCATGTCCAAGATGATGATGTGGCTTCTATTGTCCCTGAACAGCAGCCTATTGCAGTGAGAAGAGAAAAGAGAACAATCAAAAAGCCTGCAAGATTTGAAGATTGTGTTGCTTATGCCTATCCTAAGTTGATTGAGCAGCAAGGAGCTTGGTTTGTTGGTTCTGCAGGGTATGAAGGCTCAGTGAGTGCAGCTGCTGTTATGATGTCTGCAAATCTCGCCAAGGTGGAGATAGTTGTTTAG
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 gag_pre-integrs

Protein Analysis

352

Amino Acids

40.02

Weight (kDa)

5.46

Isoelectric Point (pI)

42.77

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 57 - 181 1.5e-25 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) 688
AciI CCGC 3 cut(s) 265, 560, 686
AclWI GGATC 1 cut(s) 688
AcsI RAATTY 2 cut(s) 74, 484
AfaI GTAC 3 cut(s) 85, 371, 382
AfiI CCNNNNNNNGG 1 cut(s) 767
AgsI TTSAA 9 cut(s) 346, 361, 367, 436, 544, 592, 710, 782, 914
AluBI AGCT 7 cut(s) 286, 470, 721, 743, 814, 962, 1007
AluI AGCT 7 cut(s) 286, 470, 721, 743, 814, 962, 1007
Alw21I GWGCWC 1 cut(s) 288
Alw26I GTCTC 2 cut(s) 263, 756
AlwI GGATC 1 cut(s) 688
AlwNI CAGNNNCTG 1 cut(s) 1010
Ama87I CYCGRG 1 cut(s) 167
AoxI GGCC 2 cut(s) 164, 770
ApeKI GCWGC 6 cut(s) 244, 814, 859, 952, 1004, 1007
ApoI RAATTY 2 cut(s) 74, 484
AspS9I GGNCC 2 cut(s) 165, 770
AsuHPI GGTGA 4 cut(s) 17, 386, 675, 818
AvaI CYCGRG 1 cut(s) 167
BanII GRGCYC 1 cut(s) 288
BbsI GAAGAC 1 cut(s) 309
Bbv12I GWGCWC 1 cut(s) 288
BbvI GCAGC 6 cut(s) 256, 801, 871, 964, 994, 1016
BccI CCATC 2 cut(s) 202, 405
BceAI ACGGC 2 cut(s) 288, 573
BcoDI GTCTC 2 cut(s) 263, 756
BfaI CTAG 1 cut(s) 440
BfmI CTRYAG 1 cut(s) 978
BglI GCCNNNNNGGC 1 cut(s) 623
BisI GCNGC 6 cut(s) 245, 815, 860, 953, 1005, 1008
BlsI GCNGC 6 cut(s) 246, 816, 861, 954, 1006, 1009
BmeT110I CYCGRG 1 cut(s) 167
BmgT120I GGNCC 2 cut(s) 165, 770
BmsI GCATC 3 cut(s) 10, 252, 394
BpiI GAAGAC 1 cut(s) 309
BpuEI CTTGAG 2 cut(s) 723, 750
BsaJI CCNNGG 2 cut(s) 168, 1035
Bsc4I CCNNNNNNNGG 1 cut(s) 767
BseDI CCNNGG 2 cut(s) 168, 1035
BseGI GGATG 1 cut(s) 105
BseLI CCNNNNNNNGG 1 cut(s) 767
BseMII CTCAG 2 cut(s) 318, 1008
BseRI GAGGAG 1 cut(s) 364
BseXI GCAGC 6 cut(s) 256, 801, 871, 964, 994, 1016
BsgI GTGCAG 1 cut(s) 1023
Bsh1236I CGCG 1 cut(s) 688
BshFI GGCC 2 cut(s) 166, 772
BsiHKAI GWGCWC 1 cut(s) 288
BsiHKCI CYCGRG 1 cut(s) 167
BsiSI CCGG 1 cut(s) 494
BslFI GGGAC 2 cut(s) 576, 833
BslI CCNNNNNNNGG 1 cut(s) 767
BsmAI GTCTC 2 cut(s) 263, 756
BsmBI CGTCTC 1 cut(s) 263
BsmFI GGGAC 2 cut(s) 576, 833
BsmI GAATGC 1 cut(s) 58
BsnI GGCC 2 cut(s) 166, 772
BsoBI CYCGRG 1 cut(s) 167
Bsp1286I GDGCHC 1 cut(s) 288
Bsp143I GATC 1 cut(s) 680
BspACI CCGC 3 cut(s) 265, 560, 686
BspANI GGCC 2 cut(s) 166, 772
BspCNI CTCAG 2 cut(s) 319, 1007
BspFNI CGCG 1 cut(s) 688
BspMAI CTGCAG 1 cut(s) 982
BspPI GGATC 1 cut(s) 688
BssECI CCNNGG 2 cut(s) 168, 1035
BssMI GATC 1 cut(s) 680
BssT1I CCWWGG 1 cut(s) 1035
Bst4CI ACNGT 1 cut(s) 46
Bst6I CTCTTC 2 cut(s) 341, 871
BstC8I GCNNGC 1 cut(s) 903
BstDEI CTNAG 3 cut(s) 327, 939, 994
BstF5I GGATG 1 cut(s) 105
BstFNI CGCG 1 cut(s) 688
BstKTI GATC 1 cut(s) 683
BstMAI GTCTC 2 cut(s) 263, 756
BstMBI GATC 1 cut(s) 680
BstMWI GCNNNNNNNGC 2 cut(s) 623, 1031
BstNSI RCATGY 1 cut(s) 821
BstSFI CTRYAG 1 cut(s) 978
BstUI CGCG 1 cut(s) 688
BstV1I GCAGC 6 cut(s) 256, 801, 871, 964, 994, 1016
BstV2I GAAGAC 1 cut(s) 309
BsuRI GGCC 2 cut(s) 166, 772
BtsCI GGATG 1 cut(s) 105
BtsI GCAGTG 2 cut(s) 113, 876
BtsIMutI CAGTG 3 cut(s) 113, 876, 1002
Cac8I GCNNGC 1 cut(s) 903
CaiI CAGNNNCTG 1 cut(s) 1010
Cfr13I GGNCC 2 cut(s) 165, 770
Csp6I GTAC 3 cut(s) 84, 370, 381
CviAII CATG 4 cut(s) 313, 614, 791, 818
CviQI GTAC 3 cut(s) 84, 370, 381
DdeI CTNAG 3 cut(s) 327, 939, 994
DpnI GATC 1 cut(s) 682
DpnII GATC 1 cut(s) 680
Eam1104I CTCTTC 2 cut(s) 341, 871
EarI CTCTTC 2 cut(s) 341, 871
Ecl136II GAGCTC 1 cut(s) 286
Eco130I CCWWGG 1 cut(s) 1035
Eco24I GRGCYC 1 cut(s) 288
Eco53kI GAGCTC 1 cut(s) 286
Eco88I CYCGRG 1 cut(s) 167
EcoICRI GAGCTC 1 cut(s) 286
EcoO109I RGGNCCY 1 cut(s) 770
EcoRI GAATTC 1 cut(s) 484
EcoT14I CCWWGG 1 cut(s) 1035
EcoT38I GRGCYC 1 cut(s) 288
ErhI CCWWGG 1 cut(s) 1035
Esp3I CGTCTC 1 cut(s) 263
FaeI CATG 4 cut(s) 316, 617, 794, 821
FaqI GGGAC 2 cut(s) 576, 833
FatI CATG 4 cut(s) 312, 613, 790, 817
FauI CCCGC 2 cut(s) 258, 553
Fnu4HI GCNGC 6 cut(s) 245, 815, 860, 953, 1005, 1008
FokI GGATG 1 cut(s) 112
FriOI GRGCYC 1 cut(s) 288
Fsp4HI GCNGC 6 cut(s) 245, 815, 860, 953, 1005, 1008
FspBI CTAG 1 cut(s) 440
GluI GCNGC 6 cut(s) 245, 815, 860, 953, 1005, 1008
HaeIII GGCC 2 cut(s) 166, 772
HapII CCGG 1 cut(s) 494
Hin1II CATG 4 cut(s) 316, 617, 794, 821
HincII GTYRAC 1 cut(s) 129
HindII GTYRAC 1 cut(s) 129
HindIII AAGCTT 1 cut(s) 741
HinfI GANTC 6 cut(s) 223, 391, 436, 497, 641, 763
HpaI GTTAAC 1 cut(s) 129
HpaII CCGG 1 cut(s) 494
HphI GGTGA 4 cut(s) 17, 386, 675, 818
Hpy166II GTNNAC 2 cut(s) 129, 809
Hpy188I TCNGA 4 cut(s) 51, 181, 646, 663
Hpy188III TCNNGA 2 cut(s) 401, 440
Hpy8I GTNNAC 2 cut(s) 129, 809
HpyAV CCTTC 3 cut(s) 371, 568, 983
HpyCH4III ACNGT 1 cut(s) 46
HpyF10VI GCNNNNNNNGC 2 cut(s) 623, 1031
HpyF3I CTNAG 3 cut(s) 327, 939, 994
Hsp92II CATG 4 cut(s) 316, 617, 794, 821
KspAI GTTAAC 1 cut(s) 129
Kzo9I GATC 1 cut(s) 680
LmnI GCTCC 3 cut(s) 283, 718, 959
LpnPI CCDG 7 cut(s) 274, 507, 519, 698, 864, 915, 966
Lsp1109I GCAGC 6 cut(s) 256, 801, 871, 964, 994, 1016
LweI GCATC 3 cut(s) 10, 252, 394
MaeI CTAG 1 cut(s) 440
MalI GATC 1 cut(s) 682
MboI GATC 1 cut(s) 680
MhlI GDGCHC 1 cut(s) 288
MluCI AATT 8 cut(s) 74, 331, 361, 416, 450, 484, 552, 777
MlyI GAGTC 2 cut(s) 650, 757
MmeI TCCRAC 1 cut(s) 658
MnlI CCTC 7 cut(s) 58, 163, 342, 345, 523, 628, 783
MseI TTAA 3 cut(s) 128, 411, 453
MslI CAYNNNNRTG 2 cut(s) 402, 618
MspA1I CMGCKG 2 cut(s) 814, 1007
MspI CCGG 1 cut(s) 494
Mva1269I GAATGC 1 cut(s) 58
MvnI CGCG 1 cut(s) 688
MwoI GCNNNNNNNGC 2 cut(s) 623, 1031
NdeII GATC 1 cut(s) 680
NlaIII CATG 4 cut(s) 316, 617, 794, 821
NspI RCATGY 1 cut(s) 821
PctI GAATGC 1 cut(s) 58
PfeI GAWTC 4 cut(s) 223, 391, 436, 497
PkrI GCNGC 6 cut(s) 246, 816, 861, 954, 1006, 1009
PleI GAGTC 2 cut(s) 649, 757
PpsI GAGTC 2 cut(s) 649, 757
Psp124BI GAGCTC 1 cut(s) 288
PspPI GGNCC 2 cut(s) 165, 770
PstI CTGCAG 1 cut(s) 982
PstNI CAGNNNCTG 1 cut(s) 1010
PvuII CAGCTG 2 cut(s) 814, 1007
RsaI GTAC 3 cut(s) 85, 371, 382
RsaNI GTAC 3 cut(s) 84, 370, 381
RseI CAYNNNNRTG 2 cut(s) 402, 618
SacI GAGCTC 1 cut(s) 288
SaqAI TTAA 3 cut(s) 128, 411, 453
SatI GCNGC 6 cut(s) 245, 815, 860, 953, 1005, 1008
Sau3AI GATC 1 cut(s) 680
Sau96I GGNCC 2 cut(s) 165, 770
SchI GAGTC 2 cut(s) 650, 757
SduI GDGCHC 1 cut(s) 288
SfaNI GCATC 3 cut(s) 10, 252, 394
SfcI CTRYAG 1 cut(s) 978
SmiMI CAYNNNNRTG 2 cut(s) 402, 618
SmlI CTYRAG 2 cut(s) 738, 765
SmoI CTYRAG 2 cut(s) 738, 765
Sse9I AATT 8 cut(s) 74, 331, 361, 416, 450, 484, 552, 777
SsiI CCGC 3 cut(s) 265, 560, 686
SspMI CTAG 1 cut(s) 440
SstI GAGCTC 1 cut(s) 288
StyI CCWWGG 1 cut(s) 1035
TaaI ACNGT 1 cut(s) 46
TaqI TCGA 1 cut(s) 63
TasI AATT 8 cut(s) 74, 331, 361, 416, 450, 484, 552, 777
TatI WGTACW 2 cut(s) 83, 369
TfiI GAWTC 4 cut(s) 223, 391, 436, 497
Tru1I TTAA 3 cut(s) 128, 411, 453
Tru9I TTAA 3 cut(s) 128, 411, 453
TscAI CASTG 3 cut(s) 113, 876, 1002
TseI GCWGC 6 cut(s) 244, 814, 859, 952, 1004, 1007
TspDTI ATGAA 6 cut(s) 24, 459, 474, 519, 807, 1002
TspRI CASTG 3 cut(s) 113, 876, 1002
XapI RAATTY 2 cut(s) 74, 484
XbaI TCTAGA 1 cut(s) 439
XceI RCATGY 1 cut(s) 821
XspI CTAG 1 cut(s) 440
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.