FvH4_4g14243

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000106
Physical Location & Seq
Reverse (-)
17829889 .. 17830800
912 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g14243.t1

Sequence Viewer

Length: 912 bp
ATGTCTGACACCAATATTCCTATCCCTCCACCGAAATCAAGCGGTGATGATGATGTCCCTCCACCAAAATCAAACAGTTCCAGTTCATCTGCTGATTCCTCCAAGGCAGAACCTTCCAATCCTTATTTCATTCATCATTCAGATCATCCCGGATTGGTCCTCGTCTCCAAACTTCTAAATGGGGATAATTTTTCTGGTTGGAAAAGGGCTATGGTCAGAGCCTTAAACTCCAAGAACAAGCTCGGATTCGTCAATGGTTCCATCAAAACTCCCTCAGCAGAAACCGATCTTGAAGGCTATGTGGCTTGGTCGCGATGTAACGATATGGTCCATTCCTGGATCGTCAATTCTTGCGATCCAGAAATTGCTGACAGTGTGAATTATTATCCTAATGCTTACGAGGTTTATGAGGATCTACATGAGCGTTTTTCTCAATCAAATGCAACTCGTATCTTTGAAATACAGCGAGATATTGCTTCTCTCAGGCAAGACCAACTCCCTGTTTCTACCTTCTATACTAAGTTGAAAAACTTATGGGATGAATTGACCGCATATTCAGATCCGATACATGGAGCACAATCAGATCAACAAAAACTGATGCAATTTCTAATGGGTCTAAATGAGACTTACAGTGCAATTCGTGGGCAAATCCTCTTGATGAATCCCCTTCCAATAGTTCGTCAAGCCTATGCCGCTATCTCTCAAAAAGAAAAGCAGCGCCTCCTCAGTGCCTCTCAAATCACAGCCGATTCTATCTCCAGTGCAGCATGGCGGTACGAAACAGTAGCAGACCCACTCAGAACTTGGCTAGAGGAGGACGATTTGAGCGATCTGACCGCTCTTCTTCTCACCAAAGTCGCCGAGAAGGCAATTCTTTTGCGCTCACAAAGGACGTGGTCGAGGCAGAGGTAG
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_3

Protein Analysis

304

Amino Acids

34.06

Weight (kDa)

5.57

Isoelectric Point (pI)

43.97

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 45 - 91 1.4e-22 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: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 839
AccII CGCG 1 cut(s) 313
AciI CCGC 5 cut(s) 42, 549, 693, 772, 837
AclWI GGATC 4 cut(s) 347, 350, 420, 554
AfaI GTAC 1 cut(s) 776
AfiI CCNNNNNNNGG 1 cut(s) 569
AgsI TTSAA 3 cut(s) 293, 458, 526
AjiI CACGTC 1 cut(s) 894
AjnI CCWGG 1 cut(s) 335
AjuI GAANNNNNNNTTGG 2 cut(s) 110, 142
AluBI AGCT 1 cut(s) 241
AluI AGCT 1 cut(s) 241
Alw21I GWGCWC 1 cut(s) 577
Alw26I GTCTC 2 cut(s) 169, 617
AlwI GGATC 4 cut(s) 347, 350, 420, 554
ApeKI GCWGC 2 cut(s) 715, 764
AspLEI GCGC 2 cut(s) 720, 882
AspS9I GGNCC 2 cut(s) 157, 328
AsuC2I CCSGG 1 cut(s) 150
AsuHPI GGTGA 2 cut(s) 56, 841
AvaII GGWCC 2 cut(s) 157, 328
Bbv12I GWGCWC 1 cut(s) 577
BbvCI CCTCAGC 1 cut(s) 274
BbvI GCAGC 2 cut(s) 727, 776
BccI CCATC 1 cut(s) 269
BciT130I CCWGG 1 cut(s) 337
BcnI CCSGG 1 cut(s) 150
BcoDI GTCTC 2 cut(s) 169, 617
BfaI CTAG 1 cut(s) 809
BfoI RGCGCY 1 cut(s) 721
BglI GCCNNNNNGGC 1 cut(s) 866
BisI GCNGC 3 cut(s) 693, 716, 765
BlsI GCNGC 3 cut(s) 694, 717, 766
Bme1390I CCNGG 2 cut(s) 150, 337
Bme18I GGWCC 2 cut(s) 157, 328
BmgBI CACGTC 1 cut(s) 894
BmgT120I GGNCC 2 cut(s) 157, 328
BmiI GGNNCC 1 cut(s) 259
BmrFI CCNGG 2 cut(s) 150, 337
BmsI GCATC 1 cut(s) 588
BpmI CTGGAG 1 cut(s) 742
Bpu10I CCTNAGC 1 cut(s) 274
BpuMI CCSGG 1 cut(s) 150
BsaJI CCNNGG 1 cut(s) 102
Bsc4I CCNNNNNNNGG 1 cut(s) 569
Bse1I ACTGG 2 cut(s) 81, 759
BseBI CCWGG 1 cut(s) 337
BseDI CCNNGG 1 cut(s) 102
BseGI GGATG 2 cut(s) 145, 544
BseLI CCNNNNNNNGG 1 cut(s) 569
BseMII CTCAG 4 cut(s) 288, 496, 739, 811
BseNI ACTGG 2 cut(s) 81, 759
BseRI GAGGAG 2 cut(s) 713, 827
BseXI GCAGC 2 cut(s) 727, 776
BsgI GTGCAG 1 cut(s) 783
Bsh1236I CGCG 1 cut(s) 313
BsiHKAI GWGCWC 1 cut(s) 577
BsiSI CCGG 1 cut(s) 150
BslFI GGGAC 1 cut(s) 41
BslI CCNNNNNNNGG 1 cut(s) 569
BsmAI GTCTC 2 cut(s) 169, 617
BsmBI CGTCTC 1 cut(s) 169
BsmFI GGGAC 1 cut(s) 41
Bsp1286I GDGCHC 1 cut(s) 577
Bsp143I GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
Bsp68I TCGCGA 1 cut(s) 313
BspACI CCGC 5 cut(s) 42, 549, 693, 772, 837
BspCNI CTCAG 4 cut(s) 287, 495, 738, 810
BspFNI CGCG 1 cut(s) 313
BspLI GGNNCC 1 cut(s) 259
BspPI GGATC 4 cut(s) 347, 350, 420, 554
BspQI GCTCTTC 1 cut(s) 846
BsrBI CCGCTC 1 cut(s) 839
BsrI ACTGG 2 cut(s) 81, 759
BssECI CCNNGG 1 cut(s) 102
BssMI GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
BssT1I CCWWGG 1 cut(s) 102
Bst2UI CCWGG 1 cut(s) 337
Bst4CI ACNGT 4 cut(s) 77, 374, 632, 784
Bst6I CTCTTC 1 cut(s) 846
BstDEI CTNAG 5 cut(s) 274, 482, 519, 725, 797
BstF5I GGATG 2 cut(s) 145, 544
BstFNI CGCG 1 cut(s) 313
BstH2I RGCGCY 1 cut(s) 721
BstHHI GCGC 2 cut(s) 720, 882
BstKTI GATC 8 cut(s) 145, 289, 342, 358, 415, 562, 586, 832
BstMAI GTCTC 2 cut(s) 169, 617
BstMBI GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
BstMWI GCNNNNNNNGC 2 cut(s) 692, 866
BstNI CCWGG 1 cut(s) 337
BstSCI CCNGG 2 cut(s) 148, 335
BstUI CGCG 1 cut(s) 313
BstV1I GCAGC 2 cut(s) 727, 776
BstX2I RGATCY 2 cut(s) 412, 559
BstYI RGATCY 2 cut(s) 412, 559
BtgZI GCGATG 1 cut(s) 328
BtrI CACGTC 1 cut(s) 894
BtsCI GGATG 2 cut(s) 145, 544
BtsIMutI CAGTG 4 cut(s) 379, 637, 733, 766
BtuMI TCGCGA 1 cut(s) 313
CfoI GCGC 2 cut(s) 720, 882
Cfr13I GGNCC 2 cut(s) 157, 328
Csp6I GTAC 1 cut(s) 775
CspCI CAANNNNNGTGG 2 cut(s) 875, 910
CviAII CATG 3 cut(s) 419, 569, 768
CviJI RGCY 8 cut(s) 209, 221, 241, 297, 305, 686, 746, 808
CviKI_1 RGCY 8 cut(s) 209, 221, 241, 297, 305, 686, 746, 808
CviQI GTAC 1 cut(s) 775
DdeI CTNAG 5 cut(s) 274, 482, 519, 725, 797
DpnI GATC 8 cut(s) 144, 288, 341, 357, 414, 561, 585, 831
DpnII GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
Eam1104I CTCTTC 1 cut(s) 846
EarI CTCTTC 1 cut(s) 846
Eco130I CCWWGG 1 cut(s) 102
Eco47I GGWCC 2 cut(s) 157, 328
EcoRII CCWGG 1 cut(s) 335
EcoT14I CCWWGG 1 cut(s) 102
ErhI CCWWGG 1 cut(s) 102
Esp3I CGTCTC 1 cut(s) 169
FaeI CATG 3 cut(s) 422, 572, 771
FaqI GGGAC 1 cut(s) 41
FatI CATG 3 cut(s) 418, 568, 767
Fnu4HI GCNGC 3 cut(s) 693, 716, 765
FokI GGATG 2 cut(s) 132, 551
Fsp4HI GCNGC 3 cut(s) 693, 716, 765
FspBI CTAG 1 cut(s) 809
GlaI GCGC 2 cut(s) 719, 881
GluI GCNGC 3 cut(s) 693, 716, 765
GsuI CTGGAG 1 cut(s) 742
HaeII RGCGCY 1 cut(s) 721
HapII CCGG 1 cut(s) 150
HhaI GCGC 2 cut(s) 720, 882
Hin1II CATG 3 cut(s) 422, 572, 771
Hin6I GCGC 2 cut(s) 718, 880
HinP1I GCGC 2 cut(s) 718, 880
HinfI GANTC 4 cut(s) 95, 246, 661, 749
HpaII CCGG 1 cut(s) 150
HphI GGTGA 2 cut(s) 56, 841
Hpy188I TCNGA 9 cut(s) 7, 142, 218, 245, 559, 564, 583, 800, 834
Hpy188III TCNNGA 4 cut(s) 290, 312, 359, 655
HpyAV CCTTC 5 cut(s) 123, 287, 520, 677, 859
HpyCH4III ACNGT 4 cut(s) 77, 374, 632, 784
HpyCH4IV ACGT 1 cut(s) 893
HpyCH4V TGCA 4 cut(s) 443, 601, 635, 764
HpyF10VI GCNNNNNNNGC 2 cut(s) 692, 866
HpyF3I CTNAG 5 cut(s) 274, 482, 519, 725, 797
HpySE526I ACGT 1 cut(s) 893
Hsp92II CATG 3 cut(s) 422, 572, 771
HspAI GCGC 2 cut(s) 718, 880
Kzo9I GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
LguI GCTCTTC 1 cut(s) 846
LmnI GCTCC 1 cut(s) 572
LpnPI CCDG 9 cut(s) 94, 163, 180, 322, 349, 372, 469, 513, 772
Lsp1109I GCAGC 2 cut(s) 727, 776
LweI GCATC 1 cut(s) 588
MaeI CTAG 1 cut(s) 809
MaeII ACGT 1 cut(s) 893
MaeIII GTNAC 1 cut(s) 317
MalI GATC 8 cut(s) 144, 288, 341, 357, 414, 561, 585, 831
MbiI CCGCTC 1 cut(s) 839
MboI GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
MboII GAAGA 2 cut(s) 833, 836
MflI RGATCY 2 cut(s) 412, 559
MhlI GDGCHC 1 cut(s) 577
MluCI AATT 8 cut(s) 187, 346, 363, 379, 542, 602, 636, 870
MmeI TCCRAC 1 cut(s) 179
MseI TTAA 1 cut(s) 224
MspI CCGG 1 cut(s) 150
MspR9I CCNGG 2 cut(s) 150, 337
MvaI CCWGG 1 cut(s) 337
MvnI CGCG 1 cut(s) 313
MwoI GCNNNNNNNGC 2 cut(s) 692, 866
NciI CCSGG 1 cut(s) 150
NdeII GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
NlaIII CATG 3 cut(s) 422, 572, 771
NlaIV GGNNCC 1 cut(s) 259
NmeAIII GCCGAG 1 cut(s) 886
NruI TCGCGA 1 cut(s) 313
PciSI GCTCTTC 1 cut(s) 846
PcsI WCGNNNNNNNCGW 1 cut(s) 825
PfeI GAWTC 4 cut(s) 95, 246, 661, 749
PflFI GACNNNGTC 1 cut(s) 895
PfoI TCCNGGA 2 cut(s) 148, 335
PkrI GCNGC 3 cut(s) 694, 717, 766
Psp6I CCWGG 1 cut(s) 335
PspGI CCWGG 1 cut(s) 335
PspN4I GGNNCC 1 cut(s) 259
PspPI GGNCC 2 cut(s) 157, 328
PsuI RGATCY 2 cut(s) 412, 559
PsyI GACNNNGTC 1 cut(s) 895
RruI TCGCGA 1 cut(s) 313
RsaI GTAC 1 cut(s) 776
RsaNI GTAC 1 cut(s) 775
SapI GCTCTTC 1 cut(s) 846
SaqAI TTAA 1 cut(s) 224
SatI GCNGC 3 cut(s) 693, 716, 765
Sau3AI GATC 8 cut(s) 142, 286, 339, 355, 412, 559, 583, 829
Sau96I GGNCC 2 cut(s) 157, 328
ScrFI CCNGG 2 cut(s) 150, 337
SduI GDGCHC 1 cut(s) 577
SetI ASST 6 cut(s) 115, 243, 405, 512, 896, 911
SfaNI GCATC 1 cut(s) 588
SinI GGWCC 2 cut(s) 157, 328
Sse9I AATT 8 cut(s) 187, 346, 363, 379, 542, 602, 636, 870
SsiI CCGC 5 cut(s) 42, 549, 693, 772, 837
SspI AATATT 1 cut(s) 16
SspMI CTAG 1 cut(s) 809
StyD4I CCNGG 2 cut(s) 148, 335
StyI CCWWGG 1 cut(s) 102
TaaI ACNGT 4 cut(s) 77, 374, 632, 784
TaiI ACGT 1 cut(s) 896
TaqI TCGA 1 cut(s) 899
TasI AATT 8 cut(s) 187, 346, 363, 379, 542, 602, 636, 870
TauI GCSGC 1 cut(s) 695
TfiI GAWTC 4 cut(s) 95, 246, 661, 749
Tru1I TTAA 1 cut(s) 224
Tru9I TTAA 1 cut(s) 224
TscAI CASTG 4 cut(s) 379, 637, 733, 766
TseI GCWGC 2 cut(s) 715, 764
TspDTI ATGAA 5 cut(s) 75, 118, 122, 555, 674
TspRI CASTG 4 cut(s) 379, 637, 733, 766
Tth111I GACNNNGTC 1 cut(s) 895
VpaK11BI GGWCC 2 cut(s) 157, 328
XcmI CCANNNNNNNNNTGG 1 cut(s) 801
XspI CTAG 1 cut(s) 809
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.