FvH4_4g33921

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000146
Physical Location & Seq
Reverse (-)
31964853 .. 31965583
731 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g33921.t1

Sequence Viewer

Length: 600 bp
ATGCCTCCAGTCGTCAACCATTATCATACCACCACTCAAGACAACTCGGCCTTTCCGACCAGTGTTGCCTTGAATGAAACCGATTATTCAATATGGGCACCTCTTATGAAGATGAGGATTGGAGCACGCGGTAAGGTTGGTTATCTCACCGGAGCCAAAGTCGCACCAGATGAGAATTCGCCTGAATTTGAAACTTGGGCCACAAAGAATGAGAGAGTAAAAGGTTGGCTCATTGATTCCATGGAGCCATCACTCATCAATCGGTATATCCGACTACCAACATCCAAAGATGTTTGGGAAGCAGTTGAGAAGACCTTTTATGATGATTCTGATGAGACCCGAATCTTTGAATTGAATAAGAAGTGCTTTGCAACGAGACAGAATGGTCAGCCTCTTCCTACCTATTATAATGAATTGGTGGGAATGTTCCATGAGATCGATCAACGTATTGCCTCTCAAAACAACACAATAGCTGGAGTTATTCAAGAAACGACTGCTATGATGCGTATGCGAGTTCACATGTTCCTTAGTGGGCTTGATTCAGAGTATGATGAAGTCTATGGGTCTTCCTCCAGGCTTCTCAAATGCTCCACCACGTAG
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

Protein Analysis

200

Amino Acids

22.74

Weight (kDa)

5.42

Isoelectric Point (pI)

36.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 36 - 141 4.9e-08 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000146)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g19561 FvH4_1g25371 FvH4_1g25961 FvH4_2g00352 FvH4_2g00861 FvH4_2g04952 FvH4_2g05413 FvH4_2g07531 FvH4_2g08961 FvH4_2g25141 FvH4_2g27292 FvH4_3g18164 FvH4_3g19921 FvH4_3g43870 FvH4_4g14441 FvH4_4g15581 FvH4_4g15582 FvH4_4g16890 FvH4_4g19782 FvH4_4g33444 FvH4_4g33921 FvH4_5g22281 FvH4_5g22282 FvH4_5g32571 FvH4_5g37451 FvH4_5g39631 FvH4_6g04721 FvH4_6g11661 FvH4_6g20571 FvH4_6g32791 FvH4_7g23184
prunus_persica Prupe.1G090900_v2.0.a1 Prupe.1G241200_v2.0.a1 Prupe.1G534100_v2.0.a1 Prupe.3G076700_v2.0.a1 Prupe.4G150800_v2.0.a1 Prupe.4G181800_v2.0.a1 Prupe.4G240900_v2.0.a1 Prupe.4G247600_v2.0.a1 Prupe.6G115900_v2.0.a1 Prupe.6G327500_v2.0.a1 Prupe.8G071700_v2.0.a1
pyrus_communis pycom06g11480 pycom10g08330 pycom15g04320 pycom15g04350 pycom15g12620 pycom2874g00060
rosa_chinensis RchiOBHm_Chr1g0317241 RchiOBHm_Chr1g0341801 RchiOBHm_Chr1g0341931 RchiOBHm_Chr1g0359621 RchiOBHm_Chr2g0113741 RchiOBHm_Chr2g0117261 RchiOBHm_Chr2g0138831 RchiOBHm_Chr2g0141421 RchiOBHm_Chr2g0145281 RchiOBHm_Chr2g0152991 RchiOBHm_Chr3g0448001 RchiOBHm_Chr3g0450981 RchiOBHm_Chr3g0455161 RchiOBHm_Chr3g0457401 RchiOBHm_Chr3g0460001 RchiOBHm_Chr4g0387431 RchiOBHm_Chr4g0388741 RchiOBHm_Chr4g0444201 RchiOBHm_Chr4g0444261 RchiOBHm_Chr5g0010221 RchiOBHm_Chr6g0271721 RchiOBHm_Chr6g0274641 RchiOBHm_Chr6g0294691 RchiOBHm_Chr7g0237031 RchiOBHm_Chr7g0238461 RchiOBHm_Chr7g0239981
rosa_laevigata RLG00000009017
rosa_multiflora Rmu_co7986768.1_g000001 Rmu_co8302239.1_g000001 Rmu_co8485799.1_g000001 Rmu_sc0000061.1_g000013 Rmu_sc0000303.1_g000034 Rmu_sc0000303.1_g000035 Rmu_sc0000315.1_g000017 Rmu_sc0000349.1_g000003 Rmu_sc0000498.1_g000068 Rmu_sc0000508.1_g000014 Rmu_sc0000602.1_g000001 Rmu_sc0000633.1_g000002 Rmu_sc0000638.1_g000030 Rmu_sc0000756.1_g000016 Rmu_sc0000756.1_g000017 Rmu_sc0000785.1_g000037 Rmu_sc0000795.1_g000017 Rmu_sc0000796.1_g000030 Rmu_sc0000863.1_g000023 Rmu_sc0000920.1_g000021 Rmu_sc0000960.1_g000015 Rmu_sc0000982.1_g000102 Rmu_sc0001036.1_g000008 Rmu_sc0001036.1_g000009 Rmu_sc0001643.1_g000029 Rmu_sc0001687.1_g000026 Rmu_sc0001708.1_g000037 Rmu_sc0001768.1_g000015 Rmu_sc0001790.1_g000022 Rmu_sc0002180.1_g000007 Rmu_sc0002211.1_g000006 Rmu_sc0002270.1_g000010 Rmu_sc0002404.1_g000031 Rmu_sc0002858.1_g000016 Rmu_sc0003063.1_g000028 Rmu_sc0003730.1_g000017 Rmu_sc0004087.1_g000020 Rmu_sc0004618.1_g000048 Rmu_sc0004724.1_g000005 Rmu_sc0005167.1_g000036 Rmu_sc0005781.1_g000003 Rmu_sc0005878.1_g000012 Rmu_sc0006011.1_g000003 Rmu_sc0006343.1_g000011 Rmu_sc0006573.1_g000007 Rmu_sc0006599.1_g000007 Rmu_sc0006803.1_g000014 Rmu_sc0006836.1_g000002 Rmu_sc0006849.1_g000002 Rmu_sc0007109.1_g000009 Rmu_sc0009268.1_g000016 Rmu_sc0009618.1_g000017 Rmu_sc0009674.1_g000009 Rmu_sc0010244.1_g000009 Rmu_sc0011151.1_g000004 Rmu_sc0011356.1_g000001 Rmu_sc0011674.1_g000002 Rmu_sc0011778.1_g000016 Rmu_sc0012342.1_g000001 Rmu_sc0012467.1_g000002 Rmu_sc0012574.1_g000003 Rmu_sc0012913.1_g000005 Rmu_sc0013612.1_g000020 Rmu_sc0014824.1_g000001 Rmu_sc0017869.1_g000002 Rmu_sc0018085.1_g000003 Rmu_sc0024789.1_g000001 Rmu_sc0025106.1_g000013 Rmu_sc0034502.1_g000001 Rmu_sc0034547.1_g000001 Rmu_sc0035094.1_g000001 Rmu_sc0035095.1_g000001 Rmu_ssc0000100.1_g000027 Rmu_ssc0000244.1_g000005 Rmu_ssc0000371.1_g000029 Rmu_ssc0000381.1_g000004
rosa_roxburghii Rroxscaffold_1G00015480 Rroxscaffold_1G00023580 Rroxscaffold_1G00039340 Rroxscaffold_1G00047080 Rroxscaffold_2G00095820 Rroxscaffold_2G00125200 Rroxscaffold_2G00128330 Rroxscaffold_3G00270860
rosa_rugosa Rorug06G0120700
rosa_samantha Rh3BG173100 Rh6AG089600 Rh7AG488100 Rh7DG389600
rosa_wichuraiana Rw0G001150 Rw0G001990 Rw0G002010 Rw0G019540 Rw1G013730 Rw1G024110 Rw1G029190 Rw2G018850 Rw2G021090 Rw2G022260 Rw2G023180 Rw2G027280 Rw3G010190 Rw3G020660 Rw3G029380 Rw4G002390 Rw4G002690 Rw4G033260 Rw5G011960 Rw5G023110 Rw5G025250 Rw5G028950 Rw5G033740 Rw5G033950 Rw5G037900 Rw6G009640 Rw6G011620 Rw6G027720 Rw7G010680 Rw7G042070

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 408
AasI GACNNNNNNGTC 1 cut(s) 384
AccB1I GGYRCC 1 cut(s) 97
AccII CGCG 1 cut(s) 129
AciI CCGC 1 cut(s) 129
AcsI RAATTY 2 cut(s) 175, 185
AflIII ACRYGT 1 cut(s) 519
AgsI TTSAA 6 cut(s) 73, 90, 191, 350, 355, 485
AjnI CCWGG 1 cut(s) 572
AluBI AGCT 1 cut(s) 473
AluI AGCT 1 cut(s) 473
Alw21I GWGCWC 1 cut(s) 127
Alw26I GTCTC 2 cut(s) 329, 370
AoxI GGCC 2 cut(s) 48, 198
ApoI RAATTY 2 cut(s) 175, 185
AspS9I GGNCC 1 cut(s) 198
AsuHPI GGTGA 1 cut(s) 139
BaeGI GKGCMC 1 cut(s) 100
BanI GGYRCC 1 cut(s) 97
BbsI GAAGAC 2 cut(s) 317, 558
Bbv12I GWGCWC 1 cut(s) 127
BccI CCATC 1 cut(s) 256
BciT130I CCWGG 1 cut(s) 574
BcoDI GTCTC 2 cut(s) 329, 370
Bme1390I CCNGG 1 cut(s) 574
BmgT120I GGNCC 1 cut(s) 198
BmiI GGNNCC 3 cut(s) 99, 154, 246
BmrFI CCNGG 1 cut(s) 574
BmsI GCATC 1 cut(s) 492
BpiI GAAGAC 2 cut(s) 317, 558
BpmI CTGGAG 2 cut(s) 495, 556
BpuEI CTTGAG 1 cut(s) 21
Bsa29I ATCGAT 1 cut(s) 438
BsaAI YACGTR 1 cut(s) 597
BsaI GGTCTC 1 cut(s) 329
BsaJI CCNNGG 1 cut(s) 240
BsaWI WCCGGW 1 cut(s) 149
BsaXI ACNNNNNCTCC 2 cut(s) 144, 174
Bse1I ACTGG 2 cut(s) 8, 60
BseBI CCWGG 1 cut(s) 574
BseCI ATCGAT 1 cut(s) 438
BseDI CCNNGG 1 cut(s) 240
BseGI GGATG 1 cut(s) 281
BseNI ACTGG 2 cut(s) 8, 60
BseSI GKGCMC 1 cut(s) 100
Bsh1236I CGCG 1 cut(s) 129
BshFI GGCC 2 cut(s) 50, 200
BshNI GGYRCC 1 cut(s) 97
BshVI ATCGAT 1 cut(s) 438
BsiHKAI GWGCWC 1 cut(s) 127
BsiSI CCGG 1 cut(s) 150
BsmAI GTCTC 2 cut(s) 329, 370
BsnI GGCC 2 cut(s) 50, 200
Bso31I GGTCTC 1 cut(s) 329
Bsp1286I GDGCHC 2 cut(s) 100, 127
Bsp143I GATC 2 cut(s) 435, 439
Bsp19I CCATGG 1 cut(s) 240
BspACI CCGC 1 cut(s) 129
BspANI GGCC 2 cut(s) 50, 200
BspDI ATCGAT 1 cut(s) 438
BspFNI CGCG 1 cut(s) 129
BspLI GGNNCC 3 cut(s) 99, 154, 246
BspT107I GGYRCC 1 cut(s) 97
BspTNI GGTCTC 1 cut(s) 329
BsrI ACTGG 2 cut(s) 8, 60
BssECI CCNNGG 1 cut(s) 240
BssMI GATC 2 cut(s) 435, 439
BssT1I CCWWGG 1 cut(s) 240
Bst2UI CCWGG 1 cut(s) 574
Bst6I CTCTTC 1 cut(s) 399
BstBAI YACGTR 1 cut(s) 597
BstC8I GCNNGC 1 cut(s) 127
BstDEI CTNAG 1 cut(s) 527
BstDSI CCRYGG 1 cut(s) 240
BstF5I GGATG 1 cut(s) 281
BstFNI CGCG 1 cut(s) 129
BstKTI GATC 2 cut(s) 438, 442
BstMAI GTCTC 2 cut(s) 329, 370
BstMBI GATC 2 cut(s) 435, 439
BstMWI GCNNNNNNNGC 1 cut(s) 161
BstNI CCWGG 1 cut(s) 574
BstNSI RCATGY 1 cut(s) 523
BstSCI CCNGG 1 cut(s) 572
BstSLI GKGCMC 1 cut(s) 100
BstUI CGCG 1 cut(s) 129
BstV2I GAAGAC 2 cut(s) 317, 558
Bsu15I ATCGAT 1 cut(s) 438
BsuRI GGCC 2 cut(s) 50, 200
BsuTUI ATCGAT 1 cut(s) 438
BtgI CCRYGG 1 cut(s) 240
BtsCI GGATG 1 cut(s) 281
BtsIMutI CAGTG 1 cut(s) 67
Cac8I GCNNGC 1 cut(s) 127
Cfr13I GGNCC 1 cut(s) 198
ClaI ATCGAT 1 cut(s) 438
CviAII CATG 3 cut(s) 241, 431, 520
CviJI RGCY 9 cut(s) 50, 155, 200, 229, 247, 391, 473, 535, 577
CviKI_1 RGCY 9 cut(s) 50, 155, 200, 229, 247, 391, 473, 535, 577
DdeI CTNAG 1 cut(s) 527
DpnI GATC 2 cut(s) 437, 441
DpnII GATC 2 cut(s) 435, 439
DrdI GACNNNNNNGTC 1 cut(s) 384
DseDI GACNNNNNNGTC 1 cut(s) 384
Eam1104I CTCTTC 1 cut(s) 399
EarI CTCTTC 1 cut(s) 399
Eco130I CCWWGG 1 cut(s) 240
Eco31I GGTCTC 1 cut(s) 329
EcoRI GAATTC 1 cut(s) 175
EcoRII CCWGG 1 cut(s) 572
EcoT14I CCWWGG 1 cut(s) 240
ErhI CCWWGG 1 cut(s) 240
FaeI CATG 3 cut(s) 244, 434, 523
FalI AAGNNNNNCTT 2 cut(s) 350, 382
FatI CATG 3 cut(s) 240, 430, 519
FokI GGATG 1 cut(s) 268
GsuI CTGGAG 2 cut(s) 495, 556
HaeIII GGCC 2 cut(s) 50, 200
HapII CCGG 1 cut(s) 150
Hin1II CATG 3 cut(s) 244, 434, 523
HincII GTYRAC 1 cut(s) 16
HindII GTYRAC 1 cut(s) 16
HinfI GANTC 4 cut(s) 236, 326, 342, 539
HpaII CCGG 1 cut(s) 150
HphI GGTGA 1 cut(s) 139
Hpy166II GTNNAC 2 cut(s) 16, 517
Hpy188I TCNGA 4 cut(s) 57, 272, 331, 544
Hpy188III TCNNGA 2 cut(s) 38, 485
Hpy8I GTNNAC 2 cut(s) 16, 517
HpyCH4IV ACGT 2 cut(s) 445, 596
HpyCH4V TGCA 1 cut(s) 371
HpyF10VI GCNNNNNNNGC 1 cut(s) 161
HpyF3I CTNAG 1 cut(s) 527
HpySE526I ACGT 2 cut(s) 445, 596
Hsp92II CATG 3 cut(s) 244, 434, 523
Kzo9I GATC 2 cut(s) 435, 439
LmnI GCTCC 4 cut(s) 122, 152, 244, 593
LpnPI CCDG 8 cut(s) 21, 73, 163, 180, 195, 459, 559, 586
LweI GCATC 1 cut(s) 492
MaeII ACGT 2 cut(s) 445, 596
MalI GATC 2 cut(s) 437, 441
MboI GATC 2 cut(s) 435, 439
MboII GAAGA 4 cut(s) 121, 322, 386, 558
MhlI GDGCHC 2 cut(s) 100, 127
MluCI AATT 4 cut(s) 175, 185, 350, 413
MmeI TCCRAC 2 cut(s) 80, 295
MnlI CCTC 6 cut(s) 15, 108, 111, 402, 463, 580
MspI CCGG 1 cut(s) 150
MspR9I CCNGG 1 cut(s) 574
MvaI CCWGG 1 cut(s) 574
MvnI CGCG 1 cut(s) 129
MwoI GCNNNNNNNGC 1 cut(s) 161
NcoI CCATGG 1 cut(s) 240
NdeII GATC 2 cut(s) 435, 439
NlaIII CATG 3 cut(s) 244, 434, 523
NlaIV GGNNCC 3 cut(s) 99, 154, 246
NmeAIII GCCGAG 1 cut(s) 26
NspI RCATGY 1 cut(s) 523
PciI ACATGT 1 cut(s) 519
PcsI WCGNNNNNNNCGW 2 cut(s) 53, 268
PfeI GAWTC 4 cut(s) 236, 326, 342, 539
Ppu21I YACGTR 1 cut(s) 597
PscI ACATGT 1 cut(s) 519
PsiI TTATAA 1 cut(s) 408
Psp6I CCWGG 1 cut(s) 572
PspGI CCWGG 1 cut(s) 572
PspN4I GGNNCC 3 cut(s) 99, 154, 246
PspPI GGNCC 1 cut(s) 198
Sau3AI GATC 2 cut(s) 435, 439
Sau96I GGNCC 1 cut(s) 198
ScrFI CCNGG 1 cut(s) 574
SduI GDGCHC 2 cut(s) 100, 127
SetI ASST 8 cut(s) 103, 138, 226, 317, 404, 448, 475, 599
SfaNI GCATC 1 cut(s) 492
SmlI CTYRAG 1 cut(s) 36
SmoI CTYRAG 1 cut(s) 36
Sse9I AATT 4 cut(s) 175, 185, 350, 413
SsiI CCGC 1 cut(s) 129
StyD4I CCNGG 1 cut(s) 572
StyI CCWWGG 1 cut(s) 240
TaiI ACGT 2 cut(s) 448, 599
TaqI TCGA 1 cut(s) 438
TasI AATT 4 cut(s) 175, 185, 350, 413
TfiI GAWTC 4 cut(s) 236, 326, 342, 539
TscAI CASTG 1 cut(s) 67
TspDTI ATGAA 4 cut(s) 90, 122, 426, 567
TspRI CASTG 1 cut(s) 67
XapI RAATTY 2 cut(s) 175, 185
XceI RCATGY 1 cut(s) 523
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.