FvH4_2g00352

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb2
OG0000146
Physical Location & Seq
Reverse (-)
477754 .. 478230
477 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_2g00352.t1

Sequence Viewer

Length: 477 bp
ATGTGTATTGGAGGACGTAATAAGCTTGAACTTATTACTGAAGCTGCACTTGAAATTTCTTCACTGGCACATCGTGCATGGGCCATTGACAATGAAAAAGTGAATTGTTGGCTCATCGATAACATTTCCCCATCTTTGATGAATGGGTATCTTCGATTGCCAACTGCCAAAGCTATCTGGGATGCCCTATACAAGACCTATTATGATGATTCAGATGAAACCCGACTCTTTGAATTTCATCGCCTGTGCTTTTGGGCGAAGCATAATGGAAGACCTCTTTCTGCCCACTACAATGAACTTGTAGGATGGTTGGAAGAGATGGATCAACGCCTGGCATCTCATTCCACTACAATTGATGGCATTGTGTATGAAGCATCGTATATGGCCCGATTGAGGGTTCACATGTTCTTGAGCGGATTGGATCCTGAATTTGATCAAGTTCGGGAAGAGATTCTGAACGCCTGGCGTTGTGTATGA
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

159

Amino Acids

18.4

Weight (kDa)

5.32

Isoelectric Point (pI)

41.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 14 - 108 9.8e-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
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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)
AccBSI CCGCTC 1 cut(s) 414
AciI CCGC 1 cut(s) 414
AclWI GGATC 3 cut(s) 330, 416, 429
AcsI RAATTY 3 cut(s) 54, 233, 428
AcuI CTGAAG 1 cut(s) 60
AdeI CACNNNGTG 1 cut(s) 74
AfiI CCNNNNNNNGG 2 cut(s) 393, 394
AflIII ACRYGT 1 cut(s) 402
AgsI TTSAA 3 cut(s) 29, 53, 233
AjnI CCWGG 2 cut(s) 330, 461
AluBI AGCT 3 cut(s) 25, 44, 173
AluI AGCT 3 cut(s) 25, 44, 173
AlwI GGATC 3 cut(s) 330, 416, 429
AoxI GGCC 2 cut(s) 81, 384
ApeKI GCWGC 1 cut(s) 44
ApoI RAATTY 3 cut(s) 54, 233, 428
Asp700I GAANNNNTTC 1 cut(s) 450
AspS9I GGNCC 2 cut(s) 81, 385
BamHI GGATCC 1 cut(s) 421
BbsI GAAGAC 1 cut(s) 277
BbvI GCAGC 1 cut(s) 31
BccI CCATC 4 cut(s) 139, 300, 313, 350
BciT130I CCWGG 2 cut(s) 332, 463
BclI TGATCA 1 cut(s) 433
BisI GCNGC 1 cut(s) 45
BlsI GCNGC 1 cut(s) 46
Bme1390I CCNGG 2 cut(s) 332, 463
BmgT120I GGNCC 2 cut(s) 81, 385
BmiI GGNNCC 1 cut(s) 423
BmrFI CCNGG 2 cut(s) 332, 463
BmsI GCATC 3 cut(s) 172, 344, 383
BpiI GAAGAC 1 cut(s) 277
BpuEI CTTGAG 1 cut(s) 430
Bsa29I ATCGAT 1 cut(s) 117
Bsc4I CCNNNNNNNGG 2 cut(s) 393, 394
Bse1I ACTGG 1 cut(s) 69
BseBI CCWGG 2 cut(s) 332, 463
BseCI ATCGAT 1 cut(s) 117
BseGI GGATG 2 cut(s) 187, 311
BseLI CCNNNNNNNGG 2 cut(s) 393, 394
BseNI ACTGG 1 cut(s) 69
BseXI GCAGC 1 cut(s) 31
BsgI GTGCAG 1 cut(s) 30
BshFI GGCC 2 cut(s) 83, 386
BshVI ATCGAT 1 cut(s) 117
BslI CCNNNNNNNGG 2 cut(s) 393, 394
BsnI GGCC 2 cut(s) 83, 386
Bsp143I GATC 3 cut(s) 322, 421, 433
BspACI CCGC 1 cut(s) 414
BspANI GGCC 2 cut(s) 83, 386
BspDI ATCGAT 1 cut(s) 117
BspLI GGNNCC 1 cut(s) 423
BspPI GGATC 3 cut(s) 330, 416, 429
BsrBI CCGCTC 1 cut(s) 414
BsrI ACTGG 1 cut(s) 69
BssMI GATC 3 cut(s) 322, 421, 433
Bst2UI CCWGG 2 cut(s) 332, 463
Bst6I CTCTTC 2 cut(s) 309, 441
BstAPI GCANNNNNTGC 1 cut(s) 74
BstF5I GGATG 2 cut(s) 187, 311
BstKTI GATC 3 cut(s) 325, 424, 436
BstMBI GATC 3 cut(s) 322, 421, 433
BstMWI GCNNNNNNNGC 1 cut(s) 74
BstNI CCWGG 2 cut(s) 332, 463
BstNSI RCATGY 1 cut(s) 406
BstSCI CCNGG 2 cut(s) 330, 461
BstV1I GCAGC 1 cut(s) 31
BstV2I GAAGAC 1 cut(s) 277
BstX2I RGATCY 1 cut(s) 421
BstYI RGATCY 1 cut(s) 421
Bsu15I ATCGAT 1 cut(s) 117
BsuRI GGCC 2 cut(s) 83, 386
BsuTUI ATCGAT 1 cut(s) 117
BtgZI GCGATG 1 cut(s) 224
BtsCI GGATG 2 cut(s) 187, 311
BtsIMutI CAGTG 1 cut(s) 62
Cfr13I GGNCC 2 cut(s) 81, 385
ClaI ATCGAT 1 cut(s) 117
CspCI CAANNNNNGTGG 2 cut(s) 334, 369
CviAII CATG 2 cut(s) 78, 403
CviJI RGCY 6 cut(s) 25, 44, 83, 112, 173, 386
CviKI_1 RGCY 6 cut(s) 25, 44, 83, 112, 173, 386
DpnI GATC 3 cut(s) 324, 423, 435
DpnII GATC 3 cut(s) 322, 421, 433
DraIII CACNNNGTG 1 cut(s) 74
Eam1104I CTCTTC 2 cut(s) 309, 441
EarI CTCTTC 2 cut(s) 309, 441
Eco57I CTGAAG 1 cut(s) 60
EcoRII CCWGG 2 cut(s) 330, 461
FaeI CATG 2 cut(s) 81, 406
FaiI YATR 9 cut(s) 79, 190, 204, 264, 369, 381, 383, 404, 475
FalI AAGNNNNNCTT 2 cut(s) 33, 65
FatI CATG 2 cut(s) 77, 402
FbaI TGATCA 1 cut(s) 433
Fnu4HI GCNGC 1 cut(s) 45
FokI GGATG 2 cut(s) 194, 318
Fsp4HI GCNGC 1 cut(s) 45
GluI GCNGC 1 cut(s) 45
HaeIII GGCC 2 cut(s) 83, 386
Hin1II CATG 2 cut(s) 81, 406
HindIII AAGCTT 1 cut(s) 23
HinfI GANTC 3 cut(s) 209, 225, 451
Hpy166II GTNNAC 1 cut(s) 400
Hpy188I TCNGA 2 cut(s) 214, 456
Hpy188III TCNNGA 3 cut(s) 409, 425, 443
Hpy8I GTNNAC 1 cut(s) 400
HpyCH4IV ACGT 1 cut(s) 16
HpyCH4V TGCA 2 cut(s) 47, 77
HpyF10VI GCNNNNNNNGC 1 cut(s) 74
HpySE526I ACGT 1 cut(s) 16
Hsp92II CATG 2 cut(s) 81, 406
Ksp22I TGATCA 1 cut(s) 433
Kzo9I GATC 3 cut(s) 322, 421, 433
LpnPI CCDG 7 cut(s) 50, 163, 257, 317, 344, 438, 448
Lsp1109I GCAGC 1 cut(s) 31
LweI GCATC 3 cut(s) 172, 344, 383
MaeII ACGT 1 cut(s) 16
MalI GATC 3 cut(s) 324, 423, 435
MbiI CCGCTC 1 cut(s) 414
MboI GATC 3 cut(s) 322, 421, 433
MboII GAAGA 5 cut(s) 51, 143, 282, 326, 458
MfeI CAATTG 1 cut(s) 351
MflI RGATCY 1 cut(s) 421
MluCI AATT 5 cut(s) 54, 103, 233, 351, 428
MlyI GAGTC 1 cut(s) 219
MmeI TCCRAC 1 cut(s) 291
MnlI CCTC 3 cut(s) 5, 285, 387
MroXI GAANNNNTTC 1 cut(s) 450
MslI CAYNNNNRTG 1 cut(s) 291
MspR9I CCNGG 2 cut(s) 332, 463
MunI CAATTG 1 cut(s) 351
MvaI CCWGG 2 cut(s) 332, 463
MwoI GCNNNNNNNGC 1 cut(s) 74
NdeII GATC 3 cut(s) 322, 421, 433
NlaIII CATG 2 cut(s) 81, 406
NlaIV GGNNCC 1 cut(s) 423
NspI RCATGY 1 cut(s) 406
PciI ACATGT 1 cut(s) 402
PdmI GAANNNNTTC 1 cut(s) 450
PfeI GAWTC 2 cut(s) 209, 451
PkrI GCNGC 1 cut(s) 46
PleI GAGTC 1 cut(s) 219
PpsI GAGTC 1 cut(s) 219
PscI ACATGT 1 cut(s) 402
Psp6I CCWGG 2 cut(s) 330, 461
PspGI CCWGG 2 cut(s) 330, 461
PspN4I GGNNCC 1 cut(s) 423
PspPI GGNCC 2 cut(s) 81, 385
PsuI RGATCY 1 cut(s) 421
RseI CAYNNNNRTG 1 cut(s) 291
SatI GCNGC 1 cut(s) 45
Sau3AI GATC 3 cut(s) 322, 421, 433
Sau96I GGNCC 2 cut(s) 81, 385
SchI GAGTC 1 cut(s) 219
ScrFI CCNGG 2 cut(s) 332, 463
SetI ASST 6 cut(s) 19, 27, 46, 175, 200, 277
SfaNI GCATC 3 cut(s) 172, 344, 383
SmiMI CAYNNNNRTG 1 cut(s) 291
SmlI CTYRAG 1 cut(s) 409
SmoI CTYRAG 1 cut(s) 409
Sse9I AATT 5 cut(s) 54, 103, 233, 351, 428
SsiI CCGC 1 cut(s) 414
StyD4I CCNGG 2 cut(s) 330, 461
TaiI ACGT 1 cut(s) 19
TaqI TCGA 2 cut(s) 117, 154
TasI AATT 5 cut(s) 54, 103, 233, 351, 428
TfiI GAWTC 2 cut(s) 209, 451
TscAI CASTG 1 cut(s) 69
TseI GCWGC 1 cut(s) 44
TspDTI ATGAA 6 cut(s) 108, 155, 227, 231, 309, 384
TspRI CASTG 1 cut(s) 69
XapI RAATTY 3 cut(s) 54, 233, 428
XceI RCATGY 1 cut(s) 406
XmnI GAANNNNTTC 1 cut(s) 450
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.