FvH4_3g12632

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000258
Physical Location & Seq
Forward (+)
7528174 .. 7529078
905 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g12632.t1

Sequence Viewer

Length: 831 bp
ATGGATCAACCTACTGCTGCTGGTGTTAAGAACCATATTGAGAAGCCATTTGTGTTCAAAGGCGTGGACTTCAAAAGATGGCAGCAAAAGATGTTGTTTTATCTAACAACACTGAACTTGGCACAAGTGATTACATCTGAGGCTCCAGATTTGCCAACAGAGGGTGATATCCCAGATGCAACTATTAAGGCTGTTGAAGCTTGGGAGCAAAACGAGTTTCTGTGTAAGAATTATATTCTGAATGCCTTAGATGATTCATTGTATGATGTTTATTCAACATTCAAAACTGCAAAAGAGCTATGGGATTCTTTGAACAAGAAATACAAGTCTGAGGTTGCAAGTGCCAAGAAGTTTGTTGTTGGAAAATTTCTGAATTTTAAGATGAGTGATGCCAATTCTGTGGTGAAGCAAGTGGAGGAACTCCAAATTACTGCTCATGAATTACTTGCTGAAGAGATGAACCTTGAGCAACTCATTCTCAAGCTTCGTGTGGAGGAAGAGAACAGAAAGAATGAAAAAACTGATTGGTCCTCAATGGAAGCAAAAGCCAATGTGATTGAAGGTAGCACCTCCAAGCCTAAGTTTCCTCACAATCATAAGAAGGGAAAAACTGCTGCCAAAAGAGCACCTACTGCCCCAAAAGCTGTTATGTTCAAAAAGAAAATTCAAGGTGCTTGCTGGGTGTGTGGTAAGCCTGGTCATAAAGCCATGGATTGTCGCCACAAGAAGGACAGACCTGCTGGAAATAATAATCAAGCAAACATGGCAGAAGATCAATTTGTTGTTGTTGTATCTGAGGTCAATCTAATGATCAATACCAATGACTGGTAG
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
No domains found.

Protein Analysis

277

Amino Acids

31.33

Weight (kDa)

8.67

Isoelectric Point (pI)

44.61

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 33 - 157 1.8e-16 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 745
AccB7I CCANNNNNTGG 1 cut(s) 825
AclWI GGATC 1 cut(s) 12
AcsI RAATTY 3 cut(s) 365, 373, 663
AcuI CTGAAG 1 cut(s) 471
AfiI CCNNNNNNNGG 3 cut(s) 161, 727, 825
AgsI TTSAA 9 cut(s) 58, 73, 197, 276, 283, 313, 560, 655, 668
AjnI CCWGG 1 cut(s) 694
AluBI AGCT 4 cut(s) 200, 298, 484, 644
AluI AGCT 4 cut(s) 200, 298, 484, 644
Alw21I GWGCWC 1 cut(s) 628
AlwI GGATC 1 cut(s) 12
ApeKI GCWGC 3 cut(s) 17, 82, 614
ApoI RAATTY 3 cut(s) 365, 373, 663
AspS9I GGNCC 1 cut(s) 528
AsuHPI GGTGA 2 cut(s) 176, 415
AvaII GGWCC 1 cut(s) 528
Bbv12I GWGCWC 1 cut(s) 628
BbvI GCAGC 3 cut(s) 4, 94, 601
BccI CCATC 1 cut(s) 72
BciT130I CCWGG 1 cut(s) 696
BclI TGATCA 1 cut(s) 810
BfuAI ACCTGC 1 cut(s) 745
BisI GCNGC 3 cut(s) 18, 83, 615
BlsI GCNGC 3 cut(s) 19, 84, 616
Bme1390I CCNGG 1 cut(s) 696
Bme18I GGWCC 1 cut(s) 528
BmgT120I GGNCC 1 cut(s) 528
BmiI GGNNCC 1 cut(s) 144
BmrFI CCNGG 1 cut(s) 696
BmsI GCATC 2 cut(s) 166, 379
BpmI CTGGAG 1 cut(s) 129
BpuEI CTTGAG 2 cut(s) 464, 485
BsaJI CCNNGG 1 cut(s) 708
Bsc4I CCNNNNNNNGG 3 cut(s) 161, 727, 825
Bse1I ACTGG 1 cut(s) 830
BseBI CCWGG 1 cut(s) 696
BseDI CCNNGG 1 cut(s) 708
BseLI CCNNNNNNNGG 3 cut(s) 161, 727, 825
BseMII CTCAG 3 cut(s) 129, 321, 786
BseNI ACTGG 1 cut(s) 830
BseXI GCAGC 3 cut(s) 4, 94, 601
BseYI CCCAGC 1 cut(s) 678
BsiHKAI GWGCWC 1 cut(s) 628
BslI CCNNNNNNNGG 3 cut(s) 161, 727, 825
BsmI GAATGC 1 cut(s) 247
Bsp1286I GDGCHC 1 cut(s) 628
Bsp143I GATC 3 cut(s) 4, 772, 810
Bsp19I CCATGG 1 cut(s) 708
BspCNI CTCAG 3 cut(s) 130, 322, 787
BspHI TCATGA 1 cut(s) 436
BspLI GGNNCC 1 cut(s) 144
BspMI ACCTGC 1 cut(s) 745
BspPI GGATC 1 cut(s) 12
BsrI ACTGG 1 cut(s) 830
BssECI CCNNGG 1 cut(s) 708
BssMI GATC 3 cut(s) 4, 772, 810
BssT1I CCWWGG 1 cut(s) 708
Bst2UI CCWGG 1 cut(s) 696
Bst6I CTCTTC 2 cut(s) 447, 492
BstAPI GCANNNNNTGC 1 cut(s) 632
BstC8I GCNNGC 1 cut(s) 676
BstDEI CTNAG 5 cut(s) 138, 247, 330, 579, 795
BstDSI CCRYGG 1 cut(s) 708
BstKTI GATC 3 cut(s) 7, 775, 813
BstMBI GATC 3 cut(s) 4, 772, 810
BstMWI GCNNNNNNNGC 5 cut(s) 197, 623, 632, 641, 764
BstNI CCWGG 1 cut(s) 696
BstSCI CCNGG 1 cut(s) 694
BstV1I GCAGC 3 cut(s) 4, 94, 601
BstXI CCANNNNNNTGG 1 cut(s) 400
BtgI CCRYGG 1 cut(s) 708
BtsIMutI CAGTG 1 cut(s) 110
BveI ACCTGC 1 cut(s) 745
Cac8I GCNNGC 1 cut(s) 676
CciI TCATGA 1 cut(s) 436
Cfr13I GGNCC 1 cut(s) 528
CviAII CATG 3 cut(s) 437, 709, 763
DdeI CTNAG 5 cut(s) 138, 247, 330, 579, 795
DpnI GATC 3 cut(s) 6, 774, 812
DpnII GATC 3 cut(s) 4, 772, 810
Eam1104I CTCTTC 2 cut(s) 447, 492
EarI CTCTTC 2 cut(s) 447, 492
Eco130I CCWWGG 1 cut(s) 708
Eco32I GATATC 1 cut(s) 169
Eco47I GGWCC 1 cut(s) 528
Eco57I CTGAAG 1 cut(s) 471
EcoRII CCWGG 1 cut(s) 694
EcoRV GATATC 1 cut(s) 169
EcoT14I CCWWGG 1 cut(s) 708
ErhI CCWWGG 1 cut(s) 708
FaeI CATG 3 cut(s) 440, 712, 766
FatI CATG 3 cut(s) 436, 708, 762
FbaI TGATCA 1 cut(s) 810
Fnu4HI GCNGC 3 cut(s) 18, 83, 615
Fsp4HI GCNGC 3 cut(s) 18, 83, 615
GluI GCNGC 3 cut(s) 18, 83, 615
GsaI CCCAGC 1 cut(s) 682
GsuI CTGGAG 1 cut(s) 129
Hin1II CATG 3 cut(s) 440, 712, 766
HindIII AAGCTT 2 cut(s) 198, 482
HinfI GANTC 2 cut(s) 254, 305
HphI GGTGA 2 cut(s) 176, 415
Hpy166II GTNNAC 1 cut(s) 67
Hpy188I TCNGA 5 cut(s) 139, 240, 331, 372, 796
Hpy188III TCNNGA 2 cut(s) 146, 437
Hpy8I GTNNAC 1 cut(s) 67
HpyAV CCTTC 3 cut(s) 554, 595, 721
HpyCH4V TGCA 3 cut(s) 179, 290, 338
HpyF10VI GCNNNNNNNGC 5 cut(s) 197, 623, 632, 641, 764
HpyF3I CTNAG 5 cut(s) 138, 247, 330, 579, 795
Hsp92II CATG 3 cut(s) 440, 712, 766
Ksp22I TGATCA 1 cut(s) 810
Kzo9I GATC 3 cut(s) 4, 772, 810
LmnI GCTCC 2 cut(s) 148, 205
LpnPI CCDG 9 cut(s) 6, 159, 186, 664, 681, 708, 726, 750, 811
Lsp1109I GCAGC 3 cut(s) 4, 94, 601
LweI GCATC 2 cut(s) 166, 379
MalI GATC 3 cut(s) 6, 774, 812
MboI GATC 3 cut(s) 4, 772, 810
MboII GAAGA 3 cut(s) 464, 509, 782
MhlI GDGCHC 1 cut(s) 628
MluCI AATT 8 cut(s) 229, 365, 373, 394, 426, 440, 663, 776
MmeI TCCRAC 1 cut(s) 340
MnlI CCTC 9 cut(s) 133, 154, 325, 409, 487, 541, 580, 597, 790
MseI TTAA 3 cut(s) 27, 186, 378
MspR9I CCNGG 1 cut(s) 696
Mva1269I GAATGC 1 cut(s) 247
MvaI CCWGG 1 cut(s) 696
MwoI GCNNNNNNNGC 5 cut(s) 197, 623, 632, 641, 764
NcoI CCATGG 1 cut(s) 708
NdeII GATC 3 cut(s) 4, 772, 810
NlaIII CATG 3 cut(s) 440, 712, 766
NlaIV GGNNCC 1 cut(s) 144
PagI TCATGA 1 cut(s) 436
PctI GAATGC 1 cut(s) 247
PfeI GAWTC 2 cut(s) 254, 305
PflMI CCANNNNNTGG 1 cut(s) 825
PkrI GCNGC 3 cut(s) 19, 84, 616
Psp6I CCWGG 1 cut(s) 694
PspFI CCCAGC 1 cut(s) 678
PspGI CCWGG 1 cut(s) 694
PspN4I GGNNCC 1 cut(s) 144
PspPI GGNCC 1 cut(s) 528
PsrI GAACNNNNNNTAC 2 cut(s) 305, 337
SaqAI TTAA 3 cut(s) 27, 186, 378
SatI GCNGC 3 cut(s) 18, 83, 615
Sau3AI GATC 3 cut(s) 4, 772, 810
Sau96I GGNCC 1 cut(s) 528
ScrFI CCNGG 1 cut(s) 696
SduI GDGCHC 1 cut(s) 628
SfaNI GCATC 2 cut(s) 166, 379
SinI GGWCC 1 cut(s) 528
SmlI CTYRAG 2 cut(s) 464, 479
SmoI CTYRAG 2 cut(s) 464, 479
Sse9I AATT 8 cut(s) 229, 365, 373, 394, 426, 440, 663, 776
StyD4I CCNGG 1 cut(s) 694
StyI CCWWGG 1 cut(s) 708
TasI AATT 8 cut(s) 229, 365, 373, 394, 426, 440, 663, 776
TfiI GAWTC 2 cut(s) 254, 305
Tru1I TTAA 3 cut(s) 27, 186, 378
Tru9I TTAA 3 cut(s) 27, 186, 378
TscAI CASTG 1 cut(s) 117
TseI GCWGC 3 cut(s) 17, 82, 614
TspDTI ATGAA 4 cut(s) 246, 453, 473, 528
TspRI CASTG 1 cut(s) 117
Van91I CCANNNNNTGG 1 cut(s) 825
VpaK11BI GGWCC 1 cut(s) 528
XapI RAATTY 3 cut(s) 365, 373, 663
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.