FvH4_4g15488

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000258
Physical Location & Seq
Forward (+)
19207544 .. 19215190
7647 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g15488.t1

Sequence Viewer

Length: 1071 bp
ATGGATCAATCTGTATCTTCGGTGATGAAAAATCATGTCGAGAAACCTAAGAAATTCAAGGGTTCTAATTTCAAACGCTGGCAACAGAAGATGTTGTTCTATTTGACGACCCTTCATGTGGCGAAAGTTCTGACTGCTGAGGCTCCTAAGGCTCTGCCAGAAGGAGAAGGAGAGAATGCTCCAACAGAGGCTGAAAAGGCTGATAATTTGAAGGCCATGGACACTTGGAAAACTAATGAGTTTCTATGTAGAAACTACATTCTTAATGCCTTGGATGACTCTCTGTATGACATTTACTCTACATTCAAAACAGCAAGGGAATTGTGGCAGTCATTAAAGAACAAGTACAAGACTGAGGTTGCTTGTTCAAAGAAGTTTGTCATTGGCAAGTTTCTGAATTTCAAGATGAGCGATGCCAAGTCTGTTGTCAAGCAAGTGGAGGAACTCCAAGTCATTGTTCATGAGTTGGAAGTTGAAGGTATGGGTCTTAACCCAAATTTCCTTGTTGGTGCTATTATTGAAAAGTTACCACCTTCATGGAAAGATTTCAAAATTTATCTGAAACATCTAACTGAGGATATGAATTTTGAGCAATTGGTTCTTAAACTTCTAGTTGAAGAGGATAACCGAAAGAATGAAAAGGCTGATGCTATTTCCTTGGAGCCAACTGCTAATATGGTTGGAGGGAGTCCATCAAAGGCCAAGTTTCAAAAAAACAAAGGCAAGTCTGTTGCTGCTGCCAAGCCAACTTTTGTTGCTGGAAAGAATCCTCTTGCCCCACAAAAGACCAAGGTTTTCAAGAAGCCACAAATGGGAGGCTGTTGGGGCATAGAGCTAAAGAGTGTCGCCTTCGGAAAGATCAAGGAGGTGCTGGAGGTTCTGGAAATTCCAACCAAGCCAACCTTGCTGAAACTGAAAATCAATTCATTGGTGTGGTTGCTGTTGAAGCAAACTTGGGGTTCTTCGTATGAGAATATGAGTTTCGAGAAGATGGATCAGATGCCTTGGGATCTCTTTGGCCGCCTTGGAACTCGCCGAACTCATTATCGGAGATTGGATTCGAAACCATAG
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

357

Amino Acids

40.61

Weight (kDa)

9.46

Isoelectric Point (pI)

37.58

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 56 - 214 3.1e-31 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)
AciI CCGC 1 cut(s) 1021
AclWI GGATC 3 cut(s) 12, 1002, 1017
AcoI YGGCCR 1 cut(s) 1018
AcsI RAATTY 6 cut(s) 53, 397, 496, 552, 583, 885
AfaI GTAC 1 cut(s) 347
AfiI CCNNNNNNNGG 2 cut(s) 118, 812
AjuI GAANNNNNNNTTGG 2 cut(s) 441, 473
AluBI AGCT 1 cut(s) 835
AluI AGCT 1 cut(s) 835
AlwI GGATC 3 cut(s) 12, 1002, 1017
AlwNI CAGNNNCTG 1 cut(s) 191
AoxI GGCC 3 cut(s) 213, 699, 1018
ApeKI GCWGC 2 cut(s) 734, 737
ApoI RAATTY 6 cut(s) 53, 397, 496, 552, 583, 885
Asp700I GAANNNNTTC 1 cut(s) 545
AsuHPI GGTGA 1 cut(s) 34
AsuII TTCGAA 1 cut(s) 1061
AxyI CCTNAGG 1 cut(s) 147
BbvCI CCTCAGC 1 cut(s) 138
BbvI GCAGC 2 cut(s) 721, 724
BccI CCATC 2 cut(s) 700, 985
BfaI CTAG 1 cut(s) 611
BisI GCNGC 3 cut(s) 735, 738, 1021
BlsI GCNGC 3 cut(s) 736, 739, 1022
BmiI GGNNCC 2 cut(s) 144, 663
BmsI GCATC 3 cut(s) 403, 637, 990
BpmI CTGGAG 1 cut(s) 893
Bpu10I CCTNAGC 1 cut(s) 138
Bpu14I TTCGAA 1 cut(s) 1061
BsaJI CCNNGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
Bsc4I CCNNNNNNNGG 2 cut(s) 118, 812
Bse21I CCTNAGG 1 cut(s) 147
BseDI CCNNGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
BseGI GGATG 1 cut(s) 280
BseLI CCNNNNNNNGG 2 cut(s) 118, 812
BseMII CTCAG 3 cut(s) 129, 345, 564
BseXI GCAGC 2 cut(s) 721, 724
BshFI GGCC 3 cut(s) 215, 701, 1020
BslI CCNNNNNNNGG 2 cut(s) 118, 812
BsmI GAATGC 1 cut(s) 181
BsnI GGCC 3 cut(s) 215, 701, 1020
Bsp119I TTCGAA 1 cut(s) 1061
Bsp143I GATC 4 cut(s) 4, 858, 994, 1009
Bsp19I CCATGG 1 cut(s) 216
BspACI CCGC 1 cut(s) 1021
BspANI GGCC 3 cut(s) 215, 701, 1020
BspCNI CTCAG 3 cut(s) 130, 346, 565
BspHI TCATGA 1 cut(s) 460
BspLI GGNNCC 2 cut(s) 144, 663
BspPI GGATC 3 cut(s) 12, 1002, 1017
BspT104I TTCGAA 1 cut(s) 1061
BssECI CCNNGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
BssMI GATC 4 cut(s) 4, 858, 994, 1009
BssT1I CCWWGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
Bst6I CTCTTC 1 cut(s) 612
BstBI TTCGAA 1 cut(s) 1061
BstC8I GCNNGC 1 cut(s) 80
BstDEI CTNAG 5 cut(s) 48, 138, 147, 354, 573
BstDSI CCRYGG 1 cut(s) 216
BstF5I GGATG 1 cut(s) 280
BstKTI GATC 4 cut(s) 7, 861, 997, 1012
BstMBI GATC 4 cut(s) 4, 858, 994, 1009
BstMWI GCNNNNNNNGC 5 cut(s) 149, 197, 825, 904, 946
BstV1I GCAGC 2 cut(s) 721, 724
BstX2I RGATCY 1 cut(s) 1009
BstXI CCANNNNNNTGG 1 cut(s) 537
BstYI RGATCY 1 cut(s) 1009
Bsu36I CCTNAGG 1 cut(s) 147
BsuRI GGCC 3 cut(s) 215, 701, 1020
BtgI CCRYGG 1 cut(s) 216
BtgZI GCGATG 1 cut(s) 426
BtsCI GGATG 1 cut(s) 280
Cac8I GCNNGC 1 cut(s) 80
CaiI CAGNNNCTG 1 cut(s) 191
CciI TCATGA 1 cut(s) 460
Csp6I GTAC 1 cut(s) 346
CviAII CATG 5 cut(s) 35, 116, 217, 461, 537
CviQI GTAC 1 cut(s) 346
DdeI CTNAG 5 cut(s) 48, 138, 147, 354, 573
DpnI GATC 4 cut(s) 6, 860, 996, 1011
DpnII GATC 4 cut(s) 4, 858, 994, 1009
EaeI YGGCCR 1 cut(s) 1018
Eam1104I CTCTTC 1 cut(s) 612
EarI CTCTTC 1 cut(s) 612
Eco130I CCWWGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
Eco81I CCTNAGG 1 cut(s) 147
EcoT14I CCWWGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
ErhI CCWWGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
FaeI CATG 5 cut(s) 38, 119, 220, 464, 540
FalI AAGNNNNNCTT 2 cut(s) 887, 919
FatI CATG 5 cut(s) 34, 115, 216, 460, 536
Fnu4HI GCNGC 3 cut(s) 735, 738, 1021
FokI GGATG 1 cut(s) 287
Fsp4HI GCNGC 3 cut(s) 735, 738, 1021
FspBI CTAG 1 cut(s) 611
GluI GCNGC 3 cut(s) 735, 738, 1021
GsuI CTGGAG 1 cut(s) 893
HaeIII GGCC 3 cut(s) 215, 701, 1020
Hin1II CATG 5 cut(s) 38, 119, 220, 464, 540
HinfI GANTC 4 cut(s) 278, 688, 766, 1058
HphI GGTGA 1 cut(s) 34
Hpy188I TCNGA 6 cut(s) 132, 396, 561, 854, 999, 1050
Hpy188III TCNNGA 6 cut(s) 40, 403, 461, 799, 881, 985
HpyAV CCTTC 7 cut(s) 122, 155, 161, 205, 470, 543, 859
HpyF10VI GCNNNNNNNGC 5 cut(s) 149, 197, 825, 904, 946
HpyF3I CTNAG 5 cut(s) 48, 138, 147, 354, 573
Hsp92II CATG 5 cut(s) 38, 119, 220, 464, 540
Kzo9I GATC 4 cut(s) 4, 858, 994, 1009
LmnI GCTCC 3 cut(s) 148, 184, 661
LpnPI CCDG 5 cut(s) 64, 171, 744, 857, 866
Lsp1109I GCAGC 2 cut(s) 721, 724
LweI GCATC 3 cut(s) 403, 637, 990
MaeI CTAG 1 cut(s) 611
MaeIII GTNAC 1 cut(s) 525
MalI GATC 4 cut(s) 6, 860, 996, 1011
MboI GATC 4 cut(s) 4, 858, 994, 1009
MboII GAAGA 5 cut(s) 9, 100, 629, 954, 1000
MfeI CAATTG 1 cut(s) 593
MflI RGATCY 1 cut(s) 1009
MlyI GAGTC 2 cut(s) 272, 697
MmeI TCCRAC 4 cut(s) 206, 447, 661, 914
MroXI GAANNNNTTC 1 cut(s) 545
MseI TTAA 4 cut(s) 264, 335, 489, 603
MslI CAYNNNNRTG 2 cut(s) 535, 931
MunI CAATTG 1 cut(s) 593
Mva1269I GAATGC 1 cut(s) 181
MwoI GCNNNNNNNGC 5 cut(s) 149, 197, 825, 904, 946
NcoI CCATGG 1 cut(s) 216
NdeII GATC 4 cut(s) 4, 858, 994, 1009
NlaIII CATG 5 cut(s) 38, 119, 220, 464, 540
NlaIV GGNNCC 2 cut(s) 144, 663
NspV TTCGAA 1 cut(s) 1061
PagI TCATGA 1 cut(s) 460
PctI GAATGC 1 cut(s) 181
PdmI GAANNNNTTC 1 cut(s) 545
PfeI GAWTC 2 cut(s) 766, 1058
PkrI GCNGC 3 cut(s) 736, 739, 1022
PleI GAGTC 2 cut(s) 272, 696
PpsI GAGTC 2 cut(s) 272, 696
PspN4I GGNNCC 2 cut(s) 144, 663
PstNI CAGNNNCTG 1 cut(s) 191
PsuI RGATCY 1 cut(s) 1009
RsaI GTAC 1 cut(s) 347
RsaNI GTAC 1 cut(s) 346
RseI CAYNNNNRTG 2 cut(s) 535, 931
SaqAI TTAA 4 cut(s) 264, 335, 489, 603
SatI GCNGC 3 cut(s) 735, 738, 1021
Sau3AI GATC 4 cut(s) 4, 858, 994, 1009
SchI GAGTC 2 cut(s) 272, 697
SetI ASST 9 cut(s) 49, 360, 481, 535, 795, 837, 870, 879, 905
SfaNI GCATC 3 cut(s) 403, 637, 990
SfuI TTCGAA 1 cut(s) 1061
SmiMI CAYNNNNRTG 2 cut(s) 535, 931
SsiI CCGC 1 cut(s) 1021
SspMI CTAG 1 cut(s) 611
StyI CCWWGG 6 cut(s) 216, 270, 657, 789, 1004, 1024
TaqI TCGA 3 cut(s) 39, 984, 1061
TatI WGTACW 1 cut(s) 345
TauI GCSGC 1 cut(s) 1023
TfiI GAWTC 2 cut(s) 766, 1058
Tru1I TTAA 4 cut(s) 264, 335, 489, 603
Tru9I TTAA 4 cut(s) 264, 335, 489, 603
TseI GCWGC 2 cut(s) 734, 737
TspDTI ATGAA 7 cut(s) 41, 104, 449, 525, 596, 651, 915
XapI RAATTY 6 cut(s) 53, 397, 496, 552, 583, 885
XmnI GAANNNNTTC 1 cut(s) 545
XspI CTAG 1 cut(s) 611
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.