FvH4_5g23001

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0000258
Physical Location & Seq
Forward (+)
14368407 .. 14369454
1048 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g23001.t1

Sequence Viewer

Length: 942 bp
ATGACAAACTTAGATCAAGAAGCTCTTAGTGTCAAACCTGGAAAATTTAGTGGACACCATTTTCGTAGATGGCAAAAACAGTTGAAATATTGGCTGTCTGTTCTTGGATTTATGTCTGCCATTGAAGGGCATGATCCAAACAAACCATCATCTTCTTGGTTTAGCCAAGAGGATATAGAGTATCATTGCTATAATAGAATTTTAAGTGCCTTGTCTGACCATCTTTACGATGTGTATCATTCTACAACATCCACAGCCAAAGAACTTTGGGATGCATTAGAGGCTGAATATGGAATTGTAGATGCTGGAGTTGATAGGTTTACTGTCTCTAACTTTAATAGTTATAAGATGGTTGAAACCAAATCTGTAGGAGACCAAATCCATGAGTACCAAGAACTTTTAAGAGGTATAGAAAAGAAAGGAACCAAGTTCAGTGAGGACTTTAAAGTGTCTTGCCTTATTGATAAATTGCCTCCATCTTGGAATGAATATGCTAAGTCTCTTAGGCATAAACAAGGAGAGTTCACCCTCCGTCAAGCTATGAATTCCCTTAGAATAGAAGAGAAACAAAGGGTAGATCAAAAGGGAAAAACTGAGAGTACCCCTGTTGTGAATTTAGTTGTGGGAAAGAGAAACCATAATCAAAACAAGACTAGATTCCACAATAAAAATGGGAGAAATAACTTTCAGCCTAGGGGAATGAACTTTAAGAACAATAGAGTCAACCATAACAAACAATTCCAGAAGTCTAAGGATCAAGGGAGAGAGAAGATGTCTTGCTTTGTTTGTGGGAGGACCAATCATATGGCAAAGAATTGCTTCTACAAAAAGACTGAGGAGATCAAGTCTCAAGCAAATAATGGTCCAAAAGCTCAAGTAAATATGATAGTGGAGCAAGAGTCCTCTCAACCATTATTCAAAAATCGAGTGGAGGACGTGTAA
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 zf-CCHC

Protein Analysis

314

Amino Acids

36.42

Weight (kDa)

9.34

Isoelectric Point (pI)

51.4

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 60 - 195 3.8e-20 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: 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)
AanI TTATAA 1 cut(s) 345
AclWI GGATC 2 cut(s) 128, 762
AcsI RAATTY 4 cut(s) 44, 198, 544, 613
AfaI GTAC 2 cut(s) 389, 601
AfiI CCNNNNNNNGG 1 cut(s) 126
AflIII ACRYGT 1 cut(s) 936
AgsI TTSAA 4 cut(s) 85, 125, 356, 919
AjiI CACGTC 1 cut(s) 937
AjnI CCWGG 1 cut(s) 37
AluBI AGCT 3 cut(s) 23, 539, 872
AluI AGCT 3 cut(s) 23, 539, 872
Alw26I GTCTC 4 cut(s) 331, 366, 504, 852
AlwI GGATC 2 cut(s) 128, 762
ApoI RAATTY 4 cut(s) 44, 198, 544, 613
ArsI GACNNNNNNTTYG 2 cut(s) 45, 77
Asp700I GAANNNNTTC 1 cut(s) 818
AspA2I CCTAGG 1 cut(s) 692
AspS9I GGNCC 2 cut(s) 795, 863
AsuHPI GGTGA 1 cut(s) 517
AvaII GGWCC 2 cut(s) 795, 863
AvrII CCTAGG 1 cut(s) 692
BccI CCATC 5 cut(s) 63, 154, 228, 343, 484
BciT130I CCWGG 1 cut(s) 39
BcoDI GTCTC 4 cut(s) 331, 366, 504, 852
BfaI CTAG 2 cut(s) 654, 693
BfmI CTRYAG 1 cut(s) 366
BlnI CCTAGG 1 cut(s) 692
Bme1390I CCNGG 1 cut(s) 39
Bme18I GGWCC 2 cut(s) 795, 863
BmgBI CACGTC 1 cut(s) 937
BmgT120I GGNCC 2 cut(s) 795, 863
BmiI GGNNCC 1 cut(s) 424
BmrFI CCNGG 1 cut(s) 39
BmsI GCATC 2 cut(s) 262, 292
BpmI CTGGAG 1 cut(s) 327
BpuEI CTTGAG 2 cut(s) 834, 858
BsaBI GATNNNNATC 1 cut(s) 234
BsaI GGTCTC 1 cut(s) 366
BsaJI CCNNGG 1 cut(s) 692
BsaXI ACNNNNNCTCC 5 cut(s) 830, 860, 884, 914, 923
Bsc4I CCNNNNNNNGG 1 cut(s) 126
Bse3DI GCAATG 1 cut(s) 184
Bse8I GATNNNNATC 1 cut(s) 234
BseBI CCWGG 1 cut(s) 39
BseDI CCNNGG 1 cut(s) 692
BseGI GGATG 2 cut(s) 248, 277
BseJI GATNNNNATC 1 cut(s) 234
BseLI CCNNNNNNNGG 1 cut(s) 126
BseMI GCAATG 1 cut(s) 184
BseMII CTCAG 2 cut(s) 585, 825
BseRI GAGGAG 1 cut(s) 851
BslI CCNNNNNNNGG 1 cut(s) 126
BsmAI GTCTC 4 cut(s) 331, 366, 504, 852
Bso31I GGTCTC 1 cut(s) 366
Bsp143I GATC 5 cut(s) 13, 133, 577, 754, 840
BspCNI CTCAG 2 cut(s) 586, 826
BspLI GGNNCC 1 cut(s) 424
BspPI GGATC 2 cut(s) 128, 762
BspTNI GGTCTC 1 cut(s) 366
BsrDI GCAATG 1 cut(s) 184
BssECI CCNNGG 1 cut(s) 692
BssMI GATC 5 cut(s) 13, 133, 577, 754, 840
BssT1I CCWWGG 1 cut(s) 692
Bst2UI CCWGG 1 cut(s) 39
Bst4CI ACNGT 2 cut(s) 81, 325
Bst6I CTCTTC 1 cut(s) 555
BstDEI CTNAG 8 cut(s) 10, 26, 495, 503, 551, 594, 750, 834
BstF5I GGATG 2 cut(s) 248, 277
BstKTI GATC 5 cut(s) 16, 136, 580, 757, 843
BstMAI GTCTC 4 cut(s) 331, 366, 504, 852
BstMBI GATC 5 cut(s) 13, 133, 577, 754, 840
BstMWI GCNNNNNNNGC 1 cut(s) 281
BstNI CCWGG 1 cut(s) 39
BstSCI CCNGG 1 cut(s) 37
BstSFI CTRYAG 1 cut(s) 366
BstXI CCANNNNNNTGG 1 cut(s) 805
BtrI CACGTC 1 cut(s) 937
BtsCI GGATG 2 cut(s) 248, 277
BtsIMutI CAGTG 1 cut(s) 439
Cfr13I GGNCC 2 cut(s) 795, 863
Csp6I GTAC 2 cut(s) 388, 600
CviAII CATG 2 cut(s) 131, 383
CviJI RGCY 8 cut(s) 23, 94, 165, 257, 284, 539, 691, 872
CviKI_1 RGCY 8 cut(s) 23, 94, 165, 257, 284, 539, 691, 872
CviQI GTAC 2 cut(s) 388, 600
DdeI CTNAG 8 cut(s) 10, 26, 495, 503, 551, 594, 750, 834
DpnI GATC 5 cut(s) 15, 135, 579, 756, 842
DpnII GATC 5 cut(s) 13, 133, 577, 754, 840
DraI TTTAAA 1 cut(s) 445
Eam1104I CTCTTC 1 cut(s) 555
EarI CTCTTC 1 cut(s) 555
Eco130I CCWWGG 1 cut(s) 692
Eco31I GGTCTC 1 cut(s) 366
Eco47I GGWCC 2 cut(s) 795, 863
EcoRI GAATTC 1 cut(s) 544
EcoRII CCWGG 1 cut(s) 37
EcoT14I CCWWGG 1 cut(s) 692
EcoT22I ATGCAT 1 cut(s) 277
ErhI CCWWGG 1 cut(s) 692
FaeI CATG 2 cut(s) 134, 386
FalI AAGNNNNNCTT 4 cut(s) 9, 41, 803, 835
FatI CATG 2 cut(s) 130, 382
FauNDI CATATG 1 cut(s) 804
FokI GGATG 2 cut(s) 235, 284
FspBI CTAG 2 cut(s) 654, 693
GsuI CTGGAG 1 cut(s) 327
Hin1II CATG 2 cut(s) 134, 386
HincII GTYRAC 1 cut(s) 724
HindII GTYRAC 1 cut(s) 724
HinfI GANTC 3 cut(s) 657, 720, 899
HphI GGTGA 1 cut(s) 517
Hpy166II GTNNAC 4 cut(s) 53, 321, 525, 724
Hpy188I TCNGA 1 cut(s) 217
Hpy188III TCNNGA 2 cut(s) 17, 742
Hpy8I GTNNAC 4 cut(s) 53, 321, 525, 724
HpyAV CCTTC 1 cut(s) 119
HpyCH4III ACNGT 2 cut(s) 81, 325
HpyCH4IV ACGT 1 cut(s) 936
HpyCH4V TGCA 1 cut(s) 275
HpyF10VI GCNNNNNNNGC 1 cut(s) 281
HpyF3I CTNAG 8 cut(s) 10, 26, 495, 503, 551, 594, 750, 834
HpySE526I ACGT 1 cut(s) 936
Hsp92II CATG 2 cut(s) 134, 386
Kzo9I GATC 5 cut(s) 13, 133, 577, 754, 840
LmnI GCTCC 1 cut(s) 892
LpnPI CCDG 5 cut(s) 24, 51, 291, 618, 755
LweI GCATC 2 cut(s) 262, 292
MaeI CTAG 2 cut(s) 654, 693
MaeII ACGT 1 cut(s) 936
MalI GATC 5 cut(s) 15, 135, 579, 756, 842
MboI GATC 5 cut(s) 13, 133, 577, 754, 840
MboII GAAGA 3 cut(s) 144, 572, 781
MluCI AATT 8 cut(s) 44, 198, 294, 467, 544, 613, 737, 814
MlyI GAGTC 2 cut(s) 729, 908
Mph1103I ATGCAT 1 cut(s) 277
MroXI GAANNNNTTC 1 cut(s) 818
MseI TTAA 5 cut(s) 203, 336, 401, 444, 708
MspR9I CCNGG 1 cut(s) 39
MvaI CCWGG 1 cut(s) 39
MwoI GCNNNNNNNGC 1 cut(s) 281
NdeI CATATG 1 cut(s) 804
NdeII GATC 5 cut(s) 13, 133, 577, 754, 840
NlaIII CATG 2 cut(s) 134, 386
NlaIV GGNNCC 1 cut(s) 424
NsiI ATGCAT 1 cut(s) 277
PdmI GAANNNNTTC 1 cut(s) 818
PfeI GAWTC 1 cut(s) 657
PleI GAGTC 2 cut(s) 728, 907
PpsI GAGTC 2 cut(s) 728, 907
PsiI TTATAA 1 cut(s) 345
Psp6I CCWGG 1 cut(s) 37
PspGI CCWGG 1 cut(s) 37
PspN4I GGNNCC 1 cut(s) 424
PspPI GGNCC 2 cut(s) 795, 863
RsaI GTAC 2 cut(s) 389, 601
RsaNI GTAC 2 cut(s) 388, 600
SaqAI TTAA 5 cut(s) 203, 336, 401, 444, 708
Sau3AI GATC 5 cut(s) 13, 133, 577, 754, 840
Sau96I GGNCC 2 cut(s) 795, 863
SchI GAGTC 2 cut(s) 729, 908
ScrFI CCNGG 1 cut(s) 39
SetI ASST 7 cut(s) 25, 40, 320, 409, 541, 874, 939
SfaNI GCATC 2 cut(s) 262, 292
SfcI CTRYAG 1 cut(s) 366
SinI GGWCC 2 cut(s) 795, 863
SmlI CTYRAG 2 cut(s) 849, 873
SmoI CTYRAG 2 cut(s) 849, 873
Sse9I AATT 8 cut(s) 44, 198, 294, 467, 544, 613, 737, 814
SspI AATATT 1 cut(s) 89
SspMI CTAG 2 cut(s) 654, 693
StyD4I CCNGG 1 cut(s) 37
StyI CCWWGG 1 cut(s) 692
TaaI ACNGT 2 cut(s) 81, 325
TaiI ACGT 1 cut(s) 939
TaqI TCGA 1 cut(s) 925
TasI AATT 8 cut(s) 44, 198, 294, 467, 544, 613, 737, 814
TfiI GAWTC 1 cut(s) 657
Tru1I TTAA 5 cut(s) 203, 336, 401, 444, 708
Tru9I TTAA 5 cut(s) 203, 336, 401, 444, 708
TscAI CASTG 1 cut(s) 439
TspDTI ATGAA 3 cut(s) 501, 557, 716
TspGWI ACGGA 1 cut(s) 521
TspRI CASTG 1 cut(s) 439
VpaK11BI GGWCC 2 cut(s) 795, 863
XapI RAATTY 4 cut(s) 44, 198, 544, 613
XcmI CCANNNNNNNNNTGG 2 cut(s) 153, 668
XmaJI CCTAGG 1 cut(s) 692
XmnI GAANNNNTTC 1 cut(s) 818
XspI CTAG 2 cut(s) 654, 693
Zsp2I ATGCAT 1 cut(s) 277
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.