FvH4_6g33792

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000258
Physical Location & Seq
Reverse (-)
26769913 .. 26776020
6108 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g33792.t1

Sequence Viewer

Length: 972 bp
ATGGATCAATCAGTATCATCGATTGGGAAAAATCATGTTGAGAAACCTGAGAAATTCAAGGGTTCTGATTTCAAACACTGGCAACATAAGATGTTGTTTTATTTGACAACTTTGAATGTGGCAAACGTCCTCACTGCTGAGGCTCCTACTGTACTGGTTGGAGAAGGAGATAATGCTCCAACAGCAGCACAACAGGCTGAGAACAAGAAGGCTATAGATTCTTGGGAGACTAATGAGTTTCTATGCAAGAACTATATTCTCAATGCCTTGGACGATTCCTTGTATGATATCTACTCCACATTCAAAACTGCAAGGGAGTTGTGGCAGTCATTGGAGAACAAGTACAAGACTGAGGTTGCTTGTTCAAAGAAGTTTGTCATTGGCAAGTTTCTGAATTTCAAAATGAGTGATGCCAAATCTGTTGTCAAGCAAGTGGAGGAACTTCAAGTCATTGTTCATGAGTTAGATGTGGAAGGTATGGGTCTTAACCCGAATTTCCTTGTTGGTTCTATCATTGAAAAATTACCTCCTACATGGAAAGATTTCAAGATATATCTTAAACATCTATCTGAGGATATGAATTTTGAGCAATTGGTTCTTAAACTTCGAGTTGAAGAGGATAACCGGAAAAATGAGAAGGCTGATGTTATTTCCTTGGAGCCAACTGCTAATATGGTTGGAGGGAGTCCATCAAAGGCCAAGTTTCAGAAAAACAAAGGCAAGTATGCAGCTGCTAAGCCTCTTGTAAATGCTGGAAGGAATCTCCTCGCCCCACAAAAGACCAAGCCTTTCAAGAAGCAACAAATTGGAGGCTGCTGGGTTTGCGGCATACCAGGGCATAGAGCCAAGGAACGTCGCCTGAGGAAGGATCAAGGAGGTGGTGCTGGAGATCCAAGAATGGCTGAAGCTGAAGCCAGAGCCAAACAAGGAAGAGAAGTAGTCAAGCTTTGTGAAGGTGCCCAAGCCTCCTAG
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

324

Amino Acids

36.16

Weight (kDa)

9.11

Isoelectric Point (pI)

37.43

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 63 - 213 9.1e-29 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)
AccB1I GGYRCC 1 cut(s) 956
AciI CCGC 1 cut(s) 825
AclWI GGATC 3 cut(s) 12, 876, 884
AcsI RAATTY 4 cut(s) 53, 394, 493, 580
AcuI CTGAAG 2 cut(s) 924, 930
AfaI GTAC 2 cut(s) 153, 344
AfiI CCNNNNNNNGG 1 cut(s) 865
AjnI CCWGG 1 cut(s) 832
AluBI AGCT 3 cut(s) 731, 908, 946
AluI AGCT 3 cut(s) 731, 908, 946
Alw26I GTCTC 1 cut(s) 221
AlwI GGATC 3 cut(s) 12, 876, 884
AoxI GGCC 1 cut(s) 696
ApeKI GCWGC 4 cut(s) 185, 728, 731, 813
ApoI RAATTY 4 cut(s) 53, 394, 493, 580
ArsI GACNNNNNNTTYG 2 cut(s) 408, 440
Asp700I GAANNNNTTC 1 cut(s) 542
AxyI CCTNAGG 1 cut(s) 860
BaeGI GKGCMC 1 cut(s) 961
BanI GGYRCC 1 cut(s) 956
BbvCI CCTCAGC 1 cut(s) 138
BbvI GCAGC 4 cut(s) 197, 718, 740, 800
BccI CCATC 1 cut(s) 697
BciT130I CCWGG 1 cut(s) 834
BcoDI GTCTC 1 cut(s) 221
BfaI CTAG 1 cut(s) 970
BfmI CTRYAG 1 cut(s) 213
BisI GCNGC 5 cut(s) 186, 729, 732, 814, 826
BlpI GCTNAGC 1 cut(s) 735
BlsI GCNGC 5 cut(s) 187, 730, 733, 815, 827
Bme1390I CCNGG 1 cut(s) 834
BmiI GGNNCC 3 cut(s) 144, 660, 958
BmrFI CCNGG 1 cut(s) 834
BmsI GCATC 1 cut(s) 400
BpmI CTGGAG 1 cut(s) 906
Bpu10I CCTNAGC 1 cut(s) 138
Bpu1102I GCTNAGC 1 cut(s) 735
Bsa29I ATCGAT 1 cut(s) 20
BsaJI CCNNGG 4 cut(s) 267, 654, 833, 846
BsaWI WCCGGW 1 cut(s) 624
BsaXI ACNNNNNCTCC 2 cut(s) 326, 356
Bsc4I CCNNNNNNNGG 1 cut(s) 865
Bse1I ACTGG 2 cut(s) 83, 159
Bse21I CCTNAGG 1 cut(s) 860
BseBI CCWGG 1 cut(s) 834
BseCI ATCGAT 1 cut(s) 20
BseDI CCNNGG 4 cut(s) 267, 654, 833, 846
BseLI CCNNNNNNNGG 1 cut(s) 865
BseMII CTCAG 6 cut(s) 39, 129, 189, 342, 561, 851
BseNI ACTGG 2 cut(s) 83, 159
BseRI GAGGAG 1 cut(s) 755
BseSI GKGCMC 1 cut(s) 961
BseXI GCAGC 4 cut(s) 197, 718, 740, 800
BseYI CCCAGC 1 cut(s) 816
BshFI GGCC 1 cut(s) 698
BshNI GGYRCC 1 cut(s) 956
BshVI ATCGAT 1 cut(s) 20
BsiSI CCGG 1 cut(s) 625
BslI CCNNNNNNNGG 1 cut(s) 865
BsmAI GTCTC 1 cut(s) 221
BsnI GGCC 1 cut(s) 698
Bsp1286I GDGCHC 1 cut(s) 961
Bsp143I GATC 3 cut(s) 4, 868, 889
Bsp1720I GCTNAGC 1 cut(s) 735
BspACI CCGC 1 cut(s) 825
BspANI GGCC 1 cut(s) 698
BspCNI CTCAG 6 cut(s) 40, 130, 190, 343, 562, 852
BspDI ATCGAT 1 cut(s) 20
BspHI TCATGA 1 cut(s) 457
BspLI GGNNCC 3 cut(s) 144, 660, 958
BspPI GGATC 3 cut(s) 12, 876, 884
BspT107I GGYRCC 1 cut(s) 956
BsrI ACTGG 2 cut(s) 83, 159
BssECI CCNNGG 4 cut(s) 267, 654, 833, 846
BssMI GATC 3 cut(s) 4, 868, 889
BssT1I CCWWGG 3 cut(s) 267, 654, 846
Bst2UI CCWGG 1 cut(s) 834
Bst4CI ACNGT 1 cut(s) 151
Bst6I CTCTTC 2 cut(s) 609, 925
BstDEI CTNAG 7 cut(s) 48, 138, 198, 351, 570, 735, 860
BstENI CCTNNNNNAGG 1 cut(s) 863
BstKTI GATC 3 cut(s) 7, 871, 892
BstMAI GTCTC 1 cut(s) 221
BstMBI GATC 3 cut(s) 4, 868, 889
BstMWI GCNNNNNNNGC 3 cut(s) 182, 194, 822
BstNI CCWGG 1 cut(s) 834
BstSCI CCNGG 1 cut(s) 832
BstSFI CTRYAG 1 cut(s) 213
BstSLI GKGCMC 1 cut(s) 961
BstV1I GCAGC 4 cut(s) 197, 718, 740, 800
BstX2I RGATCY 1 cut(s) 889
BstYI RGATCY 1 cut(s) 889
Bsu15I ATCGAT 1 cut(s) 20
Bsu36I CCTNAGG 1 cut(s) 860
BsuRI GGCC 1 cut(s) 698
BsuTUI ATCGAT 1 cut(s) 20
BtsI GCAGTG 1 cut(s) 132
BtsIMutI CAGTG 2 cut(s) 76, 132
CciI TCATGA 1 cut(s) 457
ClaI ATCGAT 1 cut(s) 20
Csp6I GTAC 2 cut(s) 152, 343
CviAII CATG 3 cut(s) 35, 458, 534
CviQI GTAC 2 cut(s) 152, 343
DdeI CTNAG 7 cut(s) 48, 138, 198, 351, 570, 735, 860
DpnI GATC 3 cut(s) 6, 870, 891
DpnII GATC 3 cut(s) 4, 868, 889
Eam1104I CTCTTC 2 cut(s) 609, 925
EarI CTCTTC 2 cut(s) 609, 925
Eco130I CCWWGG 3 cut(s) 267, 654, 846
Eco32I GATATC 1 cut(s) 289
Eco57I CTGAAG 2 cut(s) 924, 930
Eco81I CCTNAGG 1 cut(s) 860
EcoNI CCTNNNNNAGG 1 cut(s) 863
EcoRII CCWGG 1 cut(s) 832
EcoRV GATATC 1 cut(s) 289
EcoT14I CCWWGG 3 cut(s) 267, 654, 846
ErhI CCWWGG 3 cut(s) 267, 654, 846
FaeI CATG 3 cut(s) 38, 461, 537
FatI CATG 3 cut(s) 34, 457, 533
Fnu4HI GCNGC 5 cut(s) 186, 729, 732, 814, 826
Fsp4HI GCNGC 5 cut(s) 186, 729, 732, 814, 826
FspBI CTAG 1 cut(s) 970
GluI GCNGC 5 cut(s) 186, 729, 732, 814, 826
GsaI CCCAGC 1 cut(s) 820
GsuI CTGGAG 1 cut(s) 906
HaeIII GGCC 1 cut(s) 698
HapII CCGG 1 cut(s) 625
Hin1II CATG 3 cut(s) 38, 461, 537
HindIII AAGCTT 1 cut(s) 944
HinfI GANTC 4 cut(s) 218, 275, 685, 760
HpaII CCGG 1 cut(s) 625
Hpy188I TCNGA 4 cut(s) 67, 393, 571, 708
Hpy188III TCNNGA 3 cut(s) 458, 547, 793
Hpy99I CGWCG 1 cut(s) 858
HpyAV CCTTC 7 cut(s) 158, 202, 467, 631, 750, 859, 947
HpyCH4III ACNGT 1 cut(s) 151
HpyCH4IV ACGT 2 cut(s) 126, 853
HpyCH4V TGCA 3 cut(s) 246, 311, 728
HpyF10VI GCNNNNNNNGC 3 cut(s) 182, 194, 822
HpyF3I CTNAG 7 cut(s) 48, 138, 198, 351, 570, 735, 860
HpySE526I ACGT 2 cut(s) 126, 853
Hsp92II CATG 3 cut(s) 38, 461, 537
Kzo9I GATC 3 cut(s) 4, 868, 889
LmnI GCTCC 3 cut(s) 148, 181, 658
Lsp1109I GCAGC 4 cut(s) 197, 718, 740, 800
LweI GCATC 1 cut(s) 400
MaeI CTAG 1 cut(s) 970
MaeII ACGT 2 cut(s) 126, 853
MalI GATC 3 cut(s) 6, 870, 891
MboI GATC 3 cut(s) 4, 868, 889
MboII GAAGA 2 cut(s) 626, 942
MfeI CAATTG 1 cut(s) 590
MflI RGATCY 1 cut(s) 889
MhlI GDGCHC 1 cut(s) 961
MluCI AATT 7 cut(s) 53, 394, 493, 521, 580, 590, 804
MlyI GAGTC 1 cut(s) 694
MmeI TCCRAC 3 cut(s) 139, 203, 658
MroXI GAANNNNTTC 1 cut(s) 542
MseI TTAA 3 cut(s) 486, 558, 600
MspA1I CMGCKG 1 cut(s) 731
MspI CCGG 1 cut(s) 625
MspR9I CCNGG 1 cut(s) 834
MunI CAATTG 1 cut(s) 590
MvaI CCWGG 1 cut(s) 834
MwoI GCNNNNNNNGC 3 cut(s) 182, 194, 822
NdeII GATC 3 cut(s) 4, 868, 889
NlaIII CATG 3 cut(s) 38, 461, 537
NlaIV GGNNCC 3 cut(s) 144, 660, 958
PagI TCATGA 1 cut(s) 457
PdmI GAANNNNTTC 1 cut(s) 542
PfeI GAWTC 3 cut(s) 218, 275, 760
PkrI GCNGC 5 cut(s) 187, 730, 733, 815, 827
PleI GAGTC 1 cut(s) 693
PpsI GAGTC 1 cut(s) 693
Psp6I CCWGG 1 cut(s) 832
PspFI CCCAGC 1 cut(s) 816
PspGI CCWGG 1 cut(s) 832
PspN4I GGNNCC 3 cut(s) 144, 660, 958
PsuI RGATCY 1 cut(s) 889
PvuII CAGCTG 1 cut(s) 731
RsaI GTAC 2 cut(s) 153, 344
RsaNI GTAC 2 cut(s) 152, 343
SaqAI TTAA 3 cut(s) 486, 558, 600
SatI GCNGC 5 cut(s) 186, 729, 732, 814, 826
Sau3AI GATC 3 cut(s) 4, 868, 889
SchI GAGTC 1 cut(s) 694
ScrFI CCNGG 1 cut(s) 834
SduI GDGCHC 1 cut(s) 961
SfaNI GCATC 1 cut(s) 400
SfcI CTRYAG 1 cut(s) 213
Sse9I AATT 7 cut(s) 53, 394, 493, 521, 580, 590, 804
SsiI CCGC 1 cut(s) 825
SspMI CTAG 1 cut(s) 970
StyD4I CCNGG 1 cut(s) 832
StyI CCWWGG 3 cut(s) 267, 654, 846
TaaI ACNGT 1 cut(s) 151
TaiI ACGT 2 cut(s) 129, 856
TaqI TCGA 2 cut(s) 20, 607
TasI AATT 7 cut(s) 53, 394, 493, 521, 580, 590, 804
TatI WGTACW 2 cut(s) 151, 342
TauI GCSGC 1 cut(s) 828
TfiI GAWTC 3 cut(s) 218, 275, 760
Tru1I TTAA 3 cut(s) 486, 558, 600
Tru9I TTAA 3 cut(s) 486, 558, 600
TscAI CASTG 2 cut(s) 83, 139
TseI GCWGC 4 cut(s) 185, 728, 731, 813
TspDTI ATGAA 2 cut(s) 446, 593
TspRI CASTG 2 cut(s) 83, 139
XagI CCTNNNNNAGG 1 cut(s) 863
XapI RAATTY 4 cut(s) 53, 394, 493, 580
XmnI GAANNNNTTC 1 cut(s) 542
XspI CTAG 1 cut(s) 970
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.