FvH4_4g23911

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000258
Physical Location & Seq
Reverse (-)
26238192 .. 26239872
1681 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g23911.t1

Sequence Viewer

Length: 1377 bp
ATGGATCAACCTACTGCTGCTGGTGTTAAGAACTATATTGAGAAGCCATTTGTGTTCAAAGGCGTGGACTTCAAAAGATGGCAGCAAAAGATGTTGTTTTATCTAACAACACTGAACTTGGCACAAGTGATTACATCTGAGGCTCCAGATTTGCCAGCAGAGGGTGATATCCCAGATGCAACTATTAAGGCTGTTGAAGCTTGGGAGCAAAACGAGTTTCTGTGTAAGAATTATATTCTGAATGCCTTAGATGATTCATTGTATGATGTTTATTCAACATTCAAAACTGCAAAAGAGCTATGGGATTCTTTGAACAAGAAATACAAGTCTGAGGTTGCAAGTGCCAAGAAGTTTGTTGTTGGAAAATTTCTGAATTTTACGATGAGTGATGCCAATTCTGTGGTGAAGCAAGTGGAGGAACTCCAAATTACTGCTCATGAATTACTTGCTGAAGGTATGGGACTCAATGAGACTTTTCTTGTTGCTTCCATTATTGAAAAGCTGCCTCCCTCTTGGAAGGATTTCAAGATATACCTCAAGCACCTATCTGAAGAGATGAACCTTGAGCAACTCATTCTCAAGCTTCGTGTGGAGGAAGAGAACAGAAAGAATGAAAAAACTGATTGGTCCTCAATGGAAGCAAAAGCCAATGTGATTGAAGGTAGCACCTCCAAGCCTAAGTTTCCTCACAATCATAAGAAGGGAAAAACTGCTGCCAAAAGAGCACCTACTGCCCCAAAAGCTGTTATGTTCAAAAAGAAAATTCAAGGTGCTTGCTGGGTGTGTGGTAAGCCTGGTCATAAAGCCATGGATTGTCGCCACAAGAAGGACAGACATGCTGGAAATAATAATCAAGCAAACATGGCAGAAGATCAATTTGTTGCTGTTGTATCTGAGGTCAATCTAATAATCAATACCAATGACTGGTGGGTTGACACATGTGCATCAAGGCATGTTTGTACTGAAAGAAGCATGTTTGCAACATATGAGCAAGGATCTGGTGGAGAAAATCTTTACATGGGAAATTCTAGTACTGCTGCAGTTGAAGGGAAAGGAAAAGTGATACTGAAACTCACTTCTGGAAAAGAACTTGCACTCACCAATGTGCTCCATGTCCTTGAGATTAGAAAGAATCTGATTTCTGGTTCTCTTCTTATCAACAAAGGCTTTAAGTTAGTATTTGAATCTGATAAGTCTGTACTCACCAAGGGTGGAATGTATGTAGGAAAAGGCTACCTATCTGAGGGGCTGTTCAAACTCAATGTAATTCCTACTGCTGATATTAATAATAATAATGCAAGCAATAGCACTGCTTCTATCTACTTACTTGATTCAGTTGATTTATGGCATGCAAGATTAGTAAAGATGAAGCTTTGA
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

459

Amino Acids

51.27

Weight (kDa)

8.8

Isoelectric Point (pI)

34.98

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 33 - 206 2.9e-26 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 309 - 390 1.6e-22 Pol polyprotein, beta-barrel domain
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)
AccB7I CCANNNNNTGG 1 cut(s) 924
AclWI GGATC 2 cut(s) 12, 1003
AcsI RAATTY 4 cut(s) 365, 373, 762, 1024
AcuI CTGAAG 2 cut(s) 471, 570
AfaI GTAC 3 cut(s) 961, 1033, 1200
AfiI CCNNNNNNNGG 4 cut(s) 161, 826, 924, 1243
AflIII ACRYGT 1 cut(s) 938
AjnI CCWGG 1 cut(s) 793
AleI CACNNNNGTG 1 cut(s) 1103
AluBI AGCT 6 cut(s) 200, 298, 502, 583, 743, 1372
AluI AGCT 6 cut(s) 200, 298, 502, 583, 743, 1372
Alw21I GWGCWC 2 cut(s) 727, 1110
Alw26I GTCTC 1 cut(s) 464
AlwI GGATC 2 cut(s) 12, 1003
ApeKI GCWGC 5 cut(s) 17, 82, 502, 713, 1037
ApoI RAATTY 4 cut(s) 365, 373, 762, 1024
AseI ATTAAT 1 cut(s) 1284
Asp700I GAANNNNTTC 1 cut(s) 521
AspS9I GGNCC 1 cut(s) 627
AsuHPI GGTGA 4 cut(s) 176, 415, 1090, 1195
AvaII GGWCC 1 cut(s) 627
Bbv12I GWGCWC 2 cut(s) 727, 1110
BbvI GCAGC 5 cut(s) 4, 94, 489, 700, 1024
BccI CCATC 1 cut(s) 72
BciT130I CCWGG 1 cut(s) 795
BcoDI GTCTC 1 cut(s) 464
BfaI CTAG 1 cut(s) 1029
BfmI CTRYAG 1 cut(s) 1038
BisI GCNGC 5 cut(s) 18, 83, 503, 714, 1038
BlsI GCNGC 5 cut(s) 19, 84, 504, 715, 1039
BmcAI AGTACT 1 cut(s) 1033
Bme1390I CCNGG 1 cut(s) 795
Bme18I GGWCC 1 cut(s) 627
BmgT120I GGNCC 1 cut(s) 627
BmiI GGNNCC 1 cut(s) 144
BmrFI CCNGG 1 cut(s) 795
BmsI GCATC 3 cut(s) 166, 379, 953
BpmI CTGGAG 1 cut(s) 129
BpuEI CTTGAG 4 cut(s) 521, 563, 584, 1139
BsaJI CCNNGG 2 cut(s) 807, 1206
Bsc4I CCNNNNNNNGG 4 cut(s) 161, 826, 924, 1243
Bse1I ACTGG 1 cut(s) 929
BseBI CCWGG 1 cut(s) 795
BseDI CCNNGG 2 cut(s) 807, 1206
BseLI CCNNNNNNNGG 4 cut(s) 161, 826, 924, 1243
BseMII CTCAG 4 cut(s) 129, 321, 885, 1233
BseNI ACTGG 1 cut(s) 929
BseXI GCAGC 5 cut(s) 4, 94, 489, 700, 1024
BseYI CCCAGC 1 cut(s) 777
BsiHKAI GWGCWC 2 cut(s) 727, 1110
BslFI GGGAC 1 cut(s) 474
BslI CCNNNNNNNGG 4 cut(s) 161, 826, 924, 1243
BsmAI GTCTC 1 cut(s) 464
BsmFI GGGAC 1 cut(s) 474
BsmI GAATGC 1 cut(s) 247
Bsp1286I GDGCHC 2 cut(s) 727, 1110
Bsp143I GATC 3 cut(s) 4, 871, 995
Bsp19I CCATGG 1 cut(s) 807
BspCNI CTCAG 4 cut(s) 130, 322, 886, 1234
BspHI TCATGA 1 cut(s) 436
BspLI GGNNCC 1 cut(s) 144
BspMAI CTGCAG 1 cut(s) 1042
BspPI GGATC 2 cut(s) 12, 1003
BsrI ACTGG 1 cut(s) 929
BssECI CCNNGG 2 cut(s) 807, 1206
BssMI GATC 3 cut(s) 4, 871, 995
BssT1I CCWWGG 2 cut(s) 807, 1206
Bst2UI CCWGG 1 cut(s) 795
Bst6I CTCTTC 3 cut(s) 546, 591, 1155
BstAPI GCANNNNNTGC 1 cut(s) 731
BstC8I GCNNGC 4 cut(s) 156, 775, 1300, 1350
BstDEI CTNAG 6 cut(s) 138, 247, 330, 678, 894, 1242
BstDSI CCRYGG 1 cut(s) 807
BstENI CCTNNNNNAGG 1 cut(s) 1241
BstKTI GATC 3 cut(s) 7, 874, 998
BstMAI GTCTC 1 cut(s) 464
BstMBI GATC 3 cut(s) 4, 871, 995
BstMWI GCNNNNNNNGC 5 cut(s) 197, 722, 731, 740, 863
BstNI CCWGG 1 cut(s) 795
BstNSI RCATGY 5 cut(s) 839, 942, 956, 976, 1352
BstSCI CCNGG 1 cut(s) 793
BstSFI CTRYAG 1 cut(s) 1038
BstV1I GCAGC 5 cut(s) 4, 94, 489, 700, 1024
BstX2I RGATCY 1 cut(s) 995
BstXI CCANNNNNNTGG 1 cut(s) 400
BstYI RGATCY 1 cut(s) 995
BtgI CCRYGG 1 cut(s) 807
BtsI GCAGTG 1 cut(s) 1308
BtsIMutI CAGTG 2 cut(s) 110, 1308
Cac8I GCNNGC 4 cut(s) 156, 775, 1300, 1350
CciI TCATGA 1 cut(s) 436
Cfr13I GGNCC 1 cut(s) 627
Csp6I GTAC 3 cut(s) 960, 1032, 1199
CviQI GTAC 3 cut(s) 960, 1032, 1199
DdeI CTNAG 6 cut(s) 138, 247, 330, 678, 894, 1242
DpnI GATC 3 cut(s) 6, 873, 997
DpnII GATC 3 cut(s) 4, 871, 995
Eam1104I CTCTTC 3 cut(s) 546, 591, 1155
EarI CTCTTC 3 cut(s) 546, 591, 1155
Eco130I CCWWGG 2 cut(s) 807, 1206
Eco32I GATATC 1 cut(s) 169
Eco47I GGWCC 1 cut(s) 627
Eco57I CTGAAG 2 cut(s) 471, 570
EcoNI CCTNNNNNAGG 1 cut(s) 1241
EcoRII CCWGG 1 cut(s) 793
EcoRV GATATC 1 cut(s) 169
EcoT14I CCWWGG 2 cut(s) 807, 1206
ErhI CCWWGG 2 cut(s) 807, 1206
FaqI GGGAC 1 cut(s) 474
FauNDI CATATG 1 cut(s) 985
Fnu4HI GCNGC 5 cut(s) 18, 83, 503, 714, 1038
Fsp4HI GCNGC 5 cut(s) 18, 83, 503, 714, 1038
FspBI CTAG 1 cut(s) 1029
GluI GCNGC 5 cut(s) 18, 83, 503, 714, 1038
GsaI CCCAGC 1 cut(s) 781
GsuI CTGGAG 1 cut(s) 129
HincII GTYRAC 1 cut(s) 934
HindII GTYRAC 1 cut(s) 934
HindIII AAGCTT 3 cut(s) 198, 581, 1370
HinfI GANTC 6 cut(s) 254, 305, 462, 1132, 1184, 1331
HphI GGTGA 4 cut(s) 176, 415, 1090, 1195
Hpy166II GTNNAC 2 cut(s) 67, 934
Hpy188I TCNGA 9 cut(s) 139, 240, 331, 372, 550, 895, 1137, 1189, 1243
Hpy188III TCNNGA 4 cut(s) 146, 437, 526, 1080
Hpy8I GTNNAC 2 cut(s) 67, 934
HpyAV CCTTC 6 cut(s) 446, 511, 653, 694, 820, 1040
HpyCH4V TGCA 9 cut(s) 179, 290, 338, 944, 980, 1040, 1094, 1298, 1352
HpyF10VI GCNNNNNNNGC 5 cut(s) 197, 722, 731, 740, 863
HpyF3I CTNAG 6 cut(s) 138, 247, 330, 678, 894, 1242
Kzo9I GATC 3 cut(s) 4, 871, 995
LmnI GCTCC 3 cut(s) 148, 205, 1113
Lsp1109I GCAGC 5 cut(s) 4, 94, 489, 700, 1024
LweI GCATC 3 cut(s) 166, 379, 953
MaeI CTAG 1 cut(s) 1029
MalI GATC 3 cut(s) 6, 873, 997
MboI GATC 3 cut(s) 4, 871, 995
MboII GAAGA 4 cut(s) 563, 608, 881, 1142
MflI RGATCY 1 cut(s) 995
MhlI GDGCHC 2 cut(s) 727, 1110
MlyI GAGTC 1 cut(s) 456
MmeI TCCRAC 1 cut(s) 340
MroXI GAANNNNTTC 1 cut(s) 521
MseI TTAA 4 cut(s) 27, 186, 1170, 1284
MslI CAYNNNNRTG 1 cut(s) 1103
MspR9I CCNGG 1 cut(s) 795
Mva1269I GAATGC 1 cut(s) 247
MvaI CCWGG 1 cut(s) 795
MwoI GCNNNNNNNGC 5 cut(s) 197, 722, 731, 740, 863
NcoI CCATGG 1 cut(s) 807
NdeI CATATG 1 cut(s) 985
NdeII GATC 3 cut(s) 4, 871, 995
NlaIV GGNNCC 1 cut(s) 144
NspI RCATGY 5 cut(s) 839, 942, 956, 976, 1352
OliI CACNNNNGTG 1 cut(s) 1103
PaeI GCATGC 1 cut(s) 1352
PagI TCATGA 1 cut(s) 436
PciI ACATGT 1 cut(s) 938
PctI GAATGC 1 cut(s) 247
PdmI GAANNNNTTC 1 cut(s) 521
PfeI GAWTC 5 cut(s) 254, 305, 1132, 1184, 1331
PflMI CCANNNNNTGG 1 cut(s) 924
PkrI GCNGC 5 cut(s) 19, 84, 504, 715, 1039
PleI GAGTC 1 cut(s) 456
PpsI GAGTC 1 cut(s) 456
PscI ACATGT 1 cut(s) 938
PshBI ATTAAT 1 cut(s) 1284
Psp6I CCWGG 1 cut(s) 793
PspFI CCCAGC 1 cut(s) 777
PspGI CCWGG 1 cut(s) 793
PspN4I GGNNCC 1 cut(s) 144
PspPI GGNCC 1 cut(s) 627
PsrI GAACNNNNNNTAC 2 cut(s) 305, 337
PstI CTGCAG 1 cut(s) 1042
PsuI RGATCY 1 cut(s) 995
RsaI GTAC 3 cut(s) 961, 1033, 1200
RsaNI GTAC 3 cut(s) 960, 1032, 1199
RseI CAYNNNNRTG 1 cut(s) 1103
SaqAI TTAA 4 cut(s) 27, 186, 1170, 1284
SatI GCNGC 5 cut(s) 18, 83, 503, 714, 1038
Sau3AI GATC 3 cut(s) 4, 871, 995
Sau96I GGNCC 1 cut(s) 627
ScaI AGTACT 1 cut(s) 1033
SchI GAGTC 1 cut(s) 456
ScrFI CCNGG 1 cut(s) 795
SduI GDGCHC 2 cut(s) 727, 1110
SfaNI GCATC 3 cut(s) 166, 379, 953
SfcI CTRYAG 1 cut(s) 1038
SinI GGWCC 1 cut(s) 627
SmiMI CAYNNNNRTG 1 cut(s) 1103
SmlI CTYRAG 4 cut(s) 536, 563, 578, 1118
SmoI CTYRAG 4 cut(s) 536, 563, 578, 1118
SphI GCATGC 1 cut(s) 1352
SspMI CTAG 1 cut(s) 1029
StyD4I CCNGG 1 cut(s) 793
StyI CCWWGG 2 cut(s) 807, 1206
TatI WGTACW 3 cut(s) 959, 1031, 1198
TfiI GAWTC 5 cut(s) 254, 305, 1132, 1184, 1331
Tru1I TTAA 4 cut(s) 27, 186, 1170, 1284
Tru9I TTAA 4 cut(s) 27, 186, 1170, 1284
TscAI CASTG 2 cut(s) 117, 1315
TseI GCWGC 5 cut(s) 17, 82, 502, 713, 1037
TspDTI ATGAA 4 cut(s) 246, 453, 572, 627
TspRI CASTG 2 cut(s) 117, 1315
Van91I CCANNNNNTGG 1 cut(s) 924
VpaK11BI GGWCC 1 cut(s) 627
VspI ATTAAT 1 cut(s) 1284
XagI CCTNNNNNAGG 1 cut(s) 1241
XapI RAATTY 4 cut(s) 365, 373, 762, 1024
XceI RCATGY 5 cut(s) 839, 942, 956, 976, 1352
XmnI GAANNNNTTC 1 cut(s) 521
XspI CTAG 1 cut(s) 1029
ZrmI AGTACT 1 cut(s) 1033
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.