FvH4_3g16171

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000258
Physical Location & Seq
Forward (+)
10195462 .. 10197729
2268 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g16171.t1

Sequence Viewer

Length: 1443 bp
ATGGCAGCAAAAGATGTTGTTTTATCTAACACACTGAACTTGGCACAAGTGATTACATCTGAGGCTCCAGATTTGCCAGCAGAGGGTGATATCCCAGATGCAACTATTAAGGCTGTTGAAGCTTGGGAGCAAAACGAGTTTCTGTGTAAGAATTATATTTTGAATGCCTTAGATGATTCATTGTATGATGTTTATTCAACATTCAAAACTGAAAAAGAGCTATGGGATTCTTTGAACAAGAAATACAAGTCTGAGGTTGCAAGTGCCAAGAAGTTTGTTGTTGGAAAATTTCTGAATTTTAAGATGAGTGATGCCAATTCTGTGGTGAAGCAAGTGGAGGAACTCCAAATTACAGCTCATGAATTACTTGCTGAAGGTATGGGACTCAATGAGACTTTTCTTGTTGCTTCCATTATTGAAAAGCTGCCTCCCTCTTGGAAGGATTTCAAGATATACCTCAAGCACCTATCTGAAAAGATGAACCTTGAGCAACTCATTCTCAAGCTTCGTGTGGAGGAAGAGAATAGAAAGAATGAAAAAACTGATTGGTCCTCAATGGAAGCAAAAGCCAATGTGATTGAAGGTAGCACCTCCAAGCCTAAGTTTCCTCACAATCATAAGAAGGGAAAAACTGCTGCCAAAAGAGCACCTACTGCCCCAAAAGCTGTTATGTTCAAAAAGAAAATTCAAGGTGCTTGCTGGGTGTGTGGTAAGCCTGGTCATAAAGCCATGGATTGTCGCCACAAGAAGGACAGACCTGCTGGAAATAATAATCAAGCAAACATGGCAGAAGATCAATTTGTTGCTGTTGTATCTGAGGTCAATCTAATGATCAATACCAATGACTGGTGGGTTGACACAGGTGCATCAAGGCATGTTTGTACTGAAAGAAGCATGTTTGCAACATATGAGCAAGGATCTGGTGGAGAAAATCTTTACATGGGAAATTCTAGTACTACTGCAGTTGAAGGGACAGGAAAAGTGATACTGAAACTCACTTCTGGAAAAGAACTTGCACTCACCAATGTGCTCCATGTCCCTAAGATTAGAAAGAATCTGATTTTTGGTTCTCTTCTTATCAACAAAGGCTTTAAGTTAGTATTTGAATCTGATAAGTTTGTACTCACCAAGGGTGGAATGTATGTAGGAAAAGGCTACCTATCTGAGGGGCTGTTCAAACTCAATGTAATTCCTACTGCTGATATTAATAATAATAATGCAGGCAATAGCACTGCTTCTATCTACTTACTTGATTCAGTTGATTTATGGCATGCAAGATTAGGTCATGTGAATTATCGTTCTCTAAACAGGATGATCAACTTGGGATTGTTACCAAAATGCAGTCCTAAGTTAGAATGCATCTCAAACAGCAATTCTAATGCTGATAAACATAAATGTGAAATCTGTGTTGAATCAAAGTGCTCCACACAGTTTATGGGGTGA
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

481

Amino Acids

53.37

Weight (kDa)

8.76

Isoelectric Point (pI)

33.16

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 28 - 180 6.3e-25 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 283 - 364 1.4e-23 Pol polyprotein, beta-barrel domain
gag_pre-integrs PF13976 404 - 473 1.4e-12 GAG-pre-integrase domain
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)
Acc36I ACCTGC 1 cut(s) 766
AccB7I CCANNNNNTGG 1 cut(s) 846
AclWI GGATC 1 cut(s) 925
AcsI RAATTY 4 cut(s) 287, 295, 684, 946
AcuI CTGAAG 1 cut(s) 393
AfaI GTAC 3 cut(s) 883, 955, 1122
AfiI CCNNNNNNNGG 4 cut(s) 83, 748, 846, 1165
AjnI CCWGG 1 cut(s) 715
AleI CACNNNNGTG 1 cut(s) 1025
AluBI AGCT 6 cut(s) 122, 220, 356, 424, 505, 665
AluI AGCT 6 cut(s) 122, 220, 356, 424, 505, 665
Alw21I GWGCWC 3 cut(s) 649, 1032, 1424
Alw26I GTCTC 1 cut(s) 386
AlwI GGATC 1 cut(s) 925
ApeKI GCWGC 3 cut(s) 5, 424, 635
ApoI RAATTY 4 cut(s) 287, 295, 684, 946
AseI ATTAAT 1 cut(s) 1206
Asp700I GAANNNNTTC 1 cut(s) 443
AspS9I GGNCC 1 cut(s) 549
AsuHPI GGTGA 4 cut(s) 98, 337, 1012, 1117
AvaII GGWCC 1 cut(s) 549
Bbv12I GWGCWC 3 cut(s) 649, 1032, 1424
BbvI GCAGC 3 cut(s) 17, 411, 622
BciT130I CCWGG 1 cut(s) 717
BclI TGATCA 2 cut(s) 831, 1314
BcoDI GTCTC 1 cut(s) 386
BfaI CTAG 1 cut(s) 951
BfmI CTRYAG 1 cut(s) 960
BfuAI ACCTGC 1 cut(s) 766
BisI GCNGC 3 cut(s) 6, 425, 636
BlsI GCNGC 3 cut(s) 7, 426, 637
BmcAI AGTACT 1 cut(s) 955
Bme1390I CCNGG 1 cut(s) 717
Bme18I GGWCC 1 cut(s) 549
BmgT120I GGNCC 1 cut(s) 549
BmiI GGNNCC 1 cut(s) 66
BmrFI CCNGG 1 cut(s) 717
BmsI GCATC 4 cut(s) 88, 301, 875, 1368
BpmI CTGGAG 1 cut(s) 51
BpuEI CTTGAG 3 cut(s) 443, 485, 506
BsaJI CCNNGG 2 cut(s) 729, 1128
Bsc4I CCNNNNNNNGG 4 cut(s) 83, 748, 846, 1165
Bse1I ACTGG 1 cut(s) 851
BseBI CCWGG 1 cut(s) 717
BseDI CCNNGG 2 cut(s) 729, 1128
BseGI GGATG 1 cut(s) 1317
BseLI CCNNNNNNNGG 4 cut(s) 83, 748, 846, 1165
BseMII CTCAG 4 cut(s) 51, 243, 807, 1155
BseNI ACTGG 1 cut(s) 851
BseXI GCAGC 3 cut(s) 17, 411, 622
BseYI CCCAGC 1 cut(s) 699
BsiHKAI GWGCWC 3 cut(s) 649, 1032, 1424
BslFI GGGAC 3 cut(s) 396, 985, 1022
BslI CCNNNNNNNGG 4 cut(s) 83, 748, 846, 1165
BsmAI GTCTC 1 cut(s) 386
BsmFI GGGAC 3 cut(s) 396, 985, 1022
BsmI GAATGC 2 cut(s) 169, 1361
Bsp1286I GDGCHC 3 cut(s) 649, 1032, 1424
Bsp143I GATC 4 cut(s) 793, 831, 917, 1314
Bsp19I CCATGG 1 cut(s) 729
BspCNI CTCAG 4 cut(s) 52, 244, 808, 1156
BspHI TCATGA 1 cut(s) 358
BspLI GGNNCC 1 cut(s) 66
BspMAI CTGCAG 1 cut(s) 964
BspMI ACCTGC 1 cut(s) 766
BspPI GGATC 1 cut(s) 925
BsrI ACTGG 1 cut(s) 851
BssECI CCNNGG 2 cut(s) 729, 1128
BssMI GATC 4 cut(s) 793, 831, 917, 1314
BssT1I CCWWGG 2 cut(s) 729, 1128
Bst2UI CCWGG 1 cut(s) 717
Bst4CI ACNGT 1 cut(s) 1431
Bst6I CTCTTC 2 cut(s) 513, 1077
BstAPI GCANNNNNTGC 1 cut(s) 653
BstC8I GCNNGC 4 cut(s) 78, 697, 1222, 1272
BstDEI CTNAG 8 cut(s) 60, 169, 252, 600, 816, 1041, 1164, 1347
BstDSI CCRYGG 1 cut(s) 729
BstENI CCTNNNNNAGG 1 cut(s) 1163
BstF5I GGATG 1 cut(s) 1317
BstKTI GATC 4 cut(s) 796, 834, 920, 1317
BstMAI GTCTC 1 cut(s) 386
BstMBI GATC 4 cut(s) 793, 831, 917, 1314
BstMWI GCNNNNNNNGC 5 cut(s) 119, 644, 653, 662, 785
BstNI CCWGG 1 cut(s) 717
BstNSI RCATGY 3 cut(s) 878, 898, 1274
BstSCI CCNGG 1 cut(s) 715
BstSFI CTRYAG 1 cut(s) 960
BstV1I GCAGC 3 cut(s) 17, 411, 622
BstX2I RGATCY 1 cut(s) 917
BstXI CCANNNNNNTGG 1 cut(s) 322
BstYI RGATCY 1 cut(s) 917
BtgI CCRYGG 1 cut(s) 729
BtsCI GGATG 1 cut(s) 1317
BtsI GCAGTG 1 cut(s) 1230
BtsIMutI CAGTG 2 cut(s) 32, 1230
BveI ACCTGC 1 cut(s) 766
Cac8I GCNNGC 4 cut(s) 78, 697, 1222, 1272
CciI TCATGA 1 cut(s) 358
Cfr13I GGNCC 1 cut(s) 549
Csp6I GTAC 3 cut(s) 882, 954, 1121
CviAII CATG 9 cut(s) 359, 730, 784, 875, 895, 940, 1034, 1271, 1286
CviQI GTAC 3 cut(s) 882, 954, 1121
DdeI CTNAG 8 cut(s) 60, 169, 252, 600, 816, 1041, 1164, 1347
DpnI GATC 4 cut(s) 795, 833, 919, 1316
DpnII GATC 4 cut(s) 793, 831, 917, 1314
Eam1104I CTCTTC 2 cut(s) 513, 1077
EarI CTCTTC 2 cut(s) 513, 1077
Eco130I CCWWGG 2 cut(s) 729, 1128
Eco32I GATATC 1 cut(s) 91
Eco47I GGWCC 1 cut(s) 549
Eco57I CTGAAG 1 cut(s) 393
EcoNI CCTNNNNNAGG 1 cut(s) 1163
EcoRII CCWGG 1 cut(s) 715
EcoRV GATATC 1 cut(s) 91
EcoT14I CCWWGG 2 cut(s) 729, 1128
EcoT22I ATGCAT 1 cut(s) 1361
ErhI CCWWGG 2 cut(s) 729, 1128
FaeI CATG 9 cut(s) 362, 733, 787, 878, 898, 943, 1037, 1274, 1289
FaqI GGGAC 3 cut(s) 396, 985, 1022
FatI CATG 9 cut(s) 358, 729, 783, 874, 894, 939, 1033, 1270, 1285
FauNDI CATATG 1 cut(s) 907
FbaI TGATCA 2 cut(s) 831, 1314
Fnu4HI GCNGC 3 cut(s) 6, 425, 636
FokI GGATG 1 cut(s) 1324
Fsp4HI GCNGC 3 cut(s) 6, 425, 636
FspBI CTAG 1 cut(s) 951
GluI GCNGC 3 cut(s) 6, 425, 636
GsaI CCCAGC 1 cut(s) 703
GsuI CTGGAG 1 cut(s) 51
Hin1II CATG 9 cut(s) 362, 733, 787, 878, 898, 943, 1037, 1274, 1289
HincII GTYRAC 1 cut(s) 856
HindII GTYRAC 1 cut(s) 856
HindIII AAGCTT 2 cut(s) 120, 503
HinfI GANTC 7 cut(s) 176, 227, 384, 1054, 1106, 1253, 1412
HphI GGTGA 4 cut(s) 98, 337, 1012, 1117
Hpy166II GTNNAC 1 cut(s) 856
Hpy188I TCNGA 8 cut(s) 61, 253, 294, 472, 817, 1059, 1111, 1165
Hpy188III TCNNGA 4 cut(s) 68, 359, 448, 1002
Hpy8I GTNNAC 1 cut(s) 856
HpyAV CCTTC 6 cut(s) 368, 433, 575, 616, 742, 962
HpyCH4III ACNGT 1 cut(s) 1431
HpyF10VI GCNNNNNNNGC 5 cut(s) 119, 644, 653, 662, 785
HpyF3I CTNAG 8 cut(s) 60, 169, 252, 600, 816, 1041, 1164, 1347
Hsp92II CATG 9 cut(s) 362, 733, 787, 878, 898, 943, 1037, 1274, 1289
Ksp22I TGATCA 2 cut(s) 831, 1314
Kzo9I GATC 4 cut(s) 793, 831, 917, 1314
LmnI GCTCC 4 cut(s) 70, 127, 1035, 1427
Lsp1109I GCAGC 3 cut(s) 17, 411, 622
LweI GCATC 4 cut(s) 88, 301, 875, 1368
MaeI CTAG 1 cut(s) 951
MaeIII GTNAC 1 cut(s) 1329
MalI GATC 4 cut(s) 795, 833, 919, 1316
MboI GATC 4 cut(s) 793, 831, 917, 1314
MboII GAAGA 3 cut(s) 530, 803, 1064
MflI RGATCY 1 cut(s) 917
MhlI GDGCHC 3 cut(s) 649, 1032, 1424
MlyI GAGTC 1 cut(s) 378
MmeI TCCRAC 1 cut(s) 262
Mph1103I ATGCAT 1 cut(s) 1361
MroXI GAANNNNTTC 1 cut(s) 443
MseI TTAA 4 cut(s) 108, 300, 1092, 1206
MslI CAYNNNNRTG 2 cut(s) 1025, 1395
MspR9I CCNGG 1 cut(s) 717
Mva1269I GAATGC 2 cut(s) 169, 1361
MvaI CCWGG 1 cut(s) 717
MwoI GCNNNNNNNGC 5 cut(s) 119, 644, 653, 662, 785
NcoI CCATGG 1 cut(s) 729
NdeI CATATG 1 cut(s) 907
NdeII GATC 4 cut(s) 793, 831, 917, 1314
NlaIII CATG 9 cut(s) 362, 733, 787, 878, 898, 943, 1037, 1274, 1289
NlaIV GGNNCC 1 cut(s) 66
NsiI ATGCAT 1 cut(s) 1361
NspI RCATGY 3 cut(s) 878, 898, 1274
OliI CACNNNNGTG 1 cut(s) 1025
PaeI GCATGC 1 cut(s) 1274
PagI TCATGA 1 cut(s) 358
PctI GAATGC 2 cut(s) 169, 1361
PdmI GAANNNNTTC 1 cut(s) 443
PfeI GAWTC 6 cut(s) 176, 227, 1054, 1106, 1253, 1412
PflMI CCANNNNNTGG 1 cut(s) 846
PkrI GCNGC 3 cut(s) 7, 426, 637
PleI GAGTC 1 cut(s) 378
PpsI GAGTC 1 cut(s) 378
PshBI ATTAAT 1 cut(s) 1206
Psp6I CCWGG 1 cut(s) 715
PspFI CCCAGC 1 cut(s) 699
PspGI CCWGG 1 cut(s) 715
PspN4I GGNNCC 1 cut(s) 66
PspPI GGNCC 1 cut(s) 549
PsrI GAACNNNNNNTAC 2 cut(s) 227, 259
PstI CTGCAG 1 cut(s) 964
PsuI RGATCY 1 cut(s) 917
RsaI GTAC 3 cut(s) 883, 955, 1122
RsaNI GTAC 3 cut(s) 882, 954, 1121
RseI CAYNNNNRTG 2 cut(s) 1025, 1395
SaqAI TTAA 4 cut(s) 108, 300, 1092, 1206
SatI GCNGC 3 cut(s) 6, 425, 636
Sau3AI GATC 4 cut(s) 793, 831, 917, 1314
Sau96I GGNCC 1 cut(s) 549
ScaI AGTACT 1 cut(s) 955
SchI GAGTC 1 cut(s) 378
ScrFI CCNGG 1 cut(s) 717
SduI GDGCHC 3 cut(s) 649, 1032, 1424
SfaNI GCATC 4 cut(s) 88, 301, 875, 1368
SfcI CTRYAG 1 cut(s) 960
SinI GGWCC 1 cut(s) 549
SmiMI CAYNNNNRTG 2 cut(s) 1025, 1395
SmlI CTYRAG 3 cut(s) 458, 485, 500
SmoI CTYRAG 3 cut(s) 458, 485, 500
SphI GCATGC 1 cut(s) 1274
SspMI CTAG 1 cut(s) 951
StyD4I CCNGG 1 cut(s) 715
StyI CCWWGG 2 cut(s) 729, 1128
TaaI ACNGT 1 cut(s) 1431
TatI WGTACW 3 cut(s) 881, 953, 1120
TfiI GAWTC 6 cut(s) 176, 227, 1054, 1106, 1253, 1412
Tru1I TTAA 4 cut(s) 108, 300, 1092, 1206
Tru9I TTAA 4 cut(s) 108, 300, 1092, 1206
TscAI CASTG 2 cut(s) 39, 1237
TseI GCWGC 3 cut(s) 5, 424, 635
TspDTI ATGAA 4 cut(s) 168, 375, 494, 549
TspRI CASTG 2 cut(s) 39, 1237
Van91I CCANNNNNTGG 1 cut(s) 846
VpaK11BI GGWCC 1 cut(s) 549
VspI ATTAAT 1 cut(s) 1206
XagI CCTNNNNNAGG 1 cut(s) 1163
XapI RAATTY 4 cut(s) 287, 295, 684, 946
XceI RCATGY 3 cut(s) 878, 898, 1274
XcmI CCANNNNNNNNNTGG 1 cut(s) 1432
XmnI GAANNNNTTC 1 cut(s) 443
XspI CTAG 1 cut(s) 951
ZrmI AGTACT 1 cut(s) 955
Zsp2I ATGCAT 1 cut(s) 1361
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.